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<h3>
Roland Fehrenbacher pushed to branch master
at <a href="https://salsa.debian.org/med-team/relion">Debian Med / relion</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/445e1c8efc5108ee4508b660ef7412e70dda1058">445e1c8e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-09T14:39:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial commit with contributors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/946e508365ea58dd04e4ba329fdf67b5c490b07f">946e5083</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-13T15:38:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">UPdate of branch readme to include plan
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bcc019908ca2d758aa06c39f7c46235422deb22e">bcc01990</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-16T16:30:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">First draft: single trans test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e9343a166e928457f2d9fed483a63d78c48e4b8">6e9343a1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-16T17:11:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reproducing run.sh in test/single_trans
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bb86ed318077a01ff3c87be07c4676ba6748c667">bb86ed31</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-17T12:47:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update of test single trans
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cbad489a95f99ec08654ea9f660edb25e8fb6fbd">cbad489a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-18T13:12:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">temp CMakeLists (draft)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/00f0348194908c307e0287d6414422d31ee3b444">00f03481</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-19T09:59:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">introduction of cmake
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e72bfe71e97569204e0815dc8d339b507e246c10">e72bfe71</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-19T15:20:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cmake makes it to the linking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ec26366ca20cf0a6bfb4c92c4c0263a029fe581a">ec26366c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-19T15:37:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some changes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/776c2980dc1fb7f629bd4dd0c22b4a58e88e89a9">776c2980</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-19T16:40:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CmakeLists check for system fltk/fftw/cuda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/352a92c2197340ebcebefe96f6740403d3839d5d">352a92c2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-20T17:21:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">REL_REFINE binary links /w sys libs + external libs path
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1834c02338b3eecf2387a8c874efb1b7afacf732">1834c023</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-23T14:05:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cmake subdir w/ FindFFTW.cmake
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/010bc0712d57c6bab5d5df92c0a8cc02b3479804">010bc071</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-23T16:34:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Compile object lib once for all binaries
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/17df01a38a4ca47290d03c725157c4da349c1020">17df01a3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-23T17:42:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update to alpha-5
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/415056d32276436610e6fa6da1e25dd6eb05012d">415056d3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-23T17:47:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cuda_add_exec clause added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a1ee6fa86c04d82c5ae035069059a2c877c3be30">a1ee6fa8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-23T18:05:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merge GPU to master original alpha-5
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/46ea8f4e9474be9803b7837f4001cba1292ef900">46ea8f4e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-25T12:01:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Introduced a test hardcoded to CMakeLists: (-DRELION_TESTING)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/08502dca963c7c25bb5b02d14155b976c60240be">08502dca</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-25T13:56:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5c2da775d36a1c348e254eed979c6c1b838da42">d5c2da77</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-25T18:38:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">moved test output to build dir
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2be4bb6d76826e5bf451f0f3109169c757dd06c5">2be4bb6d</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-26T09:51:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor changes in cmake files, mostly clean-ups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/608ac3b6fba0ca13a43e0fa1086a8a44f403a8ca">608ac3b6</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-26T10:00:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Main cmake file merged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7876d42be7e0c12525f78e95d5950cd6115c1a50">7876d42b</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-26T14:00:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reduced cmake files to bare minimum
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/55bbf15aff6cb7d40540dfb2a21a1e8e4b43ff43">55bbf15a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-27T11:30:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">moved test flag and set relative path apps/CMakeLists
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/95b382782b2e1da356bdcbfd9731f080fe49535f">95b38278</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-27T12:10:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU utils
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fda04da45694add7eccb06b54594368ec3468c97">fda04da4</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-27T12:12:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'GPU-trans' of https://bitbucket.org/bforsbe/relion-1.4 into GPU-trans
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bac69a2bc9ec3a28023b1e89629e97f8ecb73f93">bac69a2b</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-27T13:40:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cmake skips search for openGL, which is not required
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f2845154870abdefe274ab6a44d9c8b1edc64570">f2845154</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-27T14:20:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cuda header fisrt draft
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e4fcc710a511b15e94ec3c0643af76e133a97475">e4fcc710</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-27T14:21:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'GPU-trans' of https://bitbucket.org/bforsbe/relion-1.4 into GPU-trans
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/56653374bbcdae14f64adc8f2a02c3b7125b17c3">56653374</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-02-27T14:24:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">first draft cuh
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5be62381741c348ea7f0a5b6c8d78964117f8168">5be62381</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-27T14:25:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'GPU-trans' of https://bitbucket.org/bforsbe/relion-1.4 into GPU-trans
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b13cb697cae7fae46ca7a3d7fecf15eab68f41a8">b13cb697</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-02-27T16:17:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working GPU kernel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb8beca39ead2e138cd44bed4cddcae445715cfb">eb8beca3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-02T16:50:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added diff2 test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/18e909d406994c713581575b262ee11106dae236">18e909d4</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-02T17:02:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CUDA implementation of diff2 calculations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/95ed9ef0937b3662a6f9f10ea1398f0c78518468">95ed9ef0</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-02T17:15:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e548b2b04882f1da8a276aabb7650760671ceda2">e548b2b0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-02T18:19:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed gpu-diff2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f20bd6fe80eaff549a58de98bb369bedcda455d">8f20bd6f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-02T19:18:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix make build hangup by sep. lib for gpu-util
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fb1d3459fcdc0623e1f05fcee395bad7ec11f92d">fb1d3459</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-03T10:41:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">--gpu flag + test deps
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64246976cfaa165b7be95408889866d5d2479490">64246976</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-04T17:24:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New layout for massive acceleration of refine.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/75ee11949937d0cf35a5db7dca929959448e42bf">75ee1194</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-04T18:22:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Draft SharedMem handle and diff-calc looped over partial images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2e782a1596ad7f473a8a9ecc14852ec6e1233a29">2e782a15</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-05T15:31:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Non-working data managment for CUDA kernel calls.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc6d73ede191aac41c6911dbb7f6025a09b6159f">fc6d73ed</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-06T11:55:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed code for non-blocksized images
Also changed test to sun with non-blocksized image
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8acd17c03e5920e451ccb9754341e10ca23d1dad">8acd17c0</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-06T12:01:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New globally modified architecture of the data managment for an optimized CUDA implementation of optimizer.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e450563e96c5f214db49f4a31d7bad51a43433d3">e450563e</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-06T14:18:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">It compiles, YEAH! Though ignoring warnings like I just don't care.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a76ee2a2c0111e9a015d63a809b1c5bb2a1860d">9a76ee2a</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-06T14:19:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'GPU-trans' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf62552f9210ecd29964bec7d75d3624437e47c9">bf62552f</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-06T17:20:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rearragements of loops in cuda optimiser.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/899fc6965196fc73a00cd590480535641a7fc972">899fc696</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-09T10:36:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rearragements of loops in cuda optimiser.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/86d36f4e622b5df1e606b9f461eb6c8d62920fb7">86d36f4e</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-09T10:52:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge within branch as a side effect of rewriting history that contained incorrect merging with other branches.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d15ea40e03796031ccf73c24cc47e4721da4f195">d15ea40e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-09T14:44:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">modularize host/device image diffs, add reduction alogrithm
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/20d0091819cf857560e084f2a623c975cddb19cf">20d00918</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-09T16:29:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some dummy code to get it to run.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/867662eb88c38b17878dd03f72ce3c23700219b5">867662eb</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-10T15:20:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">the most annoying bugfix yet
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e677ce2aee5931c19c705bfcdb124723ccd9e356">e677ce2a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-11T15:35:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">freeing cuda mem + expanded tests to diff2 set
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/75f3d39106a69bbcbfbcc00cfcc3489f44aa65b7">75f3d391</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-11T15:38:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working gigantic kernel call with trans x ref number of blocks.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c36cc3005168cbb7de71975ae454969511c0a19">3c36cc30</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-11T16:00:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'GPU-trans' into CUDA-Glob
Conflicts:
src/gpu_utils/cuda_img_operations.cu
src/ml_optimiser.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5b0cf563c464c664dbf5d790321f90ebe2d0d5af">5b0cf563</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-11T16:12:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU reproduces identical values for first particle, when not ctf-corrected.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/06634d64c4544180cc0f36c53d71386e0af6c71b">06634d64</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-11T16:12:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f84515a8adac4860ad69d4f2ada4001d781dd266">f84515a8</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-12T11:13:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working implementation reproducing CPU results.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c985c256bdb6124715dc154fc4f9d121f7f854ce">c985c256</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-12T16:13:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working implementation reproducing CPU results.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/edfbae44b23b1d852d6ca6c5c0b973bfad8bfe8b">edfbae44</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-12T16:19:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/acddf747951e5eb9f112c6dc8be281b167fbf359">acddf747</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-12T18:04:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Copied storeWeightedSums into CUDA optimiser as is. Builds and works as previous commit.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c0b3e6e1d9969607313cf87ac008be5fd9b4d10e">c0b3e6e1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-13T11:59:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Modifed test to be relevant for massive cuda-kernel call
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e366d0041e0be7f44704981436fc05edf53f0832">e366d004</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-13T13:44:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU can handle ctf-correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51efcc42d05017f807c39328ca3e27551f8e0b9e">51efcc42</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-13T21:43:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU can handle scale-correction
However accuracy when using scale_correction
may have been affected compared to CPU-based
computation. Need to validate.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/595b0eabce04266a6b90056c8b4b1c996d76d455">595b0eab</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2015-03-15T14:09:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update to 1.4-beta-1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d8ca8d65835a016301d682bb4476d254c2f2c196">d8ca8d65</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-16T11:25:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob'
Conflicts:
src/ml_optimiser.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eddaf491bdc27b2abed3a9de7d3470b58e590886">eddaf491</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-16T18:05:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Non-working first cuda-implementation of storeWeightedSums.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7707af0d40b45d094297a7ca57a07c8400216394">7707af0d</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-16T18:06:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b89622d3330fd154fe0ce65995c47085218b440c">b89622d3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-17T10:22:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Faster diff2 kernel algorithm
also some clarifying annotations in weight calc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd3101c5834df023d9bcc6e9c89881301cbff902">fd3101c5</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-18T17:45:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CUDA Diff-kernel avoids insignificant diffs
from being calculated. Some additional minor fixes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2e0e7286ab898ac2d0734a8e9416459c151fe348">2e0e7286</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-19T09:45:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Amended testing to remove old output before tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cf67c32cb4109410f68846e93e438d390c1ca46d">cf67c32c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-19T10:50:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">diff2-kernel can handle #projs>65535
by decomposing a larger number into 2 components
of size ceil(sqrt(number)), and submitting a 3D
blockgrid instead of a 2D blockgrid.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7cbf88e16d5a0f3ed0b740896a6186d605a7958d">7cbf88e1</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-19T17:37:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">(Unverified) Working implementation of storeWeightedSums.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/539c408bd20407d143a33341137d1affe1c3d5fa">539c408b</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-19T17:54:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge and small modification of cuda optimiser block sizes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a100cf7c8bea9ea57d20f06828f747d6ebdc7e8">3a100cf7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-20T16:05:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">diff2-kernel based on paired tasks
as opposed to intiating a block for each possible
task and exiting those which are insignificant.
Now this assesment is cpu-based and the minimum
(padded) number of blocks is invoked with the
kernel, utilizing references for all blocks for
read/write.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc8f9209e0b6792860396f718695b9185fe58b51">bc8f9209</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-23T12:12:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">#
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/44e10af486b72b4e853eabd80c93ee1fb0fc2144">44e10af4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-26T12:05:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">rot/transidx memleak fix (no apparent GPU memleak)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/565fa24283b4902486dedeeaa566f7ff2beee9a7">565fa242</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-30T10:37:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">~2x reduction in GPU wavg-kernel
(and alot of memory debug code)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b43cdd9266da76035dcbd87f65183b636917c84">2b43cdd9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-30T10:37:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new layout of GPU wavg-kernel
+ fewer global memory access requests
+ more scalable blocksize (more threads =
faster execution, up to a point)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ea110b126d8493e930222b5d436091c5e532244">5ea110b1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-03-30T14:12:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU wavg-kernel can handle #projs>65535
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/91a68a873591fd06f17124d979abe0f244b02f1b">91a68a87</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-31T13:57:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working CUDA storeWeightedSums
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c1b245b41152bcfbcb7fc78f8fbb93b09902517e">c1b245b4</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-03-31T15:10:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7f9c9e203d4d4899e437837ccf149bbf2a5973a8">7f9c9e20</a></strong>
<div>
<span>by Farhad Kimanos</span>
<i>at 2015-04-01T20:49:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added some utils for memory managment and data flows.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dfb1182445f9bd85f238945b8101f65a9aa5ad66">dfb11824</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2015-04-03T08:35:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revised tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6cbf66f1fb834538f192bf1e8b7ec94f7664bf65">6cbf66f1</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2015-04-03T08:37:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc5cfadd1a82338715f2d880c23a9b034a7f3d5f">cc5cfadd</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-03T10:45:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cmake handles compile on K80-machines
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a2faa82842fc815888b61c4cb8d77d6e12798ea">7a2faa82</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-03T10:46:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Expanded expectation()-tests
It is now evident that the ctf-correction via the
--ctf flag does not work on GPU resources.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/43eb00ec2cf872e46129050541db5ded63295e4f">43eb00ec</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-04T17:46:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU can ctf-correct with oversampling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4da5f81b1a4f1bfced40819c40efe79eb49aaff2">4da5f81b</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2015-04-04T20:28:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Draft GPU cc_diff-kernel (untested)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6f3dfd4b8db9f3d8b8c51f41f4a6835e4db28ebb">6f3dfd4b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-07T12:46:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CMAKE checks whether X11 and FLTK is found before compiling GUI targets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1d2af9f8089e6028bf4d302de63269adf9d07bbe">1d2af9f8</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-08T18:09:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extended cmake instructions for the non-GUI case and simple debugging-options.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a0b570c9208c53d7d9b25f2bbe226a211a0ea8e1">a0b570c9</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-08T18:30:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working ctf correction for storeWeightedSums.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb2c731ad5234c018ce91cbe53807fb9ef3641b2">eb2c731a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-08T21:18:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/491555f8971770d70cd2a70a12a7c84d9cddbbf7">491555f8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-08T21:30:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'temp' into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de7e360db66789e9886c1e5b3d783a1fca937d1e">de7e360d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-09T14:20:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added precompiler macros for CPU and GPU benchmarking.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/96f24e2ca42cfeacda592183caafcd59f62f41f4">96f24e2c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-09T14:21:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e386a888d4a27d549fddcf6232494c9251f03a3c">e386a888</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-09T16:28:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tests on relion native output
../tests/ref_Fweights.txt
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/10bec6d125e8f54fe90bf458ea5f90cecc223d9d">10bec6d1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-09T16:53:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/49bb1ef970d924c7a05c1632172beea6f018624c">49bb1ef9</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-10T10:42:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added benchmarking tool in rest of the cuda ml optimiser code. Did some modifications to names and syntax.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6bbdf296d65fe051a0480a7ca9427b1af8a6b5a3">6bbdf296</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-10T10:43:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/17588afc49d48611faba57b117192ac1d41541ff">17588afc</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-10T12:11:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better debug warnings.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/74ce65dc632302abcb9bc4abb3affe2fd7ff192f">74ce65dc</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-10T14:56:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed memory leakage caused by a drunk and code incident.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3c4e4b35d13c6387cb26505336a8b69be8cc41e">b3c4e4b3</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-10T15:36:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Kernel precision can now be selected at precompile time.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3fda9c3135a418ed257798499d514e7473e9c013">3fda9c31</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-10T16:58:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed another dunk-n-code incident and converted relevant indices to long, including pair indices sent to the kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c067740ff5390c8dd821a69fe1e03348e6e2ff11">c067740f</a></strong>
<div>
<span>by Lus</span>
<i>at 2015-04-10T23:02:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added some documentation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/382d1a8430b99708e65e8517535b0352ead43a0a">382d1a84</a></strong>
<div>
<span>by Lus</span>
<i>at 2015-04-10T23:05:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed error in Fweights and wavgs.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d30d3df98031e1047d2b8512efc0a2826a15815">6d30d3df</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-13T15:17:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updated testing reference-set
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0bf0f5335e05a12ff8165b0427c1cc60d86cc930">0bf0f533</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-16T11:21:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moved the gpu-cpu-fork in the code further up in the iteration-tree. Also introduced two classes holding all the optimisation and sampling parameters to improve syntax readability.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2e0e89bdfd77b1404895b7c7715eaba48470f34e">2e0e89bd</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-16T11:43:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Draft GPU-proj-kernel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7bb4512343b6b42ddd408380e1c02cb145b3d051">7bb45123</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-16T11:59:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf9ad69eae862532dd25061942eb538b59aa4cbb">bf9ad69e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-16T14:33:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed time unit for benchmark output and added some more benchmarking checkpoints.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cbe7eff81743411341680ec6a07ddaf1d2efb044">cbe7eff8</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-16T14:34:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc58e5cd669c4135b485169b80ca5b587c26c81b">cc58e5cd</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-16T16:35:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working CUDA-implementation of reference projection.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d206594a09f9c88c4ce89294599835a77423467">7d206594</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-17T10:24:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using build type + moved flags into debug config
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/baa5dfb3cadf66fc01c84fdcf3ed8f6384dcd5ec">baa5dfb3</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-17T11:13:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CUDA-acceleration of reference projections for both 'diff2' and 'store'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f077af3229b125d78fe8ebd8b693fc262520690">9f077af3</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-17T11:13:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b6e6365f2d96bd773ff4b896ecf769381645b701">b6e6365f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-17T16:09:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cuda (CPU) version of Euler->RotMatrix
Added since the cuda-version needs to be able to
make euler matrices with dynamic FLOAT precision,
which should be indep. of all-cpu code.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3171c3028932cd29eaa91553658bab62d977b06d">3171c302</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-19T14:09:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Small memory fix based on profiling + suggest
Further changes to wavg-kernel based on profiling
are necessary, as may they be for diff2-kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/350e38a0b14ef31e9df6839e106a7cf0c18a1e7d">350e38a0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-19T14:11:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added build-type PROFILING
However native flags are not caught, i.e. we
are not appending to current build-type flags.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb5645d31878ec4eb54c8fd55770a5c8ac46d10d">cb5645d3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-20T09:54:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU shared_mem wavg kernel 1.0
Showing some improvement of memory limtation,
but no significant performance gain (no diff
at all, basically)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/657e31298a44966ffa58d9b4eebdcb74f9389212">657e3129</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-21T20:53:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU shared_mem wavg kernel 2.0
Introduces using groups of references covered
by a single block in order to reuse image data
loaded grom global memory, but at the cost of
consuming quite a large amount of shared mem.
Attains ~2x and makes wavg less time-consuming
than finely resolved diff2.
ALSO: Switches from Complex objects of given
floating point accuracy to separte objects
for real and imaginary components, this to
coalesce memory access.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/99466b1af8ae5babd313305bd38fc24119c87c5c">99466b1a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-22T09:34:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2x better GPU diff-kernel (avoids double-cast)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/871bf72b242585cd65ce5be72a9e6bdbd85d69e8">871bf72b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-23T14:31:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU ConvertDiffsToWeights-kernel 1.0
estimated ~55ms timesave every call, but may be increased by
the time it takes to do one host-to-device copy, since diffs
are calculated on GPU.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b5bef8a126670f2f351de031167f2c8a5acefebd">b5bef8a1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-23T18:04:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build type flags are appended, as intended
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a068cd49d943355e5862b297258efc5b238ea620">a068cd49</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-23T18:04:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Thrust::sort on release build, in wavg-kernel
Speeds up sort on -O3 by ~10x
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b66296a3fd44d36af949ce6f0cd9885c61018f3f">b66296a3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-23T21:11:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Spring cleaning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/54b6178dcb48f7127ae0c42f8f52e8ecdb9d8899">54b6178d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-26T22:06:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prepared for moving euler-matrix up
When finsihed, the boolean implementation will use the full set of
orientation (euler-) matrices for all classes, making the euler-
matrices shared across all classes, thus they need only be constructed
once.
Also modified code in storeWSums() - collect_data stage, to expose
parallelism and indicate future change.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d3eecd0fb7dc7cff51ce0fb5678c3c5b2a691388">d3eecd0f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-28T18:57:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Projection using texture memory
The projection is performed by one of three kernels;
double-precision:
global memory access - explicit interpolation
single-precision:
texture memory access - explicit interpolation
--||-- - implicit (texture-read) interpolation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/959ceb1a39092519330a922ce4aef418972fc849">959ceb1a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-29T12:56:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working reorder of storeWS_collect_2 loop
Also draft (inactive) storeWS_collect2-kernel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dc9a05658bfb534d845b752485b7112ec1df94c4">dc9a0565</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-29T15:28:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CUDA acceleration of the backprojector.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/23af3c1d76c940ccefb8c5d988ee0a69094b14df">23af3c1d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-29T17:51:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ead91893bd697716b21a1ee550aecc9c0471d634">ead91893</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-29T20:26:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Partial solution GPU storeWS_collect_2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/390dff2b4a20892d4ada12a2e6bc22bfc3d4f64f">390dff2b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-30T14:07:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Faster backprojection using an simpler approach.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e2d324766db93d5418881d1fb7f7e95f3bd01905">e2d32476</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-30T15:11:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working GPU storeWS_collect_2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/52b6309a7a6c7809837392f553b633cc653dbad0">52b6309a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-04-30T15:12:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f1b41766ba8af5895eaf37b35f9fabbdbb742a7">9f1b4176</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-04-30T18:10:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New approach for backprojection.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2ab71c1ad903ec317e3bc2d3d15b10ab5aa8dc4">c2ab71c1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-03T09:27:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a95dfc78a44c1ca2c3677d90c88983a955e5f0b">5a95dfc7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-06T18:04:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Optimized backprojection kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27d79e967bfdc4c1d6213da6611c256034a45ab0">27d79e96</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-11T18:01:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Code put into functions to clean the code flow up a bit, re-ordering of projection settup to get coalesced rotational angles.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/09bd3655699c92850caa445e098614aa15add87d">09bd3655</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-12T17:18:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Further simplification of the code and slight optimisation of the BP-kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c99780b2eb8d9eaeebe394cd79db20dbb6aac1d7">c99780b2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-20T17:08:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">1.37x diff2-kernel / 1.75x wavg-kernel
This from using the __ldg() intrinsic for some of the global loads;
it routes the load through the texture cache, meaning one may score
some hits. NOTE: Not all global loads benefitted from __ldg(), and
were omitted from this commit, BUT THE DEPENDENCY OF THE PERFORMANCE
INCREASE WAS NOT TESTED ON OTHER HARDWARE. The use of __ldg() herein
may thus not be the optimal across other hardware.
ALSO: __ldg() requires compute sm_35 or higher, thus the flag was
added to the nvcc build flags. Fallback should perhaps be made.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e2e8d45a92299453913f5f1e1d26f5a332e19bf0">e2e8d45a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-21T11:38:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU Reduce_wdiff2s-kernel 1.0
This makes for a ~50x-70x speedup of the image reduction, which
before took ~50ms on my hardware (Profiling build). However, it
could be improved by increasing the number of image-loads per
block, as this would decrease loads and writes per compute.
The kernel-call should also be able to handle more blocks than
the maximum 65535 in a single block-grid dimension, which would
be partially fixed by the above-mentioned improvement. Otherwise
a simple multidim-blockgrid solution is fine.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bb4095f6d270dc20ae5a4c3584915a16b9da22be">bb4095f6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-21T15:21:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Data_collect_1 rationalized, Rel Build-type added
(Post diff2-kernel mapping)
Memcpy:s that can be avoided if the diff2-kernal can do this
mapping directly:
line 1742 D-to-H diff2s
line 2012 H-to-D Mweights
Performance increase may not be evident over an entire run on
any build type other than RELEASE.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8dba2cea223f08c3e75b214eac076c4e6ee12146">8dba2cea</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-22T16:29:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Index methods, reduce_wdiff_kernel, cuda-streaming
1. ProjectAllViews uses __ldg() on eulers, and some formalism changes.
2. Release build has thread-based cuda-stream parallelism (compile flag)
NOTE: -j 2 causes different output result (accuracy is compromised non-deterministically)
(see issue #14)
3. Reduce_wdiff2s-kernel can handle >65535 images to reduce
4. New Class "Indices" that has method to cast "ihidden_over" to partial indices and vice versa.
NOTE: this is a duplicate of a method in the class HealpixSampling, but has a bit clearer
index naming. It's better, because I wrote it. So there. Should be able to make use of
it to improve pair-list generation, but that might go away soon anyway. Has the following
methods:
- fineIndexToFineIndices(SamplingParameters sp)
- fineIndicesToFineIndex(SamplingParameters sp) FIXME Untested
- coarseIndexToCoarseIndices(SamplingParameters sp) FIXME Untested
- coarseIndicesToCoarseIndex(SamplingParameters sp) FIXME Untested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd14e87a1ab42c8389a520a64fb6ca33a5c526b3">cd14e87a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-25T09:49:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Diffkernel functionalized to same level as Proj
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/217c9ffcd1b887909dd97fbe2c7fad8ac427f1e0">217c9ffc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-25T13:41:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Release build compiles and runs with wrong output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dbaa4c0749cf7afc38c81dded46123f283330365">dbaa4c07</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-25T15:52:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Included an implementation of atomic add for cuda device code.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5625a9bf41567e51823152e28b1727d66d8b257">d5625a9b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-25T16:23:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02527698667767bf55577ac984d29679cc1a52fe">02527698</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-25T16:25:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Simplified the generation of the eulers matrices and added generation of 2D rotation matrices.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a792fcebfb4baa5d77eb7d48677c3511674907d">9a792fce</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-25T16:29:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Switching to int type for spacefill array in backprojection, due to tiny kernel speed-up.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4d22fb364739b62834f6ee627a90337a981b2f4">b4d22fb3</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-25T18:25:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed bug only effecting the results in case of multiple iterations over ipart.
- The submission to global mem in wavg-kernels are modified to additions
- Memeory for wavg output is initialized to zero before kernel-call
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd324d3761cda1009d253efb5cabf42b5cdccf0a">cd324d37</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-25T19:29:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ProjInDiff-kernel 1.0 works with single prec.
under control of bool do_combineProjAndDiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2fc509cf0660bfa12f4f73bcf75de87cf4229ca2">2fc509cf</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-25T19:30:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/75c462f0da5959f23d025ea1d02bb4f69184aa98">75c462f0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-25T19:38:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ProjInDiff' into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a72c3b3471bba979126ec1f156248c685130a11b">a72c3b34</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-26T10:47:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">wavg-kernel functionalized
This in preparation for ProjAndWavg kernel.
Also device mem usage at diff2- & wavg-time.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0bac1ef0c3722d8e58768c4340ed72ed44aba268">0bac1ef0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-26T13:29:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ProjAndWavg kernel 1.0
Works with single prec.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d30af4ad5f2e1399c2d61ee0d1c1e8a1734b83f5">d30af4ad</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-26T15:53:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleaned up the code around collect_2.
Removed extra iclass loop
decoupled block_dim from wavg-kernel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5410b53386ece63612666743f1cdac1f8ef1bfc3">5410b533</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-26T16:55:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixedd previous issue with ProjAndWavg
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/97ef6f9cf4bacaa9e97ae109e9613043e8ad1ebb">97ef6f9c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-26T19:47:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reorganizing functions into separate files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a926a0bcdaaaa361b1cd697768e71256ddce46a5">a926a0bc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-27T10:15:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bindless (object-) textures
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9ed1f948739935b315672e05fa17436504331fce">9ed1f948</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-27T16:15:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reorganizing texture-functions into separate files
Also, som preparation for diffs-grouping of images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ecde77a4aba3d6652ecafcd8151957b3cedf2e8e">ecde77a4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-28T15:04:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New block-control of PAV_Txx_D2 kernels
Currently only works with PROJDIFF_CHUNK_SIZE=1,
which reproduces previous behaviour. Higher values
will presumably reduce execution time by decreasing
the global load frequency and resuing computed
ref-values (up to) proportionally to chunk size.
NOTE: not all _syncthreads() calls may be necessary
in the PAV_TI_D2 kernel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f5c815417b20841a52fd5d496ae691c2bcbc7137">f5c81541</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-28T19:24:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working block-control of PAV_Txx_D2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f2a4005b1c91ffdcb587e57ba9aabb969a9f5ff">3f2a4005</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-29T16:10:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor performance boosts PAV_Txx_D2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/85883ad204a0a153592fe0f0c4a87642f38569bb">85883ad2</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-30T13:34:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor clean up
Removed auto athor claims
Swithed cuda.h to cuda_runtime.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1335c991ab59fb636eab7ee99ae65fc0fc31f973">1335c991</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-30T13:44:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Filetree clean-up. All kernels in one dir.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b32c95fa460dbbce0606673f55993719e98b2966">b32c95fa</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-31T10:37:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Padding_factor into ProjAnd-X kernels
ALSO minor boost to reduction in PAV_TTI_D2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc4bf4c957e0f2023d3520f970d19d4ecd3143e3">bc4bf4c9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-31T10:54:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Benchmarking works again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e4f219a747fac6d8ae1973803eec4756ca25eff0">e4f219a7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-05-31T14:28:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Map & pair_list improved ~2x
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c9c46a04a5eb00c70d44b9249f95c8a2c1df8dc3">c9c46a04</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-31T17:25:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The projection set is divided up into subsets to spare memory during maximization.
There are 8 subsets currently. This number can be set in cuda_ml_optimiser.cu:2458
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c4eb215aebd081dd70186b4ccf2e34a173f6c73a">c4eb215a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-05-31T18:35:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/85a7f2d795b82f726608436a8c9105e255ad6dde">85a7f2d7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-01T11:59:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleaned up some bad code in rotation setup where psi-values are grouped.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/14419e46da1c1224f0887cc5ddfa0e70b217fe05">14419e46</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-01T12:41:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Further bugfixes for data with sparce fine angle search.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb0c4730d187f06ef8077b370223da1f3d948ea9">cb0c4730</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-01T15:49:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Smarter projection dividing based on significant number of orientation rather than the maximum number.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7d907527fd8a549141ccab04dad1467001990a8">a7d90752</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-05T15:37:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Benchmark related improvments and some minor clean-ups.
the gpu-toc does no longer take an arg
better nameing and clean-ups in cuda_benchmark_utils
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a35da6168251f9cd4db3b5c5bcea9ec55d1d1e84">a35da616</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-06T20:39:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">PAV_D2 kernels and -usage is double capa-bloue
Also added preprocessor control of exponentiation
limits (which limit accuracy loss according to
comment on line 4129 in ml_optimiser.cpp) in
sumweight instances;
double - limit is 700 exp(700) < 1.8E308
single - limit is 88 exp(88) < 3.4E38
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c56e12cf0a08935c6543f36dd6f090b4e00efcb">6c56e12c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-07T11:10:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Sumweight kenrel does both coarse and fine sampled
passes. The previous kernel used 32 threads to access
oversampled points, which are adjacent in global mem
and therefore very fast to load. In order for the kernel
to generalize for coarse points, the access is now made
with each thread fetching an (over)sampled orientation,
which are in multiples of 32 (so as to keep all threads
occupied), but not adjacent in global memory. The mem-
ory access should therefore be far less efficient, but
the code works equally well for all healpix- and over-
sampling, provided healpix_order>1.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/05885bade914c4544d88ee5207f54806477b488b">05885bad</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2015-06-08T09:21:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Functionalised block-dim split
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e33ec5145b422340a193b7c6a2782b0934072656">e33ec514</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-09T19:52:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">PAV_TTE and PAV_TGE fixed, double build works
They had two separate issues;
1 - One input int type was unsigned instead of long,
which became an issue because it actually needed to
be signed. thus -33 -> HUGE NUMBER
2 - The padding_factor amendments were only imple-
mented on the PAV_TTI and PAV-combo kernels. This
meant that when double precision forced a split of
PAV and WAVG, it forced usage of PAV_TGE, which was
unaware that it should correct the euler matrix by
padding factor.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2745f670dffbaff5e68dc4c53e0166e971dcafa9">2745f670</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-10T09:53:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed a minor issue with padding factor and also an adjustment to the projection divition algo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6f8840584daaf9a24b9c438f1d1768006b126d4f">6f884058</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-10T10:23:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Functionalised texture initialisation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9bbb2463b9f36aacaf4012d96499cca6d33de7c">f9bbb246</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-10T10:23:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3443a43a4488bf86e5eec26d11b8c4eff9d68e8">b3443a43</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-10T15:12:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">doCombineProjAndDiff=false works
a.k.a. the D2 kernel is up-to-date
with the block-control of commit f5c8154
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/91c55207e49cc1e23e9ef67d78d2ba00afa4e3a4">91c55207</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-12T12:29:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Indexing issue in higher order coarse pass fixed
Previous code relied on the assumption that all coarse orientations
should be difference-calculated, regardless of being the first or any
later refinement-iteration. This is apparently not true, as evident by
the if-statement in generateProjectionSetup which is dependent on
pdf_orientation being finite.
The subsequent errors with/without --ctf flag and for fewer particles,
is then likely a result of the varying probability that there should
be some overlap between the orientational priors (weights) and the
erraneously mapped differences. If it happened to be zero overlap,
the result would be sumweights=0 and exit=failure, otherwise the
algorithm would continue and exit with success, but have completely
nonsensical output data, since weights and priors are then utterly
mismatched.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12b85761f7a448d77569b892aa0692600b97781a">12b85761</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-12T15:09:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minior fix, throws signal on cuda error.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/220ca77167ea8abb58096c17c6ad7df7f68db4a9">220ca771</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-12T15:09:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c8f70664f31295871aa7d7a60593ebbc40482287">c8f70664</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-14T00:03:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Diff2s in the coarse pass are taken care of by a much simpler approach, rendering a factor 2 speed up.
Program debug exits are replaced by "signal-rasing", for easier debugging..
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c83d659d5c6a9f8fc4d104e115d7a76edcf3fb0e">c83d659d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-15T12:01:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix on splitCudaBlocks()
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e8f8fba1677fcf0d536d74334bbea524a0320069">e8f8fba1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-15T15:57:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reengineered index-array use in GetAllSq (fine)
Also functionalised use of thrust min-val search
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bbbbf832cf148b45631425d4609816874313fa8f">bbbbf832</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-16T12:08:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GetAllSqDiffs() is coarse/fine-parted
Some small fixes and strategic comments
thrust::reduce on partial sumweight results
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9237f7e2a12fcf8bfe66a0b569d95ecbd8ffb8fc">9237f7e2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-16T19:06:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Partial removal of dependence on sparse Mweight
Current code relies on the implicit indexing of diffs and
weights by mapping the into an array "Mweights", which in
the gpu-based code belongs to the op class. For somewhat
converged data this tends to be a VERY sparesly populated
array by way of the low significance of many of the asso-
ciated orientations of an image. Combined with the large
size of the array with fine sampling, the cost of
a) transferring this object to and from the gpu
b) keeping a largely empty array on the gpu and
cycling through comparisons of insignificant
elements
becomes too large compared to the actual computations able
to complete. The solution is also twofold;
A) move the object up in scope and keep it on the gpu
B) coalesce data my keeping an explicit indexing, rather
than implicit mapping
This commits adresses both for the fine pass of difference-
calculation, while still mapping to the Mweight array at
the end of converting differences to weights. This because
the storeWeightedSums()-function has not yet been adapted
to handle explicit indexing rather than implicit mapping.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e485bb346563c6b43777b04bac4625508d5cfe30">e485bb34</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-17T16:38:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Major revison of projector setup.
Projector model is loaded into GPU once at rank level.
A class for maintenance of projectors and device code for projections is added.
A section presumably faulty code was outcommented in src/metadata_container.cpp.
This action did not have any effect of the data-output-file for two iterations
of both tutorial and ryr data.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/056de775ceb030acc3dd3de3bb2b118794ba8c3f">056de775</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-17T16:45:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor clean-up in code non-related to GPU-acceleration.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/640c9e80e34fc5d725f1e066d77e1dd292c6b903">640c9e80</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-23T14:36:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Supermerge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
Conflicts:
src/gpu_utils/cuda_kernels/proj_diff.cu
src/gpu_utils/cuda_ml_optimiser.cu
Major problems emerged during merge that required rewitting of large parts of the code.
Memory issue caused by varying class definition depending on compiler (gcc or nvcc)
However, code is not fully functional since further issues remain. These are fixed in next commit.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e551069fd9ba1466a7d5c516d45bdf924733b255">e551069f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-23T15:12:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor fix of the index managment causing issues in fine pass. Now code is fully functional.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/358d9cbf842f19e5c21eb4a6f6c07b0c03a76340">358d9cbf</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2015-06-24T15:14:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">collectjobs kernel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e5a4e149d1a4ef4e44588195684050e468893f9">9e5a4e14</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-24T16:17:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Backproject is moved up to rank level.
Some minor improvements on benchmarking.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41dfa9b04945dbc8c673c444cbfa381cc0222ded">41dfa9b0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-24T17:03:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/collectjobs' into CUDA-Glob
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2fa1abca049c2f75c0c7785eaa0bf871ab03478c">2fa1abca</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-24T20:31:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added a centralized class taking care of projections on the device named Cuda3DProjectorKernel.
This class holds all the parameters and the projection function, which tremendously reducing code complexity.
The performance impact have been considered and to my great surprise there was a slight improvment
on all the three related kernels except for cuda_kernel_wavg that remained the same.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/11fd7d2da80ebe078337a406ffba11805d4be59a">11fd7d2d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-25T14:26:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Project built in double precision using the cmake option -DCudaDouble=ON
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9cbe515c57488432e9d89dc5f452cfe1deea6b8c">9cbe515c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-25T15:47:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed projector for double precison.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2628c50f7685997687761a604f795a780ae60395">2628c50f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-25T16:28:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Major reorganization of code to move out as much as possible from the central file cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad4db9093ae437f1b9419d92191d778bc0025bdb">ad4db909</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-06-26T14:41:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed error in weights, caused by exclution of ctf correction in the wavg kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d00340016ca80bbceb0f94108e828126099704d0">d0034001</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2015-06-26T15:57:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to collectjobs indexing
and some excessive index-juggling in the kernel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/72bcbd3a4909f104a2dfb54567b9b14273bb6cbd">72bcbd3a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-30T19:01:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Additional index fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de076ec9eb91ef53b0479b7b1ca2077fc60d0057">de076ec9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-30T19:03:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'collectjobs' into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7eecf42a7f26ec79dafb51c90f150ec54306faaf">7eecf42a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-06-30T23:43:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removal of Mweight-based collect2-kernel
Collect2 is from now on based on a dense
indexed array, which makes it faster, but
more importantly also removes the need for
copying the largely zeroed Mweight-array
to the device for each particle.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bfb24a49b8273aed5b698138f2811796fff4dcd7">bfb24a49</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-01T11:03:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better benchmarking output and higher resolved benchmarking entries in convert and store.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24e7d1dc61526ccbaaa376426c0541b061777c21">24e7d1dc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-01T12:11:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add thrust max-reduce, removed Mweight-dep MaxVal
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/39f60a226d2000c5ff9aa29c4a2fc68507b288ce">39f60a22</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-01T14:37:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Pass op by ref, more exhaustive benchmarks
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3bc5c228d5f7fd3e4016e1938897aa642cf5ccaa">3bc5c228</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-01T17:38:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Getrow & nonZero-picking removed from fine pass
These apparently only constitute a significant part
of the CPU-bound code in the fine pass. That taken
together with the fact that the Mweight array is
used for much additional implicitly indexed checks
(like setting coarse significance for the fine pass)
makes it easier to (at the moment) let the two methods
(sparse Mweight and dense weights) coexist and simply
use the latter in the fine pass where it removes the
need to fetch a large section of an even larger
Mweight-array isolate non-zero weights.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7e2c31cda739a803e7a656c258a01bca37badf0">f7e2c31c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-03T10:01:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fine pass Mweight-dep removed
NOTE: cross-correlation will fail with explanatory
error message. Since there is some doubt as for the
functionality of the CC-based kernels we see this
as a reasonable sacrifice at the moment.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6af7e693ba54fd1f6eeaaddbc08241b3b78a50fb">6af7e693</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-03T16:49:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New class IndexedArray to care for dense data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a659f22bd8c4e9f4e009f5db493df7fce7725abc">a659f22b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-03T20:51:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New class ProjectionParams holding projection data
NOTE: Some methods added to the IndexedDataArray
are not working, commented out and "labeled" as
"NOT WORKING" in files
cuda_utils.cuh
cuda_helper_functions.cu
These methods were not identifiable in eclipse if
inlined, and producing segfaults in unrelated parts
of the code if not inlined.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1498c27c1bb8a2af91e57c07ca6155652087b1ff">1498c27c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-05T18:03:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ProjectionSetup in fine pass made global
clarification: Since the coarse pass results in a
different set of orientations and translations, this
is still local in scope, held separate fro the fine
pass.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9501eab301a0ee883de3659d10f4f86a3e1bdb22">9501eab3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-06T11:53:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ProjectionParams handles classes (untested)
Only when IndexedDataArray can handle classes as well, can we
test and debug the multiple-class-capability of this commit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68ed4086e4b075fc6ac0b7adcc33218e75f10c30">68ed4086</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-06T20:28:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Draft proj_div-capable ProjParams (not working)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58d370a232a63df0b32b1554e1e99a2b2bf9e278">58d370a2</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-07T13:08:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix for memory issues cauesed by an invalid delete and a incorrect boolean expression. Also fixed group-id in fine pass.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/08cac24172664ba65cb2e4b61813d359a75fc223">08cac241</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-07T13:08:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/093ff4520d3b84e7aaf2109005e338099c358660">093ff452</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-07T15:40:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to proj_div under new ProjParms
At som point the wavg-kenrel might benefit
from direct use of the dense weight data,
rather than map to a partial sparse object
which reduces all translations implicitly
for each significant orientation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/45c50917b0aa1c183b6195cc8914b7dd096b7be0">45c50917</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-07T15:43:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d947c83aa9df564136f221a40bf54e694301a6d8">d947c83a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-07T19:56:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor fixes which do not affect single-class runs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9248ce51fc7cd24670e01ad61cb18d78eaf4f159">9248ce51</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-09T18:16:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ArrayMasks for classes (multi-class capab. prep)
We use dense arrays with explicit indexes for the sparse pass,
where oversampling could make the very few significnatly con-
tributing expensive to iterate through with nothing to do. At
some stages, we need to perform reductions of all classes. This
offers a solution;
Make an explicitly indexed array, carrying weights and indices
for all classes of this image. That way any class-wide reduction
has access to coalesced data with direct indexing. When we need
data for a specific class, we use a mask which when fed into a
constructor for a sub-indexedArray, returns a handle for the data
belonging to that class. The mask also holds arrays which deter-
mine the job-partion necessary for some kernels to exploit re-
use of some data.
The "global" index array for all classes of an image is (in
some sense) appended by the data of each new class as signficance
of each finely sampled gridpoint is determined, and the mask of
each class is simultaneoulsy made, to be available in the conv-
ersion of weights and the backprojection of them. The job parti-
tion of the mask is independent of the indexedArray, and can be
re-defined for the purposes of any kernel designed to use them.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/08ce24f6a1f6735254cc6b28210c1e83b3ad4a1e">08ce24f6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-09T19:02:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Job-splitting in function, consistently named
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3dd36c797c15ab15942df296206e9fac738f818">b3dd36c7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-10T19:23:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2 classes works for first iteration
The only apparent discrepancies are in the usual suspects; norm-corr
and log-likelihood essitmations. Class assingment and sumweight are
correct within the allowed precision.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b38dba71f755c9e5b968a2c735349823a3d3c2ee">b38dba71</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-10T20:45:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2 classes pass second iter, w/ errs in metadata
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e3434fd0054d06f12ee9de01e5c3849097321f16">e3434fd0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-15T14:24:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2 classes pass second iter, less errs in metadata
A shift in usage compared to previous commits
to enable multi-class refinement;
before:
only the classes which had significant orinetations to be examined were
prepared, by appending any new classes and weights to existing objects.
The result of this was a difficult-to manage class indexing, since loops
are over all classes, rather than all classes which are implicity deemed
relevant.
after:
Make space for all classes in class-arranging masks and ProjectionParam-
arrays, while keeping the weights-array coalesced. This way all classes
can be accessed by explicit indices in the masks and ProjParams-arrays,
and simply skipped when nothing is deemed significant in this class
to fix:
Some stuff is being done without purpose; breaks and continues should be
injected where nothing is to be done, so as make the run proceed quicker ..
Some general cleanup might be good as well, and the error with increasing
particle number persists.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29e2aa5cf9cb1d1ef6d123fdd4a3b4d397a20766">29e2aa5c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-17T13:32:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2 classes pass second iter for many particles
This commit fixes an error not apparent for low numbers of particles,
where the first iteration produces probability densities which are so
sparse that the multi-class passes essentially only ever tries the
same class which they were randomly assigned in the first iteration.
The error was that the weights which were determined for several classes
into a coalesced array, were never actually split in storeWS, but acc-
identally just used in its entirety. As long as the sparse probability
density limited the number of classes for all particles to a single one,
this was exactly equivalent to what was inteded. With more particles,
not splitting the array with weights for all classes caused undefined
behaviour, and eventually segfaults.
fixes #28
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6108cdc124965e475464549580b8e2f70a785872">6108cdc1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-17T18:28:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup of cpu & gpu-code, no functional changes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4519a1066dde72c8a42bd06f715eac25d3311fc4">4519a106</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-19T12:11:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">no comparison tests, add ryr tests /w local files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf520de638aa30bd164a0e120c147340c8c59385">bf520de6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-20T10:45:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor cmake cleanup
fixes #29 by changing debug-flags from normal vars to cache-vars
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4ab55ba0aaf98bb63227be2461304315af6d0074">4ab55ba0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-20T17:25:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moved projection-setup to rank-level.
Introduced a new class called "projector plan" calculating and holding projection-setup.
Added a vector of these as memebers of ml_optimiser.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b46f561b40ff3df39b49ac131462d4f0b30c29e">6b46f561</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-21T12:38:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed unnecessary writes ans therad-syncs to global mem in diff-coarse-kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/153cead18aad8f5d9573871abf29c6e45d4150d3">153cead1</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-21T15:42:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fiexed precalculation of projection-plan for multiple classes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f6de4f7cfd2510aedec05a37948753864777534">8f6de4f7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-21T15:44:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed cmake build types to include definitions.
fix #32
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/def702b2d072b65353005f7910e0079f4426dda0">def702b2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-22T10:10:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed old test file output references
Files this big should probably not be in the repo anyway,
but on an associated remote resource referenced by the
repo tests.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4d800f10769408b4076ae58b38b36cb1ad9cd39e">4d800f10</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-22T10:11:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ctest' into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d3207dd891b4bbaeaf4871eb269be7874559113f">d3207dd8</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-22T14:40:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor clean-up
Removed cudaComplex and some thread locks.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ce45b0d0eafaf6b73db153892f6536897e46f47">5ce45b0d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-22T16:32:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cmake sets cufft-libs/includes when specified
cmake -DCUFFT=ON turns on inclusion of cufft libs and headers
INSTEAD of regular fftw-libs and headers. NOTE: this commit only
adds this swap-functuionality, the cuFFT usage is untested.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8acc756bed8b75fc0e7d77d8edee4f6828b3b1ff">8acc756b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-23T00:01:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Dedicated cuda stream for each backprojector.
Also model-data reduced by half hence freeing up more memory.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b776a19676f2682d7de6b7d9e1fdc3c88aca38e5">b776a196</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-23T10:03:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9360714b9e0b6b790c9b76af05bb202a878c71a8">9360714b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-23T11:08:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moved maximization to the top in store to put as much CPU-time between it and the next particle-iteration.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ca8b21af01a56b6cd771d2e48cc005a850289f0">3ca8b21a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-23T11:19:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added some new shortcut functions for cuda mem-copies.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/880b181c9ecda2d3d0c78f4277bf344b91d4f704">880b181c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-23T11:55:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed extra call to generateEulerMatrices before backprojection and instead using previously generated matrices.
And some minor clean-ups.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2fa6277bcb6837e00249a7ab269d0597a2acd221">2fa6277b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-23T14:11:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make-warnings cleanup
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b22a88453e6654af35b947a4143f063839feb2a6">b22a8845</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-23T17:16:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">First implementation of a global device memory managment for effective asynchronous kernel calls and memcpys.
New class added, named CudaDevicePtr. A light device pointer handler that can be included in none nvcc context and reuse allocated space.
All device pointers in maximization (wavg + BP) are replaced with more efficent reusable allocations.
However, the pointers are not reused for more than one particle, hence no significant perfomance gain yet.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a3b933de9b2226d7fe4ab3afce96f691a0190197">a3b933de</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-07-23T17:46:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' of https://bitbucket.org/bforsbe/relion-1.4 into CUDA-Glob
Fixed minor error impaling the results of BP and hence output data-file of iter 2, introduced in commit 880b181c.
Conflicts:
src/gpu_utils/cuda_projector_plan.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1fd6da6faf3966017dfa346dc65e0703259ff981">1fd6da6f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-25T18:13:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">re-implemented relion-native profiling
...for those parts relevant for the CPU vs. GPU comparisons
we are looking to make: Diff 1&2 + convert 1&2 + storeWS
(with sub-timing on BP)
NOTE: NOT TESTED WITH MULTITHREAD
Also: adjusted ctest refs to nethome-spcific files, so that
one can now run ctests 5 & 6 on tcblab machines with no
extra fuzz.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e701f3eb245d394caaa6b62275f3c308a5f3f0b2">e701f3eb</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-26T15:20:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Forked cuda3Dprojector-method project to 2D/3D
In current state, 3D is assumed and used, so 2Dclassification
is still not functional. This is prep for 2D-capability.
see ticket #30
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ec377f9b6acdeca3a6d8a072f633593d428d8668">ec377f9b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-27T11:33:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Forked Backprojector-method to 2D/3D
The documentations states that a malloc3Darray with a zero-depth
extent will just allocate a 2D array. We are then betting that the
cudaMemcpy3DParms Struct (doc: cuda 7.0 runtime API sect 4.8) can
also handle an implicit 2D cudaArray, and that the existing method
CudaProjector::setMdlData will just work wih mdlZ=0.
Also generalized the 3Dprojector object to Projector
See ticket #30
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a01dda0893d44da896ce9bb2b6c0364c80f205dc">a01dda08</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-28T12:32:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added apparently missing cuda-header
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf662d2214e4d60b8f746805d035a9ca0106c80d">bf662d22</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-28T14:50:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Template difference kernels based on 2D/3D-proj
This will keep a single diffCoarse-kernel in the source-code, but
expand the compiled code to include separate kernels for 2D- and
3D-projections, respectively. This to avoid an if-statement being
evaluated once for every pixel treated in the difference-kernels.
The above is also implemented for the diffFine-kernel.
There is probably some additional streamlining of the source code
to be done, for instance the calls to the templated functions are
runtime-dependent and stated explicitly for either case, both out
of necessity (the comiler should make both) and simplicity. It's
not too pretty though ( see cuda_helper_functions.cu:518:539, for
instance )
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e9b85bd650149e911484b1d4fa9c090b1919a0f">9e9b85bd</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-29T10:38:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Template wavg kernel based on 2D/3D-proj
see previous commit (bf662d2) for more info.
see ticket #30
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2df5c6fc0ad9b1d52c7e81311d1c3335cd1b2802">2df5c6fc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-29T13:17:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reorder iclass > ipart loop in diff2Fine
This in preparation for movie-frame support, which will use
ipart as primary index for all associated objects;
-PassWeights
-ClassMasks
-ProjectionData
For this to work smoothly the ipart-loop (which iterates over
movie-frames in differenceCalculation-associated functions)
should be at the highest level to pick the object according
to those indices at (function-)global scope.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc5c82e03e81905b945083f53d9c002416ca7eae">cc5c82e0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-29T15:33:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reorder iclass > ipart loop in storeWS, step 1
The safest way to reorder the index hierarchy when the second
index is divided into two codeblocks 1 and 3, is to simply make
each block exhaustive, effectively finishing everything in
block 1 before ever reaching block 3. This comes at the expense
of doing block 0 as many times as we force exhaustive loops, in
this case twice:
-- original version -- iclass above ipart in partial blocks
for iclass
codeblock0
for ipart
codeblock1
cobelock2
for ipart
codeblock3
-- new version -- ipart above iclass in exhaustive blocks
for ipart
codeblock0
for iclass
codeblock1
codeblock2
codeblock0
for ipart
for iclass
codeblock3
NOTE! : THIS COMMIT ONLY FORCES EXHAUSTIVE,
AND DOES NOT REARRANGE THE INDEX HIERARCHY.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/62218be22fbace3c7ee1d734d2f23d6459ce85ad">62218be2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-29T16:06:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reorder iclass > ipart loop in storeWS, step 2
This commit does 2 fixes in one action. The action is
to switch the index hierarchy of the first storeWS loop-
block as follows;
-- old version --
for iclass
for proj_div
for ipart
-- new version --
for ipart
for iclass
for proj_div
the fixes are:
1. The old hierarcy implicitly assumes that the same
projdivision would work for all iparts, which is not
true, thus it could never have worked for more than
one ipart; it needs to be the lowest index
2. Allows the completion of all classes for each ipart,
which is preferrable since it is building an indexed
Array with coalesced access over all classes for each
ipart. To avoid injections and reallocations of alot of
data for each ipart, this is preferrable.
Also: One associated if(do_x && do_y)-block is replaced
by a if(!do_x || !do_y)-continue case.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/19b3a67af641de7311abb9954b5cde8745ad36c5">19b3a67a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-07-29T17:41:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Vectorization of Fine-pass weight objects
This commit represents the capability of the GPU-
based algorithm to handle sub-images of what in the
code is called and ori_particle, which is essen-
tially a particle which was picked in a cryo-EM
micrograph. Collecting movies instead om images
produces precisely such sub-images of an obesrved
particle, and thus this commit add movie-capability
to the current GPU-code.
NOTE: THIS IS AN UNTESTED FEATURE, SUPPORT IS
CURRENTLY THEORETICAL, AS ONLY SINGLE-IMAGE PART-
ICLE TEST HAVE BEEN DONE.
untested fix #38
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/af55b35f69680efc0c0848a2c68c313ad825ed9c">af55b35f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-03T16:21:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moved rank-level initialization to MLOCuda-constructor, which now is called once initially at each optimization iteration.
Also more cudaMallocs and cudaFrees are moved to rank-level.
Memory issues regarding the vanilla code are inconsistently casuing problems to pop-up here and there, someone should look more deeply into this (later on).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a783bfdc067a7af9184157d1cc1480417ed05c1">9a783bfd</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-04T12:32:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The functionality for two benchmark output files is moved to a new build type, namely "Benchmarking".
Now the profiling build instead creates NVProf markers at the same points in code as the becnhmarking tool.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8783f65162d1eed9936ad90ac5c2fd595714623b">8783f651</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-04T16:22:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some more prepartions for better utilization of cuda streams.
Each CudaDevicePtr can be assigned to a stream, which is used in all copy operations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c788809dc9fca06d37506c86f60d85726ed5b0a">9c788809</a></strong>
<div>
<span>by bj.o.forsberg</span>
<i>at 2015-08-05T06:54:52-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Derived build types inherit props
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9870fb401e1e3bc9ef5e6c10a05c15380707c338">9870fb40</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-06T15:18:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'MovieSupport' into CUDA-Glob
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
Some 90/180/360 offsets in metadata angles observed,
using non-movie data. No movie data has yet proven
that movie-support is functional, but planned modi-
fications require a common codebase.
Also, perhaps slighlty larger normcorr errors than usual.
This will be investigated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a12a7f9cbbf12bfa4a3e6f467325028daad984c8">a12a7f9c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-07T11:03:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed mistakes in merge regarding benchmark timing
Only affects benchmark build, and only timings.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3eabcc2535dd1846f821ece8988c0478dd47951e">3eabcc25</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-10T10:08:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Precompiler ifdef for cufft-compatibility
This will only allow compilation of the code with -DCUFFT=ON,
those binaries still suffer from NULL fftw_plans being returned
(see ticket #34 for details).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d64512fe326e20e304a733cd8945de3820648a2">7d64512f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-10T14:12:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some syntax related changes in cuda-projector that makes the compilation more robust.
cuda_runtime.h is now included in pure GCC-context and void-types are removed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/290e7228fb8e46d339c449d6d1f465d9c124c587">290e7228</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-10T17:23:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cmake is MPI-aware
mpicxx-includes are tcbsys-dependent, this is a FIXME
FLOAT macro is reserved in openmpi, S&R to XFLOAT in cuda-files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9e9f3949f4e373e0f982b3d9832c3e3a683e2e7">f9e9f394</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-10T17:34:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'CUDA-Glob' into MultiDevice
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5bc5b57abab94aacf36f0f4d1b41ed853f185327">5bc5b57a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-11T11:38:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some fixups for the backprojector to prevent read outside array boundary..
This however does not fix the memory errors.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd55847dda7adf3300f81f724cb5bbdce1bf1777">fd55847d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-11T11:56:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CudaMlOptimiser has device_id member
Device_id is default 0 and only set to anything different in the mpi-
compatible refine-code.
NOTE:
code compiles and works for
- non-MPI runs with non-MPI refine binary
- MPI-runs with one master and one slave
code does not run for
- multiple slaves
this is probably due to either initalization on devices != 0, or
cudaSetDevice not being MPI-threadprivate.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc94a2d8b97650f6d5437acc863bae80a85b83d5">fc94a2d8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-11T13:51:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MPI-parallel device mngmt functional
(N+1) MPI-ranks will run N GPU-enabled threads, provided
there are M devices, where M>=N.
If N>M, the run will fail with a telling error message.
Possible improvements:
- if N>M, device_id could be set modulo M.
- if N>M, ranks>M could run gpu-disabled.
Mdulo will work out of the box, but take up uneccessary ammounts of
memory without increasing effficiency beyond latency hiding, at
this stage of development.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/39bec21bc8599de5400477f659772db3e90d6411">39bec21b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-11T17:36:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue related to projection division in "storeWeightedSums".
Also moved the the handling of the size of FinePassWeights to a new variable called newDataSize.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a19f5709846fcd00e3662f285fe6f432962d0479">a19f5709</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-12T10:45:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes many of the valgrind warnings within the project.
A few still remain, however this commit fixes issue #39.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/69aa2a38d5982782908d33bb8c6bf835a043256d">69aa2a38</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-12T11:19:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'MultiDevice' into CUDA-Glob
Conflicts:
src/gpu_utils/cuda_backprojector.cu
src/gpu_utils/cuda_helper_functions.cu
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/65f3ef6aa2fd8fce245f0ad4f33501deea453da8">65f3ef6a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-12T13:22:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Backprojector setup for 2D calssification.
The CPU implementation of the 2D backprojector is used for now. Data is fetched from GPU and passed to the existing algorithm.
A member variable is added to cudaMLO, named modelIs3D, that is true during 3D and false during 2D classification.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ad4beab0b05c26c6c88be468f95481f2893e26a">5ad4beab</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-13T14:46:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Forcing 2D runs to abide to psi-sammplings mod 32
Some kernels in the convert-stage of the coarse pass currently
relies on the number of orietnations to be divisible by 32, since
this is an efficient thread-wise division of work. During 2D-
classification the diretional sampling provided by the Healpix
mesh is not factored in, yielding very low orientational numbers,
the default being every 10degrees => 36 sampling points. This will
unfortunately not be compatible with current kernels.
This commit fixes this in the simplest and fastest way possible,
by forcing psi_step to increments which produce 0 mod 32 orienation
numbers. The default is then implicitly modified as
10degrees => 36 sampling points , ROUND(/32) -> 32 sampling points,
so psi_step is modified to 360 / 32 = 11.25
NOTE: this commit has issus with texture interpolation, so to see this
edit targeting issue #40, double precision build is required.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a2529ba94ba75553cfd48f0db7a326eda0aba8a">7a2529ba</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-13T16:25:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added a custom cuda allocator and reverted memory holders from CudaDevicePtr back to CudaGlobalPtr.
The allocator is not used yet and the pointers are allocated using the default cuda allocator.
Removed CudaDevicePtr
Removed cuda_helper_functions.cuh since it was never used.
Removed "--default-stream per-thread" from the NVCC flags since we are moving towards custom stream managment.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d2443078f7e060de459d61fe51f1d31cc52c036c">d2443078</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-13T16:27:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d1a63eb6b791d062f122b62628b5697253c8683c">d1a63eb6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-13T17:25:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The allocator is now working as expected. *pops champagne*
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5f61900119a4ed4dec321a193a7cea65a8c53b16">5f619001</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-13T19:00:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The allocator is distributed out to the pointers in the code. It is however not activated since this cased an unknown issue.
Some helper functions had there parameters modified to make them more generic considering input pointers.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd1efc33f62551325d7f03e971ee90795bba3353">dd1efc33</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-14T10:19:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The last bugs in the allocator was found and removed.
Hence also it was activated for the entire cudaMlOptimiser.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f06e249fc6bc86f1a2a1e19632b33f02aed0d01c">f06e249f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-14T13:45:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moved translation and scaling (ipart dependent) in maximization to only be done once for every ipart.
Added getFreeSpace-function to the custom allocator.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12711197c88b809cf1b8920f23d91335632832c8">12711197</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-14T14:11:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2D classification proj uses textures correctly
The layout for object texture creation follows very different methods,
opposite to remarks made in commit ec377f9. The hope was that the
existing method would be able to create a 2D-texture capable of using
bilinear interpolation, as per the CUDA documentation. This commit
resorts to the 'default' method of allocating a pitched (aligned) cuda-
array and uses bilinear interpolation intrinsics during 2D classfication.
fixes issue #40
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/97f4ca41f07bcb313256ad8beae32c59dc942ebf">97f4ca41</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-14T14:17:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb102d0bfcc0157d7c90dfd65d792c0054f308de">cb102d0b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-14T16:35:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Objects shared by classes moved out of class-loop
Addresses ticket #43
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ee297eae9ee140a276e7d9055627d463eae7cba6">ee297eae</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-17T16:23:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed Issue #42 (2D texture object segfault on free). Also added some new stream synchronizations where needed.
The program runs through two iterations, however the output file is not correct.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d25a1c5d1aacee28d68e94aa2e45277e90573762">d25a1c5d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-17T17:01:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Index fix in 2D priors & psi-domain control
An array reduction was wrongfully using the iorient index to read from a
reference an array, whereas it should be indexed by a pure iteration var.
The reulting reduction was used as prior in iterations>=2 during 2Dclass-
ification, so no 3D test up until now have been sensitive to this error.
Also, the first iteration produced correct meta-data, apart from the psi-
angle which was set to the [-180,180[ domain for the CPU-only code, where
the GPU code gave output in th [0,360[ domain. The reason is not fully
clear but an explicit control has been added regardless of using GPU hard
ware or not.
NOTE : the psi-angle domain control should be tested on iteration >2 when
possble, to rule out any possible issues with the extra domain check in
both 2D- and 3D-classification.
this commit resolves ticket #43, but there are further errors persiting,
which are described in ticket #46
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b6630a59598d4e49a26edabd8e3dcfcfc3c90866">b6630a59</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-17T18:32:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2D classif. runs 2 iter w/o metadata errors
In order to swiftly implement 2D BackProjection, this was placed on the CPU
hardware. Due to this, the copying back of an unused device BackProjector
caused the CPU-Backprojector to be overwritten, resulting in an essentially
NULL comparison between images, since they were compared to all-zero models.
The only difference between weights was then due to the error associated
with interpolating pixel-values of the rotated images.
NOTE: there are still accuracy errors on single precision, the "w/o errors"
declared above refers to the obvious erros in the method implementation.
fixes #46
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2656ecf5ac41f282388951d5740c61aa3d4b7f20">2656ecf5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-18T18:54:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added prioritized streams to run backprojects on a low priority stream in parallel with next particle iteration.
Moving to compute capability 5.2
Added a out of memory handler to free up backprojection datat in case of memory shortage.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/40ef03192bd33b6d3845f9d2de7a56e195a45092">40ef0319</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-18T20:01:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moved two thrust-wrapped reducts out of class-loop
It was noticed that there was a large overhead associated with
launching thrust-kernels. In the 3D-case this overhead is negligble
compared to the time it takes to run the reductions, however, in
the 2D case the problem size is so much reduced that theis is no
longer the case. This commit represent edits to the code which
benefits the 2D-classification by grouping reductions into a single
call over all classes. It will benefit the 3D-classification to
the same absolute extent, however that might not even be noticable.
The changes are made to thrust reductions
- min(diff) @ end of diff2coarse
- max_element(weight) @ end of storeWS
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d1111356d2f04ebdbbcc65c2f58e6040985aa6a">9d111135</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-18T21:53:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Sumweight thrust-reduction moved out of class loop
Targets 2D refinement efficiency @ low block count
NOTE: only tested on 2D refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/af8d38112db066107f52b9fe87773660845c0bfd">af8d3811</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-19T10:18:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reorder ipart/iclass loops in diff2Coarse
In preparation for global thrust-min reduction of diffs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/671a341d1611bcee543215f62995972d788b7d02">671a341d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-19T10:28:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12e348051d3b23a4f9ba849dedbe6fe45318b741">12e34805</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-19T10:42:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Thrust-min moved out of class-loop in diff2Coarse
This is to reduce the number of thrust calls, effectively removing
their dependence on the number of classes. This does come with add-
itional memory requirements on the device, but nothing dramatic in
the 2D case;
estimations of typical settings:
2D : 134'400 diff-vals / ipart
32 orients
21 translations
200 classes
3D : 967'680 diff-vals / ipart
192 * 24 orients
21 translations
10 classes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f6187f830d710702b001ee5321e11b6aa73ecad0">f6187f83</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-19T11:02:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added the the CUB headers to the project.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f99edbc00b3b14ce9ce8e452f29569787f8a7a8">3f99edbc</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-19T11:03:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replaced thrust with CUB for the max-search in the metadata-section.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7eef6ca83243e87b0926c7de62eac54979187c89">7eef6ca8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-19T11:52:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5e0ec00bf603f41b614ff1628b6fc29c3e7f1145">5e0ec00b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-19T17:29:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some device<->host cpys are coalesced
Mostly using temporary device pointer children as kernel input
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1194e0f8e4f239a22d5416bb2c3f2a4c558f3dd3">1194e0f8</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-19T18:29:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replaced thrust with CUB everywhere in the project.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/081506548450585f53015de2704b45a36592be1a">08150654</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-19T18:43:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">diff2coarse avoids repeating memcpys
There is a lingering if()-case which precludes copying the calculated
diffs straight into op.Mweight, which would avoid a mapping which for
a 2D run of 10 classs takes as long ass all 10 kernels.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a0d3bdba8d29644c646f3de0161261f1104bd73">5a0d3bdb</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-19T18:44:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b9d57d45a5c9d391327df801b061a49fa89c4818">b9d57d45</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-19T19:05:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ccd6155c7ca5dcf30645771a964b406bfd7525f">6ccd6155</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-19T19:22:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor fix to merge & one sync removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/933a75330f00ac6a0c910620dec9cf520d7790a5">933a7533</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-20T15:37:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Sumweight priors are prepared for all classes
This is to
- short-term: eliminate memcpy-ops between kernels calls
- long-term: allow the sumweight-kernels to be grouped into
one massive kenrel call for all-classes at once
ALSO: fix to indexing in diff2coarse mapping between op.Mweight
and 'AllWeights'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/696d91c68d875c1b6f11b66b2813be94a1b21b07">696d91c6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-20T17:11:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">"COLLECT 2 AND SET METADATA" is moved back before of "MAXIMIZATION" in execution order.
MlOptimiserCuda is plugged in as outOfMemoryHandler.
Custom allocated space is increased to 90% of remaining device space after.
New memory analysis tools added to allocator.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d7c9fec6c6c56a772458bf47398e47d191683824">d7c9fec6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-20T17:11:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ae1b1b9bda9994f444eda52964a1a867a981052">1ae1b1b9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-20T18:48:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">coalesced some memcpy-ops of collect2
Some, which are harder to coalesce in the present state, were moved
outside the kernel-calling loop, so as to enable coalescing of the
collect2jobs-kernel in the long term.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2930542041292327cb464724bbd0f5fb3bc502e3">29305420</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-20T20:19:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">last memcpys between collect2-calls removed
Just like some recent commits, this is to
- short-term: eliminate memcpy-ops between kernels calls
- long-term: allow the sumweight-kernels to be grouped into
one massive kenrel call for all-classes at once
NOTE that his changes the affected part of storeWS from
for class
for ipart
preprocess_the_stuff()
send_the_stuff()
calculate_the_stuff()
fetch_the_stuff()
post_process_the_stuff()
to
for ipart
for iclass
preprocess_the_stuff()
send_the_stuff()
for iclass
calculate_the_stuff()
fetch_the_stuff()
for iclass
post_process_the_stuff()
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f289b170c14bee8295ea934d5ef60ca3ce4706b">3f289b17</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-23T23:43:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added some error handling wrapping the cub function calls.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0ee0fcc46589b5174c9e622d5f0c22f17d60c6f6">0ee0fcc4</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-24T17:48:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bf6186bb70f74feb40c061995cf024812e21918">8bf6186b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-24T18:23:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Custom allocator can be switched off with the cmake option "CustomAlloc=OFF" (default is ON).
Reverted device arch back to sm_32, since parallel kernel execution is omitted.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d829cd15301634a63b32e3385b952e2e58862379">d829cd15</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-24T20:05:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More debug-warning handling added to CUB wrapper functions.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/66c0f22ee73b4879616eaf8edbb134cca89b1e82">66c0f22e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-26T11:15:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed error in free-type of temporary arrays in backprojection data extraction.
Also added a new constructor for CudaGlobalPtr for assigning sub regions of pointers.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6787d4efee83112814d68c7f57a9375c16517e62">6787d4ef</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-26T11:22:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moved the following classes from cuda_utils.cuh to cuda_ml_optimiser.h: IndexedDataArrayMask, IndexedDataArray and ProjectionParams
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f7347ea90d76a0c9f59a8ab6e4461bddfcd8448">8f7347ea</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-26T15:27:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">failsafe-throwback : STL-based array ops
Also fix to indexing in convert (coarse pass) inherited dev-ptr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e42ef018edcfbc7d6ad205efe632436946e2930e">e42ef018</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-26T16:33:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Separated cuda_utils into one with CUB and one with thrust.
Atomic add device-function definition was moved to a separate file called cuda_device_utils.cuh
Inclutions of cuda_utils in every file was removed, since none use these functions.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc7a78e4dcec2cf5a61fd450bb6287d88fb1f67e">fc7a78e4</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-26T17:20:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
Inserted thrust instead of stdlib for sorting, sum, min and max search.
Conflicts:
src/gpu_utils/cuda_backprojector.cu
src/gpu_utils/cuda_benchmark_utils.cuh
src/gpu_utils/cuda_helper_functions.cu
src/gpu_utils/cuda_kernels/diff2.cuh
src/gpu_utils/cuda_kernels/helper.cuh
src/gpu_utils/cuda_kernels/wavg.cuh
src/gpu_utils/cuda_ml_optimiser.cu
src/gpu_utils/cuda_projector.cu
src/gpu_utils/cuda_projector.cuh
src/gpu_utils/cuda_projector_plan.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/597610c62497ce4c5d35f62bba668b5fd4767201">597610c6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-27T10:54:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">rm:ed excessive memcpy and CPU-based reduction
in wdiff2-reduction (storeWS) which occurs over all classes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9068a3b7b249db2c994a1766351fa26321c6daad">9068a3b7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-27T11:01:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/af1520ccc933ecbc6540bf58f4cc5118f40bfec0">af1520cc</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-27T11:51:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rearranged memory allocation for the backprojector data bundle to the end of the custom managed device memory.
Data bundles are now arranged in a stack rather than a vector.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d240eff1503f86f2d7129b9dd55ec3cf0f4490b">8d240eff</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-27T11:58:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed legacy if-statement in 'SET METADATA'.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/77efaa30cf671a67c1f892f5f0cb5516f08d080c">77efaa30</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-27T14:49:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixes to STL-based utils (fallback utils)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0fb65041ad5ec00679cd9f7edc39e53afaea8ff3">0fb65041</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-27T14:50:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a075715b6d84d72f9a87614f646449180b3a9da">1a075715</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-08-27T15:25:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor changes in BP kernel, yielding roughly 20% speed-up in kernel execution time.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/946384abbf588b1476bc891ea27e971bcce591da">946384ab</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-08-27T16:19:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Coalesced some diff2Fine-memcpys
prep for coalesced kernel call in 2D (and possibly 3D)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ab096149a7f8fb1b67492cedabc0219f32003869">ab096149</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-01T16:01:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2D backprojector ported to GPU.
A scatter approach was selected due to the homogenious write load to output.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64c023bb09c53af502aac26a6ee1d68e78dee38f">64c023bb</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-01T16:03:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/75593cea28941b87076fbcc24bfc98338952ca88">75593cea</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-01T17:35:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new class cudaStager to coalesce _small_ mem-ops
Given a number of cudaGlobalPtr:s wit hthe same type, they can be
handed off to a stager which will move their memory positions into
a coalesced memory space and transfer them simultaneously.
A number of improvements are possible:
- optional use of pinned memory as staging space
this relies on whiching to management of a copy of the supplied
cudaGLobalPointer, rather than reassigning the only existing copy
- allocate space only once total size is known
this relies on the development of an appendable list
of cudaGlobalPtr:s to reassign host- and device-pointers of, at stage-
time.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/88670bdcc7ae4e53b452109dcec487b5674288e0">88670bdc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-01T17:43:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57912701a7683ce93d0765f2938a393494abab0c">57912701</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-02T17:01:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Memleak fixed
Fixed issue #51
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ee19b31b44cacc6c551adc0fa53c74af806401b">7ee19b31</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-03T12:39:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Third iteration priors set correctly
A for-loop was missing an incremental offset to its max.
Fixed issue #52
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e54bc8c6108b1cb2f14520584e7e522c768a6c4">6e54bc8c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-03T15:24:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Additional psi domain fix with GPU-code.
Peripherially adresses issue #53
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/269cf89972d8b9fe4cf5b62bbd71e3eb3bbed854">269cf899</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-03T18:32:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">3D backproject is optimized with a factor ~200 (yes, it's freckin' 200 times faster now).
I'm very very sad that I didn't try this 5 month ago (if only I knew how efficient atomic adds are).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c13effde870e125e43e4e57a2385d13b13786e2">9c13effd</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-03T18:41:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b1efabea2b4f6f472b73b1c1f6189cfe11a6d24e">b1efabea</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-04T11:28:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Actually activated the new 3D BP.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f2a6217ac3e52ebabf2dad204fe1ba2a1f0319b4">f2a6217a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-05T11:41:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added missing loop for norm-corr factor
This was somehow glanced over and manifested as a small error which
could be attributable to larger particle groups being affected by a
different order of summation on the GPU comapred to the CPU.
NOTE 1:
The errors in METADATA which this commit adresses only appear when
multiple micrographs are used.
NOTE 2:
There is still some (reduced) deviation from CPU normcorr-values
when using double prec. GPU code. This could be additional factors
which are unaccounted for.
NOTE 3:
Using a .star-file which conatins 100s of particles from a single
micrograph and a single particle from another micrograph, the error
of the norm-correction of the single particle compared to CPU-code
is much higher than that of other particles. This (possible issue
is entered as issue #54
Fixed issue #53
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6790a40de42f2217a7188001d5ecd70ccd1f684b">6790a40d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-05T12:02:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ea6b30b85abaa03c8e87ac86668061dd0d13e164">ea6b30b8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-08T13:48:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed multi-class reduction issues
Issues fixed:
- One legacy zero-initialization kept resetting a reduced variable.
- One legacy if-clause (which was unneccessary) was given a wrong
index to fetch a boolean.
fixed issue #55
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b23e1eaf81a422396071aa70419407ca408150b8">b23e1eaf</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-08T15:20:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to wavg-kernel scale correction
The scale correction was included in the ctf-object in order to avoid
excessive multiplications. However, the ctf-correction was dependent
on a an if-clause inside the kenrel, and consequently the scale-corr
was only applied to the references if the ctf was also applied.
this fixes issue #54
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4428618f259ae68afb3e7c91293f743e4c5a19fe">4428618f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-08T17:43:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">moved sync out of class loop
Result of bad implementation in commit f2a6217
NOTE: extreme degradation of gpu efficiency without this edit:
this might be worth studying closer.
fixes issue #56 (documentation issue)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ff08d28bf2f88c4e3fd3f16517ad56df59429cdd">ff08d28b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-09T14:50:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ported translations to CUDA. However, data is sent back end forth between GPU and RAM so no speed-up yet.
Also fixed an error in backproject initialization step that occured with double build.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c2a43a33688fa84a7d2889bd50042d87d850f5a">6c2a43a3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-10T10:21:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CC-support in diff-kernels (draft)
May be severely limited by shared mem, but this is mostly because
sjors indicated that --do_firstiter_cc might be needed, and the first
iteration is hardly a priority at this stage
adresses issue #11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b1a492287bf53895fb79dd5edab98598d6a1b507">b1a49228</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-10T11:13:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
Fixed error in translation caused by misuse of scales in SWS.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b909997a85a8d46b1220a1f7d7eacbb246062df4">b909997a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-10T11:19:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CC-support in convert (draft) + fix compile errs
Setting of weights on device handled by two async memset-calls,
the latter of which handles a single value, which might be inefficient
also fixed compilation errors from parent commit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/383966adcdd8853e49401495d00d9ea14acc0dbb">383966ad</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-10T12:44:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added missing is-statement in partial class-loop
The major class-loop in SWS has been partitioned into pre-process,
memory transfer, kernel-calls, and post process loops. In the final
such loop, an if-statement was missing which may have caused some
segfault under certain circumstances. It is unclear wheter this is
the fix to, but it was certainly found because of, an error similar
to that described in issue #57
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f14682758a1323e73557473f02baba3f6da20ce7">f1468275</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-11T12:05:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cross-correlation works (CC)
The kernels are NOT optimised for --always_cc, but rather just
to be compatible with the need for --firstiter_cc, whereunder we
simply assume that a stupid implementation will not affect the over-
all perfomrnace of an entire classification/refinement run.
NOTE: A third factor in the GPU-based image-correction applied to
the difference metric is introduced, which should cause some concern;
the accuracy might in some cases suffer. This commit leaves an
alternate availiable; however commented out. op.local_sqrtXi2 can be
applied either within the buildCorrImage, or at the end of CC-based
difference kernels. The present approach is the former.
fixes issue #11, creates optimisation issue #58
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/467e482a912d1bbbd1ad9ee834501d03db51b5a7">467e482a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-11T13:27:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
Conflicts:
src/gpu_utils/cuda_helper_functions.cu
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6df1feb9d5251b948ea93165fdaab945ef507fd4">6df1feb9</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-11T13:53:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added the translation-class and the plan nested class for handling of transaltion-data and kernel calles.
Some clean-up of old code in BP.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7f1706ed09fecd57ceabdf96033d901a9cb63cc">f7f1706e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-11T14:52:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ab45d84b296f683e25eb3b5eee888456c4d3145">1ab45d84</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-11T14:53:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Data prefetch to GPU memory implemented in GSD-fine and SWS.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ed9083dbab126529414a707122951f2dbc7051bf">ed9083db</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-11T16:06:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor clean-up of old translation leftovers.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/98d5e100fede3f14c952695bff1038f070aae999">98d5e100</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-14T16:50:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed xdiff reduce by introducing atomic adds to wavg.
This have rendered a slight speed-up but is mainly a preperation for a kernel call for a classes at once.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ed88444cafc8e0e025ed1113a6c13e801cf1c94">5ed88444</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-14T17:15:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed proj_diff and the second euler generation between wavg and BP by reusing the first one.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/71b195f2b8cc094cfcaf9d0fe4a92b9c7a693cd2">71b195f2</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-14T17:41:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some minor clean-up in wavg-kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/82c2e63d2f5a2763ba07ff6b937fff7ee0fe4554">82c2e63d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-15T09:49:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Separate control of doff2-coarse block size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac848b06053c6f7a49c269934f4e395669d67b1a">ac848b06</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-15T09:51:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ea586e6bed4c0650877e8dbc4597446e86627a46">ea586e6b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-15T12:07:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cuda-devices are now associated with threads instead of MPI-rank.
To run on 4 GPUs use "--j 4 --gpu".
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f854a06f91ece86e8e41688e5b600ea7a2e16e9d">f854a06f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-15T13:17:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5edaca782a1a06d5d330b022612e92f5c59f35c9">5edaca78</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-15T14:04:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed unused collect2, enable wavg block_size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/79995a47ef347a44cd2e396816793549794354be">79995a47</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-15T15:03:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">sumweight coarse update, wavg sync
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7cec93d63268dbaaf0e781364bd689e4a32cd7b8">7cec93d6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-15T15:44:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">streamline SWC-kernel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/712e05f6600586e6941d34a1ce1300ce540de807">712e05f6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-15T16:08:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better opbject integrity for CudaGlobalPtr.
Added a setter for device and host memory pointer.
Added setter and getter for size.
Added operator () for fetching device-pointer, like the corresponding [] for the host pointer.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c9035928409838f3081bf2ec8db97bb0c418a896">c9035928</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-15T16:37:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/13d6ba2f9e49ba0577e6747d4e38835fe330ee3a">13d6ba2f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-15T17:21:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">killed GPU_T*Cs + 2D test on nethome/empiar
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac4211d0f4579965fc3183f773010c5741d779fd">ac4211d0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-15T17:22:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a296be028eb3f3f4fc103cad2910bfe5761a7093">a296be02</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-15T17:50:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added 2d test & forceSTL compile option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2b002d4550406394871ff38ad7ab2e2bea46377">c2b002d4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-16T11:23:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">--gpu flag can take string of gpu_ids
--j N --gpu
where N is an integer, results in default behaviour;
trying to set the dev_id to the (--j) thread id
--j N --gpu 00...00
where 00...00 is N zeros, results in putting all threads on device 0.
--j N --gpu 01...(N-1)N
is analogous to default behaviour.
example; want 2 threads on each of 4 available devices;
--j 8 --gpu 00112233
or
--j 8 --gpu 01230123
or
...
Possible reasons for errors:
NOTE: device ids start with 0 !
Trying to specify more threads than devices without specifying id's
will result in explicit errors. This will also happen if an id larger than
the available device number is specified. For example, with 4 available
devices:
--j 5 --gpu => error, since this will attempt dev_id=thread_id>avail_devs
--j 4 --gpu 1234 => error, since dev_id=4 <=> device no. 5
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/051fbadfc53486aee41d1c795ff69be9f93ae66c">051fbadf</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-16T17:30:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cuda-owed getFour...AndCtfs copy & timings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/76b4098357c3f0fb4b54bae3762f1b8bff4b0c07">76b40983</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-17T13:45:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added some new funtions to CudaGlobalPtr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58f0efc46b19a9b64a7001b6d08dfc377d39ee69">58f0efc4</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-17T13:46:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">BP data is transfered from GPU to RAM thread safe.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6f2e316ef7c386f5ac402265d57cf91154a6a1cd">6f2e316e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-17T14:21:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">First fourier transform in getFourierTransformsAndCtfs is gpu-accelerated. 2x speed-up of this subrutine.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2000c5b73583c8a4a1f320a7a81ea6de84dda25e">2000c5b7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-17T16:33:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">SoftMaskOutside on GPU
until tested by time, a bool remains to switch on native (CPU) function.
ALOT of optimization to be done, at the moment a ~2-3x speedup of
SoftMaskOutside-block and wrapping ZeroMask-block.
This could be reduced by half; A kenrel which prepares a [0,1]-domain
filter for all particles could devote SoftMaskOutside() to figuring out
just the scaling and apply a pix-by-pixel filter without the need to
check all norms and range-conditionals within the kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eed5a4329435c1f029c7befaae5227cd9c40cf1d">eed5a432</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-17T16:34:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/38983937668304db3e3c3fda0110bd21af1f4941">38983937</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-17T18:42:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">SumW-kernels overlap, using cudaMLO class-streams
In order to keep the number of streams down, the classstreams
were made a member of the cudaMLO-class.
NOTE : at the moment we use DeviceSyncs after the only class loop
which uses this class-streaming. This might be bad, so we should
think about some way of syncing just these streams before continuing
along the CPU-code.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b494a2a56693a50754df2e101a0e3039b0bfe87">6b494a2a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-17T19:19:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">class-streams for diff2-kenrels
NOTE: using devicesyncs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6210b71e33f50702c1ee9fe32de450c7d7250b0c">6210b71e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-18T16:12:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added some currently unused functions for future reference.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/acb5b5739b65ace920d0ba2f7229a13cfbfac415">acb5b573</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-18T16:43:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">"onthefly_shifts" is automatically set to true when do_gpu is true.
Also do_gpu now works in "continue" runs.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/00bada0f6910e0ed6997e7b83866ed983c5491ef">00bada0f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-18T16:44:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9d251f52f75a73a11f28fc5b06317c2cd8e5845">f9d251f5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-21T15:55:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed the use of void pointers in MetaDataContainer to fix some memory leaks reported by valgrind.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca0f4bdae7316f1712ca50040454b9a3124917c9">ca0f4bda</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-21T18:48:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Disabled cufft (commented out) and fixed some other bits of code causing valgrind reports.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb1e6f98b7ce37484538d5e9104635294ae49c35">cb1e6f98</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-21T18:59:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The gpu memory (in GBs) reserved for each thread can now be set by the new flag "--gpu_memory_per_thread".
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb265230c419adf68d5323b91283917cb4b59fdd">eb265230</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-24T11:03:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">"HANDLE_ERROR" is now active in release build, while the old debug error handler is renamed to "DEBUG_HANDLE_ERROR".
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f9fc31372f5733327212654dbcaa99f880e7c8f">8f9fc313</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-24T11:07:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prepartion for the new setup where GPU resources (streams, textures and allocations) are reused over all the iterations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/852f3a65437b7ab4f187987cdb856efcfad1b5a4">852f3a65</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-24T15:05:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rounding psi_sampling up instead of to nearest
NOTE: still forcing nr_psi%32==0, just being careful rather than
approximately the same
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2721a69156132bd6ff184ab17f614dc42835dfc6">2721a691</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-28T18:01:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Non-working first commit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3d9c47519a245ec255596489612544b8be3921aa">3d9c4751</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-29T13:09:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some minor changes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c28d94b0e484244d8140f8abac9328bdc83dc027">c28d94b0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-29T13:25:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'reused-gpu-resources'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b87c43453e54b54477873043e149fc884bae3698">b87c4345</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-29T18:23:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed error occurring due to onthefly_shifts being switched off during auto-refine.
The translators are by-passed in case the onthefly_shifts-flag is not true. Instead the translated images are used.
However, auto-refine still dosn't work due to some other error ("trying to host-alloc a stager with size=0")
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1144ac612706b49080b0edbca1d836f2c9416fa5">1144ac61</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-30T12:39:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">binaries prepended by 'relion_' as originally
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01f08d6854a080369ba67d722834207437fd9f56">01f08d68</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-09-30T15:07:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CMakeLists-files updated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d094ea3ae7fca57dd91eeb23fbc47179c26b61ad">d094ea3a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-30T20:04:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The memory assigned to custome allocator is set to 70% of available device memory if gpu-memory-flag is not set.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ca9600be61a1d88b98194bb1045ceb8ea02df08">3ca9600b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-09-30T20:06:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24ae8be67ab6d6d97cf6897e8d328e41c16c1e81">24ae8be6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-05T11:46:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Texture can be turned on and off in single precision compilation using the cmake option CudaTexture.
However selecting double will overwrite this option to non-texture compilation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c7a07b75f52601770e5eba597aacd4ee7c9e9a87">c7a07b75</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-05T15:47:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI bool option in cmake
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ba03303b4118994e47918dc61729a9c893c2027b">ba03303b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-05T15:47:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/13c6de34a32abdc5e076556d73035c622581fcc1">13c6de34</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-06T17:59:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Devices are automatically mapped to threads in a smarter fashion.
If nothing provided (even if followed by another flag [previous bug]) the devices are evenly distributed amongs threads.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cfeb544d394c5f4b7b07285a486f00a702c9c744">cfeb544d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-07T09:59:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b324b9d93585dbc2c6a8b3bde8ecf896f2499c58">b324b9d9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-07T14:48:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor changes to get FourierAndCtfs
no changes to functionality
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf9f47b880007a40f3d2b7c02bb70c557006e776">bf9f47b8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-07T16:57:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">turn off gpu-tic/tocs & ml_optimiser-bugfix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c70ce37da21fb1e67e5eeb95a25bb2ffc13112f0">c70ce37d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-08T14:10:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">local searches tagcase works w/o custom allocator
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/236c78b75fdeaf905ce2d53172ccd27b7e7372e9">236c78b7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-08T15:04:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Custom allocator assignes aligned memory, dynamically adjusted to device specifications.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c9a74be38d275857eb1effa1c5a9f8f411b4eec">3c9a74be</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-08T15:55:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updated warns and non-0 mod 32 compatibility
Previously thew orientational sampling was implicitly assumed to be
0 mod 32 in the the coasre pass due to the healpix sampling. When
doing 2D classification the psi_step dictates the number of increments,
the default being 10degrees => 36 steps. The quick and dirty fix was to
force 0 mod 32 by adjusting psi_step to fulfil psi_step = 360/(N*32)
for some N.
During local searches and/or auto-refine 32-multiple coarse psi-sampling
might not be fulfilled or even desirable for effciciency. To circumvent
this we have now allowed any psi-sampling, at the cost of wasted cycles
on the GPU. A cleaner fix from the point of view of functionality, but
still not the computationally sleakest fix.
ALSO some cleanup of unused class_ids in IndexedDataArray
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/36166982047328766faaf7f9bc3eef660d85f30e">36166982</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-08T16:04:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/11b20c65b8e5f2b3f43d77f891f735fcae55c518">11b20c65</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-08T16:54:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Translationa are done on the fly inside diff2coarse-kernel. This yields a slowdown, but removes L2 bottleneck.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a4e3e2d09597bf83ad4890993c83be4308cbc135">a4e3e2d0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-09T18:07:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Multiple projection per block yeilding a factor-2 speed up.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad94cde4a673e263b116b72f68bc552c8fb139fb">ad94cde4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-12T14:31:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">double rplaced by RFLOAT
locations where Sjors preserved double have been similarly preserved.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/db2228e177d598e01f16f7e72d4f65b7d53403a6">db2228e1</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-12T14:49:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed output error caused by synchronization issue.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12a2cd6c9e1c52afaea970bb92e9ed371a24fd89">12a2cd6c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-12T15:04:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">sjors dev-code @a7f194b (src)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ffb71977a3a35259a9b5e531abc70cacb8c17116">ffb71977</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-12T15:57:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'sjors-dev' into sjorsmerge
Conflicts:
src/Healpix_2.15a/cxxutils.h
src/apps/CMakeLists.txt
src/apps/image_handler.cpp
src/apps/project.cpp
src/apps/stack_create.cpp
src/assembly.cpp
src/autopicker.cpp
src/autopicker.h
src/backprojector.cpp
src/backprojector.h
src/complex.h
src/ctf.h
src/ctffind_runner.cpp
src/displayer.cpp
src/euler.cpp
src/exp_model.cpp
src/exp_model.h
src/fftw.cpp
src/fftw.h
src/filename.cpp
src/funcs.cpp
src/funcs.h
src/gcc_version.h
src/gpu_utils/cuda_backprojector.cu
src/gpu_utils/cuda_benchmark_utils.cuh
src/gpu_utils/cuda_kernels/diff2.cuh
src/gpu_utils/cuda_kernels/helper.cu
src/gpu_utils/cuda_mem_utils.h
src/gpu_utils/cuda_ml_optimiser.cu
src/gpu_utils/cuda_ml_optimiser.h
src/gpu_utils/cuda_projector.cu
src/gpu_utils/cuda_projector.cuh
src/gpu_utils/cuda_projector.h
src/gui_entries.h
src/gui_jobwindow.cpp
src/gui_jobwindow.h
src/healpix_sampling.cpp
src/healpix_sampling.h
src/image.cpp
src/image.h
src/macros.h
src/matrix2d.h
src/metadata_container.cpp
src/metadata_container.h
src/metadata_label.h
src/metadata_table.cpp
src/ml_optimiser.cpp
src/ml_optimiser.h
src/ml_optimiser_mpi.cpp
src/ml_optimiser_mpi.h
src/mpi.cpp
src/mpi.h
src/multidim_array.h
src/numerical_recipes.cpp
src/numerical_recipes.h
src/particle_polisher.cpp
src/particle_polisher.h
src/particle_polisher_mpi.cpp
src/particle_sorter_mpi.cpp
src/preprocessing.cpp
src/preprocessing.h
src/projector.cpp
src/rwIMAGIC.h
src/rwMRC.h
src/rwSPIDER.h
src/strings.cpp
src/strings.h
src/tabfuncs.cpp
src/time.cpp
src/transformations.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9735ee739f66c9def96ccbaa1adb526fc1a23bb">f9735ee7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-12T16:04:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cmake fixes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/95e90613ebddb597f185e76118ccf13c38be89a2">95e90613</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-12T18:35:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More control over data flow in diff2 kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b2ff00ace57c5f5e839d611efbb966833efa579">2b2ff00a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-13T09:30:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed double device set
healpix formalism corrected
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8524c6a83e748087eb075a57635d654696dcc556">8524c6a8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-13T15:50:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relocated gpu device-set and added timings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e83c4519e01d5a66827df4c3e0aa4fc8f6d979f9">e83c4519</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-13T15:51:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">printf specifier
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4cd6de0bab9e83fc140c73bea31d28f2d1a1b141">4cd6de0b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-13T15:51:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">strcpy overflow
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c6276bae70cfa67fc987a3850a1d6f54fe55599">9c6276ba</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-13T16:07:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">return objs from sys-calls added
to remove compile-time warnings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0a3b4b28a3f69d992c04046963c60c5f982e334d">0a3b4b28</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-13T19:09:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better control of statics properties of the diff2-coarse-kernel.
Optimal properties set, should be tested for multiple systems.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd3a1c93560093a50e2b5fb509e9f35a7fbba59c">dd3a1c93</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-14T13:22:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cub appears to work, replaces thrust
The identified and amended issue was two-fold, and roughly independent.
The custom allocator was not correctly aligning memory addresses, resulting
in wrong and/or misaligned adressing.
Switching to the default allocator, the temporary storage size got set to
zero for small sorts, which resulted in a NULL temporary storage ptr, and
subsequent sort again tried to estimate the needed size, rather than
perform an actual sort.
this resolves issue #67
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/08bc0719ad565db9b35d45f5961e636ac33e6bdf">08bc0719</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-14T17:59:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added warnings for cases where orientation nr is not evenly divisible by 16 and 4, for 3D and 2D respectivly.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f00ba01b2f6b3ef3703f4f97e3e628440daa88e5">f00ba01b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-14T18:15:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added support for orientation nr other than evenly divisible by 16 (3D) and 4 (2D) in calls to diff2-kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58ad10b43d6ff253cc9a6f7282230ecec70e6b20">58ad10b4</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-15T17:19:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'experimentalDiff2Coarse'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/987492053402cd7c617442e0cc61b5c6245f39f3">98749205</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-16T17:59:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed an unnecessary stream synchronization after BP and added stream management to cub-utils.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60d79ce0d6d909ffd6092b612fe5c2543ee39b84">60d79ce0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-19T12:01:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'sjorsmerge'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d43cf71df66d5adfab3e86de5e0e8011d7d1fc27">d43cf71d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-19T15:11:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moved the mapping of AllWeights to Mweights to the gpu, hence removing back and forth copy.
Yielding 5-7% speed-up in 3D classification with one class.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02c1609d71ef6adb6751cc04042edef4fc16c3c1">02c1609d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-19T15:57:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-1.4
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/76274f9867962671ccff259d0b6789d6a89b6148">76274f98</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-20T14:05:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue 71, caused by translation data not being sent to the coarseDiff2_CC-kernel.
Clean-up in convertAllSquaredDifferencesToWeights.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8976ffa6b486c353b4c4b2839ffd39de599ba771">8976ffa6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-21T11:13:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added --average, flipZ and ampl_corr to image handler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a17ad36cdea40152df570f08046883c6de76f18e">a17ad36c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-21T16:58:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">device ids are set consistently mpi/non-mpi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/93aa3b2167f687b72c26f5b2471c8f026378b829">93aa3b21</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-22T13:40:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mapAllWeightsToMweights uses class-streams
also passes streams, rahter than cudaMLO, to helper functions.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ccfdaf0d2cde24da40125996cc682d0b5e9cacc">7ccfdaf0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-22T13:45:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed two valgrind warnings cased by cuda stream creates writing outside the data size of cudaStream_t.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd013c93d8f9e589376a8f2ac7c7c4445abb58ed">fd013c93</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-22T14:30:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
Conflicts:
src/gpu_utils/cuda_helper_functions.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/75127a2df8cd1231a6e585537d9e747eb19cf0a4">75127a2d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-22T17:10:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix for "DEBUG_ERROR: Non-zero allocation count encountered in custom allocator between iterations."
Caused by backprojector data bundles remaining in custom allocator.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/928942657cab23026e638d0107acd96776bc9f7d">92894265</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-22T17:38:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed "DEBUG_WARNING: Device double allocation."
Caused by double allocation of object in projection-plan-class.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eda3042b2c06fe92951de5c1763cabceb5b85ccb">eda3042b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-22T17:04:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">second attempt to commit changes in GUI for wrapper to Gctf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/164583637bcd016af5e87248eb526c54c57c8dd7">16458363</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-22T17:06:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">second attempt to commit changes in temp hack to allow using 2 gpus through mpi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3d0bb2b87d5f0a9519e359406bc8221e051474e5">3d0bb2b8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-22T17:09:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">second attempt to commit changes to get rid of annoying print statements that keep coming back
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24aad353f706e69b409bbb77faa5b9d3ab57ce73">24aad353</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-23T13:56:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">wavg is class-streamed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/43b46cc51a7a748968b069ea9fbffd52105530a3">43b46cc5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-23T17:23:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rearranged data flow in convertPostKernel during coarse pass.
All calculations are done on gpu, yeiling a factor 7 speed-up of convertAllSquaredDifferencesToWeights in the coarse pass.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e56c1b1cd94916459d9445fee9a92081b24f5d89">e56c1b1c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-26T09:01:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d7fcc54e6306e0d4e8137001825fec7154e2678">6d7fcc54</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-26T15:44:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Summation of the weights are moved from the sumweight-kernel to instead use the last value in the cumulative sum of significant weights.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c556d853dd16b91805672b84a4102d87f93ef392">c556d853</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-26T15:46:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0eed68b7cc9b0ea32334f65d5d646b1edd51a713">0eed68b7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-26T16:14:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean-up in generate-projection-setup. Prior look-up is embedded in Mcoarse_significant and not needed to be fetched again.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24e33e7733259bb678c8cd8ad29b907b1c89300e">24e33e77</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-26T16:21:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">timing fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b6c22af2ce87e04d3ee68bfe848864e4b14b9afc">b6c22af2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-26T16:22:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d83ea8f82c19193a8bc3e0606c04d697cdf73473">d83ea8f8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-27T10:35:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixes to debug warnings
(was checking against old stuff)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2f6265ec595a1a2801e894f967c13b287e433c78">2f6265ec</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-27T10:56:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Also convert-fine uses the cumulative-sum-approach to fined the significant weight and sum of all weights.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c0afe4d004e94a7cb22b2b4e69d5051ef1e47406">c0afe4d0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-27T10:51:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed warnings about norm corrections and made initialization of GPUs sequential on MPI ranks
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2abb3f00035753173388f5b7bb4e1adfcccf713f">2abb3f00</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-27T13:00:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2 passes on GPU to avoid --oversampling 0 issues
This due to the difference in datastructure between coarse and fine pass
in the GPU-code. This MAY clash with some local-searches or similar. Be
on the lookout.
fixes issue #73
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6067d7f12773d6497dbd000f927a70a5609a567b">6067d7f1</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-27T15:37:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed the value of the metadata field my_nr_significant_coarse_samples.
Also fixed debug and double precision build issues.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c9ec3451638fdad843742b8033dfa4b6f8a3649e">c9ec3451</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-27T15:39:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replaced cub with thurst in the filtering function.
Also setup the custom allocator to be used by thrust. Hence no cudaMallos or cudaFrees are called by thrust and memory allocation on top of the reserved amount is not required.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8197b0702f3e5d21d24c30c22e566971abe05b24">8197b070</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-27T15:48:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b54bc28dafe193b4fba3b85b2bdb3fcf1a3500fb">b54bc28d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-27T19:13:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed valgrind error in storeWeightedSum.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d94012e5fb82146bcb44f7aa6ca97b3ad995cfc">6d94012e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-28T09:15:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #1)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e028c28b01503fa7385d1fb0d744ae19dba0a101">e028c28b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-28T11:42:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">implemented option to apply solvent-mask correction every iteration of auto-refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b1963a2e72e61be773e0ed7e8618c23879709a62">b1963a2e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-28T11:48:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts in merge with relion-devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16a71a2c569ec7d1ea4044652570bc252cac7efa">16a71a2c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-28T11:52:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts in merge with relion-devel, part 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bd8517b58198b94785833ea3eddb9bd0bd047e1e">bd8517b5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-28T11:53:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2e9fec6495a952958b335ce450730e05826e52e9">2e9fec64</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-28T12:03:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">put back my changes in ml_optimiser_mpi.cpp and removal of persistent printf statements in src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/54ba25a684266a1f5636c580b00b3981fe0bbdf5">54ba25a6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-28T12:07:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #2)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/15fd471ee8bebb5f3b7576ecbb6838155613e11e">15fd471e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-28T13:14:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ee95b446a3bd3858eab4f418e14f29d44777e155">ee95b446</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-28T12:17:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">put back ontheflyshifts=true in initialise of mpi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4394ceab0a79f8fb888db873e507a5702ab93370">4394ceab</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-28T15:08:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed an error caused by omitted handling of the excessive blocks created by the obsolete block-split-function.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/79a7132cf50ec1d7369216426744ec33d3430ce3">79a7132c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-28T15:37:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #4)
Bug fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5bd32c8e22667619de04c835fae513707a2dd0c6">5bd32c8e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-10-28T15:37:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d516a1f77247d8d7bf86c785b05216dc31e0512f">d516a1f7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-28T17:52:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ba3aed03b9a3abb72f2968a72ed295275c88c131">ba3aed03</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-30T17:08:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixing a bug when there is a single significant weight
Also some added debug-verbosity by adding cudaPeekAtLastError()
under DEBUG_CUDA precompiler def, which should catch some more
errors closer to their true origin.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02feb2eab6672a3e3dc84b7e4bf24d4674134cd3">02feb2ea</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-30T17:37:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Huge revison on the custom allocator, where allocation can be marked with a cuda event which have to expire before deallocation.
Backproject data bundle is no longer required.
Out-of-memory-handlers are no longer required.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5cc9a78604b7b9cecba7c42d11ab09acd34a189">c5cc9a78</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-10-30T17:45:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de4f43a028bec9cd43fe0a3a73933fab442d48cb">de4f43a0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-10-30T18:03:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/586f54c2fec60d535d656fc03080be6076a955f0">586f54c2</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-11-05T09:48:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed a memory related debug print out.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c28e0d5b778072b655e3031c080a4903a461be25">c28e0d5b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-11-05T09:49:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cbafca7b4d074273f9defec47c38e41d5bc1ada9">cbafca7b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-11-10T14:28:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add preread_images to cuda code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cdd2b8a656c8d2a8347a210d841238e14963a6ff">cdd2b8a6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-11-12T14:49:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">implemented new sigma_rot for dna-origami+p53 refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4a9c59fe3510d6576d2c4b47e0b37a7ed9aa6b2d">4a9c59fe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-11-12T17:00:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">big merge with helical and multibody processing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/550b6de37b9977fc8a1de1aff5adfc76c28be08d">550b6de3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-17T18:25:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Forcing some intrinsics in diff2
also cleaning 2D/3D projection code, which seems to have
minor improvements (2D diffcoarse ~7%, 3D diffcoarse ~1%)
due to reduced thread divergence.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c1da926d48c7e07dbf6e373f3dc9d09e12bfd7a">0c1da926</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-18T15:42:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cmake cleanup and warns about double when single
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c77efeab2b235cbc1af83febea3d74c2de1e7c0">1c77efea</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-18T18:51:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed compilation errors
Also a double-prec computation in single mode in translator.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41890eb73c035e5fa60eab4174ea30795b70a33f">41890eb7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-19T12:26:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MlDeviceBundle introduced but not taken effect
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe764181b70e888599c115c358280b553150d2e2">fe764181</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-19T19:07:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Draft devicebundle which seems to work.
Some ugly stuff, like cuda_ml_optimiser.cu:653-656
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e300f20cf703f3df3eef9e6d1e3c0905dd2b40ac">e300f20c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-20T14:09:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Simplifying without changing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fde6a6041018fe8a5a2dc0191a7db64922faeee8">fde6a604</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-11-20T16:49:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">first moves towards a pipeline-version of the GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/533c19573b207cc404f97c43fc83f5eeabbe9412">533c1957</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-24T11:21:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">pool-flag --pool
does NOT modify block_size of pooled particles
see issue #74
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d20778ebff1edddbdeb976a2e98a594dfdec61ee">d20778eb</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-11-24T11:38:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added RelWithDebInfo as a valid build type.
Currently CUDA_DEBUG is activated when this is set, the performance impact of this is however not evaluated.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ee0f4913afb4e58809167d3a592521d0b4d1f1dd">ee0f4913</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-25T18:19:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">single/single prec on CPU/GPU is default
Some changes to names of cmake vars to clarify precision choices.
Also some changes to how the fouriertransform plans are reused
on the GPU.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2013caaeb0fc1bff7310ef834ab4c4c9a8466826">2013caae</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-26T10:39:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More efficient fftw-array allocation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/91470a18666acd701952608222edb853d63ded01">91470a18</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-27T12:00:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Include single+double prec fftw libs default
This so that we can choose prec after cmake invocation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/963abe6bfb26591267b5fd2235cc5cc3a5d8d625">963abe6b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-27T15:00:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Choose shared or static libs in cmake build proc.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/25e3466c1a34ef72f732a4187955e2bf94be87ff">25e3466c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-11-27T17:24:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">progressing with pipeline, up until process deletion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/975f8a2002d3de573328729f8cfa317fa23e556c">975f8a20</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-30T15:25:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixes to relion_mpi transformer clearing
also fftw cmake stuff refined slightly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b46c77eab3bb708c8adae7033328694a5688b929">b46c77ea</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-11-30T16:30:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cmake fix to cuda version check
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34a9f40eb8c5a439626fddedbd394181ef282103">34a9f40e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-11-30T17:02:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fftw package finder checks the require flag, required by the cmake standard.
Also if one of the paths are not found fftw_found is not set to true.
Only the required library are included in the lib-path instead of all three (single, double and thread). This is better in case one does not have all of them installed. Besides relion doesn't uses the thread enabled version anymore.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/49b15958d26c816348a844a2c0d01852cf2a7e40">49b15958</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-11-30T17:05:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d099446afd39e1b81a145f678aba86f859ee3763">d099446a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-11-30T18:18:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build type is checked and only valid values are accepted.
Release is the default value.
Some minor clean-ups.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fb81f38d976038a2394a1cb26ef3b09d116f6ed3">fb81f38d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-01T15:20:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fftw is external project which fetches fftw-3.3.4
Looks for system libs, but builds local fftw-3.3.4 libs and headers
which are automatically included in the build, if system libs are
not found.
If built in the local directory, any new build will find these and
refrain from rebuilding the loacla fftw.
The proeccess is able to modify the CPU-precision through ccmake, although
new libraries will be built if they do not allready exist in the system or
local directories.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ac67f67a80a2433467313f1319d5606a6edde48">7ac67f67</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-01T15:42:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
Included in merge is the fetaure to specify -DOWN_FFT=ON/OFF on cmake cmd-line
Conflicts:
CMakeLists.txt
cmake/FindFFTW.cmake
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/886e7a0309c34564d3c472b11df1648ecd6b77ae">886e7a03</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-02T13:58:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fltk is external project which fetches fltk-1.3.3
also, fltk and fftw are only build as local libs if the user
specifies -DOWN_FFTW=ON and -DOWN_FLTK=ON in the cmake cmd-line.
If no system libs are found while these flags are NOT passed on
the cmd-line, warnings with suggestions are displayed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3076984804bc5f3cc11ef9ac0d969254905b1ab9">30769848</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-02T17:21:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Default build type set to release
Also further fixes to the cmake procedure
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/97f2e84e0f3dd147853847cb509c197563d834c4">97f2e84e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-03T10:22:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> now can add scheduled jobs and execute them without loosing track of history
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0519509694bfd0813b6eef64461f718ea25b9c02">05195096</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-03T11:50:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">nvcc avoids float128 by ugly hack
gcc supports a type float128, which the wrapper nvcc does not support.
fftw has enabled support for this under the gcc compiler, but not for
the intel compiler. So in order to compile fftw using nvcc as a gcc-
wrapper, we can fool nvcc to think it is an intel compiler during fftw
compilation/inclusion.
The better solution would be for
a) cuda to enable float128
b) fftw to sense nvcc, rather than intel
Option bi) is possible through minor modification of the fftw3.h-header,
as described here:
https://github.com/FFTW/fftw3/issues/18
This has for some reason not made it into the past or current release
of ftw, however, so option a) is forced to provide compatibility or
RELION with past and present fftw-verisons without modification. This
is achieved by adding an nvcc-flag which provides an intel compiler
identifier. ( se ../cmake/BuildTypes.cmake)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/def34930ff7354ca0a41646189770bf0439ef19a">def34930</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-03T13:26:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added some error reporting in coarse-convert to catch invalid cases of zero number of weights.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de04ebbe5893d76cf637cb3fd66a5439cef97d35">de04ebbe</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-03T13:27:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1905ec025f6556240ef86a3e34a227c1a891eedc">1905ec02</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-03T17:45:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes to cmake fftw-search in sys-libs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4eebaf699bacf8bffa2b8c768ef1258b37854b4b">4eebaf69</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-03T17:28:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added import and motioncorr jobwindows, gctf wrapper in ctffund_runner is pending
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8136a3a042867310fa9f1de0a7cb21215094421a">8136a3a0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-04T09:30:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #5)
Mainly build environment updates and memory optimizations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/10d868206a66be5ae268db54dd8fe1f18ba7d11b">10d86820</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-04T09:50:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> trying to resolve conflicts with merge from Dari and Bjoern
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ab070a8f820e79645e094bc8b4f9cf78f68a3396">ab070a8f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-04T09:50:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b5ffdd7882b5ece07f2aa0777d545159b8683a4">2b5ffdd7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-04T09:58:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9eb5224d70cb0fa1a90ceddbe666295d6c3800ac">9eb5224d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-04T13:29:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27e545508c25245208d16237d1ef7c122a913278">27e54550</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-04T13:36:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/510b7336cf0bf259fdb76fbc01e44e7ba9bf1710">510b7336</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-04T14:01:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed compilation error and added external to gitignore
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ceb012b267b0883ba0d86e54f94fa73c9762324c">ceb012b2</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-04T14:02:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12055f48377be04508f6a8f503330223382fcc66">12055f48</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-04T15:36:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Script files are copied into the bin-dir at build-time.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/953d98cce1b4ba2846ffe4f2fd023f1348440826">953d98cc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-04T15:45:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed float overflow compile-time warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/134e9e5b29684c254e7ac2ca58d8a8b4fa8f9f85">134e9e5b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-04T15:46:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Preparation (non-mpi compliant) gpu-autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6320e588482cf3b32cc49711e845fd989fde5a76">6320e588</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-04T15:47:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fdf1eafd8cb6563aff0b8a8dbeacbda82e33b8a3">fdf1eafd</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-04T17:36:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Intall target setup in cmake.
Rpath activated for the shared-libs.
Renamed shared lib gpu_util.so to relion_gpu_util.so
Scripts are not installed yet.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e24a670c3dd2cf05d905442f31af9a29e1b5d752">e24a670c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-04T17:39:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/94d6df5746ff9afab3ba82b90206191b0223a022">94d6df57</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-04T17:21:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now gctf wrapper works
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad00c84ddfb6697481ce67d21d6ba9ee8f3726a0">ad00c84d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-04T17:22:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small debugs of update from Bjoern and dari
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d7d5cc45c39acbdeb556a96a254aac1ed46d3582">d7d5cc45</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-07T14:34:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Restructure helper_functions + autopick stuff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f260dc79820a217ae4ac5e76161385bf14a25e5d">f260dc79</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-07T15:13:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cmake-install now works for static builds.
Install targers of the shared libray is omitted in this case.
resolves issue #75
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5978d71ea542228be77bab2539e059c67541815">d5978d71</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-07T15:14:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added cmake install targets for the script files.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/44d89546300f1abfb8628a02ecff0c39f715920a">44d89546</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-07T16:13:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelWithDebINfo fix and autopicking stuff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e4f6132e7ae532a64dda3ea3d8d9b1b196a7b5c8">e4f6132e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-07T16:15:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
Conflicts:
src/apps/CMakeLists.txt
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/72d16f513ec658ae5f2a0dbd04646a4ff51e7e11">72d16f51</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-08T10:20:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopick centerFFT w/ mulitple blocks
reduced precompiler debug output in gpu code for dev legibility
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b33085b4b7781c7a2ff99d335f32b0822639b65f">b33085b4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-08T13:34:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ProbRatio kernel works
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/739875511c21c1033586511ef02b6f500bada9d9">73987551</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-08T15:17:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed Issue #77 by adding some booleans to account for the status of the fft plans.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8df19c8bb6e957120410ed25fcd299edc456dd05">8df19c8b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-08T15:18:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/40f3ae3c9470d24dd01096e9fffd28742d14c590">40f3ae3c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-08T18:55:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue #76. Changed default behavior to what is requested in the issue.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/52e4fa7f23eb2f038589a1f9fe262cefe3b4bdd3">52e4fa7f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-08T19:09:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue with cached library-paths for fftw.
Fixed linking between external libraries and internal shared libraries.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a8fc09ca3e61ebdf842a9cc0a4592065669401d1">a8fc09ca</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-09T10:09:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AutoP-texture comp. and run w/ incorrect results
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/576d2beccfcc3d638bb56e6148958ae2cd7340ad">576d2bec</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-09T11:16:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e1c7445f4f569a1408c102841b40767c8423624f">e1c7445f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-09T15:19:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working texture autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/18fd7ee7f7c3b66c86a5cc5a3d1cee1e234a0071">18fd7ee7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-09T15:29:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">A bit better error output.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a3d1bded87192071d3c75c1487ff45a8aa8abff9">a3d1bded</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-09T15:55:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed CPU double precision compilation issue caused by unhandled type missmatch.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5c4c788f19a33400883e7ca7560092f9d169ccc6">5c4c788f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-09T15:56:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e00032b212730a66776d388a552a2828cf20a5b1">e00032b2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-09T16:54:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">autopick convolution is also on GPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/136081326c06df700de2f20126579f5bd2197b23">13608132</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-09T16:54:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6dba84492c77fd37c9eba614db0514d953bd6d6c">6dba8449</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-09T17:20:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c3c739eb7ab4df33108d54017b7023fd8d719fc1">c3c739eb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-09T17:22:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now manual pick, extract and sort work inside pipeline
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/926d973c78a3b698e97622b4c91987c1a38fff48">926d973c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-10T09:55:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/17cf55e83d6d4bfb77037e313aa0353c77736933">17cf55e8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-10T12:03:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">float2-arrays are used for complex numbers
This is to maintain the interleaved real & complex components in prep
for device-bound fourier transforms. I did NOT check performance.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/73e41da40ee08329ff851dc4f693b1f32e6d69dd">73e41da4</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-10T12:15:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Allocator is made thread-safe and shared between threads.
Device allocations made by CudaGlobalPtr are not freed in the destructor but marked by a cuda event record to be freed later.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/19e309e58cb3f63dfb545bc822c2292a96381cd5">19e309e5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-10T12:19:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/da7e46967c159f75cc2ff552a50e1250fa90b2df">da7e4696</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-10T12:25:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Changed the name of the gpu-memory-flag to better suite its new purpose.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e6ec2635e2da9edc2af5f569534d8faaa2965243">e6ec2635</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-10T18:22:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleaned-up some (non-significant) errors.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61fefa86a34a78f5bb409ea0f03cb44267ae733c">61fefa86</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-10T18:23:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added the CudaFFT class that handles plans and pointers for R2C (only) transforms.
Ported the largest cpu transform to gpu in autopicker.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b367e1f638d592efdb9be8d36878fde3bd3c3e37">b367e1f6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-10T18:38:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working complex texture
Tested only sparsely for autopicker (only 2D-textures).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/23b6a8c1337eb6384d64f26535f8812130697a75">23b6a8c1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-10T18:42:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
Conflicts:
src/gpu_utils/cuda_helper_functions.cuh
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a09d755027bf50a537ede160154a44cacaee46f8">a09d7550</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-11T15:16:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enabling a single complex texture is now possible
There is some doubt as to the benfit, however. One would expect that
3D projection kernels would benefit through decreased artimetic count
during texture-intrinsic interpolation. This is to some extent observed,
but the entire beenfit does not pervail due to a slowdown in other parts
of the code, for reasons unknown.
The projection-instructions are maintained such that a call separates
real and imaginary components. If (as in autopicker) the desired out-
put is a complex array, then these components are either joined after
projection or written separately.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca186d73784bd98f1affe5ac6651cdd0d63a437e">ca186d73</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-11T16:55:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor build related changes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0e5177f74c1c4ef9996ec994eb00bfb6c43720c3">0e5177f7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-11T16:55:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">windowFourierTransform is now implemented on the GPU both for intertwined complex data and separate real and imag.
It is inserted into autopicker which primarily removes some back and forth memory copies.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de7687ce168c88b566fae57202f0bd9bf3c129d1">de7687ce</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-11T17:02:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e8712cd6da4d1dd74f69bf1edd211aa6ba6fec9">6e8712cd</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-14T09:29:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some autopicker memcpys rm:ed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/743b69fed0f0b3b6ddd28468b99b62a2e851de5a">743b69fe</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-14T14:16:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Disabled functions to fix broken standared build.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/800fb774f88582376424705e0d710cccdcc243c9">800fb774</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-14T16:40:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #6)
New autopicker code (not activated), bug-fixes, and better memory management
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ada60a2c107d2e4a0523619ccfd9d20e71117bbd">ada60a2c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-15T14:37:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now pipeline with io_node_display working
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/09e1cee6620002f848eb90b17ba958848df141b5">09e1cee6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-16T11:59:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better error reporting.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d81560859140233a95442d0760e13e34f59f0304">d8156085</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-16T11:24:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflict with Dari and Bjorn
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/487d00122a30ca3a1110045725a8bc4d7e20f9f0">487d0012</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-16T11:25:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflict with Dari and Bjorn
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d8b3c3d303d57b550fc160b88648bcd3a7f4c99e">d8b3c3d3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-16T11:28:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflict with Dari and Bjorn
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b19fd61cd78bb27a2e5d95fa3fc678c71fcd0f8">7b19fd61</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-16T11:29:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflict with Dari and Bjorn
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d27a84b63a8cf89690dc489c66b9c4cb709c933">8d27a84b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2015-12-16T11:30:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce0d5310c4dbd3822bf9f3c3ea2167cef403a564">ce0d5310</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-16T12:33:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5c14f39d0beaff51eef8c0ae4bb7183e797b208b">5c14f39d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-17T14:26:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Only devices that are used by the optimiser is allocated upon not all the devices like before.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5beb1a3c7b914e5faf5b28905967fa2cd5abdb95">5beb1a3c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-17T18:32:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Most autopicker memcpys rm:ed
also some kernel-related fixes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1066c64496fb6469f317a4b1e623a42e799263af">1066c644</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-17T18:49:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
Conflicts:
src/gpu_utils/cuda_kernels/helper.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/22543ae3d9a42774a37e4cfb995f69ba08372dcc">22543ae3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-18T10:24:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cuda_autopicker wors for SS and DS prec. combos
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/518af0fc155a212eaaba7492ef47d53ba2317132">518af0fc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-18T10:35:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">autopicker works for all prec. combos - no memcpys
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bdd537f164021e41c9cd1745a24cfd907d7d486">8bdd537f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-18T11:48:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor improvement to ProbRatio-kernel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58a7e8d51f585ec2bfd782b354c3a1129a839e81">58a7e8d5</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-18T13:55:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">buffer centerFFT instead of D2D-memcpy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c0819b4ecacf15ba82aa9a3f5194312fddb6b1eb">c0819b4e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-18T14:30:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cuda-own calculateStddevAndMeanUnderMask
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a19bc2e6c5ef19e090b5b54a38eac93a627848e9">a19bc2e6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-18T15:09:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Multiple fixes:
1) Improved numerical accuracy of offset prior by uniformly shifting values towards unity with a factor that is remove in the normalization.
2) Fixed concurrency issue due two threads simultaneously setting shared projector plan in auto refine.
3) Moved projector plan into coarse-diff function, since it's only used there.
4) Removed weird conditional raising signal.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9617e46b6fd2155f51296b97c7804e31299b6aaa">9617e46b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-18T15:16:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/07dc26b0c0c2469d3e772253b1d502ef4cd5f70a">07dc26b0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-21T12:36:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">computeStats is calculated in double-precision regradless of precompilation settings.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b860007cd35e1eb21af3e55b3053f838d68b7fb8">b860007c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-21T14:27:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">sutopick pre-calc largely on gpu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b287a056bd0a8ac1c7954d9e5e360b5fd00588c">2b287a05</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-21T14:27:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/943ad357d808fb7b3e39f60ae885c748dfb31078">943ad357</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-21T14:55:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added stream-synchronizations after all device to host copies where data is used on the CPU immediately after the copy.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/144c1a03597314e122df4b917b7cf1055560bba5">144c1a03</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-21T17:06:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Preparation batch execution (autopicker)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/46e6e1ef1a82ce91a4b48521ba39ba28c4113d6a">46e6e1ef</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-21T17:08:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
Conflicts:
src/gpu_utils/cuda_autopicker.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2f683fc5cb9df687288597c110dce5fec8baeb6e">2f683fc5</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-21T17:35:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopick makes batched projection call
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f73bc4ecbc22175c3b39edc75f7e2d00154a7778">f73bc4ec</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-21T18:05:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopicker uses batch-plans of size 1 (prep)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8897996c2272b9447013ba52d9d4b1435f013981">8897996c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-21T18:36:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prep for fourier-batches
separated first-psi and remaining transformers
prepped runCenterFFT for multiple image input
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/535991d9f1591fdacba15775161949d5c0af4e32">535991d9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-22T12:45:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prep for fourier-batches
separated first-psi and remaining transformers
prepped runCenterFFT for multiple image input
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f4e5994b4ac0765b72103806579d1f58c69d7ff9">f4e5994b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-22T12:54:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">First-psi calcs moved out of psi-loop
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1b913a195c121413b040995d25e5f9c5697fd91a">1b913a19</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-22T12:59:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
Conflicts:
src/gpu_utils/cuda_autopicker.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ea24eb49f75c903838405a0ed26b23cceb83f31f">ea24eb49</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-22T17:06:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Batched psis in autopicking, but w/ incorr results
This commit should not be ussed, it is a waypoint.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f756baa68941c81b719a1557df28fc5f60154f06">f756baa6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-28T15:54:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to WindowFourierTransform2
Also best_psi image is written correctly
Also compatibility added for cuda-Double prec. in planMany-stage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0bed3b4b7b813caa1af2f82436b941525e22f1bb">0bed3b4b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-28T16:19:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean-up and standardization of cuda-autopicker.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/979feb4fe7fcd3ff8b3ca66de2dc3341d22ef738">979feb4f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-28T18:55:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ported micrograph preparation to GPU.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cf67089e41dbaee4c9a994b1b51d0028f0152789">cf67089e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2015-12-29T14:17:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed back and forth memory copys surrounding calculateStddevAndMeanUnderMask2.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cae7db47abdf882a959ec98209425f95c5cde0ed">cae7db47</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-29T17:07:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CPU-based code can shrink micrograph
the real value of this is evident only in the GPU-code, however it is easier
to implement on the CPU and safer to test there as well.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2d3a6dc669c83b71af5d3e3f2e7606a7666cab6a">2d3a6dc6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-30T14:57:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/032d536a1e72a72f745ef1bc416295c337e12a59">032d536a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-30T15:32:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The output of CPU-autopicker is micrograph size
(even if a reduced micrograph is used for calcs)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/267332134940eceeba1bedd16edc2a8c72bb782c">26733213</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2015-12-30T18:46:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU also shrinks the micrograph during calcs
NOTE:
This may be due to the difference in FFTW and CUFFT, but it may also
be the fact that the GPU has limited ammounts of memory. I think it
is the combinations them, but anyway:
Some micrograph sizes cause issues, which appear to be due to the
accidnetal or occational occurence of large prime factors in the
fourier-representation image sizes. LArge primes means alot of extra
(temp) storage during FFT calcs.
Why was this not an issue on the CPU?
a) CPU is serial -> onlye ever 1 FFT at a time
b) FFTW != CUFFT, algorithmically
c) y=1950 => x=976, so largest prime is 61. Big, but ok.
For, instance, trying y=1940 on the GPU with 5deg orient-step:
360/5 = 72 FFTs at once (in memory at once)
y=1940 => x=971 (which is prime), so largest prime is 971 (!)
So even though 1940 < 1950, the estimated space needed to perform
the FFT is more than 8 times bigger. combine that with performing 72
FFT at once, and the space requirement is a whopping 576 times larger.
This is not so much a problem as a hurdle, which is solved by two
considerations/modifications:
1 - Reduce 1950 much beyond 1940. The smaller the number, the smaller
the possibility of large prime, in addition to smaller objects and faster
calculations.
2 - Enforce numbers which doesn't contain large prime factors. GROMACS
allready does this, but a table lookup is not that complicated if we feel
like doing our own. The formal requirement is to force a basic dimension
x such that
max(largest_prime_factor(x),largest_prime_factor((x-1)*2)) < M
where M is a cutoff which we specify as some ok-sized prime, like 61 or so.
FOR NOW, THIS IS AN ISSUE WITH THE GPU-CODE WHICH NEEDS TO BE FIXED
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c61904b6e40919e9131fec83802ad5f9fc26ae6b">c61904b6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-04T11:28:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Micrograph size during calcs uses --shrink flag
default value for --shrink is 1.0
--shrink 0<val<=1 results in a size = val*mic_size
--shrink val>1 results in a size = val
size is allways adjusted down to nearest int which is 0 mod 2,
since both size and (size/2+1) should be int.
size < downsize_mic gives a non-fatal warning, since this limits
resolution beyond the (requested or default) resolution.
TODO:
Mpsi array should also be up-sized when calcs are finished.
Large prime factors in size should be avoided by allowing dynamical
adjustment of size according to allocation estiamtes, see
cufftEstimateMany()
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f8bdbd73ce6a37c5c51b5d3e79fb4bebf1f22aef">f8bdbd73</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-04T11:48:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Psi-image is also micrograph-sized in output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ecba9e7f086d9ab678012bf49e1fc51e0bb9fdd">8ecba9e7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-04T13:49:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now with polsihing, maskcreate and resmap pipeline working
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/caf5d350165113a0a9f65efc1b1de30ecbb97a12">caf5d350</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-04T15:09:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">nicer lokking buttons on maingui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc7b3bf868a0914e208276e92de881b59de6ac27">bc7b3bf8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-05T11:23:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rearrangements & speedups for autopicker
also fix to warning-condition regarding --shrink option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1581783689519f0012210852c68ec9f9ec9adf38">15817836</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-05T14:12:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now picking with refined coordinates and even nicer-looking GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/539def1884506f35a5a226eff6f9c531548b7e27">539def18</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-06T10:42:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">finalize autopicker features for PullReq
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/140656e4f0fc57e020d04b5bba4bba0364903484">140656e4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-06T14:35:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">with gctf bfactors etc, alias of jobs, and regrouping/centering in ParticleSelect
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b02a620b1341dd8fd5b44cb27ead5a2b6871da1">2b02a620</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-06T16:43:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">PDF-offset is normalized with the mean value rather than the the minimum value.
This is done with the same factor for all classes, which is theoretically more correct.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f65b0b08b7c6130de24e8c736dfc26423f95dbf8">f65b0b08</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-06T16:53:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">PDF-orientation is also normalized with the mean over all classes to further improve numerical accuracy.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c47c2584462a320d7244259f6f4d30c3e01b0298">c47c2584</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-07T09:08:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">some debugging, also aliases in GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e656c1a17c7fe99a6e82c2d24693d226b0c80a40">e656c1a1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-07T09:17:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try to add cuda autopicker and merge new-GUI code with bitbucker from Old Year
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3bdf474f46a84a0fe2f41c822c9f6ec452b64e4d">3bdf474f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-07T09:20:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">get rid of persistent test.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ceab0e239a8f4f0164e460313cd721e06074e7e9">ceab0e23</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-07T09:27:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">for now no background image in GUI, and repaired merge error in autopicker.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3aa91d02be67b3652d6aa1218943c11390fe0399">3aa91d02</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-07T09:39:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed order of particle selection in left-hand GUI menu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fdb28bd3b11d4d95933397ac7ea88df55b8804c">5fdb28bd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-07T09:48:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">called subtract job Particle subtraction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1b6e8af80802910e7f0fc817ae09b31eeefee18b">1b6e8af8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-07T11:35:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">already add join star fiel process (not funciotnal yet, but to prevent errors in pipeline files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/35c3046b55be4be87317caeb9ec6d08ad3ccd9b9">35c3046b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-07T13:15:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aa44856abf7480014a913b922f8ab7e8beb30857">aa44856a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-07T13:09:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in import job
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12d65b51fd8092a540b6cf2375bb84afc2912db5">12d65b51</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-07T14:20:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed some suboptimal device synchronizations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0f1930c22508158c59d018db52bc4a8f6a2e33c">d0f1930c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-07T19:51:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #7)
Improved accuracy in refine and faster autopicker.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/85bce6e5d22d4a7a17c0723cf7ec57f0441004d1">85bce6e5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-08T17:01:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed debug-build false errors.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c57edd0210597e89a623fd1696b1e97d7ed791cd">c57edd02</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-08T17:01:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Inserted new code from cpu-autopicker for helical-segments; this code is commented out.
Also changed the metadata file output path and field order to match that of the cpu code.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/63006e76cbf68eec567f6378822394ff58203b21">63006e76</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-08T17:20:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> getting many bugs out, and also make aliases for node browsers
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/235f8a445352df67f33191270179eff23b29acfa">235f8a44</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-08T20:04:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed peculiar error with incorrect ccf-best for uneven ref-indices in gpu-autopick.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a9846cf6b90ba6a5f953c3255d7f8fb4a570ad6">9a9846cf</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-11T10:02:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed some compilation warnings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/88e5288bd2fec4299744408802394d0620e38fa4">88e5288b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-11T14:23:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont have model.star as outputNode for auto3D runs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/573aee1bd987d5415b2232ea2d02b6a19aaf899d">573aee1b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-11T15:41:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed some commented old code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1739e935eb05abb69413fbe6a3a311921c8466bd">1739e935</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-11T15:42:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove _movie from input filename if it already contains it
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c15636aa08144d49fe65252062558ddd187a6a22">c15636aa</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-11T15:48:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug making output directory extract_mpi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0dff4d18f3ee0b27f3ca2ba0491fe7ec29b5699">d0dff4d1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-11T17:09:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to make movie-rpocessing work
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bb0d4737c956fb671071bde65ccedec8262e56d">8bb0d473</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-11T17:23:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">program to join STAR files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1be92a0812d0e175f470b7f158a70d98b6375bb1">1be92a08</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-11T17:28:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed cerr statement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b17165383b4f19e11d5035729c879706f5002115">b1716538</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-11T18:37:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed cerr statement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a27c27180da6222f0c8dfdd2dbe795cfa845dd4f">a27c2718</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-12T09:34:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow to invert micrograph selection
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/80eadfa344feec258b866ccd62a1e52d66ac4171">80eadfa3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-12T15:10:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now with display of stdout and stderr on the GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e669bd61d092592ee513f060e6636ffb3722905e">e669bd61</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-12T16:10:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merge with Shaodas stable helical processing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/830949bdadb5d179d70f1f9f95b33b9efda5b19f">830949bd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-12T16:31:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in building of local FLTK
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58867f4ce735f78b100605319409504e6f2c0039">58867f4c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-12T17:25:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adapted some continuation settings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a92bb3c5ea232d347127b5e2d636d2d6a55d9675">a92bb3c5</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-13T13:32:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Scale particles picked from shrunken mic
Given that the calculations are performed on a shrunken micrograph,
this commit realized the idea of perfroming particle picking on this
image, then scaling coordinates to the original mircograph size. This
rather than making the image bigger simply to perform particle picking
on it.
The question remains, however; Does this affect the picking quality?
In test, shrinking affects the picked results at ~55% of original
dimesions, i.e. ~30% of original image size. This sounds reasonable,
but the resolution limit for this run (lowpass=20), is as low as ~35%
of image dimensions, i.e. ~13% of image size.
It should be noted that shrinking the micrograph only very slightly,
can improve the picking (in my subjective assesment, by vis. inspect.)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a61c07813a5231ecc40e023bb22494c5f98f6d9">8a61c078</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-13T17:13:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in moving output files away for continuation jobs in maingui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac79bc5fd2fe2fc5180cec53825515a677c4082b">ac79bc5f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-14T10:18:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further removal of minor bugs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9ace17cdf1894f0c6bf253e994640cdf37a78948">9ace17cd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-14T15:47:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> replaced allmicnames by vector TODO: file i/o in GCTF
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/992a9aa90fc0de10c8af145a0ad32efeef5ccc14">992a9aa9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-14T17:06:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further debugging ctffind runner with Gctf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/39bc9ca921d609c022c709d26eb6f1108606faae">39bc9ca9</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-14T18:14:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed some class related indexing errors in coarse-diff. And removed bad code.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/db3e0b3e75ce6fed56f6cbdb96e16b222adebbf8">db3e0b3e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-14T18:15:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/763d406c56207d2a6b1809441340ffad61968fab">763d406c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-14T17:15:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further debugging ctffind runner with Gctf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27ee6724ecac0de45ee9c4950eab37e6e53d23b0">27ee6724</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-14T17:19:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further debugging ctffind runner with Gctf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bfc761241105159f33d71234f40de0719c8bf259">bfc76124</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-15T11:26:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #8)
Minor changes fixing error in refine and also some fixes in autopick
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c3f38cfebf8bfdb395fe781052cc2cb363a6c3cd">c3f38cfe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-15T12:02:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">report errors to stderr, not stdout
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ce940af4f3b926803447e0093c9a052963d891a">3ce940af</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-15T12:03:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">run gctf on 20 mics at a time
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e8e77888ea2b06e9493919538e18837e8b423976">e8e77888</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-15T12:03:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in motioncorr logfile placement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/806d61f44f2222bd4b6bac8ecc182362ef2fe9bf">806d61f4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-15T12:06:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow selection of micrographs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cba8208ad819edf49cf5eb6b95677d1436a27070">cba8208a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-15T12:13:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug joinSTARs for empty STAR files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/441088787a8cee89890fe9aabecb9cce914ef034">44108878</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-15T12:16:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont write out to stdout which ones already exist
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dfadae1d269c819cd48ebdfbed846afa0201c124">dfadae1d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-15T14:33:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added functionality to store notes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c1ae90227eb053cadd58963c7fcd102c5f89f28a">c1ae9022</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-15T14:37:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reorganized some buttons
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8c4424a6116e67c99fb34342f340b59a20097c44">8c4424a6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-15T17:30:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repairing minor bugs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/580a99e032ddb6a7b0b87724f3f5e30dab558faf">580a99e0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-18T09:48:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make backup copy of pipeline.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/69c8cb45410e3fc8912b412c46852cfb71f40d76">69c8cb45</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-18T12:05:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fuurther debugging of minor things in GUI, eg saving hidden jobfiles, better aliases and cleaning those
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1d75d16caa2b4cf896b6d207d88c8a4501344ec4">1d75d16c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-18T17:14:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">start of mpi support with multiple gpus
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0db6f0951c8e2bc4b1dd83776dac144a4f978b8e">0db6f095</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-18T17:14:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in finding logfiles of Gctf and ctffind
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3218a13e288a12f28f68de4750aca2b4c3f47d5e">3218a13e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-20T13:52:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU accelerated first FFT transform and centerFFT in getFourierTransformsAndCtfs.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f96403476cdb493ce5b7bd8f84d910c61661bc1">4f964034</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-20T13:55:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU accelerated second transform and centerFFT in getFourierTransformsAndCtfs.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a11e5f827ea210dc71e96e605fa9e1e5cdb8b6b2">a11e5f82</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-21T13:32:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fa91dbadc385e4e09297e2f90419240d43d97df">5fa91dba</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T12:57:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">yet another bug in ctfind runner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/809086b79067564b1905cdc1a88e494a170941c4">809086b7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T12:58:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">change default outputnames refine jobs with scheduled jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60ba35dc7b93085204e1e7a2eda640834c89782a">60ba35dc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T12:59:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">schedule jobs now running in a first version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/190d3c052800014767de89f57596a08ef7737613">190d3c05</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T14:21:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merge again with Shaodas helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9ba877156df382177ddaa6901f976303c8004e6a">9ba87715</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T14:44:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> bug in continuation relion_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/921a0434fca2563c32341f95fca2d5a2a511822a">921a0434</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T14:50:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ask for repeats and min_wait in running schedfuled jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a1f84de7d17eac84d20a944cd7dd99a085cf4cf7">a1f84de7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T15:01:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bug non-defined current_job
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/86ccda596aef4773d8352efbc3377ac153caf857">86ccda59</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-21T16:50:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopicking batches ffts if neccessary (mem-limit)
Due to the scheme used, the batches are M in number, where the first
M-1 are of size X, and the last has size Y, where (X-M+1)<Y<=X. As long
as the number of batches remains relatively small compared to M, this
ensures good efficiency (no spilling)
The Autopicker CAN still run out of memory since this batching, so far,
only concerns the fft-associated arrays (and temp storage) which are
proportional in number to the orientations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01d3a268c6615ce015351d08b18ff5bafc754b10">01d3a268</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T16:14:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts for merge with relion-devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/016721723c5e7e9aca3e3b81216e80e2e4697866">01672172</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T16:21:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts for merge with relion-devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a2832a0431e3b1bc95848c793dc3d0a2b057bf0f">a2832a04</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-21T17:30:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3b4e59f6b20f991de66b6bacf098d51c0eced4d7">3b4e59f6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T16:31:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c1094c45c2d2aec89c343ee3cae87df2df9e8d2e">c1094c45</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T16:31:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #3)
put back ontheflyshifts=true in initialise of mpi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ffe14b21587f89a4b1d038a1dfb61262bfd7343">3ffe14b2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T16:33:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repairing what was broken in merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c1440d2b4bb1686b84e84a7f769250a8c8977b91">c1440d2b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T16:34:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #9)
repairing what was broken in merge (had to do some weird stuff in src/gui_jobwindow.cpp and src/gui_mainwindow.cpp because of silly merge conflicts)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f17b88e4a36b55372eec465f2f6f0a4738d1dd7c">f17b88e4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T16:37:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/052fbcb4cf9a6e3242ff6dabe9b33b776ab56efc">052fbcb4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-21T17:09:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired crash when marking as finsihed refine jobs that hadnt even started and copy pipeline.star upon calling cb_run_i
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f0f4fd88d8968401ec0548e02c8119246600908f">f0f4fd88</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-21T18:10:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge https://bitbucket.org/tcblab/relion-devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9562eecce568283f9f1694289598d8374f9b168">f9562eec</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-22T13:50:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug empty MDin from fn_data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57e49d67255cff992464dd1e33679057528a0d04">57e49d67</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-22T15:15:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed FLTK compilation error due to bad include-directives in the cmake instructions.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/621049f3294398145875ebe4d0363a4eacd2243f">621049f3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-22T14:16:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug that job files weren't saved in output dirs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02f38cbc0b5b6fc9e6a920d4b3b561af4466edcb">02f38cbc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-22T14:35:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #10)
Accelerated getFourierTransformsAndCtfs and batched FFT-calls in autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e28d46dcd1dfe514e0a2d4e0a00a54d22bea8f9d">e28d46dc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-22T14:38:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e67dcfe741d716093e82860969ea2a1f2c8a06fb">e67dcfe7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-22T14:39:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow visualisation of re-extracted coordinates thru the gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/352adb9590fc54a5bc92dce147ea7775025d3cd1">352adb95</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-22T14:39:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added unistd.h to includes to get sleep function
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bbd5250b96ae453c26d7e65ed9bcec7b4ea2e282">bbd5250b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-22T15:41:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/82cb0ea119c1ba9cec6f28d24d47d5207ebd381f">82cb0ea1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-22T15:07:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">also allow visualisation of helical segments
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dfb5a12c0ec5a05b931805acfb85e1d34d99a349">dfb5a12c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-22T16:19:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #11)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/131065ed281eb8eea85b00439f709a04707ae49e">131065ed</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-22T17:20:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6db4efacee92ed0ce6a209e6d7ed096975ca6b0c">6db4efac</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-22T16:26:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">provide alias from running and better checking uniq aliases
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c0aacc2919f24df846eab0952ae7cd044f40fce4">c0aacc29</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-22T16:55:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small bug alias of continued refine jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c69e1975793549a5ee2c3f9bd6d49f1847ce4550">c69e1975</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-25T10:24:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Single/double-compatibility fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e7d69c714558acc93bcb25b418ec64b871e148e">6e7d69c7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-25T10:25:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes to cmake external project build-process
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc3c83baaf86fd59451e2f366368186322a6756b">cc3c83ba</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-25T10:36:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding new FLTK-dep. files to GUI-omission list
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b47fca5d20977f634a6440b3a3e62cb8f4624cc4">b47fca5d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-25T10:55:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68ac5e6a858dc7f7ea915f5627ce71c0e8bdfc04">68ac5e6a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-26T15:40:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed BackProjection-specific GPU-streams
fixes issue #82
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/09881e676840db9db19c0710d5b044053e17569d">09881e67</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-26T16:25:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added memory some tracing code.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8e0383b9fe3d36394ff35bb30fb5b779ff27b774">8e0383b9</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-26T16:26:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4c1ecb90e34b37958a13669fc10df28767df2dd5">4c1ecb90</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-26T17:03:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding missing syncs which are needed in theory
Their absence has not yet caused errors, but could, if we are unlucky.
Refer to issue #82 for an example of errors and symptoms.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4480e29961e842d88eaafe3bdce28029a4b60b4b">4480e299</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-27T09:20:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better explanation import coordinate files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/79345b17a04ae4e228eb0e9fa9621350ca007cf8">79345b17</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-27T12:36:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Major revision of BP and WAVG kernels to dramatically reduce image size depenedent memory footprint.
Weight averaged translations are now produced on the fly inside the BP-kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e067aedaef25aa8bbed5506a43b760a6b6e18523">e067aeda</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-27T12:47:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fl_mesage window with metatdata
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61059459cc70ddead702f65bcc3b6df52a6c223a">61059459</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-27T12:48:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more info on imports
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c988b590430ea4f2154bccf3fdf4acb6d3adffc5">c988b590</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-27T12:50:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">toggle continue issue postprocessing repaired
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ef3830ca8a52999d9929c2acb54f5435aad38fca">ef3830ca</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-27T13:58:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New syntax for device-affinity of ranks/threads
Syntax examples and explanation, assuming a machine with 4 GPUs;
A)
--gpu
No indices will distribute threads and ranks as uniformly as possible
B)
mpirun -n 3 ... -j 2 --gpu 0,2:1,3
A colon delimits each rank, and the integers denote the devices to be
used for that rank. In this case, the number of integers match the
number of threads so the mapping will be (slave-rank/thread):
(1/0)->0
(1/1)->2
(2/0)->1
(2/1)->3
C)
mpirun -n 4 ... -j 2 --gpu 0,2:1,3
As B), but the slave-rank which has no indices is treated as in A),
resulting in the same mapping as B), and additionally
(3/0)->2
(3/1)->1 (uniform distribution of this rank over all devices)
D)
mpirun -n 4 ... -j 3 --gpu 2:2:1,3
Slave ranks 1 and 2 are restricted to device 2, slave 3 is restricted to
devices 1 and 3. All ranks simply distribute themselves uniformly across
their restrictions, which results in a higher memory-load on device 2, and
no utilization of device 0 (note that each rank resident on a device has
shared memory object for its threads on that device, so device 2 has roughly
twice the memory load of device 1, in this case):
(1/0)->2
(1/1)->2
(1/2)->2
(2/0)->2
(2/1)->2
(2/2)->2
(3/0)->1
(3/1)->3
(3/2)->1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f09ffa816241e352a3a1fd66bfbe6ab847afb157">f09ffa81</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-27T13:00:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">slightly blue background for bad-contrasty screens
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d70b8b8e9b797b520c84d7bc791b1da92a67c6af">d70b8b8e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-27T14:15:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2ec12fb4b645652e35fd698a59d39ef39c17217">c2ec12fb</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-27T14:27:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reduced the memroy footprint for wdiff2s_AA and wdiff2s_XA.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/96ea75a53eecfb53f9fcff11bdf8f085d074701b">96ea75a5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-27T14:28:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b9bb4f37021614fddf775bbe6e0051a61e204966">b9bb4f37</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-27T14:15:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #12)
Norm-correction fix, advanced device assignment options and an order of magnitude reduced memory footprint
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f2ba50eb4cb842b9c6f26f7e951ac901cdc8420d">f2ba50eb</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-27T15:20:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">device-id manipulation put into function (cleanup)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/83b3e6548965ce1b88df7d722b1bd6fb7db67f4a">83b3e654</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-27T14:59:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ff1f7723e771a989e411abff4fa5eed5d128f6f9">ff1f7723</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-27T21:09:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">non-mpi refine has new dev-affinity syntax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0a1cb27206450a5b793d4e2e9014cd42a6287fa3">0a1cb272</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-27T21:18:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7146e5b66764a5ebfe30c8f8b38110d25b38dc0b">7146e5b6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-28T11:40:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MPI-enabled autopicker uses GPUs
Same syntax as refinement, that is colon-separated indices for ranks.
As there is no thread-parallelism in the autopicker, comma-separated
indices are not necessary, and have no effect:
Default behaviour:
Requires NO indices to be suppied, and is device = rank % #devices,
so that if there are 3 devices and 5 threads, they will map as
(rank->device)
0->0
1->1
2->2
3->0
4->1
When mapping three ranks to three devices, threads (comma-sep) mean
nothing:
--gpu 0:1:2 <=> --gpu 0,0:1,2:2
To place two ranks on device 0 and one rank on device 1,
--gpu 0:0:1
Currently, the GPU-autopicker requires memory proportional to the
number of orientations (--ang 5 => 72 orientations), which can be
quite substantial. A single rank can handle the case where these
do not fit into the GPU memory, but ranks are NOT aware of each
other, meaning that multiple ranks may cause out-of-memory errors
in the present implementation. This will likely be fixed in the
future, so as to reduce memory usage and/or make ranks mutually
aware.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ccfa0da19483545257c9d6062b6a09bc8d831501">ccfa0da1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-28T11:54:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dev-id parsing uses relion-native text-to-int func
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2bce4098b08f15181ebd82291d4c535ef0efed89">2bce4098</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-28T14:20:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixes to default gpu_ids in non-mpi refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3cde65d46b067a44495427850dda692c1a0cf19a">3cde65d4</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-28T15:15:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU memory allocated by custom allocator is readjusted according to the total memory assigned by the user, accounting for additional allocations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d106437cf0c95061e2ac63202245d1af02c0e8ac">d106437c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-28T15:17:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47b90a046d574450da0a6af4a33f8a9b9bd56a7c">47b90a04</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-28T15:05:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged again with Shaoda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ffd821d82ee0a4c2cf74b96f2b0720393a7f51ab">ffd821d8</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-01-28T16:53:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Improved allocation semantics and user output info.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/37020dae71e47dfde038886f03a4ec63adf5adab">37020dae</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-28T16:28:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bug with extraction of movieparticles from Refine3D/data.star files: retain rlnOriginalParticleName!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a61f9c01fb40fb6debc28052eaf1a91b89a5feb6">a61f9c01</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-29T09:32:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">powerClass on GPU, getFTandCTFs 10-20% faster
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d7187db97557a9269f478b3f59836f6f7693b72">5d7187db</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-29T11:25:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">selTranslate on GPU, memcpy-cleanup needed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42faccfc6db92eb5f3055654705e81315f8791d8">42faccfc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-29T15:10:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">getFTandCTFs mem-cpy cleanup and some acceleration
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b80ae678fcdeeddf5b6162db1880cf36ce40fa4">0b80ae67</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-29T16:25:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor improvements to getFTandCTFs flow
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac7c095934d5b62ccc7997a3c2016a3a7b526b89">ac7c0959</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-01-29T17:06:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02cdd06eac96603aa57aa51343607186987f6189">02cdd06e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-29T17:31:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in extraction of movies from refined data.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27ac7af9ffdb5470f7b80a8afbcd53f2775f8f12">27ac7af9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-01-29T17:31:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added small functionalities
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a8f4b626a4bdbb1b625dddb169add72284a22a5">7a8f4b62</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-01T11:10:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor fixes for double-prec GPU build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f93279ccffcf3b2d1382d83aa981c9420bb7edad">f93279cc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-01T15:18:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Loop thread-wise additive reduction across devices
Each thread adds it's contribution to the weights in a refinement-
iteration. Since threads on the same device share this object, the
weights get to be too large when threads in the same rank run on
the same device, since all add their joint contribution. Instead,
each such shared device-object should contribute.
this fixes issue #84
Note that issue #83 remains unfixed in this commit, such that the
extra normalization needs to be omitted in the GPU-code for a
direct CPU vs. GPU comparison to be valid.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7391d266144140b3934acd6073241f195c4fc07e">7391d266</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-01T15:52:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added extra probability-normalization to CPU code
As implemented on the GPU-code in commits
f65b0b0 and 2b02a62
this fixes issue #83
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a289474ea4e220cfb02a94579390fd4edae52fe">5a289474</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-01T16:08:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #13)
Bugfixes, 2D-refinemnet speedup, and more precise custom allocation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a252a410be986abe29261231db283649b603a1c">3a252a41</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-01T17:26:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/225a9317d270a7d2cbd299ed8c6b7b50a9f07dfc">225a9317</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-02T15:20:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ranks without device-ids use default settings
I overlooked this case before, somehow
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e019d5a8d9ce900c26af10533052c0a3d9472bf1">e019d5a8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-02T15:29:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">system-safe memory artihmetic for GPU-allocs
The requested memory was formulatyed as
size_t mem = ... ;
int allocSize = (int) mem - ... ;
GPUmalloc(allocSize);
where the int-cast of "mem" was unsafe, in that if "mem" was larger
than the system int, a negative value was returned. The new method
uses size_t for all these cases, and where subtraction is needed,
the minuend and subtrahend (yes, that's what they're called, I
looked it up) are compared for size, not their difference against 0.
this fixes issue #85
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0bde04ee37bfefe959ed341b3504f01532df2433">0bde04ee</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-02T17:16:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d1b6d64f284f7bdc81448325f0811d96a953b33f">d1b6d64f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-02T17:16:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">import mrcs as 2d references
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/49b0d258eeb05400694e487baa9038296c0e1924">49b0d258</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-02T17:19:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont die if nodes dont have parent process
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f8c61f420ed963de7af30b2200a36cf78017e291">f8c61f42</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-02T17:19:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">display alias in current job entry
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cf8403cb3c32ebaa945514113dda73659fc373bb">cf8403cb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-03T09:12:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #14)
Memory allocation fix, minor to device-id defaults in refine_mpi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ecd008f41f2d7176b504baaa297cdc2159bf977a">ecd008f4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-03T09:15:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02ab7d5f01fe4e462a7ae8888d79dffd6f08d4b9">02ab7d5f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-03T09:16:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e6e1ec1200b3fcddf3650981fe5d1c57fe3dc72">7e6e1ec1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-03T14:57:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added syncs for exp(weights) on classStreams
There is an issue (issue #87) which was behaving incredibly sporadic,
with this commit it starts to behave consistently.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f81a2bac2fb780ffec0ad52652df55591d5bae44">f81a2bac</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-03T15:00:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/35ac601d540c6320ecffe64cf819eb2e3fb8fd2e">35ac601d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-03T15:32:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merge with Shaoda: display fourier TFs and repaired bug of translational searches with helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e078aa552ab0a42ac521410c301487fc03e0bcd5">e078aa55</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-04T13:01:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with reading empty pipeline
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/583357d03ba3bb42e8fe5b752e6f8e2d3c059fbc">583357d0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-04T13:01:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug continue manualpick and recursive alias names
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/23730a7f663df22bed15c54c7c2a666f1ec6afdf">23730a7f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-04T17:48:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replaced 12-digit uniqfilenames with consecutive job numbering. TODO: remove some code to keep functionality for 12-digit directories later
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1eca7565c818e4c15d444dc5b75895fd57b9c852">1eca7565</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2016-02-04T20:12:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Launch error checks added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/daf57c4f316f68dfa7611aa23174946dab30ea07">daf57c4f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-05T10:23:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cleaned up buggy mess with pipeline filenames
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3e9939acf0f376c20628bdcb6910559a094478a8">3e9939ac</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2016-02-05T14:07:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added launch error checks after all kernel calls
Some main kernel-launches use a thread-private cudaError_t
also repaired accidental deletion of allocator-functinalities in
previous commit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6aac6605d4e074b15a504e4d6916637c4ac75acd">6aac6605</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-08T12:15:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed explanation mask
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a4d21ce35a8380afef7f51c7297cb3221fdef9c4">a4d21ce3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-08T16:00:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired various small bugs#
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60cc113a93a045b4d87e04198601c2d4e7ec07e1">60cc113a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-10T10:36:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">size_t used instead of int in some locations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ff142a2bc11e31ae01e5c5a645ce43a49464a80">5ff142a2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-10T14:03:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> changed resmap output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7649d777cacfba9f655ad1fa20a141d1448f6618">7649d777</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-10T14:03:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try to prevent bus errors in last iteration of classification
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42e1bb01f12c64d7e20d4baf942a929ec56b8e95">42e1bb01</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-10T23:20:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">init-check of windowFourTransf. fixed
note: init-check of diff2fine NOT fixed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2a6d60df9b27077ec34dc8abe9620835f53cb0e2">2a6d60df</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-11T10:35:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed minor race-condition
this was reported by cuda-memcheck --tool racecheck,
but may not have been an issue, due to implicit thread
sequential execution.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b71506b02117dc039b763065703f97edb47f6da4">b71506b0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-11T14:32:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merge again with Shaoda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e99e3a9d80488c57f79feb6e7d3abf23236e5a16">e99e3a9d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-12T11:28:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more output for finding errors with movie expansion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/65aaa6b94d0503bab7a19d936b17ee8d5f9ac26b">65aaa6b9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-14T18:39:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added MovieRefine job-type with movie extraction and reifnement combiend
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8feb93036e5abcd57ec9cdeb6d629bd8ad87784a">8feb9303</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-14T20:35:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">started with polishing per micrograph
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c99da71080371a3a14b72986f8817a5985b3ea22">c99da710</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-14T20:55:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now polishing (without defocus and beamtilt correction) seems to work per-micrograph
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/90c7b95202d790ebcd532985d677167135661238">90c7b952</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-15T09:55:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Size_t sprinkles + rm unused streams
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/48d756a51ff37818e386cd26a795a0c544266879">48d756a5</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-15T10:04:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge commit '90c7b95'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1195c448aeca74050a81729051a96fcd4acc8826">1195c448</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-15T12:26:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed non-custom-alloc comptibility
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/634a4d5d69d5965b0221f9fcba675569bb645db3">634a4d5d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-16T18:54:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now per-batch polishing also working. Still minor problem reproducibility ber-batch refine!#
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa872c2981980937682fa4b45565ccc6da37de2f">fa872c29</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-17T18:16:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug restarting refine outputnodenames
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1722b1bea89b25fb34236fc8246117c7f2b5a36">f1722b1b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-17T18:22:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to skip static bool for only randomising once to allow movie processing in batches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ba36bd60bb055d0204ba4834615cc3a9c093d09">8ba36bd6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-17T18:22:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired small bug batch names
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2ca465c2a2063d80ef124add6a72fb8c926afd1f">2ca465c2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-17T18:27:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now movie-processing in batches gives same results as not doing batches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51c71352ac0864a10527efabd6018886fda1aa05">51c71352</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-17T18:40:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small change comment
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/19228c0b7682391eff06ff0d2a146167d5995be2">19228c0b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-17T19:37:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added phase-shift to CTF model
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d94cfb226092df2ae1300e4159211e9b137bb00">0d94cfb2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-17T19:37:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> added avg_movie_frames to movie-refinement and polishing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e4bbdf3fae5e1c85020fe384721f162b81f2c0ab">e4bbdf3f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-17T20:26:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont allow selection for manualpick/display, added selection of coords file in subset jobtype
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d50a90786156dfd878fa8b6d8d4415929ff6bfe">8d50a907</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-17T20:26:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more helpful error message to finsd what's wrong in movie expansion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c662eddda6d1845fe7c28ec7d8f7368e52f3bdf2">c662eddd</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-18T14:33:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prep for mem-leak fixes
Purposely fragmented the mem-leak to allow future clean-up and/or
additional fixes to be smoother. On this commit a memleak is made
obvious under the default allocator. It was previously invisible
to cuda-memcheck, since there was no call to cudaDeviceReset().
A un unused function CudaGlobalPtr.resize() host is added, to be
used in a future commit.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de727209802b4557a75d7a44e2a79852dc3b707e">de727209</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-18T14:37:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Leak fix to default allocator.
The issue seems to be that the default template argument for any
CudaGlobalPtr is CuatomAlloc=True, regardless of whether the custom
allocator is used. This results in calls to cudaFree() being avoided.
It is unclear to me how the allocation can remain unaffected. None-
theless, the leak is fixed. Not only does cuda-memcheck report less
leaking memory, but the positive memory gradient (as reported by
nvidia-smi) is also reduced, in fact almost eliminated.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f75ee4037017edd73478779dcf637e80747f594">4f75ee40</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-18T16:03:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Leak fix to default allocator II
I the problem fixed here appears to be that the temporary array
allocated in some cub/thurst-dedicated functions get marked for
deletion without actually getting deleted, as only the custom
allocator collects the garbage merked for deletion. When the
default allocator is used, this makes for a leak of temporary
storage.
This in part adresses issue #88
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/18b158b6a0bc0ed6444ef750f229a2f05c831f80">18b158b6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-19T10:19:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Leak fix to default allocator III
The problem herein fixed, is that the projectors and backprojectors
in the MlDeviceBundle were not cleared before program termination.
Even worse, they appear to have been NEVER cleared, so that upon a
new iteration, new texture-arrays were simply malloc:Ed and copied
into the texture space. For this purpose, both back- and projectors
are now cleared in MlDeviceBundle::resetData(), just as is the
ProjectionPlans. This should be verified to be correct procedure.
Also, this was tested with non-MPI compatibility, so the MPI-version
should be updated to comply.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a1da3eac0a71ec1c14283e7a60f64302429586f5">a1da3eac</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-20T17:02:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">continued debugging pipeline plus new option for cleaning job directories
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/012f56a3927ce1f5037c5bc25f15d3e8c623658d">012f56a3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-20T18:15:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">load previous selection
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/911caa46e99986ba3adb04fa648bdd4521b9cf48">911caa46</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-02-22T11:29:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Memory requests-numbers are in bytes. All of them.
Alos, the requested and available memory are kept separate.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02789a164f4a0db2252120c40ba6a8a1606a313d">02789a16</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-02-26T09:55:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Backproject wrap up fixed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fe6cf991391f472a6770beadb453bf48ff4d24b">5fe6cf99</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-26T17:15:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug backup_selection.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a229adfed7a4d81681860e57c140d28d5032b9a">3a229adf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-26T17:15:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">edit general notes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f52945cd8022d1e760229809ffe172fcd7fea0a2">f52945cd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-26T17:16:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bug if undefined maxres or negative bfac
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/33df062f53a7f6c4692d88f900ff0c7c1b95eb95">33df062f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-02-26T17:16:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired memory leak when clearing metadatatable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5e875dce39d7be60413561e55fb40befad98a72b">5e875dce</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-04T13:55:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">keep debugging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2bb725c889a94b0ae93e7a8ca6dd4f6291961f96">2bb725c8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-08T11:39:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add solvent_fsc to GUI, and repair some bugs minor
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b19e8524f25571a201faecfc94d156841defa745">b19e8524</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-08T11:39:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug nr movie frames in movie extract
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b0564b22430ffabe9648ef9ab9d1da290d10aa33">b0564b22</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-08T12:58:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">took out some old comments
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9251fcdc6e589a8f1bc88ce9e04cddccfed7dd62">9251fcdc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-08T13:02:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> no longer allow very small changes in orientations for auto-refine#
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f2b7689fc3c632ef1bfebc4e999c14dc11f903ab">f2b7689f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-08T15:09:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added debug_reconstruction option to write out data_real.mrc files every iteration
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/87b907363e5f573057b15ff70e0b4bbc46940d07">87b90736</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-03-09T11:49:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Custom allcoator auto-free is functional when cached allocation is turned off.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/00e82372146724a3088e0100195b56b1f92b9184">00e82372</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-09T14:22:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor bugs in ctffind runner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/36d5bc2afcc4f723d1e96cb559012cc6e2e82884">36d5bc2a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-09T17:33:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">keep stacks open for reading multiple particles in one pool
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cafce5bd4fd89493232a232ad27acaad84ccb894">cafce5bd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-09T18:00:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forgot to switch off DEBUG_SIMULTANEUS_READ
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d81d105bca2aaea7b9cae9e55ae6aabf06ba39c8">d81d105b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-10T17:34:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use stats instead of fopen for exist of file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/750552bf6ef1c53e3b5f1149171461e027589625">750552bf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-10T17:34:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">open/close only new stacks when prereading all particles into RAM
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e688a6c4b3fa99c54ac40d89436e0e00daf73e7b">e688a6c4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-10T17:35:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new Compute tabs for refine jobs, and do not remake .Nodes directory all the time in GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6906b22ee5c5290a4a43557f89655bb5e4c26c56">6906b22e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-10T17:35:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with rescaled particles and manually set angpix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a45660924e7b564b80dd0f41692a30834ac10a6a">a4566092</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-10T17:36:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont read particles into exp_imgs for subtomograms in order to save RAM
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ea31508de4c2a87fb22873673c844dfa29db9660">ea31508d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-11T15:19:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired silly mistake of commenting out entire reconstruction of half2, oops
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8537bb323e24f9993ce1500c96ba9c4e34fae0a3">8537bb32</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-11T16:57:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">another silly mistake with the new reading of particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd6fc33dcbfea0e69c78e09cf2239ddfa0541a94">cd6fc33d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-11T16:59:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">included eol
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1dbfe628edd21ae4eeb943225dde5c5fbec3cc63">1dbfe628</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-14T15:23:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use --pool 1 with preread_images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1d4ade9dc916afaf72cd7cf25dd814c792eb5b08">1d4ade9d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-14T15:24:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added touch, copy and mktree
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8f1d91a724377308989d2f14329a380349c701d">b8f1d91a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-14T15:24:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added --no_parallel_disc_io before continue read statement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/780204ab6a8ca6faa4c7fe334a15a78d554170a3">780204ab</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-14T17:00:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging new way of handling .Nodes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a475160e4fd67517fb229f00aef7511d42b451f">6a475160</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-15T17:24:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed stray cerr line
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/54937c1db339e72c422d2bcdd8b593a2b8023a96">54937c1d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-15T17:25:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">pass maxres and FOM of CTF estimation to particles.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d07bf4f58ad133a98c23666a11ffef6e9b9c54e">7d07bf4f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-15T17:25:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">phase-shifts and new ctffind4 wrapper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9fa8c3d7dfeb95f1ad549ebede702a652e6b5a37">9fa8c3d7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-16T12:43:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">get rid of --preread_images error messages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3e39e465d842909d771efc0b363a535b4215a99e">3e39e465</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-16T12:44:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">open only optimiser.star files inside current output directory
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a7b742f606690f342e3083fe3547ab308e03bf5">3a7b742f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-03-16T16:45:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Byte guards can be activated in custom-allocator with -DCustomAllocMemGuards=ON during build.
CA prints stack-trace of the allocation call if guard bytes corruption is detected during free calls.
Current implementation is suboptimal due to use of memset and memcopy instead of kernel-calls on a specialized stream.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c4e6baeeff058747ad89b1c11daeb02015c457ce">c4e6baee</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-03-16T18:34:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Demangled output from custom memguard check.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a16c260af0b1be779a36fcded19e71e090fe4d12">a16c260a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-03-16T18:35:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed faulty if-statment inside windowFourierTransform2.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a5959dd2fe4ae78823a827b2448f3a1def77af5">8a5959dd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-17T07:54:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug new browse button when default dir is NULL
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/882ebd858fc9d303a37b98dc44e0f75546ecf68c">882ebd85</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-17T14:05:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug found by Shaoda that imagesize became unequal for 2 halves because ave_Pmax was on different sides of 0.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/48832c27a70af5ab722c8d9aa2b452929865270d">48832c27</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-17T17:26:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added mpiexec flag for better restartying upon request by Jake
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/25c9a06ebbcdd1224ce50a56223bf8eb33851974">25c9a06e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-17T17:27:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont always read backup selection file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/18de002bdc681187aa0a3135240853563d4e72fa">18de002b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-17T17:28:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">double-click to open run.out and run,.err
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ace18b423715ebfb896872d544764945aa557df7">ace18b42</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-17T17:29:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now movie-refinement cornelius doesnt crash anymore, results are still not good!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/31c7a8d08dadbcdc91e6a0fd8aa8331b7bcc278a">31c7a8d0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-03-18T15:14:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix tocoarse-pass GPU-refinement scale-correction
fixes issue #91
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24f26c17b94f9b83bc57bc8484d71ecc9e9a09fc">24f26c17</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-18T17:01:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor changes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b2beedc94eb5a7da9d74b4ddd76596e655bd38cc">b2beedc9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-21T14:27:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further debugging of movie-refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/48d8cd623d1e009f60948d11c4756401a0b69b82">48d8cd62</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-03-22T10:17:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">rm:ed GPU-legacy check in windowFourierTransform2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/503a35ee2f8283319bcb9141cf030236b4ba115e">503a35ee</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-22T11:33:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added 2D plotting options by including CPlot2D
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b6b8913d8c3dc754fa52068a19373792df434e42">b6b8913d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-22T11:33:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added more plotting options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/211d50108ada2ea0c3ebf7cd182310d73ee0fe51">211d5010</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-22T14:36:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added visualisation of logfile.pdf on GUI for postprocessing and polishing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0d15ed8920bda843ade9b4d2a1e97bda4238906">d0d15ed8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-22T14:43:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">redirect gs output to devnull
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5bc7f07676d076a16310029ac512e464cb60db89">5bc7f076</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-23T15:13:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added a background image
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a9c5f0819b8760e5f70fa34979e354f9b11b3a07">a9c5f081</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-23T15:21:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont put forgot button if background image does not exist
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5764786e502e90437e33e035bce0afd7f04b26ad">5764786e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-23T16:29:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hide background image when not needed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/28bc5ae540cd12afd4850028ea3f37dda186f917">28bc5ae5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-24T11:55:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #15)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/92725142a187df32ba5117d5a1194d9d0df5bd9e">92725142</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-24T11:55:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51e0a0bc00b38eae9a04ea174707af7166856019">51e0a0bc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-03-24T12:56:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3080254c8238fd8f34e22066f55f1c2374a8b18f">3080254c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-24T11:57:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor changes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bdbbaa66d540fd61412e161b0dee9b987c2a6144">bdbbaa66</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-03-24T11:57:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5e09b0da3685e36ea7935bf6a3daaa9b09b287a8">5e09b0da</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-03-31T14:48:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Indexing fix to pdf_orientations
When a particle was classified as contributing to more than
a single reconstructed class, the directions/orientations
were always selected starting from the beginning of the
array holding the direction-indices for all classes. This
mistake was made ONLY in the summation of the orientational
distribution, not the backprojection.
Essentially, each image contributed correctly to the
distribution of directions for the FIRST class it was class-
ified as, and contributed incorrectly to the distribution
of directions for all subsequent classes it was assigned to.
This means that class 0 always had the correct distribution
(up until and including 2nd iter), whereas other classes where
roughly correct. The latter because
a) many images were assigned as NOT contributing to class 0,
in which case they contributed correctly to the first class
they WERE assigned to.
b) the orientational assignment is roughly the same, irrespective
of class, at low convergence ( low class differentiation).
this fixes issue #95
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d16f49c5d4d25469e7c9277fd1815605307321c">9d16f49c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-01T13:28:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/74c2489894f91dfae0185facf5b3b06e26db445b">74c24898</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-04T09:29:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #16)
Indexing fix to pdf_orientations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/337047712ccbcd795911aca3844e9d3eb4ea097a">33704771</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-04T09:29:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ed6a773ed903f3b9b72c0b6c6fe28ef9e514a26">7ed6a773</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-04T09:31:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added warning for empty micrographs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dbf0f36e99777c0ff879ffa8a80e3f13ca67f168">dbf0f36e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-04T09:32:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d9e87967b78d0c2fe52f87d5b52afa77673d0bc">7d9e8796</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-06T17:40:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added ctffind4.1 wrapper, to be tested...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e8693c68f3d79b191fb287d9c1f96452a8b78239">e8693c68</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-06T17:41:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added functionality for flowcharts in the gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c45c9798b3422a1b097cdf727280042a03cb5ef1">c45c9798</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-06T18:44:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The GPU-memory distribution over ranks is now aware of the MPI-context and can handle multiple ranks allocating on the same device.
The flag --gpu_memory_per_mpi_rank is changed to --free_gpu_memory that sets the amount of memory left free on each device after allocation. Default is zero.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1411dc6583f8ed40239745432a74c1e43b7413b8">1411dc65</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-06T18:47:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1c6e12df87d5cf23700c8416fbd55e2fe95eccd">f1c6e12d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-06T18:49:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a12ac3d2d193e1ab7b4407ed3d6df1544363cd9b">a12ac3d2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-07T10:29:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #17)
The GPU-memory distribution over ranks is now aware of the MPI-context and can handle multiple ranks allocating on the same device.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2a933634cc8081c307d2a7e0001d42313c216323">2a933634</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-07T10:40:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added --check_duplicates in joinstar
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/53b1a95a2191a2f37efcc5bebe7e00228f88b71a">53b1a95a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-07T10:40:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more debugging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c89084790de6a8891c4d2413ef032201076499e2">c8908479</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-07T10:40:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try and resolve strange conflict upon merge with Dari
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60e108ffe754b5d9e7f53348f69b1647235005fa">60e108ff</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-07T10:44:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try and resolve strange conflict upon merge with Dari
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/26cbbbd4c0dc85dd34d268dca50a91dd19af30d9">26cbbbd4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-07T10:44:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e025c0def7cf27290ebae39515e5095116c66d2c">e025c0de</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-07T11:18:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> still trying to resolve conflict...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a5e7846b8d23f1629a4bb700bf7099e95ac74cd7">a5e7846b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-07T13:44:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to precision issue in offfset priors
The single-prec cast of small offset priors was made
before mean-normalization, so if all priors were sufficiently
small, they all got set to zero, resulting in no weights.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a34c5be7e05d65eb5704f06a25c19a44042091b0">a34c5be7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-07T14:25:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8836f7cc6eab71c0c3f1024c8e17f902901e6ee9">8836f7cc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-07T14:16:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #18)
update main repo with relion-2.0 updates
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb7874950cd03d69520c32bc0fb14370eaea2b6d">cb787495</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-07T15:32:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2569029489d27af3a027fc36365462904d207b62">25690294</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-07T15:35:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added true for reading of pipelines
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0f524f31b950dbbf3c1e68ca997487571f0b156c">0f524f31</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-07T17:33:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed an indexing error in getAllSquaredDifferencesCoarse occurring when nr_particls is non-zero.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/706a8d8afce359c01046bbc6d94b6ce3837b5ca6">706a8d8a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-08T12:15:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">also unknown branches, and rescale genera flowcharts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4b474beab51e7545377e42121ae027a0e130985d">4b474bea</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-08T15:58:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">no more movie.star in movierefine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/33f0597c41be658fa73af8915036e4c91013a922">33f0597c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-11T12:01:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug combineAllWeights, nt thru disk
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/320dd003bd9646aedc5b57cc342fe399a498b1da">320dd003</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-11T12:02:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ad814b7274aed3057e2b7484a9c069fd6be95b2">1ad814b7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-11T12:04:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #19)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ef304b306a558bfb1e27322059fd364ea644e664">ef304b30</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-11T17:05:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check for finished CTF programs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3d3ac803de8512e5ab799b821d2b25cb3dccfb8c">3d3ac803</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-11T17:06:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed proposed by Yunxiao Zhang from Stanford
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/896ceaf9d61b153392eaac71a6cc9eaa99e7ee1a">896ceaf9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-11T17:26:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged with Shaosa: allow local averaging of helical segments for priors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a8bed2e6e36a517b0f96024acda5613613b80e37">a8bed2e6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-11T17:27:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c5945df61737e79d0a3b494152d00ade317f195">7c5945df</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-11T17:29:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #20)
included reshape from Yunxiao Zhang and merged again with Shaoda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f39a6183108d235431b9c9536fb9bea02d1fe239">f39a6183</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-13T14:26:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4cc6f0b74170eff51fab2ef973eafba3f7c7781f">4cc6f0b7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-13T16:47:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">errno was a special variable on MAC OSX
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a27577f23a6f5875bd9aefeb4062feff16872b6">5a27577f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-13T16:48:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now GPU-options on the GPU, also for autopick, ctffind and motioncorr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9049ab4e74ebfdefc2cba3ffbaeaa7700bb93a77">9049ab4e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-13T17:08:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small changes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c4cbccc605bcac5802bf309a7d4927b3c110b4a9">c4cbccc6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-13T17:09:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reproducible class assignments in 1st iteration when using threads
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e0e73528dd303661122eb0dfe1f37480c20e562">6e0e7352</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-13T17:10:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #21)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/465d856d74aae8d147ee237d1cbf33e38eff6310">465d856d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-14T09:25:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed unnecessary read
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/74101794a1d4fcb50d6ef5ddb3694b9b0c139e4d">74101794</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-14T09:45:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small changes in gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4bf7a204a04a6727549944bfcb0828f41e26b43f">4bf7a204</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-14T11:04:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/21b0b26a97ced991d2644380b2386ce80b40eb2f">21b0b26a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-14T16:03:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging shrink and gpu functionality of autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1373a747fcdab4d646b5ef4a154ea068f71103b8">1373a747</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-14T16:32:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">die when cannot write to pipeline.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fab41d9029803ee9cfd709760adf7cd3a3f63e72">fab41d90</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-14T16:39:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01973602eec32b27da7120e64f2c8cbaedd4f74c">01973602</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-14T16:40:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #22)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/21aa4e3243848e44bb9c48b45b03e409d8125cc2">21aa4e32</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-14T16:41:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c18f316111ec4d03365ce20fdf9c6992675a972f">c18f3161</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-14T16:42:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">for now no shrink with autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68d626e86e57743a82d3559f37fdadd164d89bd8">68d626e8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-15T08:11:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">gpu-side fix equal to commit c4cbccc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3bddc455eca91675366266c975250056f29c8023">3bddc455</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-15T16:53:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1983cda21934567dbb9452f84115c315e94b09a5">1983cda2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-15T16:23:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d65004d0723747a86e8b8b5785d3332d96b5695b">d65004d0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-15T17:40:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix to --shrink autopicker like Sjors CPU-mods
A few small modifications were made to the CPU-side autopicker in
commit 21b0b26. This commit mimics these edits to replicate auto-
picking results when --shrink is set to values other than 1.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ae05dbc449d995ae9585dca2612285fcc0ff211">6ae05dbc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-15T16:55:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #23)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c622632cdd54b7b694e8c17e2b65e685b0d4c7f6">c622632c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-15T16:55:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/824d93d429fb3829d23c805558a66a853fe40d9d">824d93d4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-15T17:02:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added shiny_post.mrc to outputnodes of polish to keep job in running status until finished
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f0bbcda474fbbdd7b4f0fbbff9041db194f352c">3f0bbcda</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-15T18:22:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing excessive correction to autpicker stddev
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3422fd9f56825e2b552789a515d1b01683f273b8">3422fd9f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-15T18:24:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/162881b8a5e98211690e681c4af583502634cdc3">162881b8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-18T10:01:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #24)
Removing excessive correction to autpicker stddev
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b068595e851a76cd594b6d1891311a8b7652436">6b068595</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-18T10:01:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ced057c965034dcc3e26dff03f694427381e6ccc">ced057c9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-18T10:02:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better handling of gpu_ids
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/86d1869ac1bc80a07e012ab6d7aead9988bd3985">86d1869a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-19T13:03:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resize non-square 2D images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7b7de56f34ad92bab420bfd1ef48a1a02cd6c9e">a7b7de56</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-19T13:12:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more drastic shrinking in autopicker, plus added pixel size of references
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5e680375494ed2eed08091c862d57f574d6a0341">5e680375</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-19T13:12:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #25)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/48a42f5d3a58d7224744d43f240ca500b6cb1c12">48a42f5d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-19T14:26:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Shaoda: 1D profiles in display of FFT and picking cross-overs for helical tubes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/608dbdf0670c8e81c20f98aced8438960ca35367">608dbdf0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-19T14:42:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further changes to autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c64573951afd92253f1807e6b1bcd510b4e43366">c6457395</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-19T14:43:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #26)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7cb57760f2dd79fa6fe80400c1cc14cef12c4db6">7cb57760</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-19T16:18:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a2857cf8c9a6b738cf1b315ff596eeb985f7134">8a2857cf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-19T17:01:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> back to less aggresive shrinking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/af3c68bfad9ede88cc0ebed418fd0777bc27319f">af3c68bf</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-19T19:12:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">-j >1 cmake build (make) waits for ext. fftw/fltk
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/846cb6558b43dc62a5c08055b66f914efc12f27d">846cb655</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-20T10:59:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Highpass filter added to autopick, as in CPU-code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/abda7fc7f263ec5ae5a403b3ef966b88793c0edc">abda7fc7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-20T11:00:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a9a39c98ed59d7f16df45d24103229408da081b">6a9a39c9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-20T14:36:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">back to less aggressive shrinking, now seems to work for non-square mics as well
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61a580e38983ee55207ecf4a28dbf195810fe6f7">61a580e3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-20T14:38:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #27)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/481a607f5e95ab51ed0c88e20cdfe1647b14a956">481a607f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-20T15:49:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/298900119caab1b3527ba4bb20e8fd3738af8e1b">29890011</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-20T15:47:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #28)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1cd0524ab63b4b179bc18276a5466c4009d05c67">1cd0524a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-20T15:47:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ab4d60ce15343bdb48b0b197145a8c86783e2136">ab4d60ce</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-20T16:33:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">prevent empty plots
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/66adff0412104159c1a6f3e13251f77cf32e4859">66adff04</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-20T16:33:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">warn when no angpix is available
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a63ed67c0eaa474669877797d77b5064e49d1d6a">a63ed67c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-20T16:38:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small changes by Shaoda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4bdc5ad892e64bc6a3871959ed1c3479384077a0">4bdc5ad8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-20T16:42:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #29)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2982654ed406b49837c5ab272ee29eb4c0df8490">2982654e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-20T16:42:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4086e54464d4a2405fde3178b1848d6f4f1dc727">4086e544</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-21T10:57:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">warn if users tries to submit job with too many MPIs locally
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8388dedf72d6ed7bd87ae9eec9ddb013e693b708">8388dedf</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-22T10:42:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">All devices are reset after each iteration.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/66fb7eafadab92f0bc0d35a269a7bb7e3ab0980c">66fb7eaf</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-22T10:43:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/508ca1b40d6580d81edcd62e2426514b1c574330">508ca1b4</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-22T17:33:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes an error with the bundle distribution amongst threads.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5c19c9f3628a00172d916a815de2011fe4b67694">5c19c9f3</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-22T17:44:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5387c728ee6fe6337ea24b5de4358b93ed822279">5387c728</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-22T16:56:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #30)
Hopefully fixes the "out of memory error"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fecb4f1387e90b4bd048ccf95fcac59369229ec6">fecb4f13</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-22T16:57:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/05209ad627a098bd53b4f4d55652bc780b5b1a49">05209ad6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-25T15:19:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added timing in preprocessing.cpp (extraction). Changed timer output to three decimal rounded seconds.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/83752cd3b50831f2dba4e73cd300356f0a50309a">83752cd3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-25T16:08:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopicker timings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/81b6c71e3d6cc709bee906e74445533075141eb1">81b6c71e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-25T16:08:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6878bb3a4f34eb791df57129a322aa1b7204d5cc">6878bb3a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-25T17:01:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed fftw_cleanup causing autopicker issue
The cleanup destroyed all references to fftw-objects, not just the
local transformer. Now we instead let it go out of scope and get
handled by the destructor, which cleans up the local copy only.
This fixes issue #99 (but we still don't know why that issue does
not appear when using a single reference as input for autopicking)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aadccfa74454c7d7e0f1f23501f0a651a90f214d">aadccfa7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-26T09:56:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed unused transformers in autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca1fb4f4cf00e17eb1acb10cc7fa364e6da0476a">ca1fb4f4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-26T10:46:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Batches of ffts in autopicker returns correct psis
FOM maps and psi-metadata are correct when being forced to batch
psi-dependent fft-transoforms due to shortage of gpu-mem.
this fixes issue #101
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7214040bcc53124d087d4c7130757d545e91770f">7214040b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-26T11:36:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clearing up some mem-estimation confusion
Autpicker uses custom alloc for some object, and default for others.
The code was "confused" about what objects should be included in the
overhead-estimations for either one.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7e0a57cdff675333dcc65a4f1d6db6d374f6345">f7e0a57c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-26T13:35:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Runtime setup of cache-mode for custom allocator.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd58babe9a6debd27f8ee6b9dbf4d0939f677a84">cd58babe</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-26T13:36:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">No allocator caching for autopick.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ec2b942c1ceb83d2fd64207cdf2435e93fa43aaf">ec2b942c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-26T13:45:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed the CachedAlloc-cmake-option.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6da59a01380a1736d15cc0e6e4946033bee186da">6da59a01</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-26T14:59:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Projector moved to higher scope in autopick.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7eb579a874e69f305f9ccabb4c2d79e21a7d8483">7eb579a8</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-26T15:12:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cuda FFT transformer objects moved up in scope in autopick.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8cb3965abb6a0b9c106afa59a8c3098b205c8e4c">8cb3965a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-26T15:36:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some prel prime-factor warnings in autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a0b50a61adc0c6a43db1904bd12b6fe81676661f">a0b50a61</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-26T15:38:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e715fda3ee48acafb2975b02bc8c98834d40ddd">9e715fda</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T09:15:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add clear of transformer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a4adb71c7b5119da86fc2017e0ac2550e5eff161">a4adb71c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T09:16:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">continuation of refine jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5eedacb1dbd5ce53670f75874a5aac6c765c1d8d">5eedacb1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T09:17:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">made function to print nodename
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d01586746cac42bb8463d5508a0cd375d9171ee">9d015867</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T09:18:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added sorting with autopicked coords
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1dc7817e39583ee6f51568e7d23f29e6d9f913e6">1dc7817e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T09:20:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/71414ef22591c5c617a4bbcf5a29a50ba8e34b33">71414ef2</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-27T10:29:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopick cleanup and added some new helper-functions and method in cudaFFT-class.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3ec4eafe74f6b3925af7a82e63d7ab9f4c4ff32">b3ec4eaf</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-27T10:59:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f0e2ee333917dc04d36de3ae125b57d1bb606523">f0e2ee33</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T10:50:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed cleanup from computeFourierTransform in projector, which solves problem in autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7313b69f1a6a5e1b331dc4e65996c1ba0eebabef">7313b69f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T10:51:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to copy all particle images to a local scratch directory
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d8953ad9f65eaf441f7d001c2d1c6ec871645e4d">d8953ad9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T10:52:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #31)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/87ad35d81ffd8934d9d08dfb231aff5e8e686a10">87ad35d8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T10:53:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1762630d90e01aad0c0c44dbdca74f47acab9b92">1762630d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-27T12:43:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/20511ec0f38f54e9126474e0b01804e9c3819cc3">20511ec0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-27T16:33:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">All objects in GPU-side autipicker are worksize
This affects the performance positively, as adjustments to FFT-sizes
based on prime-factors do not result in size-discrepancies. This also
allows us to remove an intermediate arrey for data resizing (FT-
windowing), resulting in a smaller memory footprint on the GPU.
In the present state, job segmentation is non-functional, but this
will be fixed in the next commit, which will restructure the psi-
batching in the GPU-code and clean up the autopicker code.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/74222ff14ea19f483c4e086e2ac3894855a0d910">74222ff1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T15:52:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added unblur wrapper and various small things
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84172c29ed35438f77d10ff781cce9bcadf5ab5e">84172c29</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T15:52:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #32)
Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c3ee4d468f51c10bc0efdddbdd7dafff47adac2">9c3ee4d4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T15:52:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a117bcb90c7cb10a2420606f8901b1d3fa726ed7">a117bcb9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T15:52:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4cfe8f7653540163962e94b98adeda8d37fefe13">4cfe8f76</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T15:54:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #33)
added unblur wrapper and various small things
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c1b2666b752b0c73aedb95c713cadd1f7067fe0">1c1b2666</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T15:54:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1d4f7fee61e2caafc9f7f2541775b5689522af1a">1d4f7fee</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-27T17:52:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Batching psi-iters in cudaFFT-method
This makes psi-batching functional again (was made non-functional in
the previous commit).
The psi-proportional transformer is now allocated fully, which does
increase memory usage somewhat during batching. Only the tranform
itself is therefore batched, which allows more expedient calcualtions
during batching, since no data needs to be moved.
Also, small changes to FFT-prime factor warnings.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0fcec49465115f9c413726a12ed47d9d8b8f4bbb">0fcec494</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-27T17:57:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42ca556095eb31e16ac4f90708be3be393c5885b">42ca5560</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-27T17:03:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging GPU IDs motioncorr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3706845b47774626eb89344b7985cf40fe7f71a5">3706845b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-27T18:03:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd10178b95f236cf0e99c38c79672f306d2253d8">fd10178b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-27T19:45:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding fudge-factor to FFT temp-space estimation
This is to stabilize the behaviour at high loads, where batching of
psis might become necessary tue to either/or
a) many orientations
b) large micrograph sizes
The cuda API estimation prior to plan allocation is apparently not
really accurate, so we can get stuck if we run out of memory. Also,
with the recently implemented mod to batching, there is minial
overhead of batching, so it is easier to just batch, even when it
might be technically possible by a small margin to not batch psis.
For now, the warning of batching will still be printed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c62608536ff4ec024479083f2ca11a8084347da">7c626085</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-27T19:49:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe4eef12c287b30dd7f14f89b6421e6e9af6e600">fe4eef12</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-27T20:03:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to estimate-fudge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d213f1fe1007fd7cf0a5ad8760541ba3c053e2cd">d213f1fe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-28T09:50:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #34)
Autopicker worksized + checking FFT-primefactors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8079de2ff992acf4611af6d7eba59536ea7e8524">8079de2f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-28T09:50:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/05ab019a38eeb36fea5d718e9c4e1fdd95dc97e6">05ab019a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-28T14:42:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enabling fwd/reverese-only cudaFFT transformers
Since the large (possibly batched) transform in the autopicker is
always complex-to-real (backwards) only, we want to make a plan
only for te backwards transform, so that we only allocate temporary
space for it and not the forward transform.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e53cbf3bc54884a885d65908e347e3a03f2d8a9b">e53cbf3b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-28T15:34:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Shaoda's adaptation of shrink for helices in autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e4538af8d64f2cd4b2b3e3b9f74e7c4ad9fe7d7b">e4538af8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-28T15:34:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Shaoda's debug of polishing for helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/249f9b93ffb7f02de45d3b51e081f88ba22b1f04">249f9b93</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-28T15:36:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">copy data to scratch with explicit prevention of filling up scratch space
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eab159b4509966e3fcedb6cc16abc028b7b1e28c">eab159b4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-28T15:37:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #35)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6eacf39743de07dec0dee5aa571932aa0e778c2b">6eacf397</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-28T15:37:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e982295b355d924586077caeb05fb5e7006dd9f5">e982295b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-28T17:48:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The exponentiate_weights_coarse kernel is batched over all classes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8dc10b8902d0d345eb869cefa31a64a86bca0865">8dc10b89</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-28T17:52:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The GPU_MEMORY_OVERHEAD_MB subtraction from CA-cache scales with number of threads.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f272115b3efc78d88decc8cf4571686e69cf4161">f272115b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-28T17:19:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Shaoda found another modification for helical autopicker in cuda code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/85508146387d3cb07ee08a9609a18119da5e0853">85508146</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-29T09:11:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">because MRC is stored in float, also preread images in float, not RFLOAT
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/22d3ee9da876b9799f5771e94dde22be3033408c">22d3ee9d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-29T11:35:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">made one generic function to generate PDF logfiles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a25ba44ecedf25f9b5b97039617da981bc8ca3a8">a25ba44e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-29T11:36:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">change psi-sampling in case of gpu to finer one that is multiple of 32
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f93cf4c2205374bfe8e8217cdab1003a95e8f384">f93cf4c2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-29T11:37:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">rescale_factor downscaling AND change dimensions automatically for optimal FFTs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c7b9c967f325060f12753b2fa85932df88391b3c">c7b9c967</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-29T11:37:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #36)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2648abf7f1028435e475a4f9b3c2c3a115d1c22d">2648abf7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-04-29T11:38:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/22674324407356a45fa91bb4841c25005e6c6233">22674324</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-29T14:07:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Batching encompasses temp, src and dest arrays
This reverts behaviour closer to a previous state, which now makes
the autopicker more stable in memory-limited cases.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe1834471ea595ced9470be2f35b90ae81530979">fe183447</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-29T14:57:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopicker cleanup and nicer warnings
warns if:
shrinking past lowpass
bad FFT-size based on prime factors
batches over psi-sampling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/096d13a7a9914959e046983c7fcefb020660dfdb">096d13a7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-29T14:59:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58f41777f4910bf7ea3bea6a30da08ec065bef3a">58f41777</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-29T15:54:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Timing for projector plan.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d1b8b3e99556e475a3dfb621d94f92969c2402a">5d1b8b3e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-04-29T18:17:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">A centering went missing in the last few commits
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f59a98388a8b6f6528cf0d7f49116ecb020cdc56">f59a9838</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-29T18:49:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed the back and forth transformation between angle and matrix representation of sampling rotations.
30-40% speed-up in AutoRefine.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a967884ae9c1dae5cf96b73c9d88f3ebd88f9bfe">a967884a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-04-29T18:51:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e176729d190d287ff953651a009ee691ec3958d5">e176729d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-03T13:01:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugged copying to scratch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4db90e915d9c53b87c68ad6788e878d6c50fa299">4db90e91</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-03T13:01:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #38)
debugged copying to scratch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f47addb8481146340ac2b555c64da5cd13c44b6b">f47addb8</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-03T14:16:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Separated preprocessor constant for extraction timing.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a394a19421947b4f3530b0b8b8fbf4616f8edbc">1a394a19</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-03T14:34:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">temp revert of autopicker shrink control
(for pull-req)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/97e6450368b302a505c899c80dda8c0e4571d3cf">97e64503</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-03T14:35:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4af35e4305ad279eadfd7399c0f35d9f02786ae0">4af35e43</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-03T14:45:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reinstating bug fix to shrink 0<x<1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ea20fe9c574fd2861a2cde6c523b8d4cd5f5898e">ea20fe9c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-03T13:48:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #39)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4ce985362727b6f159395c5dd0b373dde09a005d">4ce98536</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-03T13:49:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/74706bdf48d9b78e6e9c451d32a5ec915be730de">74706bdf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-03T13:58:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor tweaks to GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/32f8afcd79cf485595b3e3f30a8e427529d85906">32f8afcd</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-03T16:42:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better error-report in coarse-convert for zero number of significants.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/33ae8de18fe7afa1e303d8d1063f3990308f6250">33ae8de1</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-03T17:03:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU acceleration of euler-matrix calculation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1212333c81c5c292b82211f63c2cf11571ee5099">1212333c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-03T17:04:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/03e1614c6473debda1b512a4887cde08eb59b78e">03e1614c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-03T18:02:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed firstiter CC debug warnings.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ffc813cd7c79f7d1a1e49ff9f38bbf53b8f7d0d">7ffc813c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-03T20:09:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">stabilizing autopicker memory allocations
If one wants to runs insane combinations like 3600 oriennts of
4096x4096 mics with 7 refs, one CAN do it, but even on a K80 the
autopicker will need ~72 batches to do it (and it will be a lot
better at being insane than the the CPU-code).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57612678748dd4f455ed518e1038e82b254eb486">57612678</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-03T20:15:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6910e5cda4fca52c8f0c465718e570241b8d125f">6910e5cd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T13:47:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">go back to getImageScratchName in exp_model#
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a3123c1e6de66d4a2054f1e7dcfc6db53b872b1">7a3123c1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T13:48:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fl_message instead of cout
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34924260db5b528dd7ebe39cfda3064f1f7eb121">34924260</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T13:48:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> go back to providing a movie STAR file as input for movierefine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a5711bbe3cad65f1e8d15f21de49e561f64e9856">a5711bbe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T14:02:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replaced errno ddeclarations for err_no for osx compilation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5e01a052924582f861a5f4ff774ecb03ed705060">5e01a052</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T14:14:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">pass also do ctfimage in copyParticles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/424e0115a4dbba86337151af1ffd9a5231623dd5">424e0115</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T15:38:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove coords as outputnode from movierefine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ed63f4d4dc13354f1b8e6c80669fa58136569e93">ed63f4d4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T15:38:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">siwtch off PP_Timing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3bef0ac1c221a351426ef01b917aa3d73852610b">3bef0ac1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T16:17:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">synatx change warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/93bc22114fb1d051d49259ca41878cd6d87690b4">93bc2211</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T16:18:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #40)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4622f6d8a1bfd3f9e75d963b18cd222c4a8e2ad">b4622f6d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T16:18:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1f238730930e7eaf8d755d92a41a801e08f912fb">1f238730</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T17:20:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont resizebox flowcharts, leave comments for user to take out
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/309c6e0fd4c3d0f7fd04477e922eb722ba35a453">309c6e0f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-04T17:22:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont resizebox flowcharts, leave comments for user to take out
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0613905716582a6149fb97f9cc921a1d37db547c">06139057</a></strong>
<div>
<span>by Erik Lindahl</span>
<i>at 2016-05-05T22:47:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix non-CUDA and OS X builds
- Introduced CUDA CMake option that in turn defines -DCUDA for those
compiles, and added #ifdef statements around CUDA calls.
- Fixed OS X linking, library, and detection issues.
- Fixed usage of sincos()/sincosf() with the clang compiler.
- Added correct FFTW libraries to relion_lib.
- Use internal CMake varibles instead of environment variables.
- Made the detection compatible with both lib and lib64 under the
cuda toolkit directory when searching for libraries.
There is still an issue with CUDA OS X builds where clang complains
about __any() being ambiguous. This appears to be due to other
Relion files including a header that in turn uses the entire std
namespace.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/59c2eecfd80ea1c064416799b025f357ceff2414">59c2eecf</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-06T10:42:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better out of memory recovery with a large number of retries before error is thrown.
A bit smarter assignement of CA allocation size.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0e8b8a002be7a7e18ed514351b09a4220927abac">0e8b8a00</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-06T10:44:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a89770bd01327e82e048c72da5b535200d640bc2">a89770bd</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-06T11:25:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Check if the new policy exists before setting it.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f439dc4d22e2db90f2481fcc126e2ecb34358a1">9f439dc4</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-06T11:57:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Translations in diff2-coarse-kernel moved to an external kernel-function..
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8158484f96b8db74d1f8114267a2e6d4fc53803f">8158484f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-06T15:51:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> put warning of psi change after its done
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/52e6571d539c89a5c1b8b9bb63621d963e4ac4e5">52e6571d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-06T15:52:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> small changes by Shaoda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d905a99c05130602dbf68ddaa01371088060f85">0d905a99</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-06T16:57:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cut large workflows in pieces
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c5edd3abb1fc1f8fd1a083f6a16c15956f856f0">7c5edd3a</a></strong>
<div>
<span>by Erik Lindahl</span>
<i>at 2016-05-07T18:13:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed OS X FFTW3 and FLTK builds
Fixed library suffixes and detection. This should
resolve the issue with fftw3.h not being found for
local builds.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/400a167ecd98aa6df199b65d4b50c801b29fe2d1">400a167e</a></strong>
<div>
<span>by Erik Lindahl</span>
<i>at 2016-05-07T18:35:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed namespace errors related to CPlot2D
The CPlot2D header previous had a "using namespace std" on
global file scope, which caused a chain effect where every single
file had all routines in the standard namespace. This in turn caused
a clash between internal clang and CUDA symbols. Fixed by properly
prefixing names instead.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b025e5736569a7aa9cd6dccd53e1bcfcfd6d976">6b025e57</a></strong>
<div>
<span>by Erik Lindahl</span>
<i>at 2016-05-07T18:46:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added std:: prefixes to source code
A few additional files needed std:: prefixes
now that CPlot2D.h no longer pulls in all of the
std namespace.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8302946febad9b7e7d4dd200ffca4dfed2d64dd4">8302946f</a></strong>
<div>
<span>by Erik Lindahl</span>
<i>at 2016-05-07T19:31:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Cuda on OS X
Hide circular dependency errors on OS X to enable Cuda builds.
Added flags to hide warnings about unresolved symbols at link time
due to circular dependencies between gpu_utils and main relion_lib,
and avoid using linux rpath settings on OS X.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/77d2c8db5c68ffa2749849860643306d3c95bce3">77d2c8db</a></strong>
<div>
<span>by Erik Lindahl</span>
<i>at 2016-05-07T21:26:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix fltk build inconsistency Linux/Mac
Bumped required cmake version to 2.8.12, and use a patch
instead of a custom fltk-1.3.3 version for the OS X issues.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/444f1a0db1a08497dfdaa9e7083a6ebd890c2226">444f1a0d</a></strong>
<div>
<span>by Erik Lindahl</span>
<i>at 2016-05-07T21:44:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed autoconf files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f78f59a2e21ec3aa44b9f8844df51db86843fcfe">f78f59a2</a></strong>
<div>
<span>by localadmin</span>
<i>at 2016-05-09T14:12:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Warnw if non-cuda compile tries to use GPUs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9af66057ba749c4c1568f020140d6dee82753358">9af66057</a></strong>
<div>
<span>by localadmin</span>
<i>at 2016-05-09T14:20:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Warns if cuda-verison is too low
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a9bfa093f37af5ad33e7d24eaac833fdfb441bc5">a9bfa093</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-09T16:17:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8cbcf6cf44ec7f47f3746f3aed764255604db6e9">8cbcf6cf</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-10T10:33:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue with building without shared libs.
Also some clean-up.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f89f4af5e85feaaddaf207b6235bcd52d82fe8d0">f89f4af5</a></strong>
<div>
<span>by localadmin</span>
<i>at 2016-05-10T10:54:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reengineered cuda-code timings
Now activated in benchmark build. At present only works
with a single thread and rank, due to filename clashes
to be fixed in next commit.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f628dc538f1532ee1b6c694483ec5cb383bc6fa">9f628dc5</a></strong>
<div>
<span>by localadmin</span>
<i>at 2016-05-10T13:52:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Multi-reank /-threaded timing files
under precompile symbol TIMING_FILES, bewae of LARGE output for
realistic runs; averaging not yet in place.
Works for refine and autopicker (mpi-verisons included)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e3f86fb8539851d1b22e2889fd8191b806a4b0b3">e3f86fb8</a></strong>
<div>
<span>by localadmin</span>
<i>at 2016-05-10T13:54:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e69044786b7aa730bec6d3416bc873af4f0cff91">e6904478</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-10T14:33:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Translations generated pixel-wise on demand within the diff2-fine kernel..
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/848b2a00bc194189ecaf0f0044d34b1389d22999">848b2a00</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-10T14:47:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
Conflicts:
src/gpu_utils/cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d57bab8d444e37af9db95c4d453fe5e3bec4f4d4">d57bab8d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-11T11:10:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CC-kernels support in kernel pixel-wise translations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8741f653b6bcf100017b892f864512cc74111d3a">8741f653</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-11T12:23:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CenterFFT 3D introduced (unused)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/647446ed946945584478f28136c660760546d084">647446ed</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-11T16:30:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">In kernel pixel-wise translations implemented for wavg and backproject kernels.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/14544feb21b8804f48aeb17f5fa22528744d084b">14544feb</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-12T15:00:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cuda FFTs can be 3D
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a541c8156d61e6997852e9f75b99ce9fef071c5">8a541c81</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-12T15:43:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/653c3f08ce77d3cee5d3c2c4f961092ae38009af">653c3f08</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-12T16:26:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to profiling build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0f573929dc429e2c99b12c226d957c8a31f10868">0f573929</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-12T19:57:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Another profiling fix (markers in nnvp)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/842b29a5d4012a517aaf2033c712346e351e5fac">842b29a5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-13T12:24:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean-up and superficial optimization of wavg-kernel.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7f64df71b5554a72ba750c1e471560fa6c1a0563">7f64df71</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-13T13:23:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">BP-kernel optimization/clean-up.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a940d67562c40377f2c81bcafa773fc1ca62982">8a940d67</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-13T14:16:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Translations clean-up.
Removed cuda-tranlsation-class and the use of it.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e4303857277cb4ad7da3f1ede8afa5f166ea0081">e4303857</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-13T13:50:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">raise an error if one of the halfsets is empty for helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c416bd5b683a140bafd88b8fbbd530a157baf75">6c416bd5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-13T13:50:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cut flowcharts longer than 10 steps
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/92dfabf4271faec7ce3081b52f0cff4a7162b9ba">92dfabf4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-13T13:51:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new converegnce behaviour in auto-refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/46d9d09e2cee3891ef34a61b4b93a79470cef9b9">46d9d09e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-13T13:51:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added joinStar for movies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d3ace7687ac435db0b84b0477a71ee641ff9ed9">8d3ace76</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-13T14:24:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further development of joinSTAR
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9985dc6807e76c25fe03dc1f1a0309a32352f7fd">9985dc68</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-13T14:25:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/705766f7ab27b2801dfce60ccb348e2d93be47ea">705766f7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-13T15:05:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #41)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/83680dec3c4d3f77f9e690ca406f34a1122bbf06">83680dec</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-13T15:05:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29b30623acd61c9ad7c6f5ed97e60394c9f8de5a">29b30623</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-13T18:36:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge https://bitbucket.org/tcblab/relion-devel
Conflicts:
src/motioncorr_runner.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c145ad9cce063614f1f93c53efaef1bfab55a3de">c145ad9c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-14T09:56:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #42)
Better build environment and profiling, 30-40% faster autorefine and on demand translations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/487dacb02bd1942fe13c0cfd7d044e64a1317822">487dacb0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-14T09:56:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/88ec64439ac561798be86de8160c381153b29f2b">88ec6443</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-16T11:43:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Modified the automatic device assignment
Now mapps threads more intuitively and in some cases
more benefitially in terms of memory;
-n 4 -j 6 on 4 devices (before)
0 2 1 3 0 2
1 3 0 2 1 3
0 2 1 3 0 2
(each device has 3 ranks)
-n 4 -j 6 on 4 devices (now)
0 0 0 0 0 1
1 1 1 2 2 2
2 3 3 3 3 3
(each device has 2 ranks)
If we preferred, we could also choose to "unbalance" the device-
load to further reduce default memory footprint;
0 0 0 0 0(0)
1 1 1 2 2 2
(3)3 3 3 3 3
(1 device has 2 ranks, both others have 1)
This point is sort of dumb though, since one device is still memory-
limited, and these launch-configs are bad to begin with.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/763c69a4d36c7977b04e680b22b0c4c3a3f03bf9">763c69a4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-16T14:00:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hopefulyl fixed inconsistent pipeline.star when executing scheduled jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/15fa87b68b92b8ab1acd9767e06b8d5685296ef7">15fa87b6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-16T14:01:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/56266374310397f168c93b8890d37b9ff417b941">56266374</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-16T15:51:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Memory management enhancements and an allocator bug-fix.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9692aaa020007e91f304637ea7d0055fdb9b001f">9692aaa0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-16T16:02:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cafcaa29230e9bb3d1334bfe890f0451a47f376a">cafcaa29</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-16T16:15:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">no lockfile for scratch_dir in non-mpi refine
this fixes issue #102
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/522e86435be3a4c2e9e03fc2f162f9aa00ae06b4">522e8643</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-16T16:52:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autpicker fix
An oversight in preliminiary testing caused ctf correction to be
needed, as a GPU-kernel used a ctf-image as a multiplier regard-
less of ctf-correction or not.
this fixes issue #103
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/31f6bd2c3d17f0448c7b08d0150fc64407f67523">31f6bd2c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-17T09:57:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extra careful about allocation 0-size cudaGlbPtr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d2aacd0f2eb549bc9cefae531c2945a570251b3b">d2aacd0f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-17T09:57:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">All setDevice() are guarded against bad ordinals
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c1d9651a2dc12124223559ee36a3b6903c2df449">c1d9651a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-17T09:23:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed remaking of logfile for continuationn run
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f017cd0e0d43950a2a4053c3ffb127d9cc71228">4f017cd0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-17T10:54:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to debug build
(amends commit 31f6bd2)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51e85e4d008710ece23ba0cdc940a9cd2acfdaa4">51e85e4d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-17T11:52:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to Issue #105.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1783c54d7bfa266af76527a236c129c4ed8725ec">1783c54d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-17T11:59:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Additional fix to issue #105
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/051f6581fe88b63bd81fff8f7c704979f4963482">051f6581</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-17T12:00:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2acd4d019838d6f2c7025b166427d292700b08f7">2acd4d01</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-17T13:38:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Proper application exit for refine and autopick.
Instead of exit() just a return-statement is issued at the end of the main function.
This to make sure all object destrcutors are called.
A good source for this is: http://stackoverflow.com/questions/30250934/how-to-end-c-code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8937748e55781e0fddb0f80eb6609bc5541d40dd">8937748e</a></strong>
<div>
<span>by Björn Forsberg</span>
<i>at 2016-05-17T16:28:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4649e5edec8eaa682ff55312d79a051a53bc5008">4649e5ed</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-17T16:30:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #43)
Several important memory fixes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b070c02b71c54d68555bb552591809ec38f987d4">b070c02b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-17T16:30:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2befc2bfffedf5aed91ae73ec188538144e7141">c2befc2b</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2016-05-18T18:08:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to non-default dev-ids & mem-OH-calc
possibly unnecessary low-OH devicesync added for safety
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dca6054b7cd660154a280b269620301645a28b96">dca6054b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-18T18:55:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Device is set before reset
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0bb1789df23b7913ad6934216bfb3d501cbcf04c">0bb1789d</a></strong>
<div>
<span>by Björn Forsberg</span>
<i>at 2016-05-19T08:57:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4b209fb5a913048e4e5eea70aef018578284867e">4b209fb5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-19T08:33:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #44)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe49cdb3d131586ca22a2cf2ac7c8df4f5e78bec">fe49cdb3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-19T08:33:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/71decc80cdc1b1845c869abe0b7b80d7acac125c">71decc80</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-19T16:16:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">print usage to stdout, so that error message is more visible in stderr window
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/18590647fbf4e6e5d00694ab49d61129e855860f">18590647</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-19T16:17:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added scratch_dir to refine jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a29676e06ed230f64657675042bbd620057dd2f">1a29676e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-19T16:18:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">delete non-finished outputnodes when marking a job as finsihed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/865c24f32468c403cbaa195eee0ace3321f41951">865c24f3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-20T11:28:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Explicit indexing actually happens on mpi_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7456212869731326d8186500e16409ea018f9a85">74562128</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-20T11:30:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5148526a1f7e410b2c23529de4e4e4f00a241975">5148526a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-20T10:46:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #45)
Explicit indexing actually happens on mpi_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd4b29efbb3035fd382e05931f09a0cfe63735e8">dd4b29ef</a></strong>
<div>
<span>by Björn Forsberg</span>
<i>at 2016-05-20T11:51:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6cb7aeca1eb35739e4717050e82820c915245c21">6cb7aeca</a></strong>
<div>
<span>by Erik Lindahl</span>
<i>at 2016-05-22T22:10:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install gui background xpm to library directory
The relion_maingui program will first look for the file
in the configured library install directory, and then in
the source directory.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/724ac140c66288d87e239def2b6cc8c479b8a97e">724ac140</a></strong>
<div>
<span>by Erik Lindahl</span>
<i>at 2016-05-23T09:01:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix locally built FLTK installation
Install to the target library directory, so RELION works
after installation even if the source directory is
removed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/28c40ae951f3ded781abf6432dd9c2e30556ec3f">28c40ae9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-23T11:57:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow saving from manualpick window
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bee40d76157bdcc5cbb8543a4f4074883a4d3f1b">bee40d76</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-23T11:57:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">back to more stringent auto-refine convergence criteria
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/237b40bb09800b84adc15677fc56a61a821db718">237b40bb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-23T11:58:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #46)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27eabec92f65759fe603319416efbd92831e9049">27eabec9</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-24T15:58:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f60e7ef907c945784b11a2cfb3dbf6b5cd07be97">f60e7ef9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-25T11:56:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to batches over psi-orientations in AP
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dbbd7b587aba960d49426a9f372ea3c214b499f7">dbbd7b58</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-25T11:57:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reduces overhead of re-planning FFTs when batching
by checking against the *requested* size last time batched transforms
were requested, instead of the then found possible batchsize.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bc307d92fc0f2c4f152d671fe9e13d9d1f266e2">8bc307d9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-05-25T11:59:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/312411548fc67f81aa38fa0308e89be71eef522f">31241154</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-26T15:04:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merge with Shaoda#
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f4e30fa829a8bd425f3da1796a113b3d7988308e">f4e30fa8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-26T15:04:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont warn zero overlap
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/05fefb0e8e0bf879ffaaa77bde1f4ade0413e293">05fefb0e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-26T15:04:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write all notes to output file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b02557e0bca2f4291aed55d3ca97fba1a4979413">b02557e0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-26T15:05:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">main route up comes from re-extracted particles in flowchart
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3487890a1b27601d75f3a0f2f14621557a245487">3487890a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-26T15:05:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more error output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/90431dd9310ac748910dff51e5ff9b27db8594bf">90431dd9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-05-26T15:06:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better help in help-button
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4589d458d78a29d40db35facaf2cb24ff842dd6f">4589d458</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-26T19:50:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Timings in projector.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b777e7fe167bd15fe3735448a1f306105beea91">0b777e7f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-05-26T21:43:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mirrored computeFourierTransformMap from ml_model into cuda-files.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/754d372f7174ff5eb695e0edf7f945c34b3dcd16">754d372f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-08T15:04:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #47)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5579612599fd46c1d6cc169b7c7ecaf590278857">55796125</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-08T15:04:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8cd9fbdad4f96d08e8855c2600ade68669094972">8cd9fbda</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-08T15:22:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont die with errors from unblur execution
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f79d22fe6f3083dabc1eb9fced1b7f6d5e947908">f79d22fe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-08T15:22:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e6e57ef0f0d4a44d10757cf8faf01a57a4b01271">e6e57ef0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-09T10:03:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> also use master!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0f1158d8fe6a325d733727ea92e0ea9b5d83cb6">d0f1158d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-13T12:01:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix (only for small arrays?)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e3bd152bde8a32b8696b70387ef626210db47ac8">e3bd152b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-13T15:15:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adaptive OS used in fine
This should not be needed, but if oversampling is not used (i.e. if
there is only a single pass), then data-objects are incompatible with
storeWS in the GPU-version. We escape this by making a redundant calc
in a symbolic fine-pass that is NOT oversampled, but then we need
to use adaptive OS instead of hardcoding an oversampling in the fine
pass.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3768c86adf87dc98469dfd66b304d44d3bac6301">3768c86a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-14T09:27:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow import coordinates from pipeline directories, and dont let on-the-fly processing die with errors, write warnings instead
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ef5b139718ce87c83f2667b08adbcb6c21fb4222">ef5b1397</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-14T12:40:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #48)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fdcc4c88b7a583d6518d769ca4be123604828343">fdcc4c88</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-15T15:15:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Shaoda changed some default values for helical autopicking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9bc92f24c757d8cdf5b336ac79086a8ea32c711b">9bc92f24</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-16T10:04:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only save x,y coordinates in manualpicking to avoid problems with picking extra particles#
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5b850adaec8e7cd1f49687fd820ed2db2cab7b5a">5b850ada</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-16T10:04:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #49)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf7b9080b57361ef0680d62c07987bbea08e6e2b">bf7b9080</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-16T10:05:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e50ec1092301b6b1c2df5cbe49d9855f6ba0dd44">e50ec109</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-06-16T13:25:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed better memory related warning and debug messages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9058ee233581ec69f01d09ceaafd2d42ddcb0b13">9058ee23</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-16T14:19:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CudaAutopicking uses MPI correctly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f21ef0c7c420b91f6e2e539de9233a42a5d6e286">f21ef0c7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-16T16:09:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small bug in manualpicker and in main gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a49ce7147ef3f511390233acbc02ce0142750cb">5a49ce71</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-16T16:09:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/760cf4b0656667eae9b0cca7c8b2bbf1f7df3902">760cf4b0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-16T16:12:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #50)
small bug in manualpicker and in main gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0aceea1ff83381b65e0cd4f131e84051f1828375">0aceea1f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-16T16:12:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4772a6d93af86873a774486ebb0c13666f864c8a">4772a6d9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-16T17:59:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix to issue #116
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a381f1411133f35077595ce332c62f12ee9c48c5">a381f141</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-16T18:00:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> fix valgrind error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/693a59ef28c5eb99d8c808463c2c895464954ee6">693a59ef</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-16T18:04:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes under some flags
--skip_align
--skip_rotate
These flags do not work perfectly yet, but this commit does
partially address issue #113
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/71968f04b403573928d6868d83ea119d45195d53">71968f04</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-16T18:07:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1e607c867f6fc59ff7be21c10a75a2e880ab3f78">1e607c86</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-16T18:17:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">temp non-working state for merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a80a7071c0be0c7a0106d3f2742e3d71399c0bf">8a80a707</a></strong>
<div>
<span>by Björn Forsberg</span>
<i>at 2016-06-16T18:18:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c46878ee208813a4026f2bef422fd03c41ddd6d">1c46878e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-16T18:18:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Put back working Autopicker in GPU-MPI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9986679bd148094b0002c9062f3f8f50c28a744f">9986679b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-16T18:19:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/97bf428a1a252243573f046b0365d6ddc9308efa">97bf428a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-16T18:51:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">include
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9ef1018262a042eb06bec54f1e46421a509c14e6">9ef10182</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-17T14:43:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">provide random seed for autopicking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6af1b0c9d7945eebb7e7412e59cf316e95228157">6af1b0c9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-17T15:04:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #52)
provide random seed for autopicking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b4552ef616e8a04903e5208002c7d744f2fa819">6b4552ef</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-17T15:04:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6f73c1d12e5ba43c99a39beb4feb5efb3805e63d">6f73c1d1</a></strong>
<div>
<span>by Björn Forsberg</span>
<i>at 2016-06-17T19:06:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/62a9b703f7c68c316192294607fa98fce571c473">62a9b703</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-06-17T18:15:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #51)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7d98788ad1f5ec2130f237c168320d625d855d4">f7d98788</a></strong>
<div>
<span>by Björn Forsberg</span>
<i>at 2016-06-17T19:18:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/07e9f02f05f6c49df60f96a67bd2c729c70595cb">07e9f02f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-21T10:57:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix to fedora-like linktime requirements
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/50d7e5ed78fd0e79cceca96fa8e064a22b3d8bda">50d7e5ed</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-21T11:32:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix compilation error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c80642be38c9eb40325d6bad2d24f61daa06415a">c80642be</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-21T11:33:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">A bunch of single/double compatibilities
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a1a6e0cf88bcd8d8187cd7ca44f56141ccd5c4d">3a1a6e0c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-21T11:36:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor build-time print fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1070902d3c041f3164740103a1946739ad597494">1070902d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-21T11:36:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a6cbe60f4227b1256544cbff56e5b28212270d6">9a6cbe60</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-21T12:27:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to recent change in sum_weight initalization
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fac5670aadd66216ce1eea18a5774764e502e341">fac5670a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-22T14:08:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CC-kernels (coarse less smem-dependent)
This adresses a reported issue in the relion2-beta and is effectually
a response to the original implementation which hadi these deficiencies
noted (see commit 6c2a43a).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/111aa805b0cc7391b443499b196a072ab89db21d">111aa805</a></strong>
<div>
<span>by Erik Lindahl</span>
<i>at 2016-06-22T22:33:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable SSE/AVX when building FFTW ourselves
Detect if the architecture is x86, and enable both SSE/SSE2
as well as AVX if it is. FFTW will time routines and pick
the best supported alternative at runtime.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8ff656801522c8755001f900a0c85314b05b18e">b8ff6568</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-06-27T10:09:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better handling of the different build cases: no-GUI, no-CUDA
Fixes beta-repo issue nr 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2007cccc838874597d0f249ab26ef4843cd277fd">2007cccc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-27T10:24:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to ctf-values being zero
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fba995e64eea507fca172dd7d6170a48202af00">5fba995e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-27T10:24:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29886201a3c43c9a46203e382211c49dab1a8cc4">29886201</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-27T12:03:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed compile-time warnings, mostly GUI
some non-returns in std::sys -calls
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e5db9cc549c931987ba4b07b4accbb3ac32e58e3">e5db9cc5</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-28T14:01:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Scripts are installed with the right permissions.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a48bdf544c57835d7e9b555ea884e29a753dedff">a48bdf54</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-30T17:53:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding 3D-kernels use in getFTandCtfs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be83a51f9e37b51b16033f03d79b0df5ec272c33">be83a51f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-06-30T17:54:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes to movie-refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/31da19a479ff7d614f43b58c7f61db56c5bca09d">31da19a4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T11:36:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ecf74998130d3872a858faabb52bc7d60b27d529">ecf74998</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T11:59:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #53)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6f96227a843cf976d8ea9b88f4d52a85126bf3f7">6f96227a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T12:06:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/05b46b49eb4419d4b687ed277b618fccb7d703b1">05b46b49</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T12:10:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow helical_outer_diameter change in continuation jobs and set phase-shift in ml_optimiser.cpp and .cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a44b58259c0ac13f1563e56c015b1dd7315367c">7a44b582</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T12:11:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont set pool to 1 when prereading images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ba8ee84ecb8c6a6b298274d23b6cfdec6724a245">ba8ee84e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T12:12:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolve issue of hanging GUI when deleting job without output nodes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dbcf2fce23866f3d29a6bc3dc7c8418dfa9542ea">dbcf2fce</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T12:12:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #54)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27943e421f2d153851ef1a753db9ef0eef289074">27943e42</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-01T13:14:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/274e389a1c7b3d10ef28fd19d134b564179fc77c">274e389a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T12:18:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> repairing typos...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be5186039998ef0e8d1ed5e2cd6b93f980574fee">be518603</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T12:19:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #55)
repairing typos...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/22a0b8df85656586185e54aa53e1779a4c695137">22a0b8df</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-01T13:20:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6342123f479396f69f1a7690eae80e58dc788abb">6342123f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T12:24:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ba4576449c868ea1a02561cb16b26b56418ab1f">5ba45764</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T13:52:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont die GUI if fields are empty, raise warnings instead; fixes 2.0-beta issue #34
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d085c5aed24c56172eb206dfe07886885747cf7d">d085c5ae</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T13:53:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #56)
dont die GUI if fields are empty, raise warnings instead; fixes 2.0-beta issue #34
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fffebc5fcd5ceab0b6c0e097bdf38b3e93bc92b2">fffebc5f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T13:53:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f2e35150132b2c2a071566eb1ea79a379aba591">9f2e3515</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T14:48:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolving issue #36: setting angpix correctly from STAR file in manualpicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dca38edf9bdb5ff9c6de1d17d3e0030ae7e20ffd">dca38edf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T14:49:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #57)
resolving issue #36: setting angpix correctly from STAR file in manualpicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b63410c50ac9a71f226eb497ed4b739a7bf49a1d">b63410c5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-01T14:49:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8621d09bf0fa89cc879d7363e5b4089a483226ab">8621d09b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-01T16:26:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Massive commit for added support for helical refinement.
Warnings removes for non-support for gpu runs on helical refinement.
Slicker code in and around precalculateShiftedImagesCtfsAndInvSigma2s.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ea5a8607c9299494d9e0f24c32b484900175f3f">3ea5a860</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-01T16:29:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24098756335d88828de26210758d1fe5c6c208a0">24098756</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-01T16:30:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/66f206f5be4b7c86c5c702835c83581bed82a004">66f206f5</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-01T17:19:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Multinode jobs get devices set based on host-share
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f668448214f3f82931718294a0c68f89b383b99">3f668448</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-01T17:20:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cf8ab0ab68100e845b762382a5a64fbbaaaa8c7d">cf8ab0ab</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-05T09:22:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix to single/double choice.
In this case, even single prec. was less than single. This fixes
issue #114 and possibly also issue #113
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42801af90ea934afa9c971d15472b309e3f0de57">42801af9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-05T09:24:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Addintional single/double fix
(not symptomatic, but could be in future, so fixed as precaution)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/65030586e463286b0b663338aa71d777103675c3">65030586</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-05T09:35:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #58)
Added support for helical refinement.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cdde80e9680cd7dced764da4b0a0ce8ab7406f36">cdde80e9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-05T09:35:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a43823aae50624172dbf48c776b5593b6275606">6a43823a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-05T19:12:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/587758c3146d3fd94422cb5e55ff6bd11a52cf2b">587758c3</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-06T16:19:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor cmake related cleanup and bugfixes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12d9713608dc037115a37561455e862bfe1b602b">12d97136</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2016-07-06T21:08:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix to device id MPI_send in MPI refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/88e9bb57fbe167bce7cb6025cff3f3253e2cdfb2">88e9bb57</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T09:19:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #59)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a0218a93d2a1f434474c9a546b07b46132df6a2e">a0218a93</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T09:20:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0096315f5e00b5c7dc77fcf1166b276478fa248f">0096315f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T09:44:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolving issue 18 in relion-2-beta
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8c541c1c0e63eb72c6e5f41394757037027ae9d">b8c541c1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T09:45:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #60)
resolving issue 18 in relion-2-beta
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5169b0a36be20d4e2bf59fd3fe60bfe3b055ddd8">5169b0a3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T09:45:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/25c28f7b8f9c0e3be21f93b78af48eefe90b09c7">25c28f7b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-07T11:07:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b77837d14bc8d2f3a47132675c2a788eb760c262">b77837d1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-07T11:09:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">movie-compatiblity amendments
related to issue #119, and solves major symptoms, but may have
lingering issues.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4d45beb2c5181274fe69ed14302f399320e72215">4d45beb2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-07T11:10:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b08f2b6a8e7835d0756b0c361ee46fdf38a4705b">b08f2b6a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T10:20:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new io of ctffind4.1 according to Alexis Rohou
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/89cce59bcb129360ad4f0c664d3ab6c07c02c5fb">89cce59b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T10:21:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f4d5c0ffb1d177b571f0d6aab5102608871a785f">f4d5c0ff</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T10:21:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #61)
new io of ctffind4.1 according to Alexis Rohou
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34b885a58fe0b146ce2b5150fa143a5560469cf8">34b885a5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T11:39:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug manualpicking reported by Rafa Leiro at LMB
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5e71a17867f6f41e38cdbc140f47aec02e2637c">d5e71a17</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T11:40:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a5f865341a5a51363c6fcfb94ae84115cf1d0d6">3a5f8653</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T11:40:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #62)
repaired bug manualpicking reported by Rafa Leiro at LMB
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68f6c7ae832719a61cfdf1bc012864724f1f1b22">68f6c7ae</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-07T11:40:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b979959b4f7ab1b0593e1e90fa85f16bd312dcd2">b979959b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-08T10:42:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolving issue 15 of relion-2.0-beta
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa2751d053529210635543cc4a7994c95edc2ef7">fa2751d0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-08T10:42:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #63)
resolving issue 15 of relion-2.0-beta
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/53b54113da865935bd72dc9ca3fd3ab178b7319d">53b54113</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-08T10:43:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/70ac67d6200aac427ceb1a84e5fe130ca46b7fa2">70ac67d6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-08T11:16:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">also have multiple subdirectories (for subtomogram averaging) treated OK
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29c3e1f9d3c3fbf9b283bd3cc17181741ffd1dff">29c3e1f9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-08T11:17:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #64)
also have multiple subdirectories (for subtomogram averaging) treated OK
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/56d2f8182eb5d1e40ec58c608532ad20dbbb1ab8">56d2f818</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-08T11:18:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/186ffad63a450038f9e84914ce50898f0870449a">186ffad6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-12T10:01:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adapted for latest ctffind4.1.3 from Alexis
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2f53e248c15c80d9d9627a40bd5c6fab785e6464">2f53e248</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-12T10:04:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better io for errors with helical search ranges
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d7187f6ee48a8f7e0817db4e34d2370010cbb865">d7187f6e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-12T10:04:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #65)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f3ad6d45e2577a8464958de5d2412849bd74a0c2">f3ad6d45</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-12T10:54:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better indentation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c580bfab80bcbcfbc7e6678e51860715b1c9b365">c580bfab</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-12T14:19:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Improving accuracy by moving the exponentiated diff2-values towards the center of the single precision numerical range.
This is done by permitting resulting values above one, i.e. positive exponents.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f6d6a8eb157c552fef56237e7fa8f473095c80a3">f6d6a8eb</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-12T14:25:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e9da1c1bdb1256972ab9c136ba959127fc89208">6e9da1c1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-12T13:43:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #66)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ce48150594a319ad1ae348559e36b637412eba0">5ce48150</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-12T13:43:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bbcbd3f888efd96e8fb060348c255a74f5cd8917">bbcbd3f8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-14T14:17:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">carry on pitch and tube id for helical segment extraction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c31ca860175a8a237056272b421370f80331eded">c31ca860</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-14T14:18:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a863ac049a444e8a0cf6603af6470d1c9f4eca2a">a863ac04</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-18T10:20:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">max_weight is based on coarse/fine weights
This amends/fixes issue #119:
max weight was occationally larger than the sum of weights, which
was algorithmically ok but resulted in meta-data probabilites
larger than 1. We now raise segfault if this happens, and collect
max_weight(s) and sum_weight(s) from the same array of weights,
i.e. it should never happen.
Also, max_weights are stored for all iparts since they are now
fetched during convert, and subsequently used in storeWS.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c7770f3ed6eb6bb6b8d0ba1da220917904edd02">0c7770f3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-18T10:26:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
Conflicts:
src/gpu_utils/cuda_ml_optimiser.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68ea4ae3bff4d658caecddbcb1d8598a8a63e33c">68ea4ae3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-18T09:54:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added local resolution option in relion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2540fe9fc4e9cba85a4eb7650b53e323f0236d36">2540fe9f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-18T10:06:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small changes in help boxes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a98cecf7a83fcb0c814872ec8fa9e40b5d6947ab">a98cecf7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-18T10:08:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow threads for resmap
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6eea0884afaf7b9d67922ce87af5e241f43aabd5">6eea0884</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-18T16:51:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small changes in locres estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/125957e183df6f98bd80a13cab61cd610d231cba">125957e1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-18T16:59:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small changes in locres estimation 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9880c851a46e81d349e1ed20a9d8f764810f8eb">d9880c85</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-19T10:27:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">min_diff is only updated when fine is meaningful
This fixes the remaining discrepancies in issue #119
Also, LogLikeli is correct using avg_diff subtraction, by changing
definition of dLL accordingly. NOTE: sum_weight is still uncorrected,
so there appears to still be "hidden" discrepancies in LogLikeli
which are completely overshadowed by the diff- and noise-terms.
Also, I changed mean_diff -> avg diff, because having both min_diff
and mean_diff is just confusing.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/96181c5243a80dc35d85d3d307eed8c28408a27a">96181c52</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-19T10:41:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d8108066c01c1e29ffc7abbce66ac0ef4930ea93">d8108066</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-19T09:48:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #67)
Movie-refinement works and diff-subtraction corrected
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a9bc027a8e2262d52d30f12aa07a1e76146603e2">a9bc027a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-19T09:49:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/605f5e4d01b89b901186061630178c9233f109a0">605f5e4d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-19T12:32:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed options of relion locres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a5f8b011c26bcc92fea9dc948811d0a3cde8fe66">a5f8b011</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-19T12:33:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d35262543458e87afdbcaced2a0bd1bc60e54d22">d3526254</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-19T12:34:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">defaults to 25A in locres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d585daecf2456751ec0ea4702bef9c4782fad6a">8d585dae</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-19T13:59:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mpi includes are included correctly and sys-indep
related to a FIXME from way back when: 290e722
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4da3e2c4c88383e7b2d332d596f59af252d1a6b9">4da3e2c4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-19T14:01:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/72f493a3ce938677e0a2f0e862f9d2eaaa0a745d">72f493a3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-19T14:21:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added helical to symmetry expand
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/10f5a0b2fec8e45b75a1c5024b651aa3df193fed">10f5a0b2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-19T14:22:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to remove NaNs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8197df5c45d86fdb613fbc0eba2f974d9671fb3f">8197df5c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-20T11:08:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont try to read fn_in as a STAR file if it isnt a STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e5b04ba3bb031435032e5b625b4d92e2ad463a7">6e5b04ba</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-20T12:43:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">import/export blocks of scheduled jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe5971f4cf11260b34b1ebb539cfe31a40c69f9b">fe5971f4</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-21T11:54:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes Issue #117
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/937b8a4b7559fe4f72e1d6803e70668cbbe0a2a8">937b8a4b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-21T16:31:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Average square diff (avg_diff2) is set in the fine pass as well.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cf9430d030c7e5dfd7bd8badba80c4ff068c0bd8">cf9430d0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-21T17:07:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mixed multi-rank (non)default gpu sel.syntax works
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2157871db71b92c2ae96a53d1401ee2c4bf4e8a6">2157871d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-22T10:19:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to runtime installation path
librelion was installed, but the installed binaries did not reference it.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/89f0e1f1875e8c083918a1cde20d86fe89a6763a">89f0e1f1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-22T10:38:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #68)
Further improved numerical accuracy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a4694545958ea3cd7484e8e1ca0e5c1f79d91e56">a4694545</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-22T10:38:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29826fd3d97cdc8a5c7cd485df61465aa647c2bf">29826fd3</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-25T13:54:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clarified warning message.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b592231eac93cb2ebf27b302f0cced63cea7d212">b592231e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-25T18:04:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added a flag for running asymmetrical padding factor for projector and backprojector models.
If the hidden flag --asymmetric_padding is specified the BP padding is +1 that of the projector.
The purpose of this is to be used in combination with --pad 1 to reduce the GPU memory requirenments.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d75a37b7ced653e9f7a5b798376d205dd27f338f">d75a37b7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-26T17:47:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">draft subset flag
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5e2b4a32d095db97abd1675923749705bd3c517a">5e2b4a32</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-26T17:18:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added extra_gctf_args
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/552bea95f1f2e64977000130a0b83f6b510ef0d9">552bea95</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-26T17:29:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #69)
Local-resolution in RELION, import/export blocks of jobs, and some fixes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/44a086929630ef07093f3c243a023bcabb73dfe7">44a08692</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-26T17:30:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c0cffee23c9d7ebbe02dcfecc14299515720915">6c0cffee</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-27T09:11:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Runtime cuda compute capability capacity control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/125857f983808d0f92422faac01c26101d89585e">125857f9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-27T09:12:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a734a0f80c47a50b73a0a9d761f95d70e83cfca1">a734a0f8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-27T09:54:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'subset'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b95e8d0440d57ff587c9436d1aa22c5d74264e6d">b95e8d04</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-27T10:08:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to subset during split random halves
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9b304896de9de0b66f489f49a24e4f26dc553e94">9b304896</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-27T11:43:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New hidden flag "maximum_significants" than can be used to set the maximum allowed significant weights in the coarse pass.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/408c368b8a526d6a6ffdf62fbfff68ec65bde5b3">408c368b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-27T11:44:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e563f1a467bf63cff0394eeae2dada4d7601fe2b">e563f1a4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-27T11:55:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPU sel. for exactly one rank used by all ranks
before on 2-gpu system:
mpirun -n 3 -j 2 --gpu 0
slave 1, thread 0 -> device 0
slave 1, thread 1 -> device 0
slave 2, thread 0 -> device 1
slave 2, thread 1 -> device 1
mpirun -n 3 -j 2 --gpu 0:0
slave 1, thread 0 -> device 0
slave 1, thread 1 -> device 0
slave 2, thread 0 -> device 0
slave 2, thread 1 -> device 0
new behaviour:
mpirun -n 3 -j 2 --gpu 0
slave 1, thread 0 -> device 0
slave 1, thread 1 -> device 0
slave 2, thread 0 -> device 0
slave 2, thread 1 -> device 0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/66515d0919edeb0f9b6364ce2c63a33973eeb4ec">66515d09</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-27T11:59:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc884c31bcbaba06add43746b9629151d323229d">bc884c31</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-27T12:18:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Diffrentiating hidden from invalid flags in output.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/061d6af9ee3091a936035ee8ded039e52dbbf133">061d6af9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-27T14:58:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0fd1b1b94661060bcccb704222033d92a6e3d32d">0fd1b1b9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-27T15:31:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #70)
Feature bundle
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0aa963f5b59971e8c4f026f5b2c6f7df54bb1bd3">0aa963f5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-27T15:31:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/37be342e68c3ac882616ab3a5ce454e7dccf60e5">37be342e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-27T18:01:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> added multiple schedulers, and their parallel execution to pipeline
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4fbb95868a15867e608bfcc22f5e4547907ef057">4fbb9586</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-27T18:02:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to apply fourier-mask to projector (debug3) and added functionality to skip gridding in the reconstruction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e2681d7a88f4219eb93edb994c30d25546bad77">6e2681d7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-27T18:10:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #71)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/461537607677f0b54e9b009bac8c03ed99ea552f">46153760</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-27T21:23:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to subset progress bar
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4337d7f492bc13c64313dde18d3a984c7e0e738c">4337d7f4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-28T10:24:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with continuing refine jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac92066443a9c6d0dfea1390809f81ee6f7f8893">ac920664</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-28T10:41:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forgot to add skip_gridding to copy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5c1fb01781d63c84f64cf9b8611b08094645a1fb">5c1fb017</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-28T10:43:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed some spurious attempts to auto-uopdate window
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/234b9603eb786561ec09c3068d644238f45991d0">234b9603</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-28T10:43:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b259b68b212adb7c985124f1e5b929e9813c0eb1">b259b68b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-28T10:44:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #72)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47da6231aebe3e2737d945fcb9bef46b3904bdde">47da6231</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-28T10:44:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7139743eaedcfe12b0eeda1d90faf3f49efe96cd">7139743e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-28T11:13:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added functionality to automatically update stdout and joblists every 2 seconds
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ad0a6dc659100161c70815193967a883e56e285">6ad0a6dc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-07-28T12:25:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">go back to old position in joblists scrollbars after autoupdating
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b89fef9707d28639021463c913934d9306ec998f">b89fef97</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-28T17:11:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cbe4724f1568f7d46ed4546cc86954f960029fbd">cbe4724f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-28T17:15:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Editable filename in displayer + default rev. sort
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e585684b7fcf4d49caf5d8707de773b2a06b5af3">e585684b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-28T17:16:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/25c0dae6ac4760c52ecaef5059c8abd97ff8817b">25c0dae6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-28T17:55:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The elegant (less fun) way of handling hidden flags.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b9a8878ea0c72eaa2504377387eea3bf200a0721">b9a8878e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-07-28T17:57:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/315704126869eb514147b2f3b13e445de7809817">31570412</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-29T12:56:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Proposed defocus displa in manualpick display
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f13ed30947c0ae998ec8202600fc1de0e749e919">f13ed309</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-29T12:57:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/38bbafeda65b664da1990e1e35e2962200fc6eb0">38bbafed</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-07-29T13:49:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor additional fixes to manualpick display
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d534569a7b47c74378a2a5141e406acf27ac009a">d534569a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-01T12:09:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove error message with GPU found
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2d823806d9b9631e95ced29fdebdaaf04c9e0dbc">2d823806</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-01T12:09:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">control refresh rate and idle-die time of main GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e408ad565e988469c24f920c97aaa6749f79a16f">e408ad56</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-01T12:10:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #73)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb1db5aeeb561d926c206bf1e01a3dd11fcd2720">cb1db5ae</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-01T12:10:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5f7a0bb7b8a20d3ed9f1c139d48fa241abb5bf5c">5f7a0bb7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-01T14:25:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug deleting last job
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84dbf6bb197332184c47822f57adf0660eb8c737">84dbf6bb</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2016-08-02T07:56:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert "Editable filename in displayer + default rev. sort"
This reverts commit cbe4724f1568f7d46ed4546cc86954f960029fbd.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d3417b059ca920b86dd6843c44cf4b5f5679cb9">9d3417b0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-08-02T08:44:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a2fd216df50e549aad41f956223a71b497266971">a2fd216d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-08-03T10:15:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed legacy code in getFourierTransformsAndCtfs.
One transformer is enough, removed the other one and reuseing the first one.
Device init of fouriers and reals in transformers are not required, also removed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ba706fd1b47b8b8c8b6e02441e82f36aafc4d3d">8ba706fd</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-08-03T10:23:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Change flag name from maximum_significants to maxsig, for simplicity
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ae268c120bb7f18da9325b48f7b2b4125504db52">ae268c12</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-03T10:04:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #74)
suggested version v2.0.b11 in beta repo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce51455653e677eaf275b9413acdf2d1f9196e1d">ce514556</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-03T12:17:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f12d5cd9ccd48b5a5de6d38eda4641289ca8e284">f12d5cd9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-08-03T17:57:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Auto-refine does not use subset
This avoids issues with the subset-option which unfortunately broke
auto-refinement in commit d75a37b.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/accb2bedfe9ac621fc91732836af222976fc5cef">accb2bed</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-08-03T18:17:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fail-safe mode introduced to handle "filtered-size-zero" error and recover from it.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1d87c1f3f068b278d5ca1e0e701fab47447d6fbe">1d87c1f3</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-08-03T18:18:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7123d843b84642a08164429aef24b094091a57c">f7123d84</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-08-03T18:33:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dditional fix progress_bar mpi subset stuff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6aa0fdc2ce528ef3a716d6e79cf5696d0c7a3514">6aa0fdc2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-08-03T18:33:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c59248386071b5c965b42112857e49b87907c269">c5924838</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-08-03T18:55:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b28fb498c39f92cf31a70c3e136444eda588ff58">b28fb498</a></strong>
<div>
<span>by Erato.bjoern</span>
<i>at 2016-08-03T20:29:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">inactiveate randomisation during subset selection
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29b4817e6907c7c9c8ee82d974bd7d1432c7c6ad">29b4817e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-04T11:33:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow float-values for padding_factor in projectors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f00ae3a96d8809b940f302aeb386e374d51bf606">f00ae3a9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-04T11:34:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired small bug reading when setting alias
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b09c05b5a9e3ea6ff8d0381b07eb77bf5d01c409">b09c05b5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-04T11:38:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added options for flipX and flipY
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/03fd26b1b4dd3b22cca50814442db247311930d1">03fd26b1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-04T11:38:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d6a865da71d39634a4d77859be90534ede7c0e67">d6a865da</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-04T11:42:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #76)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60b3d48b4d5e9d671b1d9da8053564d0f8d89265">60b3d48b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-04T12:25:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added comment why closing isnt necessary
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/35112f4a4c7c3bbb83762f407d0ddd54bf404324">35112f4a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-08-04T13:52:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor revert, no functional changes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ff01b592ede24203b8f899ce4545f173568d8e81">ff01b592</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-04T13:07:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #75)
Auto-refine bugfix + refine failsafe mode
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/803b38984ff0cdbb08a70894cebf48c34dad2fe2">803b3898</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-04T13:07:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e3b83e635526ba7ed5c0427fd1c9e83cb33ae9e1">e3b83e63</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-08-04T13:08:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3b357c8836ab5c253a93fba61f0a2026681fd19d">3b357c88</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-08-04T14:08:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/146f38077eac1405844f6fe998f39e6166d7a1cf">146f3807</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-02T09:31:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont die if header wsa set incorrectly and max < min
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3e681abc20e7a41b433ae1eaf82461ea64ef6eb4">3e681abc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-02T09:49:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug not updating particle count first micrograph
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7de18b1153e09e0e60765b0cb629e12eb1fd294f">7de18b11</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-02T15:52:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolve bug movie-processing reported by Shaoda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/80c38203edc292773f5570facd04c2c69f7fe0ec">80c38203</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-02T17:40:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">specify that relion GUI has died
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be4e3453b69e8031aa6cfb0245ba311dc4984863">be4e3453</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-02T17:42:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mention bug non-unique directories in browse button; added motioncor2 wrapper to GUI; added movie_name to refine-continue for Shaodas movie refinement bug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8eaa185dbe5a5408f2618049c158797fc18460fa">8eaa185d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-02T17:42:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> added motioncor2 wrapper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e676fd5dfc05eaed0af2c0d0a4767ea32822cc7">7e676fd5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-02T17:43:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #77)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0ecf8dc1112f12650519d36b4e3d4ab9a5663991">0ecf8dc1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-02T17:43:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3550701e32c2c55f15e5aa329c76facc2ac9c340">3550701e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-05T10:05:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont allow highres_exp limit to change upon continuation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/693fc6caa6e2126742793d9dd908d20f7bf756de">693fc6ca</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-05T10:06:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug in cancelling job and .lock file reported by Shaoda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5eb9e82acd9b93042069ca2dbf051c0eaa949bc4">5eb9e82a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-05T10:06:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added motioncor2 to mpi version of run_motioncorr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4ba2b7e54554c72d841c8156aefe230ddd8ce6fc">4ba2b7e5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-06T10:40:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to autopick with gaussian-blob reference
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7a68525933d8f9346ed6bc0c003990378edd30f">a7a68525</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-06T10:40:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">run motioncor2 three times in case it fails
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2522d3881401c60fec893a866f1273a890039873">2522d388</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-06T10:41:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #78)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f54bd53e75f5bba4ecf1d4bd41c0157bcba24abb">f54bd53e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-06T10:41:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/13efa09b24e8a6a932febed921c82d2bcb6790b0">13efa09b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-09-09T10:26:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/20146fc135e4adad5495a43ce15ca81e32a05f87">20146fc1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T09:34:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow changing gpu ids upon continuation motioncorr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1e89e2381c11952d2036cab558de6aa0179cc779">1e89e238</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T09:35:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only move after successful motioncor2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5b18326bc7b0bd055f487d160d4d5601888c376">c5b18326</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T09:35:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #79)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/54174cd0dc0ca1eafaa37bc7f180c9b2ad3cdcb7">54174cd0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T09:35:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0973cff01cb1d22a6c4771c7aec49265118fc59d">0973cff0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T09:38:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only move after successful motioncor2 partb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a02157ffed45d7dba0f6cf0c867f511ff6aafaed">a02157ff</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T09:38:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c3586ba2732efbb04bcb09d804b0158111e37891">c3586ba2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T09:39:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #80)
only move after successful motioncor2 partb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f64e993a9a4c6f7bedb9da3b2abbaca3ee5a0ab4">f64e993a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T09:39:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2dee3145caccee30e2fdc976641a1c1d49c7211f">2dee3145</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-09-09T10:40:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed compilation error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/65762a08781d772aeef98644fd65929c63321c29">65762a08</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T12:48:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflict with Dari
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/027d02759452910dc20ea007a2e119ea6b467f08">027d0275</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T12:48:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #82)
trying to resolve conflict with Dari
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c0db491bda1f987d7b81af66a56e81e201275ba">6c0db491</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T12:49:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #81)
Fixed compilation error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ba4c8a7cf00abe8948fb9d1a6a975fb4ab765baf">ba4c8a7c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T12:49:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c57436eaf9ba9d56abe9b1eae57301c2e4fd1cf7">c57436ea</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T13:06:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove 3 attempts motioncor2 as it no longer is needed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b4341d7c157c332c78924c5e218928316df036a">6b4341d7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T13:07:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #83)
remove 3 attempts motioncor2 as it no longer is needed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b1fd9fdc202d041ca2dbceb090aa28296947bd5">2b1fd9fd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-09T13:07:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c17c14d834d24335daa1927e54d70474b59b7472">c17c14d8</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-09-09T14:37:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c7545316bdba693935d68287857188bec21c31dc">c7545316</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-12T09:21:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug lowpassfilter non-squared micrographs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f0c13b97654c1e246dc1dc4a15bdac864d49d68">3f0c13b9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-12T09:22:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b35e543272a124b1c6f219cbd90fea4a87e671b8">b35e5432</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-12T09:32:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed default motioncor2 executable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b01e4c6d0a23f67262f07bdd99b4869f15e8185">2b01e4c6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-13T14:29:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug non-squared images lowpassfiltermap
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/acb7aa098869634dd1a87f112de24660db900f51">acb7aa09</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-13T14:29:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to debug scheduler with rafa
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd2d488ecb57b2652ac5dbbb3fb27303ef680a73">fd2d488e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-13T14:30:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check at end whether all output files are there or not
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fc94665385bb0858a0c188a428d4bd82ce00124">5fc94665</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-16T12:47:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reapired bug in progress bar MPI picking on GPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d104b1d0d2efa11be76e9361bfd36cdfcab08d3">5d104b1d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-16T12:47:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added citations unblur motioncor2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/63fecbfaeae4a08e86cb237454df9dc104dfa790">63fecbfa</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-16T12:48:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more decsription for deletion lock file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e11827074506b440e5a5e1828b4c5a9cb579b3df">e1182707</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-16T12:48:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug motioncor2 wrapper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1cfc0690e487ea660f3bfb1ae7439efac6e92805">1cfc0690</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-22T11:38:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add option to reuse_scratch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc84a3526b0e593f90e81948661a02ecaa36f8d5">bc84a352</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-26T13:22:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bug passing pixelsize to motioncorr2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5582e8f69e9b83445c5e95c02d70bb371576ca7f">5582e8f6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-26T13:28:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #84)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a737ab1f950019f988f2d8d06cb482bf73bbd49">5a737ab1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-26T14:31:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolves issue 110
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0da468fb437f171bce178ce431f161327fbf04d3">0da468fb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-26T14:31:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolves issue 111
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c8f917dce343a99f3e2999d3e6c0483793a65cc">9c8f917d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-27T17:21:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added time to logfile of scheduler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cfcc40f74fc040f89cd40557a68f90215c081a37">cfcc40f7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-27T17:22:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better explanation frac_range
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3630b070c1c7f78f98c38b8bff37f4ba2080dad1">3630b070</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-28T10:02:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #85)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fdf61d4ed2a73ccae9d9342abc6ca0b1d38e38b3">fdf61d4e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-09-28T11:12:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0585630759c574e20d4dff1cce5a2e8a8d339237">05856307</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-28T15:24:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added hposition to scrollbar resets in running/finsihed jobs lists
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa174c123e0e4ded3a45180c26175619089a211d">fa174c12</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-28T15:24:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> warning about softer mask postprocessing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/39294fe3a8aaf116b8f8a0b558220f5107528e1a">39294fe3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-28T15:25:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make frac_range work with helical particle expand
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d33a21a8f13d7a8602af7f310d5d17b4ec29ee7b">d33a21a8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-09-28T15:25:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added fourier filter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/274080f1c459a3279969f738b4b080ca9ff8a4c6">274080f1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-04T16:42:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reset optimiser.star input for refine jobs, and de-link coords suffix files for auto and manual picking (issue nr 114)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/553cea3df2f93baa9ed7580d44ee7398f18062d6">553cea3d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-04T16:42:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #86)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/791d4fbe7ff8f5fa1c69f5d4d2166b73bf401d0b">791d4fbe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-05T12:57:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">default psistep of 6 degrees, so GPU will do 5.7
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a28890babff5d6a675bd31c5f0061aee497874c0">a28890ba</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-05T14:37:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3cdbc744451397845b1906fd22b329c13771661">b3cdbc74</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-10T15:37:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with D1 symmetry, reported by Jaime Martin-Benito
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3d722f4bc1f798508f80aa2b307346e46bba1ad6">3d722f4b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-12T10:13:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use install instead of mkdir to create scratch dir with correct permissions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1484086bd0d544ce4eca96cc6a9187dac3d3b792">1484086b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-12T10:15:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/33634691558b985b5e379df36f67e70f910185ac">33634691</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-12T10:21:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">save min_dedicated to file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/799a5f6b29cbdf16668a3927031a500ba176e933">799a5f6b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-12T12:01:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check for empty autoopick references, issue 124
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0ae7160fb71f757cd17485d7b6d20687d03be6d">d0ae7160</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-13T16:14:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only print estimated memory if verb=2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8131c5b4843549573b0db0184e0e1ba971b74ad7">8131c5b4</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-10-14T16:15:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More precise error reports. And better exception handling in threads.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/beee00f017933ac2432ce75d6633ec1f30e691f0">beee00f0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-10-14T16:24:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/040e0ecc88edd9e46b6afd588eb21501deda2402">040e0ecc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-14T14:45:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #87)
More precise error reports. And better exception handling in threads.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc9d3a56cb3cb46dd4f74390c517c807cb8b9a3d">fc9d3a56</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-17T09:07:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa91c71e674a68339d46475e2ef03b6fd0aacb62">fa91c71e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-20T10:11:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added -Bft and -InitDose to motioncor2 options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/83c66959c5154328f279738a20c4967c75e095ea">83c66959</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-20T10:12:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/26250a8beb3dfb039f3e5a48d82e9c7d5e1d3fe2">26250a8b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-20T09:19:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #88)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/356e8ef413ff8d33e79c309b549afb796a8c1911">356e8ef4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-20T11:00:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reapired bug last_frame and gpu passing for motioncor2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f7b235136a54f15a0d9096230a90c89d2c3b532">9f7b2351</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-20T10:00:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #89)
reapired bug last_frame and gpu passing for motioncor2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe596c5744c372008b39f444ae75c2feb55f66b9">fe596c57</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-10-20T11:02:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/828e76620de2980a28d24c9d5ec2d6546508d87e">828e7662</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-08T09:28:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added 3D rotations to subtract option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d67e01fc65262d3340a7746ad67103be2e45cdf2">d67e01fc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-08T09:39:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolved GUI buggy behaviour with symlinks, issues #152, 137
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2010e702dc34ed261bd1c30ebfee4e0f9d05bc3">c2010e70</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-08T09:39:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolved GUI buggy behaviour with symlinks, issues #152, 137
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d209617d751d8aa03b46a9470338cfd2a8f0ba4">0d209617</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-08T09:40:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6abd8e78252dfe9c75cb5a283c733c7b8e28b705">6abd8e78</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-08T09:40:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #90)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ec5766ca383121d0dfe2b103cee0b2875e7cb48d">ec5766ca</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-08T09:41:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dedba476ac9a61f62bc70a4b2a58f5ac3de96234">dedba476</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-09T16:45:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair issue #157 with mpirun in front of echo commands
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0a4baf21f5ae21a7b374f804e584cd682d53d840">0a4baf21</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-09T16:45:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47eb3455c48823c5cb6c7ba3b2d03b3f779a4d48">47eb3455</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-09T16:47:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolves issue #122, problems with helix_toolbox on some systems
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc51c494331025e69ba670875205a3a70d647d0d">cc51c494</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-09T16:48:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #91)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/701c383b2df80c245d624096f6fd6331930f79b4">701c383b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-09T16:48:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bb8482bde189304019167982d26231c29e2acfb4">bb8482bd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-14T14:30:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug introduced 5 days ago
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5f1f600cd3a5a43441cb2e3369ee37a315ae313d">5f1f600c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-14T14:35:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #92)
repaired bug introduced 5 days ago
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/05a2b184577b1680f45356c195fda5554006f005">05a2b184</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-14T14:36:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dc760071c09d75ff1d3c60293d2df2749f0e57ea">dc760071</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-14T15:45:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bug was still not fixed...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f657321e454926107a212661dae29dc71d153a31">f657321e</a></strong>
<div>
<span>by Shaoda He PI Sjors Scheres added 15092014</span>
<i>at 2016-11-15T16:33:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changes by Shaoda in helical code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/556fc43f39b4309ab7b8e8314092d8cda8f46451">556fc43f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-15T16:37:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #93)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2551b02941bf250498dfbbb713ff0bea1485f9bb">2551b029</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-15T16:37:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b70a71bfcf4652a36a14621e8b24b415dd85e85">2b70a71b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-11-21T12:45:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added support for up to 1024 coarse translation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/86934259c59bd5aafe62826e1ce2198a12228480">86934259</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-11-21T12:45:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4092f7f031e2c7185b7c200def2ae280f27b9c6e">4092f7f0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-21T16:53:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #94)
Added support for up to 1024 coarse translation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5aa3c963e33546963c5957415e3ea06fe7bee718">5aa3c963</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-21T16:53:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4a40f43b57b8eb9190368a0ef442a8c84b14a25f">4a40f43b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-11-23T15:58:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to automatic GPU mapping for multi-node jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f6157c7c217bb45ea1aaa2b1cc134d1d0d71894e">f6157c7c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-23T16:13:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug local averaging in helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/56418b2ca0112511f245f632d8b7468f598436ca">56418b2c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-23T16:14:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/212f9dd347e81df4b11e90352518df7385350cde">212f9dd3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-23T16:15:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #95)
repaired bug local averaging in helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/46327310aec3556dc53d96be675c0ea3d9051eda">46327310</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-23T16:16:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60630fc458e343cd85a99b8e3e34edd27e63aa44">60630fc4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-24T11:43:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make readonly version of main GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cbba8460f2e0de3212839534f86a4cb4c6fc40b0">cbba8460</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-24T11:43:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #96)
make readonly version of main GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd5838f7014aa92bbd710b16979399226448cee4">dd5838f7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-24T11:44:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f71f79c57eef3cb01007f491ab4f0a5836ebc699">f71f79c5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-11-24T17:51:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/30ef4bf2fb1a526064d16778a34ce129f65fc43d">30ef4bf2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-24T17:06:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #97)
Fix to automatic GPU mapping for multi-node jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/80ca2ed99f28c48382ab56fa87c46bc18d2a16cb">80ca2ed9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-24T17:06:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/40299364e549e889383f89079f15d3cf93849c01">40299364</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-29T08:41:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolves issue 171
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a51d79075ece4d96de61876e693624d646c625e4">a51d7907</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-29T08:41:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eedf6c7ef51b40e44f45de946fd7cc1e81c90fc9">eedf6c7e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-29T08:42:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #98)
resolves issue 171
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/94eed3389567a69b8a44b70376a75bdde9fe90cc">94eed338</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-11-29T08:42:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d344374f050d98b5394977eb17e67a01013e6b41">d344374f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-11-29T17:39:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Allow direct use of _model.star as --ref input
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d2fbe70c6926073bc1ca8e18ea67f9697f3daf49">d2fbe70c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-11-29T17:39:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/877f40d8b4740fb843c9fe680dc6ba08a0b78714">877f40d8</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-11-30T18:08:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch for reported issue, when building coarse kernel in double precision.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d4bf630b489d4b393eba78433221925aa426bce4">d4bf630b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-11-30T18:09:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cbdf88e74c0e9b15dc5f0c75f5793e70cf489939">cbdf88e7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-01T13:50:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">SoftMask kernel is 3D
inital kernel (commit 2000c5b) did anticipate 3D input data, but
disabled it so as to save cycles (?).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb9f44ce52d9f7952dacddd564b078f8a6e3ef95">eb9f44ce</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-01T17:09:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GFTAC entirely compliant with 3D-input
NOTE : subtomo still not working, but endof GetFTsAndCtfs show the
same Fimg and Fctf as evidenced by spotchecking.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d843468ae9ffe2fc52f12e3e1eda93c3a6c23098">d843468a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-02T09:10:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleaning GFTAC
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5033b8c7c7ad39d9e2c44233b6a82b57f4da08d6">5033b8c7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-02T10:23:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">template PowerClass kernel on 2D/3D
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0ad4d607cec06d88f1983b110822a677f54bbf4a">0ad4d607</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-02T10:52:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">prep subtomo-GPU; trans_z device arrays
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ddab97bee54928f50fcfc329ad2241178a48e5a8">ddab97be</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-12-07T17:02:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rearrangements and clean-up in cuda convert
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cdc6da355ef45237c0b31dfb93f4635a97113063">cdc6da35</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-07T20:03:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GASD-coarse is compliant with 3D-input
Correct raw weights are given after first pass, using a simple testcase.
Template diffcoarse-kernel on 3d input data to preserve 2d input perf.
Label some x-y-z index extraction as optimization TODO, but since we
have not profiled it under subtomo, I don't know the importnace of it.
Also reduction of default softmask block size due to excessive resources
during debug session. Its a fairly light kenrel (I think) and boosting
the block size isn't the way to optimize it.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd3f6149d9d375d9f7a71f6157d47eb9898e6ab8">fd3f6149</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-07T20:04:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61954915e05e65c9d1f7a0835e2c3c56e344b229">61954915</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-08T15:08:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">collect2jobs + wavg are
collect2jobs wrapped to hide template args. Forced to use extern
shared memory allocation to avoid uneccessary smem alloc. It should
be fine since all vars are expanded compile-time.
wavg is untested but compiles and runs with new template var added.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f2b19e4b8e952d984a5771dbf270447f83a5df5d">f2b19e4b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-08T17:02:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Backproject 3D template on 3D input
More instances of index checks that seem excessive, removed with
reference to the fact that we do fine without them in diff_coarse.
Prelim. tests (ctest no. 5 + subtomo_case) indicate this is ok,
but this should be furhter tested on much larger cases.
also: untested complementary changes to BP_2D
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/54f32652c5eca6981528bc63d2bb539c75d708c5">54f32652</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-08T17:03:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ecae26153fcccfaf243308aeb9211f9ce6cf3c3c">ecae2615</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-08T19:03:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix implicit cast in runCollect2jobs wrapper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f1ef2a57a594a42bf07bdcda3b7e7448cf392a7">9f1ef2a5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-12-08T19:13:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added double-mode
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/696f48609a9947a4fa30112385293645fc7a402b">696f4860</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-12-09T09:09:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolving issue #131
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/49fff5843134d06def24c9315801bf37daf1b070">49fff584</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-12-09T09:10:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/89d47d90efac97ba37f0d5b2f6a3aad575959b0c">89d47d90</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-12-09T09:10:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #99)
resolving issue #131
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3b0c798ceec9b1545ed914c30427d4c87e2992d6">3b0c798c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2016-12-09T09:11:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/49a3f5c7219e9fe14cd8cb641f2d772e42ffa888">49a3f5c7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-12-09T15:07:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f07d6abeb4e521f6be337d5b62d7e46454ab3c83">f07d6abe</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-09T17:04:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to subtomo z-trans copying
also just allocate excessively for now; translations are not the biggest
of arrays...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6626c7235bdeaea01be4d7b9c8d481c91a827251">6626c723</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2016-12-12T18:18:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed firstiter_cc on GPU
Fixed issue #122
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ba98aef96b516bfdf2a386297023895aa47dd7c">1ba98aef</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-15T16:54:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix to BP in 3D input
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c789f7e106728d3a69b24570d3870ce21217ab1a">c789f7e1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-16T10:29:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Critical bugfix to diff coarse
diff2 coarse cuda kernel broken during 3D input compatibility work
(commit cdc6da3), last functional commit is commit ddab97b.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5f3b6c51bd141fa93b013f5b196ddfa1d346e8a4">5f3b6c51</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-16T10:30:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/78f9e28f02d5211ae1d970d27eec06cd37e23b88">78f9e28f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-16T13:16:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix to reduced sum in backprojection
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ccd2e5feabe87f3ab9b8489747d61ab409aeebc0">ccd2e5fe</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-16T16:33:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">range check in some kernels fixed
conservatively set to match CPU code maximally
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5aa8e27fc307d47cd11c1c348ffbc450d3b0ef28">5aa8e27f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-19T10:09:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">3D input CC-kernels added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf990d4ecadbfc75bb4c1610725ae73a2ff31690">bf990d4e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-19T11:45:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Softmask kernel split
Much more efficient, especially for large images (also 3D input)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2cf78b02e6691f8d4e73e7152ee8194d27c66f59">2cf78b02</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-19T17:01:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed apparently unnecessary D2H cpy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f68fb31293264500b2f6af6fc4d4c08dbe9ba64">3f68fb31</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-20T13:10:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added specilaization to compile-consts
also, identified issue #123
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1709fb5a14f1b910446973341799ada27bdbcfab">1709fb5a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-20T16:18:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Further block-size tuning available for 3D input
Display notification about 3D input data on GPU as dev feature.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c988fbf8eb21669b952fc1f14c901d2603d428e2">c988fbf8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-20T16:24:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cee76cd89246d931d9cf94bfefa47114bc29f5db">cee76cd8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-23T15:26:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to cmake 3.7.x compile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/387c2e1b98e640e61e070441d2e34cfee1369732">387c2e1b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2016-12-23T15:27:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c51b3b4567303a125d59369a4ec9b907eab7be3">1c51b3b4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-03T09:26:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #100)
subtomo on GPU, CC-fix, and _model.star as --ref
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/36e9360fdcfb5742fe056fa4fea4b50017ddc0d2">36e9360f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-03T09:26:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7302dfdce5375a666601a94b81155168694174af">7302dfdc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-03T11:30:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix issue #178 always_cc only CPU part now works. GPU still gives segfault.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9946e0c685ce8b929e5eef3631308272fb48758b">9946e0c6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-03T12:00:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check reference size before noise estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68ccdec73c06e0115fa9865d9a1a9b4a88c9e58d">68ccdec7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-03T12:05:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check if output directory exists before doing anything else
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5071b968aded4e9d1f293dacb9102123742536fb">5071b968</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-03T12:56:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only show limited number of images in multiview displayer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1bdc981dcc5a205ae2163addb51d45133bbd87d3">1bdc981d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-03T13:06:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">default random_seed is 1 for autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bdb912ef6d0a9bd017f2747011df8567263798d9">bdb912ef</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-03T15:00:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow --angpix_ref in sorting
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aa5de7633d09dbfcb74942f41c064c0817dbf022">aa5de763</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-06T09:46:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed long long int for unsigned long long in response to issue #180
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d901cba90393fe8db68d990be9c5d1938a943d22">d901cba9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-06T09:46:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor change in I/O
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ae7431a7750a2f45dab6e2993845e658ba91be41">ae7431a7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-06T09:47:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #101)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/efddedb8e8ac12a28ecf14e6c50563816fe38cc4">efddedb8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-07T11:49:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/44eb96dcc4a5bc8f120eb4b1c99a622672ba76c2">44eb96dc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-13T12:56:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">for compilation with C++ 11, as suggested by Javier Vargas
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e652a86342024990c6dbcb4a8883e80b796aaef8">e652a863</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-13T12:57:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a3a30a535babaf74e844d35617e485e5607e9503">a3a30a53</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-13T16:28:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">to solve problems with particles.star files as in issue #143
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/680303a6664de44f1110d980dee1057be7e96a6b">680303a6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-16T14:57:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to euler matrix init
identified by Sheng Fu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2ccadfff64b4fa86b423f2bd1dd1112a06b8f63">c2ccadff</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-16T14:58:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CC-diffKernels use single-prec sqrtf when possible
Identified by Sheng Fu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/97fe4e10072ad36638810478615c5adaa4b15d4c">97fe4e10</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-16T16:00:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Only include re-extracted mics in new particles
Previously, the _extract.star files of all mics included during
re-extraction are joined to form a new particles.star. If re-
extraction writes into a directory with existing _extract.star
files (which pertain to mics which have no particles for re-
extraction) then the joined particles.star will conatin these
pre-existing particels as well. This can lead to the unintentional
inclusion of additional particles to those selected for re-
extraction.
This commit only includes the particles from _extract.star-files
which were found to contain re-extracted particles, and thus only
the particles selected for re-extraction. This increases stability
during uninteded use without affecting "correct" behaviour under
intended use.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/301c0f8517d03290f96449989dfa2ba9cedad0eb">301c0f85</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-16T16:57:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2a8bea8a947867f795a25872c0c356c1bde6a649">2a8bea8a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-16T16:58:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c25bd5cb1518066f8cd06c0aff2240b2615efca">1c25bd5c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-16T22:00:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use env-vars for c-/xx compilers
As suggested by Johan Hattne on 2016-12-15
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9efb1500dab673fa0dd0ea515df9192836ad92e1">9efb1500</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-17T10:03:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Allow parallel writes of fom-maps
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2002222d23f3ef35eb57efe9c971eb85b7830dd4">2002222d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-17T10:18:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Limit number of fom-maps without manual override
If one tries to write >20 fom-maps, the run is aborted and the user
is required to continue/re-run with the addition of --no_fom_limit.
This prevents accidental cluttering and high I/O loads, since the
previous commit enabled parallel fom writes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/797cae855df7adf6082a379589aac683aa7950dd">797cae85</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-01-18T14:53:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue with skip_align
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b2afb009d67422eebe8b36e158f1d4f3fb441140">b2afb009</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-23T19:04:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">stated fom limit is actually default
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc54eeaeaf8b1abe41a486beed9e9ca0f6ac27f1">fc54eeae</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-24T11:13:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #102)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6945cbdc063d210a01d0a7ec5b2807bad5bce0e9">6945cbdc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-24T11:13:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f699868ba696fdcb85ebf0724f0321f82708227">3f699868</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-26T14:46:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">last additions from Shaoda to stable release
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a83d9dccf55777fe48c32404095e7f80315c19a">5a83d9dc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-26T14:47:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/91024134e51c3a563057d5f3a7f988d2f0915216">91024134</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-01-26T14:57:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02eba2427cddb261a21dac0ccf6a259c636a0169">02eba242</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-26T16:48:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d61272b9ddbbed3f46b6f2d2ef9a643f96be77e8">d61272b9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-31T17:21:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update ctests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f150f1be7b2ae0c1f4c5eee0a2e9c531c12042a">3f150f1b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-01-31T17:22:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0fe1cae66783d07e3fe4f88b17d85e026e2ec6e">d0fe1cae</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-02T14:32:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">file->about + window displays version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/140b89802a02523dd41f748af82cd1cf432d028c">140b8980</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-02T14:33:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">included math.h in marcos.h for compile support
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ae9a5d6fc55e0bac33026b6fffa2cf06bea8655">8ae9a5d6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-02T15:57:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added (tergeted) Benchmark timing for Maximization
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/19607e852202ace7ecc2bcecbfd90487d8dce7c1">19607e85</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-02T16:18:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">oversampling can be set >1
ctest no. 1 works GPUsingle/CPUdouble (prec.)
this fixes issue #96, but further tests are required
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b8adbcbd189a0b38bfd431a3fc7f48b84e9be49">7b8adbcb</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-02T19:22:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some segfaults replaced by nicer errors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5c0e9cb4f64ad910b6ecd00f065cb3802b3f8be3">5c0e9cb4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-02T22:08:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More segfaults clarified
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f68e1ffe37ea1ea6c5664cd77b46389a4326b431">f68e1ffe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-03T11:23:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">corrected typo in error message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/744decbbe012c301f477d8ca1552bfac2e499d85">744decbb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-03T11:31:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">express ranges as fractions of helical rise
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4bae6013e26e5c7200e23e10a733280ee5627f2a">4bae6013</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-03T11:31:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">red color for devel-gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a7c1c42f19e4a92d0f8d64cc6374c3c4e362963">8a7c1c42</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-03T11:36:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added first version of Stochastic Gradient Descent (SGD)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3fbb8e20ddff56e9be2304579179ca08835930b1">3fbb8e20</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-03T12:18:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in normal auto-refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be14326a4cf862ae054b76ae01db01d5d6e131a4">be14326a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-03T12:45:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add options for denovo model to Class3D
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c67ee6a355f9adbdb3c6984f162b90bd0e99f1d1">c67ee6a3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-03T12:45:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forgot semi-colon
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f483b8a0cf0b82d5e4930f782213dd9c5ea21e6">8f483b8a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-03T12:46:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small edit of jobwindow class3D denovo ref#
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/013198d9efa7ff242eb5a812a63e37a35e273179">013198d9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-03T17:11:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added max_effective for SGD and extra break when autorefine converges
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2894ade94d6d69d2265b230c45595121e6a24428">2894ade9</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-04T14:15:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed legacy cmake option cufft
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/82972b34810c0e1e7b6a3f8da6429f542158ee58">82972b34</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-06T15:02:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Nicer error messages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fe8942dcadf1eb93d381eabafa12a3b1d406029">5fe8942d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-06T18:38:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Device mapping occurs before noise estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ede4456cd72523ffbc441341bad9d0e40c4b9660">ede4456c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-06T20:19:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">draft warn - box dims and GPUmem
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/272f75c40d66ac36e4a1e455ee43e25f0ec61ed5">272f75c4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-07T10:52:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more verbose and helpful image-size warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3dcef86aa002587ab50da51eb648c621cede8d9e">3dcef86a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-07T11:43:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">REDME github formatted
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/79cc704366182ab4974a4be213a7c2c974203060">79cc7043</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-12T17:45:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extra timings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/346890eb9e7fa31a0fe3163068af2c39cd24975b">346890eb</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-12T18:06:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">output ppref after expSetup
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2775a734f8b300b68f3571569054b0eedb49d5a4">2775a734</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-12T18:16:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mod output to .dat
easier to compare directly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8abf24a365c06a19f6825188a0370994b049c230">8abf24a3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-12T20:23:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added ref files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2eb4d68d9d76657134991d792d414f13c9f83c36">2eb4d68d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-13T10:20:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">One rank does expectationSetup() + MPI Bcast
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aa0d3c5f625572751590ab8b82b7f870db1e4c19">aa0d3c5f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-13T11:24:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working for nr_slaves = nr_classes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fb4d27411b4b027b2ee82da0e207b8f1e3db8ff">5fb4d274</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-13T13:39:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Working (but ~untested) PPref slave-division
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/581d2b1d3dec1f4904d7d0188764f51eb96e905f">581d2b1d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-13T16:12:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Slave comm working
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/823bd253901fc46511e994f74db64b9abdea0a44">823bd253</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-13T17:34:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move PPrefRank-control to initialization
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c42a4e99be7b0f992a9d68575db83dc579f7df59">c42a4e99</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-13T17:51:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes to non-mpi 2D classification
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ebc94dc691265ba6679e77032e79fe7bbaf940b2">ebc94dc6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-13T17:56:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mute PPref .dat print unless debug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8459899a0c88d31078b6c9ab629d105315d5efde">8459899a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-15T14:02:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update about-tab & version number display
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/004fa4ec2a1016a5ab36c3087d99710376df7a3b">004fa4ec</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-15T14:09:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'scaling'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3e923303a85416a4b64e1eb0248e86d31390a892">3e923303</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-15T14:40:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #103)
new ctests, more informative errors, and faster expectationSetup with MPI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1233bef3f6cc44a46dc699e91c75ca8ac4be9eba">1233bef3</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-15T21:10:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">continue append is 3-zero padded: e.g. _ct004
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/474658402404e299c4b1a8b03cbe5d158b73af58">47465840</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T14:22:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts in merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/90d8412f1c24ff74b888639c089a9d31cfa66d3f">90d8412f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T14:24:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts in merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/43104746832dbc072f074b0e52b55da02cab99ee">43104746</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T14:35:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts ml_optimiser.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ee006e069660b2f46ee0318efca7dc4b96e7d14">3ee006e0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T14:39:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts ml_optimiser.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1f05b1e56510eb0a24cb4ddb00f838fb7513c172">1f05b1e5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T14:41:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts ml_optimiser.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/48795fe1d97b47c2cd9cbc7277c6891b1a41beda">48795fe1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T14:59:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts ml_optimiser_mpi.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/69837eff501424b368351233c9b4c5037062a1a5">69837eff</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T15:01:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts ml_optimiser_mpi.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/783119d3c304331c15c05d5045f8f0febdb06017">783119d3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T15:14:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts ml_optimiser_mpi.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d7a7841c26e247a52f4c906d52655ca07ad53546">d7a7841c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T15:15:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts ml_optimiser_mpi.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6690f1f095c6fbed0977b869921f839d5b4c4916">6690f1f0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T15:27:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts ml_optimiser_mpi.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a53166d4c90aca9db4775dadadc9fc405677c1a1">a53166d4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T15:27:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/547786f8609d9ad7b6f842c1d236e8aceddb1983">547786f8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T15:35:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged with Swedes, put do_sgd back into initialse
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b596e128f36bde336f234c35518a8f5ef62a7f9">6b596e12</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T15:38:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired back again after merge with Swedes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/913c69479b0466ada9d052705c3365e5d83b3e49">913c6947</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T15:54:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to merge things back together again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/520f4e2189d9f57aae390bc21b8f0b7c8f698ae6">520f4e21</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-16T18:08:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">put sgd back in after merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a1f5c277ec1d501e69e4f91f72e41e4d11f717b">6a1f5c27</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-20T18:10:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Safeset MRC header
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ddfed47661ec236be5e6cbd06126c4530fd4a66">5ddfed47</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-22T15:53:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">just before mergeing with Shaoda: strict_highres_sgd
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2f45b1824f5ceeec464804d8b409de08fb93a528">2f45b182</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-22T15:56:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merge with Shaoda: subtomogram averaging for helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad630c7169ee952fa21cb7e62132b509205df59a">ad630c71</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-23T16:58:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc1a8c49f669881227e59c514635fff481a85ff3">fc1a8c49</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-24T11:31:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with None-reference and CTF in initial noise spectrum
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bea9b09191865554f45bb9d9533138cb6e859d5a">bea9b091</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-24T11:31:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove comment from mask
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f0302ddea2c2ad8839afcd6810a57737f035dac">8f0302dd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-24T11:33:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bjoern says this prevents stalls
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/128749b7feb8e459921d153f5a368d903091d627">128749b7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-24T11:34:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34030c95f5290d45c4ebb0251f6ef28bad2279cc">34030c95</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-24T11:37:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">still have to add MPI_COMM_SLAVES
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e37f45e773526438eb6e74fad38f3bb3edc05caf">e37f45e7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-24T16:02:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">option for groups in motioncor2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/220a10e7b216fae40f3a544273ac6aa821fb09de">220a10e7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-27T11:01:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added subset options to Class2D GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca9898561aa11103b6e38100b2efa9f6d06636ff">ca989856</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-27T11:05:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #104)
Master
Approved-by: Sjors Scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a88273b29ca88667a35209956308021eea0cf31a">a88273b2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-27T11:15:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">die if do_sgd and do_gpu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3b5a63ab5a86cbbe9d4d03e2eecfc1c2d34b1a0a">3b5a63ab</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-27T11:16:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #105)
die if do_sgd and do_gpu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c35458a8bffca0bac50c414b2bcaef4bbe3f25d5">c35458a8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-02-27T11:17:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a7cff1e345d16a9f4d660caa85ef198d2ab6962">9a7cff1e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-28T10:13:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Lock-class for scope:d mutex locks
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e38aa82e455acd9cf6b99f69ce639f4882c9fa52">e38aa82e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-02-28T10:14:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1548206022c27e8c62e418134bde101f55e1b1eb">15482060</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-01T11:54:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> put initial seed generation back into after taking that out for SGD
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/43be3a747dbeaa24306e6c0a55324ca87d0f442a">43be3a74</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-01T11:55:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc9a6504df5689e5958bb8fa3a8088b289529a8d">cc9a6504</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-01T16:05:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ignore FSC-true if unmasked FSC doesnt go below 0.8
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84743fe0a9642ac46ef87810b504ca4c1f865127">84743fe0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-01T16:05:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ignore FSC-true if unmasked FSC doesnt go below 0.8
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1d59b3dffd58914710dd5377557f2f8ae5d95dfc">1d59b3df</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-03-02T15:19:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Syncs necessary for non-block classStreams
NOTE: use of non-block classStreams still OFF by default.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dc6ad4d124e1f02065fe0db13c4a0f8e7e26d404">dc6ad4d1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-02T15:18:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">deal with FSC never below randomize_at
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/815d4745f08d18ab4313216c875b0aaaa4d846a7">815d4745</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-03-02T17:18:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Each thread gets its own private cuda stream. Some thrust calls still runs on default stream.wq
Should reduce risk for internal CUDA thread-lockes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b59168c52ecd188872304a978002e89810b7855">8b59168c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-03-03T10:05:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replaced thrust calls with CUB. Speed-up of 15-20% in expectation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0731b491a82ed5df49b62ecbc0d139daeb69b873">0731b491</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-06T09:14:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor tweaks
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b50f5ab08c3f11c604bf50701488d556abbf5a18">b50f5ab0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-06T09:14:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forgot to initialise back exp_random_class_some_particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bbc94475cff5b4bf1c69dcaf846de377406394ea">bbc94475</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-06T09:15:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #106)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/007dc9c02b0f031a2f98078b8b713deebf4f52a5">007dc9c0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-06T09:15:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8d1f3f8ee50dd0c2a3b5a68131a6fca2e3501f5">b8d1f3f8</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-03-07T14:55:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make install OWN_FFTW/FLTK follows install prefix
As suggested by Merlin Hartley
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fbbb4371bad66b970ff35a9d4474b2b4b67958ad">fbbb4371</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-03-07T15:19:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1629f12ccf49f1c1b23dace612c7fc2d98e14b20">1629f12c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-03-07T16:10:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert "continue append is 3-zero padded: e.g. _ct004"
This reverts commit 1233bef3f6cc44a46dc699e91c75ca8ac4be9eba.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/509fe45fd815786bc597bca2df940bc68f5d5b97">509fe45f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-03-07T15:23:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #107)
v.2.0.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c4c49ba4a7547e8948325a3eb64a1b6dba0b9fd6">c4c49ba4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-07T15:24:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/619f6c6148dbb3babccb7a2e21e22242adce2a95">619f6c61</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-08T09:29:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adapted for LMB
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/875c22215609ded366ecd63b0a2111833b78587f">875c2221</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-09T09:31:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">put back sp.iclass_max in cuda part of optimiser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1fd555edbaad2b48e266ceae2a9b3ca634051be5">1fd555ed</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-09T09:32:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated wrappers to Gctf and Motioncor2, remove MMOTIONCORR and CTFFIND3 from GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9d25a485d81f392afb3dc5dfd91ebbfa6eae6e4">f9d25a48</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-09T09:36:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replace qsub.csh with relion_qsub.csh
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/694001e5fb8761ea53f3728dc2ca85ec70ac9f1d">694001e5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-09T09:37:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/67385899f5f2ff030919fb6b8ba8628ff491fedb">67385899</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-09T09:38:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #108)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d13489e2b9d255b68cfecf2aefc54afbf8f5ea79">d13489e2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-09T10:48:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add trainingset saving, off by default
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c752436f2ac338fd254250854b5c4d73f9d8cbe">3c752436</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-09T17:00:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow restarts of subset-calculations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ffa1ed40997732109a20b3a84c8426340cc692c7">ffa1ed40</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-03-11T14:28:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">args via --help/-h/<no flags>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/671130e2ce25ed86c05e93c4abd85da5817e6763">671130e2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-13T09:17:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a2c6cfd2aab04b41b8d610649ab1a1c974fcb93b">a2c6cfd2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-14T12:39:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bugs in SGD and made InitialModel GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e11114565209f6c1353bbe0c2bca793ddc9f3809">e1111456</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-14T12:39:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/26af2d90fc8a562a41f4aa273659c9568ce66938">26af2d90</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-14T12:53:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed default sigma-fudge inimodel on GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47fea8602fbc61db6696c38d66a5895c0d0a295a">47fea860</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-14T12:55:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed remnants SGD from Class3D jobtype GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/25f8dc2e3303e992006169adffab488ef2d04329">25f8dc2e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-14T14:14:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added new options from Shawn Zheng in Motioncor wrapper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2409bdc5f833e16ce242af495f62c50ebabd4f5b">2409bdc5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-14T14:15:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #109)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e4de2b488ecede8527f8bbf0746b55933c585adf">e4de2b48</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-14T14:16:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">switch off ask training again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d06912168b547f25866d34ac10c953b496988b06">d0691216</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-14T14:17:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #110)
switch off ask training again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7dffd78459c126216260c896f69991c565248a6e">7dffd784</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-15T10:59:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added subset option to Class3D GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4a21ed125726767301322a0fa6279caf2ccec742">4a21ed12</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-15T11:00:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5875e3d919681363e7b209162efba6c2cee12a42">5875e3d9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-15T11:00:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #111)
added subset option to Class3D GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01b26fa53ae02aa525811710de37577e9f45d2ab">01b26fa5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-15T11:00:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e41d48168d3215eae85d14aca9aebb55399b84e9">e41d4816</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-03-18T22:58:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More general help flags
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/82e82b58ddbfe590f0d9e83ad57a8a04bd297fea">82e82b58</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-22T15:23:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set FSC solvent-corrected to zero beyond current size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc9a7981af01bd34835c42498db5312fb152c8d9">fc9a7981</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-22T16:58:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MAJOR OVERHAUL of the entire GUI, separate from pipeliner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/165d0aa21c98bf7f8fba833b83cf0ef847584cd5">165d0aa2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-22T17:01:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed hearde inclusions new GUI files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c0cbbec1b63f1528ebb920ae57df14919547707">0c0cbbec</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-22T17:02:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed error printing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02ca74a5e7856f6c2999be6e31430c0fbd3dc7fb">02ca74a5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-23T11:49:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further debugging new GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd15c2ce933080b0368718c86580cdca70eac4ef">dd15c2ce</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-23T15:04:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small bug helical options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/711c926b95bafc3f9a1dabe232b94f404f70a337">711c926b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-23T15:04:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed debugging statements
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bb4da40b20c3907cec9fde70f75b59a04ae0a644">bb4da40b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-24T11:54:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">still getting out bugs from the new GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7593c1b8b0bdadf8861fe884a6b86ccb96a17f90">7593c1b8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-24T16:20:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">keep debugging new GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/97c4b9c321fdead8c8f9c2a1f17596145c7ae9fc">97c4b9c3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-24T17:21:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better behaviour GUI after clicking Run button
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/636f7220e3ff9863043098aa20f822bc8d2c2cab">636f7220</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-27T12:19:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug select jobtype from coords reported by Xian
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/55ca2b016b9669c3f95c024bd109dea6071c1de2">55ca2b01</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-27T12:37:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removes clear from gui_entries and gui_jobwindow to prevent segfaults
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f2a49f0a305226a0087a0042affe3947a11d804b">f2a49f0a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-27T13:52:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">group of d-ohelix in polish window
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2abde687271813f9821efb97faff268ee0f26a0e">2abde687</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-27T13:53:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">group of d-ohelix in polish window
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fb2bf979298712717990f77d000363f475366e41">fb2bf979</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-27T16:58:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added CTF toolbox programme
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/587c2917419b2c194fa8b8601b4bf6c38125b6a3">587c2917</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-27T17:17:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added first peak intact to ctf toolbox
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6250ae073989083570effeeff899d7a9f7fc8524">6250ae07</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-28T09:30:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove floatToString from inner_helix diameter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c3ecf61d8a85745446a18515eadfc893c7efd470">c3ecf61d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-28T09:43:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug directory browse for files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/463a7217d9c83aebb69a8e1ccbcd852ba0f9040a">463a7217</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-28T11:27:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed bug initialise empty directory
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b95e4f40db346ee114f4b1351928ec05be5a9df">0b95e4f4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-28T16:16:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug manualpick job from display_io_node
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/db2e93331ebc8da95e4d877ba8d9088764f7efa3">db2e9333</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-28T16:18:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">just renaming global_manualpickjob to manualpickjob
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/696bea8636c942625d9c6f347f3a1beac7216164">696bea86</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-28T16:29:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">initialise manualpickjob upon reading
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/20cb2267f11503861035136b86f6fdc7575a1b93">20cb2267</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-29T10:11:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed classes and zero-mask options from the HUI for inimodel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/14a0d20a83f0ab16e91e467ed960680b0e07880b">14a0d20a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-29T10:11:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed classes from inimodel, and repaired bug scheduling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c19bc03fe2ee7944c3a842a856ce504132a4f83e">c19bc03f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-03-30T16:08:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> tried to fix bugs pipeline reported by Rafa
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f411d339611882f9584e089bf8b2e9957406224b">f411d339</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-05T09:51:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update cub to 1.6.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/07c68404edcefa02079cd04f6f0db8c1f49960f2">07c68404</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-05T16:59:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Gaussian blob good warn + good help
Gaussian-blob picker tells you what's wrong rahter
than a segfault
Autopicker listens to --help / -h / no-flags
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2602f3c6089321629f7a11b68caffbed5aa03436">2602f3c6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-05T17:16:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">All apps refrain from printing usage on err-catch
instead, rely on --help / -h / <no flags> for usage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d3a6f9547679e938f9b8b86127470dd9f2401f15">d3a6f954</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-05T17:17:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CPU-code listens to --maxsig
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/54709bc7dc7abd8da3988673c005a148b020690d">54709bc7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-06T20:22:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Header organization
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a8371e134c6f22316fadbf631caf603968779b2e">a8371e13</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-08T11:15:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ba3efc0f31dfe70be1fba6adb27ec84c4f6ed13">3ba3efc0</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-08T11:16:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f70ed533a2dd4bf7afcf02226bdeff3901dfb18c">f70ed533</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-08T16:00:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CPU code listens to maxsig (correctly)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f99be475487318409aac89fe3f36e6ce78d5dadf">f99be475</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-09T15:47:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed some old subtomo test files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/133df200d086090275458bb04fe192564789da03">133df200</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-09T16:41:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tentative SGP BP-kernel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/edda4090c9dd1a3eb5e9c324bed1cd775470f8c4">edda4090</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-10T14:42:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to maxsig on CPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4d7ffcdf907784d52185257b251b39838fe3a206">4d7ffcdf</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-10T14:44:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to SGD GPU kernel
CPU/GPU multithread BROKEN
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5aff3bdc79d2e9e53fe5ca6d7e97c6a3f1eda94">d5aff3bd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-04-18T12:42:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug not reading manualpickjob when jobtype Select
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7cacd16148bcc9a3471cfe43fe7fcebeb55f2183">7cacd161</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-04-18T12:52:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug setting alias upon running
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5c6adec38f1c7c6cd09ed47dd691577272e2570">c5c6adec</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-04-18T12:52:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small bug active gpuid line upon continue
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/90f0c30e8af2294c6de00fbb15c8fd749e0a98c4">90f0c30e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-04-18T12:04:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #112)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ab1d32263a1e1080984d1b6f60c1380c9ce9471">8ab1d322</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-19T14:05:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d7a29a4ab0d7b1afd3737336902377006d241f2b">d7a29a4a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-04-20T09:23:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Compile-time warnings fixed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/59ff0a7d0c53cdb11f08ba95fb75fc0bdf7dbb92">59ff0a7d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-04-25T10:00:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/23e3ec9fee28cb414dd79648e84cc59adba83e14">23e3ec9f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-05T16:46:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont deactive gpus in autopicking window
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5fe0a096525c7957d2c5ee56eabb713f86400ea">d5fe0a09</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-05T16:47:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41811d50ba06e89201740b6b2c667b3e522b7c53">41811d50</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-05-10T12:07:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Framework for a merged accelerated code base.
acc_ptr.h defines a handler that manages two pointers similar to CudaGlobalPtr.
Which of the pointers that is used is defined by the second template parameter.
Some additional functionallity have been added to make the management more general.
Example setup in "main" code-flow can be found on line 282-304 in cuda_ml_optimiser.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47c708202fc0d15e5bc5c88ef2950b10c093b36d">47c70820</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-12T09:20:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add Fourier Completeness to output of model.star file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7697f4895fd2926717e392fb525954ca7ab9ec3d">7697f489</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-12T08:21:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #113)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/59adf06d2fe36b239c14f9836e8827b3957137bd">59adf06d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-05-12T12:16:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Expantion of the AccPtr to incorporate the realspace translation helper-kernels translate2D and translate3D.
Code now works with boh ACC_CUDA and ACC_CPU as template variable to getFourierTransformsAndCtfs.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/964b373f4fd644d78911ddbef3818647c0fd883c">964b373f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-05-12T15:08:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Introduced a new image-datatype that extends the AccPtr class to further compress the code.
The mereged accelerated example code can be found in cuda_ml_optimiser.cu line 319-349.
Switching between ACC_CUDA and ACC_CPU on line 3091 in cuda_ml_optimiser.cu sets the code up to be compiled in either implementation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/721f1b947001b3ef3b9f2e49949b2c35e07e9ccf">721f1b94</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-05-12T19:09:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add check for solvent mask value before first iter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9b0234f7b471ccaca4ba46b2761a16464b5554b9">9b0234f7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-15T09:52:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">distribute fourier_completeness over MPI slaves
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2c6acc32edc97cce64d2a9928674551c00d3781a">2c6acc32</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-15T15:29:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adding support for local symmetry by Shaoda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5563736be04662fd4a2784888388d6b59987c057">5563736b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-15T15:30:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added extra option for helices to GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/436fdc6b870b32a687daf5e79232969548827485">436fdc6b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-15T15:30:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68e71afb964b5034b0c817eb6dd57fa4f08ca599">68e71afb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-15T14:31:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #114)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/15abd4f386e6af08d9dade48e67d61c8f42fc4fa">15abd4f3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-15T15:32:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7775cca266dfcffb682eb0a3e9ceabac52c5f7cc">7775cca2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-17T10:33:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added functionality to project random, uniform agular distribution
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9797057aeb7dca637917745cc5a9b3d67315750b">9797057a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-18T17:20:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> going back to multibody. This works perfectly on phantom2d, 3d to be tested still....
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/06017a2d8cbd53c647448423b3b244cf4b359f6a">06017a2d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-19T16:56:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">also checked 3D transformations of new multibody
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d5678e05a308ff759cc7af6cfe4c2854c792b9e">0d5678e0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-05-23T17:07:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More consistent naming and a few new operators.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2c63f2067971ab1b8576d6eaec946fba8e692164">2c63f206</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-25T14:50:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now multibody with solvent_correct_fsc works: multiple fsc_halves per model
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/37f30fe51840c0eca39ed0dbe79e4a3e7ab8b999">37f30fe5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-26T15:53:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now multibody refinement continues from autorefine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e0cd0d9f1b524a244d43c3391100786d3eb4bc87">e0cd0d9f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-31T08:58:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reorient bild file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e9421480b96846ba8f509b3ef5d66f63233996e">6e942148</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-05-31T14:45:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added skip body option in multibody and kept debugging that
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b6777ded2b7d0343f4e8fcc973c33e6143fa2c36">b6777ded</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-05-31T12:39:57-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move cuda files to src/acc/cuda from src/gpu_utils
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/81f00bfd6ac8a612ecab5f23dace6a3a01e26513">81f00bfd</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-05-31T13:18:04-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Get everything building again after the move
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f160b8223277b74642b6575918f1bb2010f332cc">f160b822</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-05-31T13:51:47-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create accelerated generic common file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/169ca4df6e01b6991a476f7277d32afc13d06a0c">169ca4df</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-01T11:54:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">warn if fndata_extract is empty
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c497ae87a3b596aeaca82457d774eb2738ec584">1c497ae8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-01T11:55:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">always use pixsize for motioncor2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fca768d70bf720ddf7c051282d3211fcfb90847b">fca768d7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-01T11:55:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added random sort and maximum number of particles per class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41ab6d981f9921c2d55e534f7b1ad7b1868193c6">41ab6d98</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-01T12:44:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">random sort and max particles per class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/87074d1394a89c66686a5e1122e4b8b4a0fe325b">87074d13</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-01T12:44:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">max_subsets only within 1st iter and write out message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3263186c2a527de6f8fd7cd78b7a2b170843226f">3263186c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-01T12:45:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">always pass pixsize
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0cbd0c03e3a7a244b0f1b4ca3954997566f86e78">0cbd0c03</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-01T12:45:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">warn empty refined particles star file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f50250303bca766eb1402b61590eb3afca1ab079">f5025030</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-02T10:08:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with new max_patrs_per_class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c6f35c389e660fc6f22c0d54d094907a52a87093">c6f35c38</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-02T16:23:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">green buttons for relion-2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1b1032083093cab078fc14879bc70c3392df3f08">1b103208</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-02T16:24:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bug reported by Rafa Leiro about picking extra particles in refined coordinates
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b84f34ce7a2c953fc1064bb422595b35931f2e09">b84f34ce</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-02T17:17:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set version to 2.1-beta and make better explanations SGD on GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/387225ecf94fed61bb0563ec7e8a46fa4eb1abe3">387225ec</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-06-02T18:44:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12de721e63e43a915d09d38d4b402324d7222c97">12de721e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-06-03T09:09:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #115)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be1e8e0624656b723c2bda19194aa339729d4945">be1e8e06</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-05T09:36:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">correct display of options with --continue
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02a201e3d1dce6301f7b09369ef5bbaf6f589822">02a201e3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-05T09:36:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">green run button
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84a222940f7391f65d84f7376bc688be3c195c89">84a22294</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-05T09:36:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added gpu for inimodel and better help text
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d1b9cbd85d5c2b9c8b82b86ee1fa1a70474958e">5d1b9cbd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-05T09:37:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">display errors in refine program without giving any options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf145c054c1173dfadaf2a7cc3a7ce84f8b7b31b">bf145c05</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-05T09:46:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added SGD paper and motioncor2 paper in about
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c45d6cb6b1aea9d504ea502db5253525347fdfc">6c45d6cb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-05T10:50:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">let fsc_true become negative
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d1c9aebee9b742deaa26bd8e99e3339ec086eb6b">d1c9aebe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-05T14:24:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging SGD
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2091910eecbc5180114bce397b60eb1991330f7">c2091910</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-05T14:37:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added ScLileLab logo to background image
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f11e20dde2f360e7ae332163c90962cebdc03e65">f11e20dd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-06T09:34:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set version to 2.1-beta-0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1580f59c0391f6191e61fc2fb9e294dc49b1e02f">1580f59c</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-06T11:07:55-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Start segmenting code, fix build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e8aa459cf90cb9395522392b0ca2bbd46b758b1e">e8aa459c</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-09T13:33:35-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">WIP - segmenting CPU and GPU code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/db4d3667ca0f09058369adde176706ee21362a8a">db4d3667</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-09T17:00:10-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">WIP: Convert the rest of the world to the new shared pointer class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b6312d15ae2f62a879e32822e6352c88aece080">7b6312d1</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-06-12T13:45:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a5d6aaa95325cb7d2c64fa7cee6acf640744fd7">6a5d6aaa</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-12T16:19:22-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">WIP: Clean build with CUDA on; not run-tested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2da5db4f55ace6d843d77248d5fcf029be37e6aa">2da5db4f</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-13T14:16:07-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Change CUDA_DOUBLE_PRECISION to ACC_DOUBLE_PRECISION
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4db6d76f4ebaf7a018298f2e390fbf9b84a5af08">4db6d76f</a></strong>
<div>
<span>by Sheng Fu</span>
<i>at 2017-06-13T15:52:20-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add CPU kernels
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ba1658ce9c43f3ae259472f72f0fda058f43d95c">ba1658ce</a></strong>
<div>
<span>by Sheng Fu</span>
<i>at 2017-06-13T15:53:09-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'cpu-cuda-merge' of https://bitbucket.org/tcblab/relion-devel-tcblab into cpu-cuda-merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/634c4a7127d09fab77dbd40b452868512a6e91e7">634c4a71</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-14T11:32:47-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move single-particle expectation into common code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5c583dda78fa435028e553bc7cc327aad06ce94">c5c583dd</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-06-14T17:03:11-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix build errors and crashes in CUDA debug build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7f6ff7267df7ae50ded5b328cbe06ba47fa38ab3">7f6ff726</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-15T15:46:25-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix some error checking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a665271871381040e632fbf18e52c807bbba2f2">5a665271</a></strong>
<div>
<span>by Sheng Fu</span>
<i>at 2017-06-19T16:06:00-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check in the kernels that include sincos lookup table
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b146b216e952ac5b406e5d9422ce97d7f1af81bc">b146b216</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-19T17:04:06-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">WIP: Try to start bringing the optimized CPU code back on line
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3d539e1f3cbef4b29546229737dfabf58af70587">3d539e1f</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-19T17:04:52-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'cpu-cuda-merge' of https://bitbucket.org/tcblab/relion-devel-tcblab into cpu-cuda-merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a7bc35ba03de8e51fa56cc7805860f20936814e">6a7bc35b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-20T14:54:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changes for relion-2.1-beta release
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/633b4fd2a31bb5f47365f4be76bf716e6b76cacc">633b4fd2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-20T14:55:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merging with Shaoda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/81692c6fde365afec2668fff52a6298a39fd5af7">81692c6f</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-20T11:08:55-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Intel MPI build, experiment with CUDA-free ALTCPU builds
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ebc80d9c09f74a1172b9e6f069909d65e555dfad">ebc80d9c</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-20T16:41:47-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop some templating for AccPtr, start getting ALTCPU code to build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24552daba27ede5d7702145e077a6abc1561a6d0">24552dab</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-21T11:52:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug nonsquare mics for premultiplication CTF
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0de16d04f8e147a94f0dbb1a29d26cd7261e27f1">0de16d04</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-21T12:51:35-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix runtime error and selection of files to build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/38725147f529a8266eddf94ebdeffe2c56db3a96">38725147</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-22T11:18:03-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bring new CPU path into ml_optimiser, plus more instrumentation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9193690ca6e3305a4c7a1432d5bc13985db4aa6">d9193690</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-23T11:44:59-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert to using original code kernels for utilities, continue CPU merge work
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ba6807e1f438b8569f454f089e2188da8574fde">3ba6807e</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-23T16:51:41-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Attempt to merge slightly further
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/94a5ecb0e1e59ec674623911f813c7ad5b18cf2a">94a5ecb0</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-26T16:47:58-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Firewall ..onDevice functions in AccUtilities
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7dbb6c03d662505b408269bb540eae3fc68439a">f7dbb6c0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-27T12:48:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">draw lines for start-end coordinates in helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/db894e92c24a5f40c58f730c31ea6b1436c3146f">db894e92</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-27T16:26:53-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Convert more CUDA calls into wrapper calls
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f8938727a8b5cecb433fce5be5b1c64f48d6c898">f8938727</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-28T12:53:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">functionhelp in helix_toolbox
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0ab7efe6957d0f184289b6abf199361bc28e443e">0ab7efe6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-28T12:54:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add --noscale and --no_norm in refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4699bcea5fd0e009f6ff383169d3df689898697">b4699bce</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-28T12:54:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">typo bining to bnning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3e4efa7290af49432977abb3314799a4d5e9d98f">3e4efa72</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-28T09:28:16-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Convert another CUDA call, remove CUDA ifdefs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a91009bf76b027d77eb0e66d4f8f7deb58d1d6ef">a91009bf</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-06-28T18:44:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">image_handler --o fn.mrcs is sane
per-image ops on stacks used to be
--i in.mrcs --o out.mrcs -> in_out.mrcs.mrcs
--i in.mrcs --o out -> in_out.mrcs
now you get
--i in.mrcs --o out.mrcs -> out.mrcs
--i in.mrcs --o out -> in_out.mrcs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2030bbb232c575f1a2cb76ffe85144775f61469c">2030bbb2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-06-28T18:47:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a349386ec7527dc089b1d378dbb76596041a297b">a349386e</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-06-28T16:19:05-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move to a shared projector_plan
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/da18875741bc337c2e47c83376b56202966f2668">da188757</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-06-29T10:02:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">displayer can lowpass 2D-stacks
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eea00b1737dc8a018b504cb45c43d606645c35aa">eea00b17</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-06-29T15:17:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bug reparted by takanori
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f5facd5e7609db85af7dc51017e1a42122bac0ef">f5facd5e</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-07T14:00:43-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Touched 3rd-rail - shared projector, backprojector, helpers and resulting fallout - only a little more refactoring needed on CUDA side
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e4abe20eb409eb81ddc046bd45c37fda0151ff6e">e4abe20e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-10T14:47:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">oldstyle GUI option added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8416d0b88b04dce5535e372c5f680b7a868e3f02">8416d0b8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-10T14:47:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make angpix compulsory
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f714945b205465398b4bb3f1d741016e3d62e1a7">f714945b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-10T14:49:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added safeguard for gold-standard separation and made specific local searches angular distributionin healpix_sampling for multibody refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a2a6986b55c69c3b2c06563841877628d0f32846">a2a6986b</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-10T11:22:59-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Complete initial refactoring, fix memory leak
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8e7d03a92db3a90490cfc196a35aeec5f5f7a6ce">8e7d03a9</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-10T12:02:30-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do away with AccT parameter - currently serving no use
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d6fbf1663caee41cfa003e4d6ee53d9ab557ac0c">d6fbf166</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-10T13:38:06-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up duplicated code on CUDA side
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/40492a4e64c4c95b157b5adf136294de2a7f73bc">40492a4e</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-10T15:58:41-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up, including unnecessary file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4b3ee5fe57afe3cb468c5080f402827d9fe6d33b">4b3ee5fe</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-11T12:51:32-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Early WIP to get CPU code building
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f6219c7e6a124bb8b2edc282f1b41f2ceb3d6962">f6219c7e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-12T09:38:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug oldstyle gui filenames from browser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b73d7812d46dba4c24ab928d1a988ce2bd5a431">8b73d781</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-12T09:38:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">diameter in angstroms not pixels in help manualpicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2e65be9f49e676be8c3a20f933e9d3bc3967076f">2e65be9f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-12T15:59:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now multibody seems to work OK, but it is very slow because psi-prior has ben deactivated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/28e8564f732af5a3f6a6d3d4bd65b12cdeab712b">28e8564f</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-12T16:59:59-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up CPU build of everything but missing FFTW calls
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e9d60a701c650baf0b7ecc21c97cfa80adb48134">e9d60a70</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-13T16:30:24-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Solve a few link issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bdd2f2de5b212cc5602e0fc86fe9ee471c28f209">bdd2f2de</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-13T16:52:20-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Optimized CUDA and CPU branches build cleanly. Now to go back and put functionality back in
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ddcf679e44cf40a8d48431a270d9e4815dd572eb">ddcf679e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-17T16:12:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merging with Shaoda's local symmetry
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3549ca689a4fbb02d83c0a383d1971abff24c345">3549ca68</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-17T13:38:39-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added global support for lambda functions (c++11) in cmake config.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/758a2c4cfe45e344eb66f9e6fc0ee1fbe1576d1e">758a2c4c</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-17T16:44:21-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AccPtr always allocates aligned memory
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac84bac349c49fcdebfd37fe15f6c3b33f60e989">ac84bac3</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-18T09:35:59-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">A more cmakey way of linking to TBB that resolves linking issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/79a296c4e289135ee6c9187c58bdaef93c1d522a">79a296c4</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-19T11:03:50-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Hook up optimized CPU projectors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/443892856903a736b9f373d66a6f02b93fdebb0e">44389285</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-19T15:12:54-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Complete CUDACOMPLEX to ACCCOMPLEX transition
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9fa2bff6380d86b3e5f211f7c015428c2d40e983">9fa2bff6</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-19T16:43:16-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Visit a few TODO items
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16aa54bca26f498d7d37754c681471e40da10755">16aa54bc</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-07-20T18:19:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Compile bug fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3550fb1d1cb766188e0e27a89116d73e7971dfa2">3550fb1d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-07-20T18:54:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed exception pointer bug.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6cb6eb17cda7dee910d1f9d276c43faf646a890b">6cb6eb17</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-20T14:05:12-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make some bugfixes, including some from maineline
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/21039fbdceedf5570a8b87efd8f59193e012347d">21039fbd</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-07-20T14:45:32-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix double-allocation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/37a27024963f527d236cefdb2a86f62865897631">37a27024</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-07-21T12:53:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to compile issue with CUDA enabled combined with DoublePrec_ACC.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a37f20763fc0fd18d8248db517d64c50661d462e">a37f2076</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-21T15:32:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">angpix optional again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a957d54d03817360f1250ce1b0dc5ec0c5cf6ecd">a957d54d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-21T15:35:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now multibody rotations are around (0,90,0) to avoid problems with psi-prior
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/88769db0f9b4c844ec7438912bc38d3264afadff">88769db0</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-21T15:08:58-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bugfixes to produce CPU signs of life
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7950b2e58a8456a323fad5edab7c4abb194ac879">7950b2e5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-24T11:52:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now multibody has correct translations and rotations?
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7eba2039b804282a46323d8d6ad5d5384f12d846">7eba2039</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-24T11:58:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small error in psi prior
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a6174e09f96ad94fde910b8ce8c38c2bea9100f">3a6174e0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-07-24T14:44:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix segfault when compiled with CUDA enabled and DoublePrec_ACC=ON.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/65bbc65e0b9553981d3cf9a21e9fe69a42785e4e">65bbc65e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-24T14:23:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bug in origin pixel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/97b7d874330aab1c2fa81a93f690edb6eb85eb40">97b7d874</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-24T14:24:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out BILD file with body COMs and rotation directions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/250b0bb3b1395c2d908f0818064dbf9449aaacb5">250b0bb3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-25T09:45:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with sigma2_rot for helices when starting from local searches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e5d1e53d656a6b3dbe2b4e29b2f65c872191b9e7">e5d1e53d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-25T09:45:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed --help for --function_help to not clash with args.cpp anymore
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c0fcce98df736bcddcae0a77c001ac8ce6498ad5">c0fcce98</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-25T09:48:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added warning sort and max nr images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0e6546dc16b1f1f84db480deda65b186d8ed46f">d0e6546d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-25T09:49:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed archive from GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3162db2a2acd7aac051edc2080faaac56eb3e789">3162db2a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-25T10:43:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #116)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/097af6333b412b73dd97668c966bd51c42962d50">097af633</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-25T14:15:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/26c29c98148a38a9da3d1f4bf48e8628dc11ab19">26c29c98</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-07-25T17:23:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f6821c1a7ddcc0b2302db7f64e200de276de0f98">f6821c1a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-07-26T10:44:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2caccd5c89e3c411b25c95d2a3cf9ae1d8523d26">2caccd5c</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-27T13:57:30-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Memory initialization bugfixes, etc. for CPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1e639af30de5965529e2048363de206cc8490be">f1e639af</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-28T13:28:37-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Centralize CUDA subouts for CPU, use different back-projector
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f159b98e5f9e009883790b165422d9e92d309460">f159b98e</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-07-28T14:53:19-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">A few bug fixes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b34698dc348a0ae37756291d76efd92422fadad">6b34698d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-31T08:48:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added 2D->1D (back)projectors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f220f48d92d7bee4798b3b207c5e2b509db9fddb">f220f48d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-31T08:52:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added new functionality to make 2d (xy) initial model for amyloid-like helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3697eae331aa40df9f62afe0a2301c43bbc6b85e">3697eae3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-31T08:54:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9729f4dc352af4aea558bd8cf764a86b6699d1bb">9729f4dc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-31T09:00:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in tilt prior multibodies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e348c266ef2df1c9dcb8d7a6eba95895d8b29d54">e348c266</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-31T09:01:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added multibody-specific mask-radius
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9fb6c050c66e5ee84d767ff3eeddf24cef3d41a9">9fb6c050</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-31T08:03:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #117)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf80e591acc9dc5c5995122271016795cfe3041c">bf80e591</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-07-31T09:03:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9013c3e69af599458ccd0c01b768e4fed9abcefd">9013c3e6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-07-31T17:01:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Alloc before init fixed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c85e9734de8f0ce9297c36d9e306fc92d36d9f8">3c85e973</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-01T18:02:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">back to red GUI for devel version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/643b0c404c65a6e46eb77a97b0ed9bf0c6e5ac41">643b0c40</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-01T18:03:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2D->1D (back)projector normalisation for greyscale in inimodel2d helix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa3ea6749f26b27ad83e4e07932f1da77225ee49">fa3ea674</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-01T18:04:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug multidoy affecting class2D
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f366ae157685038ea4c6e17d67bdb970c41676cb">f366ae15</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-01T18:04:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">also read rlnReferenceImage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f8c81e89b101915ae95cb704573a979c16e0ad38">f8c81e89</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-01T17:04:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #118)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e3a60c789c47dc2febf34f99fb45e0910d0601c6">e3a60c78</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-01T18:05:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/449a6d9c60dc78b2b8ef41fc73012417a0a315b9">449a6d9c</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-08-03T16:47:00-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Memory addressing and size fixes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/17bbb85e6a5745f6acb36aa54e2bacb749362572">17bbb85e</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-08-04T08:55:15-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'cpu-cuda-merge' of https://bitbucket.org/tcblab/relion-devel-tcblab into cpu-cuda-merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b79021be3b2abaecf7bbf409055028e08c30a03a">b79021be</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-07T09:27:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bugs reported by Andres Hernandez and by Takanori
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/453f37560ba33278725a0adce03cf2d31c3af669">453f3756</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-07T09:27:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug reported by Andres Hernandez: delete a single job in any menu segfaults
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4e74a8cb377f240081e933c383f23b4ca8f72790">4e74a8cb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-08T12:50:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">disable utf8 error messages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c998ad8097d90e5c26227ff55dd2881b39b0263e">c998ad80</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-09T09:33:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug with pad1 reconstructions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a8b3c1e0a852199a8835de5396650ac85634d305">a8b3c1e0</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-08-09T10:05:49-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tweaks and bug fixes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4caeaba9f3841e1d3c9297d0fe5289cf42fe49e2">4caeaba9</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-08-09T13:23:26-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">First attempt to reduce number of ifdefs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ef315eaeecbed71a5386a1eb3b869239d3c5fd0">1ef315ea</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-10T10:58:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont allow saving stdout, as it is a temp file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/30dc3bfe59f92d45d3f53c6461605e57cf422e61">30dc3bfe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-10T10:59:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">deal with overlapping masks in multibody refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d8cdaa82a9c9e44a87a477187dd5fec689ced34c">d8cdaa82</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-10T15:43:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">print out cl errors without giving options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f38edadcc593aa706b2a86a18130b47fe13cdee7">f38edadc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-10T15:43:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug in overlapping masks for multibodies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca302bf4cc29277351ad5996640c0e6a529f344b">ca302bf4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-10T14:47:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #119)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/94c8b0c7f80da0a0affe66c99f30fb0eb4fc7797">94c8b0c7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-10T15:47:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dbf3e62076cf493ba1e7183085bcfc8e17fc2b68">dbf3e620</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-08-10T09:45:17-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up legacy code from CPU-side source
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/882cdef6c112dd9274e7ae309f88f56129150f86">882cdef6</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-08-10T15:46:04-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove compile warning building with ICC
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/833651ad84ca0c59e56f5584cc70bb3604277821">833651ad</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-08-11T15:54:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b477078f7936f6b0a1c1e0d63ffda8cda475ceb5">b477078f</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-08-11T16:18:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to zero-distribution classes @ reconstruct
Especially obvious for small-set / subset runs. E.g. segfault occurs
for a 600-particle 2D-classification on 10 2D-classes, whne using
~100 particles subsets. This is not of tremendeous importance, but
for debugging it is preferrable with stable execution.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ccb42f8fecd2a6bdfac09a223508e6afea239148">ccb42f8f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-08-11T16:38:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add program to analyse results from multibody refinement, and perform better subtraction for focussed refinements
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/21da208f0ee01f3c15b8f58e56410e4b63cdf839">21da208f</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-08-11T10:38:02-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use accelerated back projector for 2D case
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c76679d4080f1bdfe4003d83f9bc6044e4b1087">0c76679d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-08-14T11:10:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2dd23dff5e21a67adc31d2ad9674f94fd8262cbf">2dd23dff</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-08-14T16:46:22-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add optional MKL build, parallelism to more serial sections
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/df4463586cbcd54006adcffe2bbb9116d7143492">df446358</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-08-15T13:15:33-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix linking issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2293d66519385068b6f94b0bcd13e923f7b75c28">2293d665</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-08-16T11:27:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check against clesses/bodies in PPref setup
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a25345463ad4d6d73ce48d20b5f41366882172c">5a253454</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-08-17T13:27:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Default format .spi for file-write is consistent
running e.g. mask_create with "--o test" produced a spider-format
image named "test", rather than "test.spi". This is now fixed.
The code is a bit unclear on the distinction between "extension"
( traditionally "suffix" such as .spi ) and "format" ( auxiliary
specifier to override filename, such as :mrc). This should probably
be revised, but nobody want's to spend their time doing that.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b980948c45e5c82e186ef7c4b4a0e73b18ebf0dd">b980948c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-08-19T19:47:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Auto-refine bugfix
This fixes a critical bug affecting half-set (gold-standard) refinement.
Starting with version 2.0.4, each iteration of auto-refinement incorrectly
uses the same half-set reconstruction as for alignment of all data. The FSC
and resolution reported is however still based on comparing two half-set
reconstructions which contain completely separate image data. A
degree of reference-bias is however present. The effect is to report
a resolution higher than what should be under gold-standard conditions,
since, reconstructions are subject to a degree of over-fitting.
In order to claim a so-called "gold-standard" resolution, use any version
before and including 2.0.3, or after (including) this version.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4dea187b82118d4ef8b88a67200b5e6363b41f1d">4dea187b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-08-22T17:43:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to CPU side issue in runCenterFFT
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47601608aeaa9d40f102558005fec002c18d3dc9">47601608</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-08-22T14:20:15-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Generalize centerFFT across serial and parallel invocations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2f219cf5717aed9af3ab4d6fe2a6448c6a4c8945">2f219cf5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-08-23T12:45:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Number of failsafe attempts adjustable by user via new flag: --failsafe_threshold
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c6e72eb2b07a8246ff47ef47d6fb8c9e5a18811c">c6e72eb2</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-08-23T13:04:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better error reporting for failsafe-mode.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/81661d8ed5602dc324f069ab133b256e87ba83cd">81661d8e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-08-23T16:39:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Critical bugfix to random halfs protocol in auto-refine.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc792be3a0f740e4a91b2737a341b98712f624b2">cc792be3</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-08-24T16:00:10-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Switch to unoptimized backprojector as an experiment
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0e87d56674b9c005a6b74abd288cfe7a132461ba">0e87d566</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-09-04T16:04:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #120)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/602c7adf1f95b97f17b2718bc6be1184cb9a3827">602c7adf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-04T17:04:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/631dcd9c93050d2ce027a4e115ad92b94e94703a">631dcd9c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-05T09:21:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">after merge with Bjoerns stuff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8effdc927fa3bb97557154cf4ed9a43c7f1e3dae">8effdc92</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-05T08:22:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #121)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e093e5b141f9073a1b067bf481b18431f45e810">7e093e5b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-05T09:22:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2bf94987ca877186c934e350a3075bc3bfc0a4d0">2bf94987</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-09-10T23:13:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/22edb93697309b1f524e4296404ac7b764914dd9">22edb936</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-09-11T15:38:22-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Go with alternate backprojection
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f98d344e12c7fe4a03f6e65d1615518724f7eb56">f98d344e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-09-18T10:07:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix SEGV when opening .mrcs files (not .star files) with relion_display --gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf9f4bc763f847138ff9072d0131fb4be28aafa6">bf9f4bc7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-09-20T15:25:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix a bug that "relion_preprocess --operate_on" creates filename.mrcs.mrcs.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47b3a8a60b474c2934717fe7a7e2ed6db59e1ab1">47b3a8a6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-09-20T15:31:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set pixel size in --locres map.
This is my pull request on Github #266 that solves the issue #239.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2adb960ca684af4232689ad95b4466ae5da1a177">2adb960c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-20T15:31:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new flex_analyse functionalities
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8e36ffad5c8f957dd62115990a219217b5bf0147">8e36ffad</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-20T15:34:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small bug in flex analyser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bdfd79690e546440db749fc8a2cdcb25519ef7e7">bdfd7969</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-21T13:53:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">keep debugging multibody, joinTwoHalves opn higher ranks than 1,2 only
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/caa9155014373fc88e272c9e23c44ffa4f66649a">caa91550</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-09-22T11:12:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix a normalization bug in relion_preprocess when rescaling.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01b83b6b20d912ff2a87e689e72e296665f84bcf">01b83b6b</a></strong>
<div>
<span>by tnakane</span>
<i>at 2017-09-22T10:44:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in fix-preprocessor-bug (pull request #123)
Fix a normalization bug in relion_preprocess when rescaling.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57abfa9388a7ee1f01f9444d07e23b9128fdca37">57abfa93</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-22T16:58:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">how to deal with selfRound in multibody offsets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/35bcb707f39fc67ca31cf197b67b8e42a2b27f86">35bcb707</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-09-25T10:24:07-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unneeded link option when not using Intel MKL
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1f8964dfa4f1d47ff113b98a07698064bb814650">1f8964df</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-09-25T10:25:24-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'cpu-cuda-merge' of https://bitbucket.org/tcblab/relion-devel-tcblab into cpu-cuda-merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c174c7568a64ec356bab5841b43a3ecc33112501">c174c756</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-27T13:49:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added do_map_generate to flex_analyser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2f14f88b53ece8c8a7c93e001e3421637cd7fe69">2f14f88b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-27T13:50:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug for multibody last iertation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f3ea5abb437f5320acfeac4a9c9fec1df510d8a5">f3ea5abb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-27T13:50:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug negative numbers
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/76b5aadfc90eeeb9d948a8f7c863fc7436a8aab2">76b5aadf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-27T13:50:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add phase randomisation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8cd8b564b2e3c1e9dc3d1e927885ee859dfea8f">b8cd8b56</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-28T09:40:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix bodies if they dont have angular accuracy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3e2ab46f793e6e39c73127af7d310baedf159913">3e2ab46f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-28T09:41:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4aab626f2ab69a5a2ad0f40189d2cb128aced569">4aab626f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-28T08:43:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #124)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7258c2134028c58fa36c27667dd9ad00c21a2d97">7258c213</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-28T09:43:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/433c40101f43c737efc2c63661f7820f9bf35445">433c4010</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-09-28T09:57:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">stop multibody angular decrease earlier
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4d02fc157265f9990df3cf5338cad6d72bcc40be">4d02fc15</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-09-29T16:16:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d2d1721be76e3744553615b82aa65bce79f4637e">d2d1721b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-10-02T09:36:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cannot change padding factor during a multi-body refinement...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac7cbbbca1d5e341f58bfd3859a846a2fe359048">ac7cbbbc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-10-02T12:03:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug phase randomisation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3bd28636f0879e085c3383028ad1b305ae59f89f">3bd28636</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-02T16:21:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean-up
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7aca98f019abd7b72b97aab15e8e2f01c6e69f7f">7aca98f0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-02T17:04:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into cpu-cuda-merge
Conflicts:
src/acc/acc_ml_optimiser_impl.h
src/ml_optimiser.cpp
src/ml_optimiser.h
src/ml_optimiser_mpi.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ab12c16df0060ac372c1772e5a44d8e647cd4ad">3ab12c16</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-04T19:04:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Improved precision in convertAllSquaredDifferencesToWeights
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cbff6c5d4affd8a5474da49481032cd60bf728e9">cbff6c5d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-05T17:15:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Improved precision in convertAllSquaredDifferencesToWeights on acc-cpu side
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ccec0f544a80f15e39be2850e57ff881d68214f0">ccec0f54</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-06T11:26:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Making code hardware-agnostic
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ef56845f5a158d0a6dcb84a8b1692edb0382ff2">7ef56845</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-06T12:14:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Code made more hw-agnostic
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4126e861112ba0f4b6f9e31320cfb7db71cb529e">4126e861</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-10T13:24:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AccPtr usage clean-up
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d64b4f3e2f8f6439b2617adf76d6ac2b4b423b71">d64b4f3e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-10T18:04:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Introducing AccPtrFactory and AccPtr with a state-variable for AccType
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c8c6e05fd8bd7fb29b8ab05a5ec4b0a19f87dd8">6c8c6e05</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-10-11T11:03:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug hanging multibody refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/21bf310a3d593b6cfc35ce6cb96fd4b5df6c3585">21bf310a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-11T12:05:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replaced metadata REPORT_ERROR with exception to track line number of issues in star-files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bceecd1ade9116b0890d0ef5399fce625915de9c">bceecd1a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-11T12:19:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue with nvcc not picking up the c++11 std.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d097273aa9989a6e80663f7e20c25b43c85ed39c">d097273a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-10-17T11:16:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reset mu to zero when SGD or subset have completed.
This ensures rlnClassDisribution sum to 1.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/40ba4a74dd47b600e2754d209d4a59ea8087c365">40ba4a74</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-10-17T16:30:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed a coordinate bug in singleViewerCanvas, where the amount of scroll was corrected twice.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27755d8fc6156bbfed5c4530b10fd506045e69cc">27755d8f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-17T23:09:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed max value issue
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b89334d36b0c1934f5225bb60424d64ff0f5a2d7">b89334d3</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-18T16:13:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Further improve maximum exponenet management
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ecdc1544e6b8ea14cbc46c4ad0f1b4b258836bb6">ecdc1544</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-10-18T10:16:58-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replace CUDA_DOUBLE_PRECISION with ACC_DOUBLE_PRECISION
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/14e38ccb2fa45d25d4dc8cc25a552f4e1f2176cc">14e38ccb</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-19T15:25:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean-up Image
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/923850fbdc8ff5d21725efd629656ff1c4ad6eed">923850fb</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-19T17:26:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing warnings and rounding up some functions for mutual cuda/cpu acc enabled binary.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bff86a6399062fb8f2b1dcd9e667f11f0fe83882">bff86a63</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-19T17:26:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'cpu-cuda-merge' of https://bitbucket.org/tcblab/relion-devel-tcblab into cpu-cuda-merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/343b0d16af81808bd574502d1fc042983b1b2f73">343b0d16</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-19T17:37:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Dropping COMPLEXTEXTURE to reduce complexity for enabling dual CUDA/CPU builds.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc03af21ffbc49ab0346579a81f27d2d60b45817">fc03af21</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-10-19T11:45:03-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">All projectors share the same complex-number data structure for accelerated CPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cdf18d3d0758826e50090c55a3e58a0de95fe46e">cdf18d3d</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-10-19T11:45:55-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'cpu-cuda-merge' of https://bitbucket.org/tcblab/relion-devel-tcblab into cpu-cuda-merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3dc6589b9c18879c164bde17545439fe38bb912d">3dc6589b</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-10-19T16:20:52-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix bug in CPU-side backprojectSGD
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8dafa02af096be95f4eb2299f7d0361d2b51031d">8dafa02a</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-10-20T09:28:02-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix race condition in CPU MPI initialization
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/311f69634320e0eb7a442a3c61f362ee81648633">311f6963</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-10-20T09:47:15-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unnecessary memory allocation/copies of data from CPU backprojectors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1b2622638615e506869710598abfa392fcae2a87">1b262263</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-10-20T11:21:47-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Pass pointers by reference rather than value - sigh
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/67748168933057008508efcae4091385d74e1910">67748168</a></strong>
<div>
<span>by tnakane</span>
<i>at 2017-10-23T08:18:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in reset_sgd_mu (pull request #2)
Reset mu to zero when SGD or subset have completed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c8eeafbad7786b581c5636530cdb10704df40342">c8eeafba</a></strong>
<div>
<span>by tnakane</span>
<i>at 2017-10-23T08:18:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in display_scroll_bug (pull request #1)
Fixed a coordinate bug in singleViewerCanvas, where the amount of scroll was corrected twice.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6fb53b8fcdc5a18ca7788e209af9069a4428171f">6fb53b8f</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-10-23T12:43:07-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add multithreaded FFT operations to ml_optimiser_mpi, mirroring what is in ml_optimiser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/45e08504a98f55d43d8829d2298a62307e975347">45e08504</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-10-23T14:44:49-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix build error for CUDA target
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/399b105230773da12d1079d8ac84408b1893789c">399b1052</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-10-25T09:51:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed an integer overflow in relion_stack_create.
(calculation of the necessary memory size)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/19d7d2cdb81e87b2cc0ede7b41a7c9104c4a6122">19d7d2cd</a></strong>
<div>
<span>by tnakane</span>
<i>at 2017-10-25T08:57:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in fix-overflow-in-stack_create (pull request #3)
Fixed an integer overflow in relion_stack_create.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f35dfc8236fcede5fd6d8b6926e1b6d590c27abe">f35dfc82</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-10-25T12:55:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">"Show metadata" in relion_display now tells the total number of selected particles.
Also made clear that the metadata shown is of the last-clicked class, not all of the selected classes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/af877d2b08feb6b0251e6cb63b2eecea1f5210fe">af877d2b</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-10-26T14:51:18-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Various tweaks to try to get CPU code to run
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a1654cc5ab2bb679846d4b633ba608f7e86a910b">a1654cc5</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-10-26T14:51:58-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'cpu-cuda-merge' of https://bitbucket.org/tcblab/relion-devel-tcblab into cpu-cuda-merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9325939fa6b83a8846b7373e9b2311abab91261a">9325939f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-27T12:19:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed compile issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/88b0fa6e9b55b376367cba743467fe0586c45371">88b0fa6e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-27T12:28:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Unwinded allAlloc back to accAlloc, we don't want to allocate unused RAM when on GPUs.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c92e154c47191342111b55e778fc9ca19c4380e9">c92e154c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-10-27T12:40:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue with min value caused by the C++11 NOT so intuitive definition of min/max.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fcaeb97ef6a877c47529f700b3802d39ce045608">fcaeb97e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-10-27T14:16:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add -LogFile option to MotionCor2.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47623d8e84a07f7c22205024fa265cad5e759a4c">47623d8e</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-10-27T11:00:17-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replace numeric_limits::min() with numeric_limits::lowest() for float/double
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd1c326cdee41afb1f46546545f756f7c6fb5f5c">fd1c326c</a></strong>
<div>
<span>by tnakane</span>
<i>at 2017-10-30T14:37:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in motioncor2-logfile (pull request #5)
Add -LogFile option to MotionCor2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/71f09609a2dcba79864915b23ec3fba9e1a9c18b">71f09609</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-11-03T14:33:52-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Limits and memory leak fixes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/82d476d66bbe1fef77983565e90f76d8d7bc1dd9">82d476d6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-06T09:30:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #125)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/faec8f5ef0afd03c68898fe5290f705604d50053">faec8f5e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-11-06T14:41:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix boundary check for MRC stacks.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2672f153cfd5b7e63453c78875eeede38fe55c92">2672f153</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-11-06T16:26:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Supported TIFF (only for reading)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1b21d1db6ec8a8169627434d9ec9058da5183ff5">1b21d1db</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-11-06T16:28:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/31a1e8a7e8175c7ef65e20e8861af7c4b97c0560">31a1e8a7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-11-07T11:24:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Respect readdata flag in TIFF reader
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c12d2d779203fc421c12075878bd21194cab4c7a">c12d2d77</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-11-07T11:32:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_run_motioncorr can handle --last_frame_sum for TIFF images now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/642f1fd81d58a2fba292998ce20250f4adf4f943">642f1fd8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-07T16:16:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired restarting multibody refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e88254cbe2a6bdfd2af4d78c79c8630e8bca0c54">e88254cb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-07T16:16:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired restarting multibody refinement 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5117b884a65cb58c2a70f395f7b538f19dc8567e">5117b884</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-07T16:17:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging thread-safety FFTW
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aceae6080f2944ecc0210cb4aa18aa4bb38969cd">aceae608</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-07T16:17:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">expanded flex analyser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/478e357a121083d44dfc849ea2f05e06836dd4e4">478e357a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-07T17:11:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more tweaks for convergence of multibodies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/62d9835e7f36b7aeae218cad50cbc261f0e2b3c4">62d9835e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-07T17:12:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42ec39eadbe47be9a948bf571e7059f69677a7ad">42ec39ea</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-11-07T10:32:29-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix unitialized memory on CUDA
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6fef8688868571a76e80bce29ac765de3b6a137e">6fef8688</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-08T14:28:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/383338250075842a48e2b14b3941810de35b0bd2">38333825</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-08T14:40:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into cpu-cuda-merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e25d93d2b76cc1d6c2962102b3406077a5125e4f">e25d93d2</a></strong>
<div>
<span>by tnakane</span>
<i>at 2017-11-08T15:09:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in improved_show_metadata (pull request #4)
"Show metadata" in relion_display now tells the total number of selected particles.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/abbaca5eb531094e5ed23614384e64657e07e2c2">abbaca5e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-11T09:23:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Texture switched off when ALTCPU is enabled.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/df7b1ef0914884d9d1347229a93d7d140a8ad000">df7b1ef0</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-13T08:36:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed cmake warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/953012e6aae243499c320e5b94732db699ae3fbf">953012e6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-13T12:39:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set nr_sign correctly for non multibody refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b157418fa18df45f3b6bec6e072de149affea832">b157418f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-13T12:50:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added Chris and Richard-style Ewald sphere correction. Still developmental...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ed9e701cfda5c7c41c5beadca602315ed6165634">ed9e701c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-13T12:50:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29aabc8a42408c8f0a0d3555841b31b821bc136e">29aabc8a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-13T17:03:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Backprojector on shared memory using whole-kernel mutexes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/03443459356a760d45385c66b186b44b4af2d2c4">03443459</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-13T17:27:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MPI support for shared memory backprojection.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24783ac07604ce02fa933b4e31fbde141aba55d4">24783ac0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-14T12:21:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mask and write out eigenvectors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7fd89e478e3a50a382e60a312147c1a9318dd3d6">7fd89e47</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-14T16:14:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Code clean-up
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ddb7bf56203f988aa85e37544cae4af0866319b">6ddb7bf5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-14T17:02:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed double free bug for MPI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d43b6bcaa25dfdf2eab27d1e8ef2c07da8a1f085">d43b6bca</a></strong>
<div>
<span>by Charles W Congdon</span>
<i>at 2017-11-14T14:41:41-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Only free shared projectors/backprojectors inside do_cpu for MPI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68a2d2f14dfed1bbedf5d2d527a699a731b71f73">68a2d2f1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-15T11:34:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Jasenko new metadata libraries....
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84e76866565440e3513402650cbfe3e956ab0ea9">84e76866</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-15T15:09:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Granualar mutexes for CPU backproject kernels.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2057051a2ad2398cd4e683429ee220a5dea4ed07">2057051a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-15T15:09:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'cpu-cuda-merge' of https://bitbucket.org/tcblab/relion-devel-tcblab into cpu-cuda-merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e92b6fb85961b9a4d71d3cd551c3db66beee1001">e92b6fb8</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-15T16:49:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed error on icc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d46a418765d452f5bac4d74b197d9755d1c56105">d46a4187</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-16T09:13:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont do solvent flattening when doing multibody
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eac1a885a992830af6923e176c112b74069973b8">eac1a885</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-16T09:13:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ede23e082b101f9df6abe25c4dea2621de7f2249">ede23e08</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-11-20T15:04:48-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CUDA build should not use TBB
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e3a263365b323dac369ae65fbe93d7dde39d9bd9">e3a26336</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-11-20T16:30:04-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clearly label this as a test version of the code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bbcbc986ddbf01accb7fa44003130dd6280cdde4">bbcbc986</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-23T11:15:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> also do beamtilt correction on imagfe used for alignment
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/527dbc6643cac38310f882355a3e885bb3235a7f">527dbc66</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-11-23T14:28:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix Jasenko's MetaData container for single precision mode.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5de7aa42959f3916532f4ba2cc2d4b8224407cb7">5de7aa42</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-11-24T12:14:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix boundary check for MRC stacks.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2d4998cf14a5c37c669971657f3db0fec925c45a">2d4998cf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-27T16:21:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #126)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4699d3513a544ea27c2550b1118565ea71a1aebc">4699d351</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-28T11:23:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f924c87bd4aadd4b50987656a298018a6338bfc7">f924c87b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-28T11:32:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to missing sort-button in the displayer.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce90586e9d3f14e106c9bdf7c778fc2645236d57">ce90586e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-28T11:34:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix to github issue #291.
Issue description:
This line causes an error when compiling with clang on macOS Sierra with latest Xcode installed.
Please consider changing the comparison to page > nullptr.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5db48c21ffd3f1094f9d6f6f0d774bd991f25d0f">5db48c21</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-28T11:44:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed help-output for the last binary with this issue.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41747061ff709740feb9a54499480b3c96e1b8b9">41747061</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-28T13:57:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More extensive information about actions related to external libs during cmake configuration.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a74e925beb95bf24b7ed27c576c276b608b1849">8a74e925</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-11-29T09:04:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #127)
Fiixes, for release 2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0560f35abb1c00295df954bbb5c222196f587377">0560f35a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-29T11:55:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow tau2_fudge in Refine3D
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/501ea28d08dffbb65c53b3d8a2c8a49b83eed72e">501ea28d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-11-29T11:55:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6fa18c343e50fef74a29aa7790841c87d20e699b">6fa18c34</a></strong>
<div>
<span>by Andreas Schenk</span>
<i>at 2017-11-30T15:00:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added write(DO_LOCK) to release lock file again in the case somebody tries to mark a not yet started job as finished
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/10fb779caf8bd6b75ed92ebec56cebd6d0c510eb">10fb779c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-11-30T15:21:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update README.md as suggested on GitHub with minor modification by Takanori.
- pull request #233 by Andrew Jewett
- pull request #218 by Shyam Saladi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2cfeb1ed8fe392ee140dc8e58fe20b7bda1024ec">2cfeb1ed</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-11-30T16:40:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2a41959e56f86ccda0da5799bfa67fe78637f15d">2a41959e</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-11-30T16:55:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CUDA 9 compatibility
Fix to rarely used diff-kernel
Upgrade cub to 1.7.3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5b28b2cc3e162f453388b2db597292c71b16bfd0">5b28b2cc</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-11-30T17:01:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prevent int underflow in packing
resolves issue #180 (github)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/10fd2e178af9b3c8f5ec20abc8761a702caf2772">10fd2e17</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-11-30T17:34:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subset reconstruction handled sgd-like
Reconstruction should only occur when there has been something
back-projected. Using SGD, subsets might be small enough for
that not to happen, which results in bad estimations for the
cumulative weight. Code was written to deal with this, but it
did not cover the use of subsets under conventional (non-SGD)
execution. Runs which used subsets in conjunction with --maxsig
could therefore crash. This fix should avoid this issue.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/014c93f4376ce03a3ac79f6afabeee275e90cace">014c93f4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-11-30T17:34:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More general null-check of buttons
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1dd8467ba6e30843740eb28e3ce61eb5ecb54ab9">1dd8467b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-11-30T17:34:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #128)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d05ec6a4881d0a333366026205e4ff4402ffc911">d05ec6a4</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-12-01T08:37:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MPI-subset recon (and activate for non-SGD)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9bf06f6e3df3b33c03e33436543738abc23ceb8">f9bf06f6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-01T09:28:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add tau2_fudge to refine3d, hidden option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd5fecd04edbe8c4c723f4bde9143b340bbeb23d">cd5fecd0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-01T09:28:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">last changes by Shaoda
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8430f85d3e0dd5fbf765c5944571ce60b96660d9">8430f85d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-01T09:28:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated references in about window for release 2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/69bf03bddcb34eb0f6a700db5eb933f50b4f40e8">69bf03bd</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-12-01T13:11:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51412ceedf2ff82e5d92482e529842e188d147b5">51412cee</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-12-01T13:29:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tau2_fugde is NOT adjusted using non-SGD subsets
Mild confusion;
The issue that commit 10fd2e1 and d05ec6a was trying to solve was due
to the lack of an accuracy-check under the else()-case covering non-sgd
reconstruction. Those commits then removed the else-case to achieve this,
but also activated the tau2_fudge adjustment for non-SGD subset runs.
This commits reverts the latter effect, because tau2_fudge should ONLY
be subset-adjusted when using SGD, due to the update-formula used.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1fcdf2ef16a8474dc3ba3b67c2a54f2c9b5df5b6">1fcdf2ef</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-01T14:12:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed my strange formulations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64814406385b1e6fcdd69b90288a078ebfb61432">64814406</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-12-01T14:37:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Separate FLTK-deps by gui-lib
As suggested by Matt Williams (https://github.com/milliams),
with minor alterations to be cmake 2.8-compatible
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/019abdd2d1e4ff866f98f0eb710b625f38176181">019abdd2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-12-01T14:39:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3bdc8f66804bc756deeb28fbced7d6dd3d8721f0">3bdc8f66</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2017-12-04T09:58:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #129)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fb43d542d540d73c304825667dd11d3b6cc1cb40">fb43d542</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-12-04T09:47:41-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Version 3.0 alpha first stable version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5b473f9b40dd6687f363691f2eb09f7b15c1d81a">5b473f9b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-05T09:48:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">do recompute plans if pointers change
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f73d2c51061715be1cbf428a2a67d14e134e660d">f73d2c51</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-05T09:48:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ebcfd193fa91197090d8847e35def9189f2f80c0">ebcfd193</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-05T11:31:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug windowFourierTransform ambiguity even/odd ydim
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8cde6465c35c793c6b53d8440cd8a3a036ddaa73">8cde6465</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-05T11:35:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired single precision code with plans_are_set variable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/426f21efe538422a0f8674e8ae1d32200c42abde">426f21ef</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-05T11:44:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #130)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/50289ddaddc3f7ca6783d706337361f51a7294f3">50289dda</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-12-08T10:54:46-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes for large images and memory diagnostics to run when building debug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0bc6c6bf40475e8b0d4c2771e91e5903b2e6d163">0bc6c6bf</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-11T16:56:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/879ae79f176c0ad087c219a0027ecd354ebc5fd8">879ae79f</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-12-13T10:42:22-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Correct use of some existing timers, add a few more to improve coverage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0361ee35cc716140b84ad43213e1cbe2d712a461">0361ee35</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-12-13T15:37:37-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Actually initialize new timers
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a978614976a5a7ef5558627797f6add523051be6">a9786149</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-14T13:33:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'cpu-cuda-merge'
Conflicts:
CMakeLists.txt
src/acc/cuda/cub/agent/agent_spmv_csrt.cuh
src/acc/cuda/cub/agent/agent_spmv_row_based.cuh
src/acc/cuda/cub/device/dispatch/dispatch_spmv_csrt.cuh
src/acc/cuda/cub/device/dispatch/dispatch_spmv_row_based.cuh
src/apps/CMakeLists.txt
src/metadata_container.cpp
src/metadata_table.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/74ca8b66b2ea46966fc56935d91a3c852f0c0b81">74ca8b66</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-12-14T13:43:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed a bug in relion_image_handler --threshold_above and --threshold_below when re-windowing at the same time.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a2cc1a0bf47b1c16a69b3efa119962e194115605">a2cc1a0b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-14T15:42:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed 2 instances of usage in ml_optimiser_mpi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/09a63b3fe1032944420a35dccf6944ef58e1fef8">09a63b3f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-14T15:43:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/05d21ee70073db7f4d4ba07e230b6b832797ce51">05d21ee7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-14T15:52:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #131)
removed 2 instances of usage in ml_optimiser_mpi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a9f5e9e6136feada14b079d795c03ce27aea769c">a9f5e9e6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-12-14T15:55:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Synced AUTHORS to that of the GUI.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/04fcbe0a355c8e3e3299dbfb9a2c2f04eed1ec53">04fcbe0a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-14T17:40:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Stable accelerated multibody port up to diff-coarse.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/32b5f360852fab8565f7695ac7a309aeee7f85b3">32b5f360</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2017-12-14T15:53:51-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Also add additional instrumentation to MPI side and reuse some existing timers
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7cf7bf43052db55c0984526c10d3efe15216b69e">7cf7bf43</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-12-15T10:08:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27c7d1ef4a6c4caba148d7b186b91ccba1aaa21c">27c7d1ef</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-12-15T11:02:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f67ae00b9c9e50f686843bd94600f8a904aeab8">9f67ae00</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-12-15T12:17:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use "Slower, more exhaustive search" in CTFFIND 4.1 unless --fast_search is ON.
"Slower search" was OFF by default in CTFFIND 4.1.5, but turned out to be
less accurate (ref: http://grigoriefflab.janelia.org/ctffind4).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2d997c74d90e5b59da0002230bb8dad2cce2f658">2d997c74</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-15T12:32:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged ctffind4-wrapper into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1be3f829aceb5565e6abfa0f209de27deb11c67f">1be3f829</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-15T12:32:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bdee9757012295a6b31a5c7d19f7899014d43693">bdee9757</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2017-12-15T12:33:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #132)
Use "Slower, more exhaustive search" in CTFFIND 4.1 unless --fast_search is ON.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf8fc4939f406ae55c0692cb2bff8a4cb6f3c1e8">bf8fc493</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-12-19T11:58:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed a bug where broken texts appear in the GUI instead of hard-coded defaults when environmental values like RELION_QSUB_TEMPLATE are not set.
(The cause was that "char mydefault[]" is valid only within the scope of the "if" block)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/651990f183478cbb294860cc15a5568f1ce2f768">651990f1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2017-12-19T15:40:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Check if the extract_size is even in relion_preprocess
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/46358bcae26d1cb07dc7b7e2b78104eadefb7d39">46358bca</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-20T19:01:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up diff-coarse
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cdd6f119133b13b8c6f38123f5edf37fe1143539">cdd6f119</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-20T19:02:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd3a28081188bd983c7a288345a6baf2463ce4b5">dd3a2808</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-22T10:33:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4b7eee885af3a661daff2d19e2fbeb0d6c27761e">4b7eee88</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-22T11:00:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Expanded multibody port to the fine-pass and storeWeightedSums.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7059baac451e8dafde20be7c8a60710e8f371b0">a7059baa</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-22T11:00:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2a117707b9ac05a8be613864f4b3e451332d2114">2a117707</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-22T11:25:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GCC compile issue fixed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2d2699016373f5d60ff7800b90c65e05d045d03b">2d269901</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2017-12-22T11:26:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed legacy files.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ee0d28d8ee51e46f05f228b9f4052ccf7104b3b">1ee0d28d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-01T19:16:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Unified code with pointer bundle.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fb1bdc5da2f033b2ef00297326d77e1403a98d5d">fb1bdc5d</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-01-03T14:22:23-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Restore fix to diff2.cuh made in commit 2a41959 that was lost in merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b25e862f24033e93a37d8fe3f6af575ee3e0879">0b25e862</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-04T09:50:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair segfault display class withour sort
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/357f7b91d9c9e0ac35265879e61e70ca8edf77ad">357f7b91</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-04T09:50:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">put version back to devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ddad957de64aeba1ede260b6a87551c7aac0c373">ddad957d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-04T09:54:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added flip in rotations and remove hand1 from reconstruction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb71103909ac8832d5f06ab81993cf4fbebe2ae8">eb711039</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-04T09:55:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60a873b7d32ba40835c07cf033cfd347a68da219">60a873b7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-04T12:07:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Array size issue fixed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7fae5fc51aea9d80120c71f74abee32a31b6978b">7fae5fc5</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-04T21:01:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Matrix multiplication issue fixed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4fd6b7905145fb8c4042c3eb2a348e394144a071">4fd6b790</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-04T21:01:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/422976028a3f77f8df36eab6e2788a498f29b657">42297602</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-05T17:24:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add laplacian-of-gaussian blob detection autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4a7869a0b401a57e3336978020474c81e4179fa3">4a7869a0</a></strong>
<div>
<span>by Dari</span>
<i>at 2018-01-08T13:22:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue with both required double- and single-precision FFTW-lib when base-relion and acc-relion are compiled with different precisions.
The find packaged function for FFTW is made more cmake-like by enabling the specification of components used to specify the need for the precision-types.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be646ec40a7f7b3fd42030890e71f28372c5e86f">be646ec4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-09T14:51:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">LoG-picker improved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ca2ea9cb68f58e155377220c322e4ae2dc29324">5ca2ea9c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-09T14:51:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8426c1c999421a741ea545b1fe16ef80050c7ddd">8426c1c9</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-10T19:37:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Inverse and correction matrices applied in right order.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01206199871a01d48abcf62a0e8e1adef6ed3e0f">01206199</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-10T19:44:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a31fea78a2ad69604a5ffdb5e63716befc6f9620">a31fea78</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-11T14:52:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow scheduling and executing pipeline jobs from the command line
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd344430cb3ce7184317c53d147e0a560d8e56ef">fd344430</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-11T14:53:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">also for command-line scheduling of pipeline jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e6263546fbc0e94fd856e1d16197314db7dc4090">e6263546</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-11T14:53:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair verb bug autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/49b305095b089a4c0deb718a10f671fbcb0011c5">49b30509</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-12T16:06:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/30848d5c70e4ff35c2e50be7f7a6d0342177ee89">30848d5c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-17T14:55:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Started working on Micrograph class.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ff8d3604880f82045298e3fdc681f74df8d67867">ff8d3604</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-17T15:45:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Store global motion from MotionCor2 into a STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aacfa039d24c8e77cb643c798bdddde0b9ae0e97">aacfa039</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-17T16:12:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Repair error output from run_motioncorr_mpi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1f172d0278197bb99bce9e4df6912bd21ac9b5bb">1f172d02</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-17T16:24:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added amyloid-specific functionality to autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a9c3ff9679148cd6fa41e0a3ad09641c6b9de21">8a9c3ff9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-17T16:25:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cef9c5907399204807f92d6e9cc490841055174c">cef9c590</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-17T16:51:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Global motion can be saved from MPI version of run_motioncorr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01ab8b82753164b7a06ca795d6df1df5c12caf36">01ab8b82</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-17T17:26:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Force MotionCor2 to always take the first frame to be aligned as the origin of the motion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/388fa0547b75d7d8177d230f2ad38acd2a07c2a7">388fa054</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-17T20:27:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue #132, both single and double precision FFTW libs are actually built when required simultaneously.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/10c95c2ec63d3493c6c5b54417248a8c4116b3e9">10c95c2e</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-17T20:55:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix for undefined cmake variable warning.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b9775ee80edc99f73d4ccd5f63168ee1fc4d6bb1">b9775ee8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-18T09:12:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add option to recenter re-extract images on a 3D coordinate in the reference
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f87dfd832fa0490a3a1d93dd2eed61a88bd084be">f87dfd83</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-18T14:17:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Distinguish unaligned frame(s).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2367931dc55d51ce5e518505abb7a55789066e6f">2367931d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-18T14:26:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Made micrograph-model STAR filenames consistent with the image filenames (replace . with _)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b07e310ed02876f5ceb769b8a771c222ae23d9f">2b07e310</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-18T16:29:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">preparing to incorporate Jasenko's code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1b980546736dc71ef36047eef0375eb4470b5104">1b980546</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-18T17:36:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Correct created number of projectors and backprojectors in MB.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a126e436421f6001083b63be634096fe0d92bb4">8a126e43</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-18T17:56:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix number significants
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/06bc925ad92aa861bb01d4ea8dac7afaaa7f44bf">06bc925a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-18T17:08:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #133)
New accelerated code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/790d8b961816af291d33f488454dda9ce625e285">790d8b96</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-18T17:08:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed memory leak on GPU with modified autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3207a31af58a11a594468d2af32e9051dc4e9f65">3207a31a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-18T18:10:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/28e14ee9219cb4db89c4532302a19a216e6974c3">28e14ee9</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-19T10:15:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Forgot about this.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c9b6311006768c8de28bc0436a57bd3ed4f05ea0">c9b63110</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-22T17:52:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Deallocate unused CPU-memory allocations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0236bc0d934baa8660dc4b22934276ae92c01f79">0236bc0d</a></strong>
<div>
<span>by Dari</span>
<i>at 2018-01-23T23:04:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed issue in FindFFTW.cmake
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dfb9455fe18666ea123f5ba12cae13990e68301e">dfb9455f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-24T14:03:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">decomposePipelineFileName before looking up the group table in relion_project
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51df10df272b7adadb60153ffc846f525bd26cef">51df10df</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-24T15:38:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed a bug where relion_image_handler skips the first image in a stack.
Also clarified the meaning of select_img in Image.write().
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bfd538df0f6c2592b4ca762b7972c3973839e33">8bfd538d</a></strong>
<div>
<span>by Dari</span>
<i>at 2018-01-25T10:51:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed yet another issue in FindFFTW.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34abfd8688b3769878a844354bc79f1cad34afae">34abfd86</a></strong>
<div>
<span>by Dari</span>
<i>at 2018-01-25T11:04:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TBB include issue fixed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/14f7286c1ad2d346408aa5bc21e9f66a5e05f0a0">14f7286c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-25T11:01:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improved version of amyloid autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58564657396f331c7f445107d7e1bc8831b12ffc">58564657</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-25T11:02:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8abc93e193773f74b683c976eb9be317b21c5278">8abc93e1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-01-25T15:18:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged master, tiff and jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9fbe6f0f0d0ddf68df13494b9f841d9e09ee3ad1">9fbe6f0f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-01-25T16:38:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged master, tiff and jzivanov; adapted to C++11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42be736c191dcd809331b09d22ee25b33a4b8927">42be736c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-01-25T17:07:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with new GUI jobtypes, revert back to numbers to avois lots of trouble in transition
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ae6d0d981d77fa3fd1492f40795f77ac4ac5581">5ae6d0d9</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-25T18:56:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix for compile warnings and handle memory allocation failure.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b705fa745db3d47138d92fffd80f575a7b6e25a0">b705fa74</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-25T19:45:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Handling different number of projectors and backprojectors.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/462f26448a059693082fea32e8500e6df0d47141">462f2644</a></strong>
<div>
<span>by Jasenko Zivanov PI Sjors Scheres added 28022017</span>
<i>at 2018-01-26T00:25:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tilt_fit now uses the FSC as a weight
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5797bd664c42eb8beaa59c5624f9fcd8e50101cf">5797bd66</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-26T09:39:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #134)
Multibody fixes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/00e76b859ef43c7a39c27dbc9bd05dc4840c85aa">00e76b85</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-26T13:14:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed out of bounds array access in symmetriseReconstructions for multibody.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b2773f49542f224541ef8dd2b53eddfa7811858">6b2773f4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-01-26T14:36:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed libRelion to static linking - this makes the programs archivable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2bc23443e5a3e91e6e21b8239208472f4e577f5d">2bc23443</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-26T15:27:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #135)
Please double-check this edit.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2376ad1b0baccabfe057978b8f3949a9506fc077">2376ad1b</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-01-26T15:37:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">defocus and tilt fit now display the usage when called without mandatory arguments
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e80290a80e6b6d12373f132d083695f26dcdc17b">e80290a8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-01-26T17:11:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tilt fit refactored and untested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0f28a341d1b964bff77b58496b332931fc44a358">0f28a341</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-26T17:46:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use Image.setStatisticsInHeader and Image.setSamplingRate to reduce code duplications
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/09adae07b5596654be6750527981f21c1450cb79">09adae07</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-29T15:50:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Require TBB when compiling with ALTCPU and completely remove requirement when not.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4e30bb159252efcce62903398d1486d278648f04">4e30bb15</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-29T16:41:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added --half_maps to relion_postprocess to output post-processed half maps for validation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ac8e998554cdf09d6a89ed9360927511d608c4f">7ac8e998</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-01-29T19:50:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit refactored, reconstruct_openmp updated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/73d38ef2dc815a722db1f18a7aad30ffb0cb5742">73d38ef2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-01-29T19:51:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit refactored, reconstruct_openmp updated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2e7f37c0c898897bb18891dcc329e118d0e28fe">c2e7f37c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-01-29T20:25:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reconstruct_openmp bugfix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e29b70b48c564b891f3d5d275ff4aa6a367b23e3">e29b70b4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-01-29T20:27:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reconstruct_openmp bugfix 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dece2347b8c76893cc7bda240d78fea967f2b615">dece2347</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-30T02:43:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor: an tbb include not wraped in ALTCPU.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f31badab61eac5e03012deb064b8ae6d6eee2eb1">f31badab</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-30T03:44:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop min required cmake version to 2.8
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9515f1c38f25a85c67c70c81b3bdffa0ad9ba967">9515f1c3</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-30T04:14:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Sjors' bug fix, including oversampled translations in storeWeightedSums also for multibody.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b3bb326a6059222010eb978c12935ffae6ca810">0b3bb326</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-01-30T08:23:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #136)
Drop compilation requirements and multibody bug fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/687a665b9f935bf6e9a02ad09440e4277edbe937">687a665b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-31T11:58:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix CUDA autopicker (shouldn't write combinedCCF for non-helices)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/165ed3101acabe7fa2e3135dd8cdd049cb6c2ada">165ed310</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-31T13:55:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in fix-autopicker (pull request #6)
Fix CUDA autopicker (shouldn't write combinedCCF for non-helices)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/17e2c97ffd60515e15eca786059e503884ecb9be">17e2c97f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-01-31T14:54:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Keep track of binning in micrograph model
(NOTE that shifts and coordinates refer to UNBINNED pixels in the original movie, because binning should be done AFTER motion correction.)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/98c13ab12687aecfc486636439baae2e4c06b282">98c13ab1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-01T14:20:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Our own implementation of motion correction.
Work in progress. Implemented global correction.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a0181494842b7f76c9f3d90859883dd0fa9a6f0a">a0181494</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-01T14:23:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged with master, fixed helical_rise bug in reconstruct and reconstruct_openmp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/59f4bcba1daff8d3b4c6f5e18d64e7d4b322d28a">59f4bcba</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-01T15:57:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Implemented patch based trajectory.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f19c386511f011d04bd1614ae20fe5c91bb46e4">9f19c386</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-01T21:11:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e47afc4ac718ad6af3cf3fdac5ac539077fc4023">e47afc4a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-01T21:13:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3cc1f87b067d5b93c07f8e49632032f2630126e1">3cc1f87b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-02T10:11:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Implemented polynomial fitting and binning.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5a363216af21fea2092522865fbc102a99f6902">c5a36321</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-02T11:29:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polynomial fitting is working. Real space interpolation next.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/abf6cb06fca2c1e88606e0acc0060ac84c8d6516">abf6cb06</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-02T14:40:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Implemented Real space interpolation. (do we need gridding correction?)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/92d767312c2652f32f56eb345f0c80be76cca453">92d76731</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-05T12:44:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trial commit curand Noise w/ img-printout
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dcc1e8ca0069032adfb5e296a4a8a4537a16d525">dcc1e8ca</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-05T12:16:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cut out binning of non-square images as a function.
(Probably binning and shift should be moved to fftw.h eventually)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3d348095ba91c45f03a6c85d3a9cc86be7ba15ac">3d348095</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-05T13:51:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleaned up new noise-mask code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c7e18e310d4cea79fda3e58c96d2dbe5ac3e904">9c7e18e3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-05T16:31:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Dose weighting. (WIP: Testing needed!!!)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/af21aa5a56b1f398cc8b77e4aea7d099cc28c722">af21aa5a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-06T13:52:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Show stack trace in REPORT_ERROR.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f3a1a8ba7554276cc18033a80a36f517851e0464">f3a1a8ba</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-06T14:32:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Explained how to decipher the backtrace.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01f53553b96e8f99656244e4f8d0a00cee4fedf1">01f53553</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-07T09:55:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean and make safe
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b06be64c0ee1dc097ca6c90b8e67a8f3ee146b01">b06be64c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-07T11:15:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Read multiple frames from TIFF images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b329917ceec588264f1ef801ab7d1d422f9c5d01">b329917c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-07T11:16:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Supported MPI-based parallelisation in motion correction.
(WIP: TODO: output should respect "verbosity")
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d04870bddbad142f3f3ffc6d41c80e3e12a7537">9d04870b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-07T15:17:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added directional lowpass filter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/965c4df4b239fac9ccf0ad8d2a02a8ec938223b9">965c4df4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-07T15:19:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">also write out unmasked references in 2D classification
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/30f756e627b1a07f79678e1b9c796472a97bb621">30f756e6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-07T15:20:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set default repeats to 1 in pipeliner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/78d2ff377934f7b252a5b981dc8cf0f02d0d1aac">78d2ff37</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-07T15:20:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add output directory ooption to reposition particle program
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fef2d6fdee87d4a1734fa52aa37e4f9e49649ec2">fef2d6fd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-07T15:21:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in relion_rconstruct rise was in pixel, not in Angstroms
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d6f5e2165084d2dff5d077fa87355dfe53d64de3">d6f5e216</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-07T15:21:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2214d0413b73618ebd2908b9c4b0d3f91c0bac48">2214d041</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-07T15:47:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forgot to remove directional filter from ml_optimiser.h constructor
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1003573896a0b51bc6ff398fe7bd8add7600d2fb">10035738</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-07T17:33:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update GUI windows upon reading default .gui files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a0730587277fa051100e3ff1bebab8438f8fe808">a0730587</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-07T21:39:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new motion_fit; not fully tested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/75ea2db2136121e8ee7e6371e744846ffc7090b3">75ea2db2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-08T02:22:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new motion_fit debugged and tested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b847988620ff3d0f98c40f9d9d0d8d0cbb84815">8b847988</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-08T15:17:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in recenter of tomograms
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bd2564238177cf85299a43d15dda30cb25405871">bd256423</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-08T16:36:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug re-extract with tomograms with Dustin
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/36e847a7e31e67a003758333e0eb9083bb293ee2">36e847a7</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-08T17:58:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reorg getCTFs-block and re-enable >1 iter on GPU
Rec_img auto-refinements work on acc-path (GPU tested, ctest #9)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/320373e1562f7443383b9dacc5debbef1ac7c84d">320373e1</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-08T18:21:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Compilation error
missed due to cached compile config.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9ca9ad9407bd109da86039e2dec6c4cd6e09cc2">d9ca9ad9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-08T20:28:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Flip the Y axis when reading a TIFF. (see code comments for the rationale)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c62057b63545a05c8e36dc8d86c1503805d682ee">c62057b6</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-09T04:20:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed heap-corruption bug in motion_fit; motion_fit now produces near-identical results on unextracted images as it did on pre-extracted ones; split off parallel version of FourierTransformer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/216cfb78f37aa6010c0b08e5714ea6fb22d08da8">216cfb78</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-09T04:21:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/tiff' into jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d2d67296b04999fac2858d2467e47ebb1c7a4f63">d2d67296</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-09T04:29:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed y-flipping of tiffs from StackHelper since it is now done by the tiff-reader
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5b600294ee85c13169c4933296116fed8bc41d5">d5b60029</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-09T04:32:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added parallel FT class to repository
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d88617157faf13d0c7de628123cc26c8ceb5c203">d8861715</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-09T11:25:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed dose weighting.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/119dfff367c0faa8aff62b8843a14f3ebaf0f82e">119dfff3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-09T12:47:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired error for permissions in saveTrainingSet
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c4966559bc72e895c110a8472b1692da893b0a93">c4966559</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-09T12:47:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow sorting on selected subsets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fc70951923004e4742af2b00da3652dee8b6779">5fc70951</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-09T14:33:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix MRC header (pixel size) from ml_optimiser.
We had to call setSamplingRateInHeader(apix) only AFTER X/Y/Z SIZE were defined.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/df1a3f8655765aeb0f9bb0c2d6dab43b831004e3">df1a3f86</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-09T14:37:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2a12e245dfc0350f1ef36460e03800fc2e4a83b">c2a12e24</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-09T19:50:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added timing codes. CenterFFT is the bottleneck!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/623d2acb9556021f4536dbc94b125eafebf2ea9a">623d2acb</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-09T20:28:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">recombine_frames refactored and made compatible with unextracted movies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4dd11283c6789f155c4792d84d574c7b1c6e752d">4dd11283</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-09T20:32:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed CenterFFT from argmax CCF. This greatly improves global alignment performance.
(But not patch alignment performance; related to cache size?)
Now the bottle-neck is dose weighting and FFT.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa2501ec5bf7b531d5bace0de578b91e5f9bdd3b">fa2501ec</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-09T20:42:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed a parallelisation bug in Fref calculation. Now results are identical with or without threads.
"schedule(static)" did not improve performance.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8e1161db5086b9a7fd13101cb4debda9c278bcd2">8e1161db</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-10T06:45:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Profile FFTW
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c9982ff2db0180d2d8a052374549c4a661d050d0">c9982ff2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-10T07:01:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired and improved program argument logic: all refinement programs can now take an external Cs and kV as inputs; tilt_fit no longer requires an input star-file when a precomputed pixel fit is provided
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/af7cd43fb2c4130900eeb2b5dae6871234bab9b1">af7cd43f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-10T11:00:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">implemented iterative tilt optimization; further work needed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b184d766a1eebf9165f0f76db58b063d5fb395a1">b184d766</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-02-10T16:30:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eaa13e215f35450bcf2e3e6a3a43027480a62633">eaa13e21</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-10T18:59:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Parallelise FFTs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a408000c17f5b75ae3b6ac2f8d016a78e6d5411f">a408000c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-10T19:40:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Parallelised alignPatch().
Now ~ 70 sec for TcdA1 with 6 cores.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/727e4c46c8669136a3e54fee17652174047bbf1a">727e4c46</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-10T22:54:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Parallelised patch preparation.
WIP: results not identical. Investigating...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d3ffbe3ea7354f4f294a1ee992c75ffaa283c3b">0d3ffbe3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-10T23:29:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure patch sizes are even. This fixes the threading bug in the previous commit.
(But leads to slightly worse RMSDs. Is padding better?)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4cf700e9799651284c48ad09a4dd341fc1bdb0df">4cf700e9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-10T23:40:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix timer labels.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a745e8eb18e1c72e975588688fc9264872c5cd1">1a745e8e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-11T10:33:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix parallelisation of real-space interpolation.
Parallelise reference calculation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/74af370f32bf95e908c5da9563fab96f64b6d374">74af370f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-11T11:00:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Anisotropic tilt fit implemented and tested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e7a8c22649ca3ba2456023b1cfcab0e92a30909b">e7a8c226</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-11T15:18:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reduce calls to SINCOS from nfx * nfy to nfx + nfy.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b5b304890da459fd7f6a3c5c5b9b8593e9ff9193">b5b30489</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-12T00:22:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">defocus_fit now supports anisotropic coma correction and reestimates per-micrograph astigmatism before per-particle defocus estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c8c65913a13c35468728955da0b243cc15a8109a">c8c65913</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-12T03:16:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Support for anisotropic coma added to reconstruct_openmp; activated timing switch in BackProjector
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b88fe3b272804b2ca4fc5a0f297a69e674bfdc52">b88fe3b2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-12T05:13:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">BackProjector::reconstruct partly parallelized
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2228a6778eabf24f091b55f9b83008f265818cf4">2228a677</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-12T05:17:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed --jfft parameter from reconstruct_openmp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f54519420bc61df0d915dba2d98b7cd074dfa4a7">f5451942</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-12T05:58:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed parallelization in BackProjector::reconstruct; replaced by progress indicator
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b33d7db82cef2a1970763f1c5b5057cccfcc2106">b33d7db8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-12T06:31:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed bug in anisotropic coma correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2904229bec81926ec8b18e5d623c0c3e58683641">2904229b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-12T19:08:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unsafe de-allocation of host-projector
CPU-side allocations were deallocated to save RAM, but when
multiple deviceBundles (accelerated code path) are used,
this de-allocation creates null-pointers for all but the
first such bundle.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/df9b9011deb1863ac0e4e3b30b94c0f9b5ee384f">df9b9011</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-12T19:11:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/50c112a20173c7f82b1f173b4e73ddb0f5eb9132">50c112a2</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-12T18:22:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #137)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e9f8af249e5127eaea3b50413f21a7cdf269ee98">e9f8af24</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-02-12T15:46:19-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix issues with ALTCPU build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3b6d3ce42171781d43f692db162d9ac601e4a79c">3b6d3ce4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-13T04:29:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tilt no longer applied twice in defocus estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/56b59d0ada4733b0aba75666b17ba3368482ccea">56b59d0a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-13T07:59:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">corrected units in anisotropic coma model
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/37ac67b4c7f1f049f3c5f2626f786aa6124911d1">37ac67b4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-13T08:56:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reverted units in anisotropic coma model
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1daef6e75e549530d87af8c8b294663158750f42">1daef6e7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-13T14:32:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improved SGD initial model generation and subset handling in general; now subsets are just shorter iterations; particle order gets randomised at every iteration
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5d75df798516e9df5864040cda26304140ff51c">d5d75df7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-13T14:42:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forgot a comman in rlnSgdFinalRsolution
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/96b011a940b45167ae9f261b54e61cfbb1798379">96b011a9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-13T18:08:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make micrograph model C++11 compatible.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd6721a72ece54064879335e45a91e49596fdcd8">cd6721a7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-13T18:31:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added GUI options for fast_subsets in 2D and 3D classification
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/66c547486bd4c1148592268587ec230a620906b3">66c54748</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-13T18:32:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed I/O of postprocessing, to allow post-processing of multibodies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ebcfee3b2db07239a91966a0eb79c37724662ffe">ebcfee3b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-13T18:52:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added own_motioncor and multibody jobtype to GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f662b48a3ab3819ba7f825f22aaad5b33e3a4dfd">f662b48a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-13T18:52:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1d9aa4204ef7ef325804e1cf0e1cde58ba8f8bf2">1d9aa420</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-13T19:21:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added tilt test option to tilt_fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2460092723187c0b092594a73674515bfa9e4681">24600927</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-13T19:49:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed aniso-tilt bug in reconstruct_openmp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0e9904d66d6741717d9cd20d04f495fa0ba6b9b4">0e9904d6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-13T20:02:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Write rlnMicrographMetadata column to corrected_micrographs.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/22ee8144246a642890334fc3da210e33625afb22">22ee8144</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T09:40:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">attempt to resolve conflicts to sync relion-devel into relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/171b9a110e80bf59b11b7b7af560c8b50d86a5c3">171b9a11</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T09:41:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f77abbe50edf79fc02c4b7f12aba31e576dc68b0">f77abbe5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T10:32:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolving conflicts from merging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/44e3f26310f321d45d8b552968295dd57d55d939">44e3f263</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T11:54:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolved conflicts after merging, still need to test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9daca5c2130377d913919af3b5adb05838e13eec">9daca5c2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T11:55:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tried to solve cuda_autopicker after merging, but failed to do Mmean calculation. STILL PENDING
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/967fb1d590805379c81ca1824dee001396581030">967fb1d5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-14T12:04:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Save aligned but non-dose weighted micrographs (--save_noDW).
This flag is always on for MOTIONCOR2.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4210f81c88d5df8eb81d4827b3aab5a98a0575f3">4210f81c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T12:24:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">change GUI colors to orange for 3.0 alpha version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9831f6830867dc3d8463fab1ee3b40ce6b518098">9831f683</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T12:25:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hide amyloid picking from the GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/767c6f7265a345b5d27ade749bc4b001d51ff36f">767c6f72</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T12:52:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now have Mmean working again in cuda_autopicker.cu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58dbf2ac4cf2376b7cb27554b8299d4c3de5c55f">58dbf2ac</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-14T13:57:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">global aberration plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/14428517b07b4ea56840ba3f856960b8a646845b">14428517</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-14T14:02:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">global aberration plot added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3fd51ec2cf1a65906747e5e1d1b82571f94fd1d7">3fd51ec2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-14T14:06:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
Resolved Conflicts:
src/apps/CMakeLists.txt
src/fftw.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c38e62f4da0dc574f83087c2a4d88854f3648b8">3c38e62f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T14:13:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tiff (pull request #7)
Tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c7a97fe24ae45ce875b5cd6ed680e502c639dcc">9c7a97fe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T14:26:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add option to skip padding to multibody refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/127cf52348943aa34410ed0a57bc41420ef3ccf4">127cf523</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T14:28:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add option to switch padding back on
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be9180c9514d41f33ba191ce7dff3c1f55f96525">be9180c9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-14T15:04:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added pixel size, voltage, pre_exposure and dose rate to the micrograph metadata.
Fixed voltage (it was always 200 kV)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/32e3def54ee0d2a19c8eb4dff475daba8ce93e95">32e3def5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T15:32:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired cuda autopicker after merge. now confirmed tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bb7dd64bf41186fb69cdb5ad8259ad8fddf8bcd8">bb7dd64b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T15:34:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed debugging statements from own motioncor implementation and reactivated threads in GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9b8e5d688693a770424ddd20055a55256f343eb7">9b8e5d68</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-14T15:48:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added reference-based aberration plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1345469b2d2ee9d8cdaba691df427a65eea8a234">1345469b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T15:54:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tidying up multibody jobtype
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/09bcc9036cdb8eb884d2adead829bbb2e5557529">09bcc903</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-14T15:59:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moved shift calculation to MotionModel class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b166369c9552d881894185f247d4c8294b0c29f8">b166369c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-14T16:10:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
Resolved Conflicts:
src/motioncorr_runner.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7decc4056f1da030a71b12607144ff86c7456c93">7decc405</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-14T16:21:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in reference-based aberration plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/644eed76a8f05614d68bbb976133128f462da5ae">644eed76</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-14T16:52:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix 2 in reference-based aberration plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a5f7c3c1a48b32100b433213bc91aba947e1bf0">5a5f7c3c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-14T17:28:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Write fitting coefficients.
WIP: Reading needs more work.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/910945303d1019be218c5812c651dffe0e6b009f">91094530</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T18:48:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write to stdout that we're reading optimiser.star to prevent apparent hanging of multibody job
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61bae3adbbe4f664866d63e43dd145ce41c78abf">61bae3ad</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T18:49:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired dangerous bug of mixing gold-standard half-sets with new subsets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b9893c19a6efe6a2e6bbff16fb7946272bc00aa7">b9893c19</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-14T18:49:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added gold-standard test for bugs in acc code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f6425eba079192372ee47ebbf95e0c65d38696ff">f6425eba</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-14T19:09:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added relion_recombine, a greatly simplified version of relion_recombine_frames. Removed deprecated parameters from relion_motion_fit.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7436f2653f43891db0d5f4ee6c360de8f5f622ec">7436f265</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T08:44:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugged new io of postprocessing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0a86fe7431b89294da8ccddb0aac5e17b9a0e0b9">0a86fe74</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T08:45:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed handling of randomsieOriginalParticles call
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a1f3e6ac95f9aed4a6c943c8b68ce52af92cfa1e">a1f3e6ac</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T09:27:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed very old jobfilenames in pipeline
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c44ab817d690f43b8b00f4fb5afeb84a41213efb">c44ab817</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T09:28:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">in chronological order: show job nr first in lists of jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16cf61fd933ac7a764d25164c005ea08d4c05391">16cf61fd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T09:29:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> removed coreAllocate and DeAllocate of backprojectors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d3c8598542ab04644f94cd19e346c1104d83781">0d3c8598</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-15T09:44:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hot pixel removal added to movie refinement programs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ed122c9c438f03b84cd875b7775cfb168802cf0">5ed122c9</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-15T09:49:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hot pixel removal parallel again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/50ce4806ccca9c89e2bd73d9d1782ff5a6cb3466">50ce4806</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T11:24:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in ppipeliner of multibody
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02eac8a1783a7d6954581aa138bbf2deec87a72e">02eac8a1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T11:32:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try to repair bug reported by Takanori about decomposeFileNameSymlink
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c80e8ba06dcaf32c5deb15ad11cf4c9817ea7d85">c80e8ba0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T11:34:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try to repair bug reported by Takanori about decomposeFileNameSymlink
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/39234bf7cab7cc2c33366413a2fdf23aced2adea">39234bf7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T14:57:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">store ints as longs and floats as doubles in MetaDataContainers
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/435b9ced983203677145db466e064356eb813dbe">435b9ced</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T14:58:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired old debug statement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/005fd0a7c92f3f3fdfc6f2dec1a398bcbc3b0e92">005fd0a7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T14:58:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">raise errror is not enough particles for PCA
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d090c8503cf864922fc3fd69738bde5091e053ec">d090c850</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T14:59:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added flex_analyser to MultiBody job type
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b78e788852f98756748c25b8b7eb79279f1f121">8b78e788</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-15T16:22:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added ctf_tilt option to reconstruct_openmp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/33ddc6209f27ddc14cc50c3eaaacb08557f97757">33ddc620</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T16:56:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">swicthed tab 3 & 4 of multibody gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c027ae833b95cbc8a22de8a530974bfe6a1404ba">c027ae83</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T16:56:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set minimum step size [progress bar
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a36bcd67792baa1df58da32d2c1510abd17a6c15">a36bcd67</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T16:57:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> set version to 3.0-alpha-2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2d24f9e55f4f671b12d3f2908ce7b30f4f6a5b14">2d24f9e5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-15T16:57:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired outputnodes multibody jobtype
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c7c6bef7e8e3dcbaf7d8afbd1d3cad827912f570">c7c6bef7</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-15T17:40:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in ctf_tilt code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29f52415267d2dc41b51a81a49785c5bfd5dac3c">29f52415</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-02-15T20:23:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac7aa06286092f3e569bc6f28070fd8e34050d51">ac7aa062</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-02-15T20:40:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reverted expectation memory free-ups. This was never a good idea anyways since max memory utilization is during expSetup and maxim.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c141ea618d82eb8064451e585df49101c5ab2ad9">c141ea61</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-15T19:41:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_tilt option added to defocus_fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e2481c277b1ee20a404217ee26eae42f996728e9">e2481c27</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-02-15T20:54:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Don't raise signal in release mode.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3260b96faaa5433cf5376ef6d2600a2838251f4a">3260b96f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T09:01:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resend data_vs_prior for each body to all nodes in iterate
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4b4b964384c75e951b02c18208272d38038915b8">4b4b9643</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T09:01:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">also show job number in current job field
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/882a962ac5f601e5a414be677b77632bcedb6497">882a962a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T09:02:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set minimum number of movies in slidebar to 0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a4b4bf1dbc4784543b0396ac40267943cd6471a0">a4b4bf1d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T09:04:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #138)
3.0-alpha-2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e11326d832e5e3105bf7f01fa09ee655f0e8caf0">e11326d8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T14:59:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired error in filenames for flex_analyse command line generation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c4c45691910281be62a050a6d5766aad6f217977">c4c45691</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-16T18:12:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Draft duplicate removal (WIP, does not take effect)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/38d4695c38402d916d7ac16553ccf1d5ff030c7e">38d4695c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T17:33:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed forgot button and repaired nasty bug NR_BROWSE_TABS
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c8f3b5732e15b153513b2c3ce0a83e6952422b09">c8f3b573</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T17:34:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont move away old nodes from initial model and multibody job types
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d56c8a14d3303e0f405d6a8bc93f4f56da9da448">d56c8a14</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T17:37:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/729e7fe5159322fd121cf7d404466e4468af4460">729e7fe5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T17:38:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #139)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ae44a61441fea3b625cfc4c40371e8f3ea97df39">ae44a614</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T17:47:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">deactivate buttons on initial screen
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/464dc72fe4fbde16896148f279daf822efd24d8a">464dc72f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-16T18:30:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cannot deactivate other buttons: will stay that way
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0553c6ac5a54864c47e8567a9ecbef08f004ae28">0553c6ac</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-17T16:34:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">phase shift / amplitude contrast fitting and extensive diagnostic visualization added to defocus_fit; tilt removed from ctf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dcfd27da36d208bc91df9b3dc5c64780223b1ccc">dcfd27da</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-17T18:27:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added experimental Cs-estimation to defocus_fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c02ea23e573f8fa1b11a19c19ad8a0344cecc64">9c02ea23</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-17T19:28:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">start to port Jasenko's defocus_fit and tilt_fit into a single ctf_refine program. MPI doesn't work yet. tilt-fit gives an ERROR. work-in-progress
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7861f6d714ff7cd093760e2e4484865421ce9061">7861f6d7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-17T19:28:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jzivanov' of https://bitbucket.org/scheres/relion-devel-lmb into jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d3ef6e6f0b077d5b6e2b36aa851f2aba20c13840">d3ef6e6f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-18T05:55:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">deprecated ctf_tilt functionality removed from ctf_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5f0e8e4484e14cc92be86fd7a06b79255052db42">5f0e8e44</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-20T15:48:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new experimental aberration plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/af8ce3c3821aa1922037de0a1d021cd608e84b0b">af8ce3c3</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-20T21:09:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improved aberration plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5523f0b5d1bb5c9859239a7c2b864bb00530e85d">5523f0b5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-02-20T21:44:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed sign in aberration plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/98a7eba09c19f59348d5d470ba3cc8af81e11644">98a7eba0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-22T14:00:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/35b58c5912a56ba2cfae361615df6c23d3d54f5e">35b58c59</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-22T14:08:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9df91cb443389aeae43ca5607a41813f5ac95cf6">9df91cb4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-22T14:12:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed TEST VERSION warnings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/503eef5b37be3af3cb332a47a14dcc2c693d6fb3">503eef5b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-22T15:00:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> bug upon convergence of auto-refine: combination of multibodies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/231c0b2fd0271082872d26924d876442fedb601b">231c0b2f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-22T15:00:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">report resolution to one decimal only
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/247e7d60e182ce9ec67357c0b5a19f71b0f095fe">247e7d60</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-22T15:27:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed error in multidimarray when not necessary. Somehow this suddenly caused crashed in refine with GPU...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d4e09b27d755dcaa8535e924274df92e820e5f0">6d4e09b2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-23T10:06:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed --do_fast_subset sizes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/abba3c680d4e391c9a8e704643e8067aeead6f28">abba3c68</a></strong>
<div>
<span>by Dari</span>
<i>at 2018-02-24T20:21:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added print-out of version and build-info at the start of some important executables.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/48dd2b5a38c557a2db79baf16ad7e4fcd17ea076">48dd2b5a</a></strong>
<div>
<span>by Dari</span>
<i>at 2018-02-24T20:28:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'remotes/tcblab/relion-devel/master'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bceb88b4f8273441571961ffe886afce9f933183">bceb88b4</a></strong>
<div>
<span>by Dari</span>
<i>at 2018-02-24T20:36:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed compile issue for scope of isnan().
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4302b959c69efaff1f55979ca434904afae6762c">4302b959</a></strong>
<div>
<span>by Dari</span>
<i>at 2018-02-24T20:44:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed build with RELION_SINGLE_PRECISION defined.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be29959e4f219c92acb5da9a2f1d0cd8959ded82">be29959e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-26T12:21:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug FSC higher bodies in last iteration
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84cc659d036d7c10c947002a1a8063219d79664e">84cc659d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-26T12:21:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">put amyloid option back onto GUI for autopicking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2d93807ef5bf23d8e68f26df95681f39aa08a85e">2d93807e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-26T12:22:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d1d83a5aff033bf2ff7c857def04b92311bd512">9d1d83a5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-26T17:09:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">OpenMP parallelisation of relion_mask_create (--j option)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/469428c75de699ca0db57f7caf92ed72aa0a6cb8">469428c7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-26T17:14:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bd89d4f4260d0b9a5e66951978ec21dbbe51ea9">8bd89d4f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-26T17:20:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add threads for maskcreate jobtype
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a1f9daebda7e24242fb119cfd9ee6090e7271b7">6a1f9dae</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-26T17:23:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added --j to relion_mask_create command
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/603b392128b4c66e25b183e700db1df19c152c8a">603b3921</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-26T19:40:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">own_motioncorr: write a log file for each movie, removed a duplicate definition of --j.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5479ff5f77020340b2e9bac3be1758e8957f97d1">5479ff5f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-26T20:21:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Read and write local motion model.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f004e14570cdbe135daaf4a4c4e5dc648a98d3c">9f004e14</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-26T20:21:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42fc2eda93ddfed8c2cc1632259dbbbef7858b4a">42fc2eda</a></strong>
<div>
<span>by Dari</span>
<i>at 2018-02-27T09:20:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Alternative merging scheme for overlapping multibody mask regions.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2aab21a4524c7cccd7d0027d408a979b1a2a031e">2aab21a4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-27T09:11:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed suprious debugging statement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/71d75c85e7e86eac0ab305805f77c0f453d4bbb4">71d75c85</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-27T11:42:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b9325af4e26ceb136958e8f7f8efb66cdd1c899">7b9325af</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-02-27T11:42:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Version print-outs are done on MPI master only.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/91af1d95096077222e89a594a1d01ac0a52e9af5">91af1d95</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-02-27T12:15:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Droped the discontinuity warning.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/20765a15f4882b35d06d793801a45a18c787a2b2">20765a15</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-02-27T12:49:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Max box size warning adjusted by padding_factor.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1da2b38271886f75c07a5dff79ce256b7b3366fa">1da2b382</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-27T12:18:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Skip patch alignment & real-space interpolation when patch_x and patch_y are too small.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ae126d8799a34382d8394ad691ac2668068a0f57">ae126d87</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-02-27T12:23:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added warnings for non-implemented features.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be306e7d3ff9280ceb7aa3ce74155758db4642ce">be306e7d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-27T13:34:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixes to helical on gpu-noise
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/916a554691a754ff38b2dc5ff03872c2cd6afeb2">916a5546</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-27T13:35:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/83afe0d6d3eee0ae9704a86410ef2c80bfbe51b9">83afe0d6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-02-27T15:43:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Segfault fixed (one-liner)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f798da6e998fff5b7859da59f5c46524d17f5d1">3f798da6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-27T17:59:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">get/setHost methods passes multidimarrays by ref
These methods are currently only used by the helical code where
GPU-side functions are missing and we copy down to host-side
temporarily.
With this commit, the helical tag-case test works ok. It
became broken in commit 14e38cc.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1e76f6cbeae67bcce78729c1437d00003f50276">f1e76f6c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-27T18:02:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16a3dddf322ed87f65ca35c2a1299a610309d19e">16a3dddf</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-27T17:36:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #140)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd7e9e6d1d41d50c0db966e643258a4417c90da6">dd7e9e6d</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-02-27T18:57:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added tag_case test targeting helical (zero-mask)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c7debcaa5240625dc59f0e3f3081ac717a1e5ec3">c7debcaa</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-28T09:34:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d51661dca3c25476cffa4f32ffe3b533fb6cb4f">6d51661d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-28T09:40:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolving conflicts after Bjorn repaired error helical class2d
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2fef87dcc560e25f82953336870f0fac021c2026">2fef87dc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-28T09:48:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed TEST TEST statements and renamed VERISON into VERSION
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ab433564348c53007b13c2d53e507e8b3d17e0da">ab433564</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-28T09:49:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #141)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/640d80fefea486c077736893c20c051171513489">640d80fe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-28T10:04:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed do_remove_duplicates suprious entry in extractjob, amd added little spacer on select job gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad1dde3193fae591785687087877068df09e4263">ad1dde31</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-28T10:04:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd495de87c6420ecda5bba7878854df6628be034">cd495de8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-28T10:05:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #142)
removed do_remove_duplicates suprious entry in extractjob, amd added little spacer on select job gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ece17c961c207fc54108dfd036fbf16e6063ab1e">ece17c96</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-02-28T10:05:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/336d263e140cde80c84782e9b656cf156fab086e">336d263e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-01T10:01:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed VERISON to VERSION
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/405a2ee3d6947b52d880d4b486961e97ebc67e96">405a2ee3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-01T15:18:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed GUI to support local resolution estimate of body reconstructions.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47311f7401159bcfca0e9ed4c765deaf82058c14">47311f74</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-01T16:26:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Started working on frame grouping.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d3c548d2e90595853237c3aa3dade24019ea5cee">d3c548d2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-01T17:03:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Frame grouping in local alignment.
WIP: RMSDs remain rather high and convergence is slower. Need to try another approach.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b14ecbe2e3ac1698dab307b0f23481763c5b0586">b14ecbe2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-01T17:53:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Another approach to inter/extra-polate.
TODO: test which is better
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a39e7a308db94c7bf81cf948e0b8c75801d8ee1">1a39e7a3</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-01T19:19:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">phase fitting implemented in ref_aberration_plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/031cdb2e41ce081acc9bf1f55cc74037c5cc691a">031cdb2e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-01T19:21:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added missing files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3de1250d523b5ff26f48b889c0e7588848aeeaa">b3de1250</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-01T21:31:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">aberration plot/fit improved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/910e66ba44c349c3af74eef407e497f57167a033">910e66ba</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-03-01T16:36:42-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Attempts to use std::complex for projectors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/499088fc9f8cd38ed77872eaf4a7be08d7273b2f">499088fc</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-02T13:45:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed interpolation. No need for special codes for extrapolation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4beacfe5cd89c1aacb66dd1591d5aa5276ac6105">4beacfe5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-02T14:54:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tidied up interpolation of shifts.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dc1970ff07543a2a0ab6fc4f6ae97532f2a52b3a">dc1970ff</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-02T16:42:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed uninitialised first_x in 1D->2D backprojector
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e2bff2cf0924b592bbfff242822273451f489e1a">e2bff2cf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-02T17:06:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug allAlloc -> deviceAlloc autopicker cuda code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b29a221da1f6d133bf65caf827cf3e10bbdfb8c9">b29a221d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-05T01:34:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">additive astigmatism in defocus_fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5c4c7dd0d1c20eaea5df7efc60497c9552edfd71">5c4c7dd0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-05T13:00:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Respect n_threads in mask_create.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d3ca5ddf6d9a23390dbe35c999385f47d1d8e904">d3ca5ddf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-05T17:17:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired dirty bug in helical refinement, reported by Jan Lowe
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ba509b7c22bd458dc7a181239c48856bcca89ff">1ba509b7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-05T17:18:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired dirty bug in helical refinement, reported by Jan Lowe
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cbcb8fe7cb3498ab9adecec8485736ea5b9c2ef4">cbcb8fe7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-05T17:18:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2cffe77e5fccf810353f007ff3502a435297a31">c2cffe77</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-05T17:28:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added comment warning about bug reported by Jan Lowe
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c2910c6e04838421b9fad772827ee2ac96b3dc3">0c2910c6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-05T21:14:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MPI parallelisation of signal substraction in flex_analyser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58434d67e1d4b29ae9532c31499ac6071fe58e50">58434d67</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-06T17:53:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix libtiff linking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d32d41662108f47468df30eaf5b6328671ad15f">7d32d416</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-06T18:10:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged with tiff branch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3004d150d5b954e29cb5bb9418b2192eb8841e56">3004d150</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-06T20:02:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #143)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/311e8a13b28994315ba4cbb028cc47407c16b298">311e8a13</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-06T20:07:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">movies are now being loaded frame-by-frame during extraction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/524297366252b247f71fc94e25e9426119294718">52429736</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-07T02:35:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">binning parameters replaced by pixel sizes in motion_fit; all binning types besides Fourier cropping removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3630db6cb705a92f98f3985fede884fda0dab894">3630db6c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-07T03:35:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">std::numeric_limits<T>::lowest replaced by -std::numeric_limits<T>::max
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d338ac0eb77d690e4c15191b45b40463047c4d1">0d338ac0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-07T09:38:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">some more shifts 3 to data_dim changes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64341b3ce398d024109e875331ed7e2fd501395f">64341b3c</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-03-07T13:14:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9fd79ca47546baf8f41fa75dde5ee0e4f534c05">f9fd79ca</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-07T14:32:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added center of mass to relion_image_handler --stats
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7129507f36f44d37a86b0f4543b4f9b9e0133c61">7129507f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-07T15:46:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca0db35c133fc295a8c81920ca1d15df0ffd3970">ca0db35c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-07T16:23:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added search-and-replace hack for movie names
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/405c4bd4f1209203190bc636bf0726ea5885a50e">405c4bd4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-07T16:40:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">search-and-replace hack more robust now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27012c9f5531357b02a74b4633df54699104cb9d">27012c9f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-07T16:44:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed frame numbers when --first_frame_sum is not 1.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/acd22762e1d2f29caa98cb18903669a8895ebf2d">acd22762</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-07T16:45:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more debug info
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1a2463ea6f4363df96aac9c142b49a6c8f81f45">f1a2463e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-07T16:54:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Described why we don't scale x and y in Ewald sphere correction.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e3c99ed8e062423d361fb7b7044a0e5edf9856a4">e3c99ed8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-07T17:30:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added support for particle coordinates given at micrograph resolution
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3730be5297db63745747b1b319b0cc425d98cf79">3730be52</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-07T17:34:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Combined map from relion_postprocess should be in the same scale
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1155af71982ccffb616477dd2e4552642e13c521">1155af71</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-07T17:35:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b229f6bbdb9d539d89bb1bc2939714ee1017a39">6b229f6b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-08T11:27:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Don't complain about angpix for movie extraction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb99c5e8a7274396984ded8ebafd0ce588a4a7ad">cb99c5e8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-08T15:10:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">B/k-factors are written out by recombine if --debug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/921218df3c366aca3c8860b3cf5bcb61e9982e23">921218df</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-08T16:52:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">flex_analyser: re-center to the COM of the mask, combined STAR files from MPI slaves, removed unnecessary codes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d775c25d7f1750045a2db6cc5266651a35335bc">0d775c25</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-08T17:00:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tiff (pull request #8)
Tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d9ba5525859c220374e698d1046c2fc363dd13d">5d9ba552</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-08T17:01:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replaced error of normalisation check with a warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cce8c9900f082c09205fa79425a4f8e2eb1bf069">cce8c990</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-08T17:02:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e055959f21c9f33014320c0acec78e42e7b9513b">e055959f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-08T17:10:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replaced float for RFLOAT for many shift vectors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dc68a368c104a8fa9155155c994e12561913b4be">dc68a368</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-08T17:26:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">freq. ranges now given in A for recombination
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a7e01a200da43f053222097fe9dc60e1141ac97">6a7e01a2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-08T19:45:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">No residual offset in flex_analyser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b750025b2cdad93d57c1b097fa1ffa8c3b36d42e">b750025b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-08T19:47:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge commit '921218df3c366aca3c8860b3cf5bcb61e9982e23'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce6528d412dd92375c0bc72e66959b4823fdc00f">ce6528d4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-08T19:48:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into flex
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/399b11b65e7962628c1b92cd339322b4bec0eabd">399b11b6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-08T21:22:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">flex_analyser: removed one Fourier shift for performance.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/325ec705de091ed40ffff701a8e4b086773751e9">325ec705</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-09T02:14:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit parameters now normalized by pixel size and electron dose
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bd3a717f528e20865d8c5e4c700baba161cd823a">bd3a717f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-09T03:21:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed default arguments for motion_fit with normalized parameters
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/024070867cbb4dcaf69d2493c3d98e76d1f320c7">02407086</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-09T04:32:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">movie pixel size parameters now separated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de1af8dd79130b4530a993182031569da906c0df">de1af8dd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-09T11:47:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improved error handling when noDW labels are not in input starfile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c994f255a7bcfd660e77ef74b82a434bc231c9fa">c994f255</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-09T15:39:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">own_motioncor: improved error & warning messages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/14b49d180308ff0d890a43ca3379a7f6491b8d63">14b49d18</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-09T19:59:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed logic with noDW
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a2b007ded9ba3568e78e8c129b5bdc3c3f6374c6">a2b007de</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-09T20:36:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed SEGV when save noDW & do binning.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/79015470235f8b18451fb49d0dcc0ff8f8120470">79015470</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-09T23:13:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed SEGV in binning. (see code comments for FourierTransformer pitfall)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b466bc2987ada04ea1d225b98a1e8e72a0d6146b">b466bc29</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-10T11:09:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed binning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ccd600bb51107b0bdd554db324e95dc42476beec">ccd600bb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-10T19:24:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Convert Unblur trajectory from angstrom to pixel
PLot local trajectories from MotionCor2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3d61e256781f77eca0a3d4f6318ec554c1377cca">3d61e256</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-11T03:54:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in motion_fit; added option for unregularized global motion and distance threshold for divergence term
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6fc196902395bc69084257cc4fbea28f62c8d30e">6fc19690</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-11T20:09:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added support for custom frame ranges; input dose is now per-frame
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad1d3a9821557799a5f3e7f09525f0245804bd85">ad1d3a98</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-12T01:21:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tilt_fit now writes out a *_particles.star file with the estimated tilt values
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aa73117737225da8fa1bc701fbbe6751bd992bc1">aa731177</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-12T02:21:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in recombine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0cd95474106159f8e48f1be73b41207c197c5472">0cd95474</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-12T03:02:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in reconstruct_openmp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/862a4a15047af44c28f7fb8535e60b2135656cc3">862a4a15</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-12T12:28:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow reading/writing backup_selection.star with information for liyis project
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f35762f44f2c130ece22c2297294aebe92755570">f35762f4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-12T12:29:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b99cf738f4d816221e46c7af7c8147d435602df">6b99cf73</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-12T12:29:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow rescaling output 3d maps in flex analyser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/690ba830e716e3e8f280243d7e0dc8163ce47c8d">690ba830</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-12T12:45:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_postprocess: added a hidden option --seed for testing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/80068bd8f076e95b6cb3dd6e4bb220ab86a95873">80068bd8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-12T12:46:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84e6b06864d306d94da514e14b730f4f908b850b">84e6b068</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-12T13:53:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_image_handler: COM calculation moved to --com from --stats
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9de2d2147117e96d02ceec3d05d266c3c3465a64">9de2d214</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-12T22:48:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed debug output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/53cf0f3e4997016125653897ba9068d67782391a">53cf0f3e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-12T23:11:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">preliminary merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/62f68d735ba34c76743bdc3f3c84d931d30370e8">62f68d73</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-12T23:11:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/tiff' into jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb8f8a4f70fe4c394a309e58bb66032ef751e392">eb8f8a4f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-13T01:03:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added support for corrected_micrographs.star to refinement_program
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4bff2eea11c998b6573609cce4b655ff854b0fbc">4bff2eea</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-13T03:19:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in motion_fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/93054667e67145fc66a9c712e461a89a5a276b60">93054667</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-13T11:07:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/724d06d46a4e83512b11a49b7141b33709095526">724d06d4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-13T11:08:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #144)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0478656918a4c5cc5efb65a87e1ac9d05d5d020d">04786569</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-13T16:03:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in refinement_program
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/74ad5e63b682b4ef7eda9b7e00dc8fab6ed2b29f">74ad5e63</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-13T17:47:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cherry-pick Jasenko's Micrograph class refactoring
Conflicts:
src/micrograph_model.cpp
src/micrograph_model.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01ebe42b73f1aae3e832c42d9436dc79e701f8be">01ebe42b</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-13T17:59:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cherry-pick Jasenko's Micrograph class refactoring (2)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b88e1ae958eef59da70888a5698123da9e0349b5">b88e1ae9</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-14T06:43:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added (center-weight) prior to initial per-particle offset in motion_fit; this prevents confusing particles with better visible neighbors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0762c909a590a14d0ce5c42cfdcb7d5e0931de28">0762c909</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-14T11:35:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit accelerated (initial particle offsets parallelized and made optional); some vtk output replaced by general image output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2404953f93d671ec42c9738f948a96575691f195">2404953f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-14T11:37:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/146acb983e7fa5399942497276aa6a24de38feb3">146acb98</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-14T12:56:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">all vtk output in the applications replaced by generalized image logging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dc95a8989d062cdc00899a56559fc164cebdc439">dc95a898</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-14T17:00:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_display: Initialize do_remove_duplicates to false
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/edeb1fd38020ac5de06a53faabff90689096af76">edeb1fd3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-14T17:12:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e2acd9559851ce9a02e5f9eac90f7a71af128431">e2acd955</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-15T17:16:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug with MDbackup in displayer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f034a91f71ce5f4c1fdfd1ae8098a54b2a928cec">f034a91f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-15T17:17:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">always perform 2D classification with pad 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cbb852957319285e794ac1db6132e8e6e42b1389">cbb85295</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-15T17:17:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1693f353aba2f1e30af5aa7b8fb68857c186e8e1">1693f353</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-16T08:42:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit heavily refactored and parameter estimation option added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c6d989836fa19dfb29c84ecf191e17f14679cf13">c6d98983</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-16T09:16:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit parameter estimation improved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ef592b8caac4b9d7f7ddce346ec5c68858d2b0f">8ef592b8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-16T13:58:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit parameter estimation: quadratic extrapolation of optimum added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4193be69307b8c30fe5821f96885816806d288dd">4193be69</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-16T14:49:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow multiple color selections in multiviewer display
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fa5ca1210acf3b79da0e976d6107370a5d60c1a">5fa5ca12</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-16T14:50:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed position set selection type in popup menu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b2e4d2d6d887ef76698e1f3f885eec46fe02d7e">8b2e4d2d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-16T15:35:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont need to specify fn_imgs or fn_parts for loading of backup_selection.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/76ba73ef3e1f2083956c5c2170b2d8f1b720cd16">76ba73ef</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-16T19:27:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit parameter estimation: bugfix in quadratic extrapolation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ccfed4d299194375b09cc2227431da615217b19">3ccfed4d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-16T20:37:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/82c86b329dcebbe2c50886c6c4b2cc0137a0774d">82c86b32</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-16T20:48:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: always treat .mrc files as .mrcs files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a0240cb23fdf6348d6b523030203c9005563f1ad">a0240cb2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-16T20:58:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed file handle leaks for TIFF
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ed74c86f9adb13e03e65719daf98d4e0f348e0f">1ed74c86</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-17T15:10:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">progressive 3x3 grid search implemented for motion parameter estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f46b9e7f1af2e87d4cafa372e40a13c2c2ec07d">4f46b9e7</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-17T15:32:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion parameter estimation console output improved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/39df208eefdec705aea771d8dcaefd1b46c402a4">39df208e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-17T15:50:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Avoid crash in very bad movies. WIP: need to think about more robust way..
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ba78eadcaccb81c362019dfc4f2aa235f20b5b43">ba78eadc</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-17T15:52:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in motion parameter estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce7a345e7e0f37c95b20f3d276497a5dc82a07f1">ce7a345e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-17T21:20:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reconstruct_openmp now survives missing images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ec75770ddb7128964e2119222d98fc96da6c78c">6ec75770</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-18T07:01:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_stats added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/99dbe406b85f4ed6386879a9ae376fa6360f3c73">99dbe406</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-18T07:02:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_stats really added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e3772262f4210ab78304d36f93d016e9a528d234">e3772262</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-18T07:17:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit can deal with non-positive parameters now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ca4201f8988bfef1ffc5dbc3b96a30a17978e69">1ca4201f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-18T07:33:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfixes in motion_stats and recombine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c13ad5e7fd1ee51f8b7496343b6888265448d8d8">c13ad5e7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-18T10:28:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">--use_own does not save movies.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc0b523b29f85c46db0211f3be1954c98645e066">fc0b523b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-19T10:43:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34cc75c23238967ae57df0dbdc25463c6cc40798">34cc75c2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-19T10:44:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #145)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/49caf151c622d90e2363d7e744039284cc7e4b4c">49caf151</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-19T14:24:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add command-line usage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/253353dbdcfb08316297f968b7172c1cb39236d5">253353db</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-19T14:24:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b77940ff57d68233b01a777bc3657806c0ec9495">b77940ff</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-19T16:40:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added wait_before to pipeliner and usage function in CL parser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e53011bb1829489fc311267bf09c024ce1a2f89">7e53011b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-19T17:05:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix bug in interpreting links in the "browse" button.
Previously, a link from "mask.mrc" to "../somewhere/mask.mrc" was expanded to "somewhere/mask.mrcmask.mrc".
Now the link remains intact.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0a0636a614768e70e217635cd7271145e05a01ee">0a0636a6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-19T17:08:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c713c9bb5a4dd59dc577da8b3bebe181261ba80">0c713c9b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-19T17:26:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugged new --wait_before option in pipeliner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a6029fad8d9a76fe86811e0b8f4139f167b323b">3a6029fa</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-19T17:30:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added --check_job_completion option to pipeliner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f10f61cc1c5d628c3cc3341d24d7d6ead83c77b5">f10f61cc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-19T17:32:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added --check_job_completion option to pipeliner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8ecb372314218395cd822ab254bee7455dc90a9">b8ecb372</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-19T17:33:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #146)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e8c231e2984fc15f536263f6eb0e8155eab12faa">e8c231e2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-20T12:46:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9dd67689f7cc160e782bc11a9fac092197548e28">9dd67689</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-20T12:53:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolved conflicts upon merging in jzivanov branch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/99df682f362bab9f35490724cf8d299c4d957521">99df682f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-20T12:54:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a9eebf48321426392b8378c02c5580a8a1ecdc31">a9eebf48</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-20T13:02:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">intoduced underscore in EMDL_IMAGE_SIZE_X Y and Z
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0253bfce3b2aad6b1665994337431f553df89277">0253bfce</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-20T14:01:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/074fc027998c9d9c9fbd25568fef94d7fb4693d7">074fc027</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-20T14:34:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Downgrade from c++11 to c++0x for compatibility with gcc 4.4.7 (in e.g. Scientific Linux 6.8)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/144f8250d7888cff99efee881801de0c55dc2f44">144f8250</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-20T14:39:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c463efca7c2211abc409b65c1c76867b2e90d33b">c463efca</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-20T14:40:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/567e6a087b4f2e81eeeda04bff8e66dc490096d2">567e6a08</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-20T16:41:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">made MPI version of reconstruct and moved code to libraries, also removed debug statement from backprojector
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1b1b6a97d8db3f7e63f71178a80863152cf96d99">1b1b6a97</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-20T16:41:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47e30942db2110ab5f34bb331ce70c778250cf9a">47e30942</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-20T16:55:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add_compile_options(-std=c++0x) is not necessary as we use CCFLAGS and CXXFLAGS.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/878443526acb864e244899fcaf3df5c08aae74c8">87844352</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-21T09:13:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed --j option from reconstruct, now mpi parallelisation only
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8db72c746c221b1ef8ed1848ab4051986d36c4e">b8db72c7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-21T09:55:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed annoying version print from all programs, replaced with --version argument in any program using the IOParser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/911a66352ce9e6f408ef6fdc741016b6b7495db6">911a6635</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-21T10:26:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">switch --reverse_curvature, now default should be mostly correct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/906784a2487ae2b202021913a8394e4a5f952e96">906784a2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-21T10:26:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12407d81f1a175d8b6d4e8f61cb99eece7329f94">12407d81</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-21T11:45:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Change the color of the global trajectory to blue
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c788c56308349d14959cf26d11af20542487e85">3c788c56</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-21T11:46:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d5eb869d62d8ab7f6defcc5ce9bec0008726b04">9d5eb869</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-21T14:53:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit: Gauss process regression implemented
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2a90d3a8d605b0daeb30c70df5baedf243525715">2a90d3a8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-21T14:55:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">svd_helper added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/385bcf41b3e61c6b9e2a4c7041a68fef185d5018">385bcf41</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-21T16:19:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in refinement_program
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bed06d4766db7d7e670310818e075743c76bf6fe">bed06d47</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-21T21:18:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">exp-kernel option added to GP-motion regression; acceleration term adapted to new model
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b60cea3ebc90647d80011f8013015c5d10b9b6eb">b60cea3e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-22T14:15:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tracks are now stored in .star files named after micrographs (including path); FCCs stored per-micrograph and summed up by recombine_frames
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1e860e0a4be700db032ba93263e9e3869dc6c756">1e860e0a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-22T15:50:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bfactors are written out as .star files by reconstruct_frames and can be loaded from there (instead of computing them from FCCs); reconstruct_frames recreates the directory structure given by particle .star files, like motion fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ec5d08ad3efcbaf1900cf8717e799b0a6ea08a8">8ec5d08a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-22T17:21:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The corrected_micrographs.star file can have any name now; recombine_frames now writes out a star file with exchanged image filenames (particles.star)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ada12f0d71c829ed636786682ecf5cf8e572cd2">1ada12f0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-22T17:23:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">writing additional info to postprocess.star for handover to Jasenkos programs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aef14c07c1265b5c0f42dbfc4466630acaa7c03b">aef14c07</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-22T17:23:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">writing additional info to postprocess.star for handover to Jasenkos programs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9b2a6f086bbc32c401192dd509ae48b08e712d75">9b2a6f08</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-22T17:24:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">WIP: initial attempt at jobtypes for Jasenkos programs, not functional yet
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/26b9d69c0553dc0b97a2190629d2fb7d0891f9dc">26b9d69c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-22T17:25:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">WIP: implemented latest version including Csfit from Jasenkos defocus_fit into ctf_refine, also made --only_do_unfinished and MPI version. testing pending...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ae7c2afdba26230d690f4cdf09caf703563c0d97">ae7c2afd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-22T17:26:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4b5e47aee7f63d22b2d75e9822b87ff4fb8fe7a4">4b5e47ae</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-22T17:33:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">divide data set by rlnMicrographName, not the StackName of rlnImageName, as the latter may be one for the entire dataset, for example after subtraction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe5eba0ba38679667ce0e7e1128ed93384e2dcfc">fe5eba0b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-22T17:33:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make sure output directory exists
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c11fa56fb56f66cfb2428009fb66a1de738730f">6c11fa56</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-22T21:49:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">initial trajectories read from metadata file - work in progress
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a940d6a3610652c5b288e5ea84af38a78dc0fbf1">a940d6a3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-22T22:39:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed Micrograph::read().
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16bf5f8bfd75abd02f42dc783632fda35818f923">16bf5f8b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-22T23:06:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Further fix for Micrograph::read().
Thanks Jasenko for finding this.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b8bb9685275ddd6f444478d71e0a3c043a5ac6f">2b8bb968</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-23T01:59:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">head reattached; two files lost
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/59ea13ee4de9e60971d740e6be5e0f9e4ae3779f">59ea13ee</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-23T02:05:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mrc2vtk restored
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e6ef3a26f9aa25f8693e0dd0a9c2dced42962df8">e6ef3a26</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-23T02:22:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cherry-picked a940d6a
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aaee5e74ecc478384a8722aa70e800983aa15c51">aaee5e74</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-23T02:24:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">simulated cherry-picking of 16bf5f8
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1c4e4e54283ac764d2c577e168c82195f22179e">f1c4e4e5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-23T16:18:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed ThirdOrderPolynomialModel::read(). Thanks again to Jasenko for pointing this out.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dfd27a71fad32f95c101161a17157b9a1e2bf550">dfd27a71</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-23T18:00:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">memory-corrupting bug fixed in micrograph_model; derivatives corrected in gp_optimization; slice-by-slice loading of micrographs now optional
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/867176ded1679299d258aefb4722fcd44c71d884">867176de</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-23T18:19:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">parameter optimization no longer crashes on fewer than two particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2944b99afc927743613d6784cb2cd622a5965559">2944b99a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-26T11:57:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging and further development of ctf_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5fecf2e3d5dbad79206ffe4492b8497b0b8643d">c5fecf2e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-26T12:34:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further debugging and improvement of ctf_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/822461f15eeba6925acff37bbabb760b52a93088">822461f1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-26T12:35:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/21fcb407166e85de0a27e09dcf7f9f916a2d44f1">21fcb407</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-26T12:48:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added "Use exhaustive search" option in the GUI for CTFFIND4.
This is "No" by default because it is > 10 times faster and CTFFIND 4.1.10 fixed a bug in the fast search.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6918df935b93030e04ca93dcfe6155269d833a55">6918df93</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-26T12:50:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d87139922503af82d5f8075bde014a942cb75e8">5d871399</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-26T13:44:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">pre-merge commit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/44379fdfea72c277db5202d51cf7f5092ec1c6f7">44379fdf</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-26T14:18:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged with master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a78ec9725e6aaeb4ae18d41ac2b770297b6170eb">a78ec972</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-26T15:54:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">kmin for both defocus and tilt fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64b3f5425948031c9399054ab0d79bd6fc5b88a0">64b3f542</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-26T15:54:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c957bdac115d49a58fee8e3247107c43d71860be">c957bdac</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-26T14:58:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jzivanov (pull request #10)
Jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/736599128f0ba9ab1649de3f05fb683a4c74fa2b">73659912</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-26T15:58:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c78c22470ecaaadc1bef7c07718014a0a7b7d64b">c78c2247</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-26T16:08:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed duplicate kmin definition
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a15cb5ad9bcb30fb53c453db04cce833b689c7a2">a15cb5ad</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-26T19:35:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit now allows for the estimation of all 3 parameters; parameter estimation is now recursive
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/501dd74c9de24f2e4f345dfa8176fbff742e618d">501dd74c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-26T20:46:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fit parameter estimation deals with zero values more gracefully
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ad607608ee402cb6b2b080886b07f56276ed551">7ad60760</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-27T02:06:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Single precision support added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d0b3a643a54bf39a83a2fb142733bab4454b76d">0d0b3a64</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-27T13:29:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jzivanov (pull request #11)
Jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8cf7e486686b8f82ced7479c8feb1492fa948e46">8cf7e486</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-28T11:44:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e71b03730e7fdb78e0ec1f8e184159079911027">6e71b037</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-28T14:20:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">getShiftAt(): clarified the meaning of x & y
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ea50c172fbc69cae9deb97d7579163342840ee1">1ea50c17</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-28T14:54:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Disable local motion correction when the fit is too bad.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3aed2adb49f97e49e9eddf21a879ae011a07bc58">3aed2adb</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-28T15:10:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Particle origins are now considered during movie extraction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/883fc76178f3601189ae6462fbe8ea773ab0689b">883fc761</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-28T15:24:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cleaned up ctf_refinement a bit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/46bc99229e5932082ad42daa2c4d014cf24fab6b">46bc9922</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-28T15:24:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed order grey and black lines in EPS plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4f6cb365244c6f65d0f17f79a19e36b5b6f28ed">b4f6cb36</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-28T15:26:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added motion_fitter library and motion_refine (mpi) programs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ccd9fe8ca4d7a9531f4ca0b1b4da673d773d5a5e">ccd9fe8c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-28T15:59:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make 'preread images' and 'use scratch' mutually exclusive.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/780d56e44f3732fabc80097305b9261f793d6641">780d56e4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-28T15:59:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f726ed31f46bc2965cfa65614417314c4cd2d3f1">f726ed31</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-28T16:00:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in handling micrograph filenames inside pipeline
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb27b9d2cc870ec4ad1b1740d5e78917dc325973">eb27b9d2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-28T16:01:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d2f9158abd840782b4724570d743e39abefa09e6">d2f9158a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-28T16:17:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tidy up the Motioncor2 tab in the GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cdb03926d72bcbbe00a9bcf9228ae14dc78bc4fa">cdb03926</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-28T16:19:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/10371249cb122d0bebab3e44ea9e2efbce36bcf5">10371249</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-28T16:25:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Parameter search can now deal with negative initial parameters; offsets removed from extraction again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4c122e70417251f63403b8e8b363f998887f79d4">4c122e70</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-28T16:39:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small changes to GUI for motioncorr runner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a04de3a35420875614ef641e78a4bcfff19acf77">a04de3a3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-28T16:39:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out combined PDF logfile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c7ad9cb19b07c613b18233e612b7c2314552f1f">1c7ad9cb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-03-28T17:11:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'tiff'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac004b062067b2bc8e737d26c61b72460439cf8f">ac004b06</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-28T17:11:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GP-based motion optimization parallelized
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2d4eee64371199e2908bfbef75e8cde6c59aa6f8">2d4eee64</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-28T17:56:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion parameter estimation now returns a sensible value even if it aborts because the max. number of iterations has been reached
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9ddfedf13ce0103f9fbaaa9868487e9370c48545">9ddfedf1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-28T17:57:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/master' into jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9afd23b4c22f9ffb5b39b69b044a620e2045ab12">9afd23b4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-29T01:54:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Accelerated parameter optimization implemented (not --exact_params, --mot_range); Added option to set max. nr. of eigendeformations (--max_ed)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c837227c3d4213cbed037fdb3905b2c0c5baf96">9c837227</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-29T01:55:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/699c88e406a59c96238cd33f4e2e015552077dc5">699c88e4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-29T02:16:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">number of eigendeformations can be set to the number of particles by setting --max_ed to a negative value
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5c6911d1d39489878095ff4d3be6738deca25e65">5c6911d1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-29T12:05:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> added combine_frames to motion fitter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d39fd4d8aa7c8d0cf47d5bd350f7dbe7a47b5129">d39fd4d8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-29T12:06:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/492156027731efb4a3e4a9143fb2de82abf3897e">49215602</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-29T13:37:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in 3-parameter-estimation; motion optimization further parallelized
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/96a1b0bcbbd2047cf1aa1ac3dc8a5e6eb57b461e">96a1b0bc</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-29T14:26:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in 3-parameter-estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3543b46743f1e75a13506b6b1982ef41507a58c7">3543b467</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-29T15:54:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging combination of combine_frames into motion_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2924d10f9bdada04e2949b0dddbe4c0330d9d359">2924d10f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-03-29T16:27:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write RELION_VERSION as comment to STAR files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/669eb3e61f2ea74874f727b887b18404fb1c18e4">669eb3e6</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-30T01:43:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfixes in motion estimation incl. GP-model derivatives (slower now due to unhindered convergence - 1000 iterations appears sufficient); motion model accelerated (~4x speedup per iteration); optimization interface (and all implementations) changed to accommodate external temporary storage; minor bugfix in strings.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/74618c32dc77dd17de77851907b66d147c1dffaf">74618c32</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-30T18:41:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">libLBFGS added to jaz/lbfgs; optimization code moved to jaz/optimization; motion fit now performed using LBFGS (in motion_fit)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c03de8a3d5840a2547110553cd74807a692621b5">c03de8a3</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-30T19:33:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">LBFGS motion_fit parameters exposed and optimized
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d8d6733240a798a07464edc782727b9138c20526">d8d67332</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-30T20:09:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">damage model is now being considered by TSC evaluation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/491a57d1966cf523d7b12b03743456f5d651d91a">491a57d1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-30T20:12:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tiny bugfix in parameter estimation printout
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1349384c37fca527a6bf863a831ce803947ddfa6">1349384c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-30T20:46:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/master' into jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ddce7da53d743c7227184db7fe7ed480bcdaaf13">ddce7da5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-30T22:26:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine now works on Relion2 datasets (hasCorrMic was uninitialized, --mov and --mov_replace work now); motion_refine switched to LBFGS; support for a max. number of eigendeformations added; motion_fitter code sanitized
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/523778054dc020a22a4fbe30b929fc397a3831b7">52377805</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T00:44:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">control flow bug fixed in motion parameter estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47e45b9555da9c2fcd6b9fff779bc100b9e7b39f">47e45b95</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T12:15:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fitter prepared for parameter estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3b4deaebce4a1790cf31599bfaf1ec655e9d1c6e">3b4deaeb</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T12:45:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_fitter renamed to motion_refiner, since it does two other things now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0dc245fa63d641f1eb2e9a7dcfe9fe1bf0a2dda9">0dc245fa</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T12:46:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16a02a0a799a6ae4e71728b84e7aecc73a5adcd0">16a02a0a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T12:57:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion-related code moved to jaz/motion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4329d872ef853a7e057b604ef3bda4e5fd216925">4329d872</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T14:04:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refinement class renamed to motion_helper and reduced to necessary methods; some deprecated code moved jaz/archive (not being compiled)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e6735e5f406f1080d0b3ac8c0979522820bb9389">e6735e5f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T14:05:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1b33349f4e230af72bcc9c053d90a7e0122c10e1">1b33349f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T16:01:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion estimation functionality from MotionRefiner factored out into MotionEstimator
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe8c171ef4fa7a3c4419c294cb33ddc7556ef995">fe8c171e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T18:17:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MotionRefiner refactored further
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/46d6bacdd3c56cd759afc167889ba8a303f5c16c">46d6bacd</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T20:07:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">frame recombination functionality from MotionRefiner factored out into FrameRecombiner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/59809daef2133304d3f266ec557a6677fee7ffd3">59809dae</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T20:09:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d6b2eb588c5a45f09954f2eb69b4c3fc7aa753a">0d6b2eb5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T20:55:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">preemptive bugfix in FrameRecombiner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de3a310c5581df82f2ef54b6011e64d372f444f7">de3a310c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T20:57:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">unsaved files updated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/99fdefa3078d393b20d6bef2da8fdfb901b84c73">99fdefa3</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T23:50:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refinement further refactored and debugged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5a2178d0788c15e81989263d4702b40130adac9">c5a2178d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-03-31T23:54:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tiny bugfix in motion_refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7116865068466eb1ed37c033e86d30cb4c5402ba">71168650</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-01T04:25:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfixes in motion_refine and motion_fit; results consistent again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad394c15b7bb46469dd3e3b6a715e2213c5766c1">ad394c15</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-01T19:36:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">preemptive bugfix in obs_model
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/054acf1fc34712c2c61daf368a2ad8a4fb98a9bc">054acf1f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-01T21:48:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">freq. cutoff for motion estimation at .143 FSC now optional; bugfix im motion parameter estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/63f03583888167cab4f8fa8c51f95b173499c2d1">63f03583</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-02T00:19:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix im motion parameter estimation completed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e8f8a674be60c981f0f5668089f9cb650daf0a58">e8f8a674</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-02T15:17:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">functionality for the loading of micrographs and initial tracks factored out of MotionRefiner into MicrographHandler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/167b9e33749db6ef2aed2e0d146555141b4f01b6">167b9e33</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-02T15:54:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MicrographHandler now robust against metadata-star-files missing in corrected_micrographs.star (it throws an exception now instead of returning unallocated memory)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c24f01f2cb9d010a16595c1bcdce937205c7bfd8">c24f01f2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-02T20:33:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reference map handling from MotionRefiner factored out into ReferenceMap
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8d11248458f4e17e5a1bbb80c90de4653b6be2c">b8d11248</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-03T01:55:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion package further refactored; MotionParamEstimator, MotionEstimator and FrameRecombiner no longer (cyclically) dependent on MotionRefiner; all public fields removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c35c534e9f456531831674779016cd7d69f455c5">c35c534e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-03T02:48:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine now survives one-particle micrographs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa1f629176fe4615e7485fca18610c8bc68b5b9b">fa1f6291</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-03T20:20:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">parameter estimation implemented in motion_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/da855ba2bb06088b6ba75509f6b7fc071e2f6e0f">da855ba2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-04T01:20:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine now supports --first/last_frame for relion3 datasets as well (i.e. polynomial initial tracks)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a29b82cca0ff315e19929b6a1def0ca7e61029fe">a29b82cc</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-04T02:09:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine: initial tracks are now returned exactly the same if --max_iters is set to zero
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/990fb5efe88d103b4a6a2b1bcadc83fc78a2a786">990fb5ef</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-04T04:06:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">experimental Nelder-Mead-based hyperparameter optimization implemented in MotionParamEstimator
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8809931e0de4f7e928f180ec11c049b564443728">8809931e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-04T16:45:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3dfaa54296a399833387707a59efbb8a5ba1caac">3dfaa542</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-04T19:06:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MicrographHandler now determines the max. safe number of frames in the chosen part of the dataset before loading any movies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/32ee3340cbcfaa8a79c8431455c7fa0588788b42">32ee3340</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-04T22:01:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine now supports the --find_shortest_movie option. If set, only the frame range available in all movies will be loaded. If not set, all movies with an insufficient number of frames will be determined beforehand and ignored (the user will be warned)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/53e509d1f280e6b320d9c838fbda416c85173284">53e509d1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-05T03:14:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion hyper-parameter optimization now fully transitioned to the Nelder-Mead uphill-simplex algorithm; definition of sigma_div no longer includes the dose; single-exponential kernel is now the default
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f4459f1748a079b88b37b49c55ee211ff20005d">8f4459f1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-05T03:45:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">value of ThreeHyperParameterProblem::accThresh tweaked
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ffe88597bcb9b13c164a16df55064659faf1c06">5ffe8859</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-05T03:51:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">output of parameter optimization clarified
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9bd1de976c2632cca545072af8fed9712496063">d9bd1de9</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-05T04:05:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ParameterEstimator: sig_acc now clamped to 1/eps
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eda9c5946f6282d305fae799f7fc85e9b72cbd9b">eda9c594</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-05T18:45:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ParameterEstimator now supports separate frequency thresholds for alignment and evaluation, allowing for a gap in-between
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/673ef2beeb2e6ff8c9b843a559ba60aa0d102157">673ef2be</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-06T01:45:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more debugging annotations in motion_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/85b616ef60b5bc76ee2a81b38187db6665431c37">85b616ef</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-06T02:52:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed memory leak in LibLbfgsAdapter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e89d9998e28414f1a81544c4c44afbf2bee72dfb">e89d9998</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-07T04:32:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">memory leak fixed in MotionModel; memory footprint reduced for ReferenceMap
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a1f3eb38530f81a22cf2c61b172e208e99e21ca">5a1f3eb3</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-07T05:02:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added --seed option to motion parameter estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4bbdbfb2e5b9f886ef3ead8547c4095726c90cde">4bbdbfb2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-07T10:32:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MotionParamEstimator: optimized allocation order of alignment data to minimize heap fragmentation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b1e2af4e8b30cb4898860c9d534758dd780ceeda">b1e2af4e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-07T18:39:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed duplicated 'scratch_dir' in Class3D.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0101a7528b47c7ec332aa5f1be06ddc2b7e6175">d0101a75</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-08T10:57:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New, experimental FFTW wrapper implemented in jaz/new_ft
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57e31b5205560522f397d360f6b8419c3e912f03">57e31b52</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-09T03:47:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AlignmentSet now a template; used with floats in MotionParamEstimator now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16531fbe5b57dcba5a29140cac695f7ac7735504">16531fbe</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-10T19:52:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Crop cross-correlation map (WIP: still testing)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f4bfcddd6a1f74781c78a49fc7447ee6601b6744">f4bfcddd</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-11T12:43:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CCF downsampling tested on two datasets. Debug statements removed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c1909678ca4d34a89606040ad6d9361124f2114c">c1909678</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-11T21:57:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">potential memory-alignment bug fixed in new fftw-wrapper; --no_glob_off parameter replaced by --glob_off
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3bdd6ef2be60c6d57643af1d2bcc03a061f0634">b3bdd6ef</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-12T17:27:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tidy up binning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c76414dcca98cba115b919ff7442f1d706c8201b">c76414dc</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-13T10:51:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Pitfall disarmed in BackProjector::reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/087a11d4177eb83ac774faf2aa725945b8756d47">087a11d4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-14T15:34:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added experimental double-reconstruction program
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/784b7744a07992f7d6cdc3f8de047dba1d4fe26e">784b7744</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-14T16:34:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging in double-reconstruction program
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c1b6f9e6a0397ceb4e088de8e4fe471c107be26f">c1b6f9e6</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-14T16:41:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">include statements slightly pruned
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d1c2453812850f97f712d67ad56393df0f4cf382">d1c24538</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-14T18:29:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">double-reconstruction program debugged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/497d2894e40c28547ffdd8e8e26ba54169bc31b9">497d2894</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-15T15:50:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">double_reconstruct now only writes out debugging data if --debug is set to a non-empty string
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c910012ee6e7b7a2b9c7aee4c3b547cee5b62bc2">c910012e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-15T15:53:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">double_reconstruct now reads the .star file even if --debug is set
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/817fb0106a552753c76005e2877437fa2d4600f4">817fb010</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-15T15:57:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">progress indicator debugged in double_reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/08eab721565f605b59e4ece9ac3087e8017ed30f">08eab721</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-15T16:59:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed resolution-rounding from postprocessing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5b1071f11811afd26e4badbd52e416dc1568f459">5b1071f1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-15T17:25:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added an option to divide the per-voxel average by its weight prior to computing the preliminary FSC (which is needed for regularization)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/20657149c458db5256542172fe7de95f09d832c2">20657149</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-15T17:35:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">double_reconstruct progress indicator further debugged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ee9e19c0ba9065aacd528b7343fd22c573208833">ee9e19c0</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-16T13:19:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">experimental L1-averaging added to double_reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60c9415b82c6b97077b32bff0c624b8b7db27f13">60c9415b</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-16T13:35:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">altered weight-formulation for L1-averaging in double_reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9b46f01b8d7c657f924223c1216cdd145bef70d">d9b46f01</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-16T14:20:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in L1-averaging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2e006457699bacce1fc45b5f93b75a1c1f11447">c2e00645</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-16T18:30:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in FourierTransformer: in setReal(MultidimArray<RFLOAT>), the plans are now also recomputed if the *complex* array has changed in the meantime (only the location, not the size is being compared)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c02bf7a169be7ed07f65c5888641b8303341f559">c02bf7a1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-17T11:23:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jzivanov (pull request #12)
Jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/056ace5dbab3126de469e75cccab8bbf3ad04dea">056ace5d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-17T15:10:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed some old program files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7cb2182a88fb6cb1e4c47ab91c72d198c3c49a5">f7cb2182</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-17T15:13:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small error in help text
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce9a4ee871e9a1301e4eeee75a59d1a823ad890c">ce9a4ee8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-17T15:13:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added help text for first and last frame
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0016402f134348e2c9292db66b6d94e3b5356d53">0016402f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-17T17:09:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Early binning in motion correction to save memory (but not used by default).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7637959233504379b869124dd04817a51bdae020">76379592</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-17T17:41:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed UNBLUR wrapper, movie refinement and particle polishing from GUI, and updated the pipeliner for motion_refine jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5762b398503e7a036f227fb1ebcb8766cd73b6c1">5762b398</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-04-17T20:27:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5b8729a7b0bfb910a16ccaedb75905112234541">c5b8729a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-04-17T21:28:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix TIFF-related compile issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/734780c45bd37930b5bdc0bfc8bd93d23de434a6">734780c4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-17T20:32:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor changes made at the LMB
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f92ec5f1bf127819bd2501ce49d6317ad42dc75">4f92ec5f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-17T22:11:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">single precision build compiles and links again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/635845b29d36b3d82548ac0a20d8f43aa0720cdd">635845b2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-18T09:07:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adjusted motion_refine command line defaults as per jazsenko
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e179db00e87fe4357449270c33a13fab14e2ec94">e179db00</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-18T15:03:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in NewFFT; NewFFT::XPlan now knows whether it is reusable and it answers isCompatible() accordingly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a686c7a5722b93eb1bed1b0bbe7869256d462ee">9a686c7a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-18T17:16:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">NewFFT: output array for on-the-fly transforms is rescaled to the correct size (if necessary) prior to the computation of the plan
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/49a2dd64c84824f30866608f27e6c4034469d8e7">49a2dd64</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-18T17:39:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">NewFFT further refactored: both on-the-fly and reusable-plan methods perform the required size-checks and make an optional copy of the input array, then they both call the same private methods that perform the actual transform and normalization.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bb3dd08f0de44b5101697e487e01f654903d63b2">bb3dd08f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-18T18:37:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ft_test app added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c92a255a1b40ca72cb24e77c52044b36b3b14d1">3c92a255</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T10:46:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added keep_tilt_prior_fixed on GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/576f02fe0cccf8865eef46d6b35a699f6f416979">576f02fe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T10:47:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow keep_tilt_prior_fixed and local averaging in helices, also repaired bug in NrOrientations for skip_align
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6338dde140f838b1259b067a988799170a912e00">6338dde1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T10:50:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">setting version to 3.0-alpha-3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f75c7b9b5615937d408b5108dd5774190ccc55e3">f75c7b9b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T09:51:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #147)
relion3.0-alpha-3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa8dfe12136fc10f5526d374889413b530a656f9">fa8dfe12</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T10:52:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e3f99cd48ede9fccb78f553c4bbc5727e5ac8e1">7e3f99cd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T11:31:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dynamic library linking, otherwise ftlk gives errors..
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3950b63c178b309967accf128e10dc0638280af2">3950b63c</a></strong>
<div>
<span>by Public</span>
<i>at 2018-04-19T11:40:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dynamic librray linking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5182d7217af5d8a166bacb8daecd8788229877a1">5182d721</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T10:42:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #148)
dynamic librray linking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8511700d7dd40d86e580e05be6ee2782e31e3b81">8511700d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T11:42:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/95856e2431aa49489941bd2333357eb95daae42e">95856e24</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-19T14:04:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in newFT: plan creation for rectangular images corrected
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/522e8e9b3704ea386e66bd299bc0436c89a8d014">522e8e9b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T16:05:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tau2 can be both input or ourpur. repaired bug introduced by jasenko a few days ago
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b454472b5ce8f91df7781b33c8b64082d8b2496f">b454472b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T16:06:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64030743836981d5ac72310d2b928472212581e6">64030743</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-19T16:10:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine: support for --mov and --mov_end arguments reestablished for Relion 2 datasets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f5741cf749c2faad2c8971e63999d602fdecab9c">f5741cf7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-19T16:10:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jzivanov' into tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ee27f792e09c8b4ebeb8d11d2e9f152791ea60cc">ee27f792</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T15:11:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #149)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b77503889e753c469a04fbc8b531f5dd6d69eb6c">b7750388</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T16:11:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c6a2d4f34d0602a7b97808048aeaf1a91c1e888">7c6a2d4f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-19T16:14:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">...now including the initial micrograph
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3802506af26aaaa788c6997ae236bf1b1d1a22fd">3802506a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-19T16:38:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> added --ctf_multiplied to new reconstruct progra,
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c2a56ec3deaa6f9c593c3e7d8aee0848b50b00d">3c2a56ec</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-19T16:43:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/master' into jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bef826382f6908a99af2e1bd0d8878016522fa3c">bef82638</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-19T17:14:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged with master; movie path parameters and support for preextracted movies removed from motion_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/18c82d76d3c17e80b7ca6ac368b8881f410ba08c">18c82d76</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-19T18:48:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tau2 handling in BackProjector::reconstruct() made slightly safer; ft_test emptied
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b7d1b715b4f81abbd286f4f2cc2dbeadc1b0c4c7">b7d1b715</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-04-20T10:37:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12c35300db77cc177985deb96fa41de8f214dfd5">12c35300</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-04-20T10:37:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">3D particles can be shown from model.star display
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4131686bf24a21987123a975bb4eba1abd2b35a6">4131686b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-04-20T10:39:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d8bb8ea6b7f190e92dea0fe68f17ff1178c8241b">d8bb8ea6</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-04-20T10:58:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Particle displ. uses the "apply orients" tickbox
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/80d19045cc62fa6821a74dd0a4066932d938c5a4">80d19045</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-20T11:03:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Always use float in motioncorr to save memory.
Confirmed EMPIAR-10153 gave the same resolution as before.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/89f966ebf4926a5b74bf2623b826f2244fdc1f1c">89f966eb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-20T11:04:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'tiff'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/07e09b0c6decbdbe1b478a23191bb963fad17169">07e09b0c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-20T11:20:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added RELION_TEST cmake flag to prevent test programs from being built.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e09b244dc25ca6b6d82c88c6e1979015adfe9a12">e09b244d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-20T11:24:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c41c55f09b16213b028c3bdbca85a9f1f9f00b9">7c41c55f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-20T11:34:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unnecessary transformers.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e0bdd3877a991539bc76e8b6336fecc87fff737c">e0bdd387</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-20T12:14:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/master' into jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cf053a605aef7ee2db78f82b5c5088e3c22dae0d">cf053a60</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-20T12:33:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine now looks for all missing movies at initialization
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bfe8bd2fa1a6d004a9bfeb90ab649c931e34f1a">8bfe8bd2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-20T12:49:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_stack_create: mkdir when necessary as reported by Max Wilkinson.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/142091483707a0c190b602a440b3c4852ed9b45b">14209148</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-20T12:58:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">It is no longer necessary to use mrc:mrcs to load stacks stored in .mrc files in motion_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/936a15156568ffb3d5b0385042567fca9ff57a9e">936a1515</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-20T13:34:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">image stacks are now loaded slice-by-slice in ctf_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/def78c662115b71db8f9c4f26460623f8ac1641c">def78c66</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-20T14:47:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging statements added to defocus_refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0f7bbb2a522410771a89c5d91a59ba1f6996df27">0f7bbb2a</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-04-20T15:50:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Acc. noise-masking runs with 3D input particles
Seems to give erraneous output though....
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/892d8bc5c17d48b014e1a4e4e5ea9eaea6b64603">892d8bc5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-20T15:11:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More help in GUI for motion correction.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/206c30011073e9903548482a71b24aa7cc65c554">206c3001</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-20T15:44:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed motioncor GUI and added "save non-dose weighted as well?".
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5b4eb9c14ec18a69e87aeb1c0629f92f2746e342">5b4eb9c1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-20T15:20:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #150)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34a2ef84d8377e2083eda63982ceabd0436e731d">34a2ef84</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-20T17:50:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix minimum inter-particle distance in autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/994d6f251a993cbf28f0c369965523db6b4e61b9">994d6f25</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-20T20:55:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_refine now uses ReferenceMap; prediction for defocus estimation now considers current tilt assumption; prediction for tilt estimation is now taken from the opposite half-set
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/35a82d0d2c7b94e41980c83f80661e1b70aa5bc2">35a82d0d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-20T20:56:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/035cf51d2d6c567620613a45d26d186bbe96a272">035cf51d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-21T00:03:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CtfRefiner: tilt refinement factored out into TiltEstimator
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e4fc5bfd8e1e01b296e23c3df2aacc03dba0b9e">9e4fc5bf</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-21T11:55:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tilt estimation now considers per-particle defoci
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/160fc3193993dbb50b1b2dbaec4a14e541533fcc">160fc319</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-21T15:56:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">defocus estimation factored out of CtfRefiner into DefocusEstimator; defocus and tilt estimation can now have different kmin
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d31420e5ec5fcc1bd2978729e23b53780acce258">d31420e5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-21T16:33:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in ctf_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2bdef4a3f88c350b141c9cb412ba7460ac5c3c8">c2bdef4a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-21T16:36:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_refine: no longer printing out particle index on --diag
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/784a9384b8ef2a262c40a3fe5ded7abb1a324d19">784a9384</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-21T17:34:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in TiltEstimator
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7afac3aeafa61d8a9d71475e8931fa7ead753e25">7afac3ae</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-21T18:54:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in defocus estimation; diagnostic output improved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7da5d92bd7722d19e744ae32a192f76562eb732f">7da5d92b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-24T16:32:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed a bug in "combine STAR file" and tidied up indentation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c64674d488b28b92ed7d3f969fb0c9e72ecdb3f2">c64674d4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-25T09:05:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/598ea88f2374becdbba965778e9b9c9625f4495b">598ea88f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-25T10:21:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">spaces at the end of logfile.pdf filenames removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/92a87fce08b9e41908dc9221eba6eec90b27da84">92a87fce</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-25T12:59:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">FrameRecombiner now uses the outer freq. of the reference as the outer limit for B-factor estimation, unless a value is provided through --bfac_maxfreq - this requires loading the reference in that case; CtfRefiner slightly refactored in preparation for anisotropic mag. estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/83dde660deda083ee1e81a24cb1a8a009e4a0568">83dde660</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-25T17:12:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tentative anisotropic magnification fit added to ctf_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1bedbb03073887eb3a4733a1410e33a57cec5098">1bedbb03</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-25T20:04:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed reconstruct_openmp. Marked double_reconstuct_openmp as testing program.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f326aa40a2f8f80f8477c8dc78ecc12e300e3baa">f326aa40</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-26T15:07:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out debug maps in reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0ebeace9023a690ee0d38bf0721f1e7e8ef18661">0ebeace9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-26T15:29:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Manual picker: treat shift + left-click as middle-click and ctrl + left-click as right-click.
This is useful for touch panel users.
Also tidied up indentations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/adc748b178010b5a676896d1043c3bcc844602bf">adc748b1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-26T15:31:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84ee51c1877426908228bcee0e543aad2c93fc97">84ee51c1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-27T12:01:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_refine now works on centered particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e1ee1c677d928f082ec8928937518a2bd2d11738">e1ee1c67</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-04-27T13:10:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_refine and motion_refine now warn about missing star-file columns that are required for forward-projection
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7aecb45ae912757a7f0b26c7e4dabde896042552">7aecb45a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-04-27T16:55:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Made motioncorr more robust.
WIP: We still need better GO/NO-GO decision before fitting.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/19f43c921d802128b1cac693fe6b18397c07455e">19f43c92</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-30T10:08:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">rescale originXYZ as these are in pixels
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24c927ec078f96bce80f5ce894871937b749ce53">24c927ec</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-04-30T10:09:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1e5db96108a6ad9428661f8652158be1d22af1f6">1e5db961</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-01T02:42:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine: B/k-factors scaleable, noise-whitening optional
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57b1cf49a839868fa15226573336816e3682ab0e">57b1cf49</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-01T13:00:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed garbage in the qsub template field when the environmental variable in not set.
And tidied up indentations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de8b0d7b0d16a87be13ce4e7cc9ecba6fec4dbdc">de8b0d7b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-01T13:02:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/39e88dc17f1ea8099b2a43b8f4a578326b293ea6">39e88dc1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-02T09:05:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add unmaksed 2d classes to trainingset
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b745f839dfdecb16aa5777cfed046b687c375841">b745f839</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-02T09:06:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/317c6570938b910378c311aa680ef48d882c6972">317c6570</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-05-02T17:34:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de56860ed36851f494b57df602b7d8791f1ad882">de56860e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-02T21:58:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine: initial per-particle trajectories are now aligned rigidly with the data if --glob_off is set
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6373b95ef05683d7175188c23aff5c983a17c988">6373b95e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-02T22:23:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_param_estimator: internal scale of sigma_acc increased to 10,000
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/46e6e35acd8739e82311cdbac6d7a1f4af9f1e8d">46e6e35a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-02T23:53:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_estimator: scaling of input parameters by dose now optional (--params_by_dose)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29bf55fc6e204d0eeeaac6e89f59df955473cc7d">29bf55fc</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-03T00:37:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_estimator: input parameters scaled by dose by default (turned off by --absolute_params)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a20387a7e6209838009ce0dec001f7c7f2b113d">7a20387a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-03T01:11:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_param_estimator: internal inversion of sigma_acc removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bdcad7b1996c5a200335e19186effdad2dc7103f">bdcad7b1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-03T01:25:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_param_estimator: internal scale of sigma_acc reduced to 100
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/902f2c0b43b2c4992616e45fcb3742bd282fa447">902f2c0b</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-03T01:49:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_param_estimator: internal parameter representation further optimized
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f502d8d2ac84a24f2bd642031d7a8a0e116650ef">f502d8d2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-03T04:08:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_param_estimator: initial step size increased to accelerate convergence
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ab46b358ce92ecf8f9bb4ed87d8adf80d863dbe3">ab46b358</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-03T13:36:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Stop if RotGain or FlipGain are given to MotionCor2.
WIP: gain rotation & flipping will be implemented in RELION.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/14afb1b87b770928539c7407568e4f1f682680f0">14afb1b8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-03T13:36:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27209a41fa34b8548768013310e6669e375fa387">27209a41</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-03T14:23:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_image_handler: Fixed typo.
And tidied up indentations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/38c6b93aad93ae1cef0c29d2240f2fb22deb2292">38c6b93a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-03T17:03:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rotate and/or Flip gain within run_motioncorr.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a8f46151a98b7471e3b3bc8bc5d5040d5c55f6a3">a8f46151</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-03T17:22:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_estimator: --unreg_glob option working again (only useful for Relion 3.0 datasets)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ae32026da6173ee80bb5f2aea163a2fbf22e693">8ae32026</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-03T22:19:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_estimator: more debugging data written out
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4bd9a7e2a612606ab15f8916595e3fee362eda5">b4bd9a7e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-04T17:33:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Made gain rotation & flip as drop-down lists
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/55a1fd5995b73977247c98fb120eaa0592e820f7">55a1fd59</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-08T16:12:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #151)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/96c948b5749fbe623d5587c9397bc3c34acc081e">96c948b5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-08T23:23:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cubic interpolation is now numerically more robust
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/234a08ef1f5bd736b282fb625f9aa3a245764cd1">234a08ef</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-09T12:31:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug autopicker helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c7b332c2d3e7f3cf5e702f80c9abc81d17dfdc8a">c7b332c2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-09T12:32:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">call jasenkos motion_refine bayesian polishing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/71a1d9f4d3810a2c19ab8c7e9fc9bdcfcfda328c">71a1d9f4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-09T12:33:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug mysize when reading debug files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8be1b3a3e99b8f5e9bde3758ee44aac616eaf31a">8be1b3a3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-09T12:33:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added debug option to keep debug files for reconrtuct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b2c98583f21ec6aeaf0abf6e01bb2af2a51eba8f">b2c98583</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-09T12:39:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added do_fsc0999 option in reconstruct to avoid artefacts in some helical reconstructions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d725c6281a1c51ab5623717ae809c93f7bd3591">5d725c62</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-09T12:58:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c12ab79e7c5e4c7b88c63890898042ec676c672">0c12ab79</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-09T17:42:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added functionality to select micrographs or particles based on metadata value in the STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fdc4bff6ca866e3dc48340fb42b93fb0df41b556">fdc4bff6</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-09T23:41:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">--k_cut[_A] and --k_eval[_A] arguments in motion_param_estimator replaced by --align_frac and --eval_frac
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a149c30b2f3d287827fa4b0634355a931341421">7a149c30</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-09T23:42:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/master' into jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9eccc52ef67c95cff6f3eeac01f666d2ce3b171b">9eccc52e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-10T00:03:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged with master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd6dc20dc00303367924f356850013b47888c3e2">fd6dc20d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-10T08:34:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jzivanov (pull request #13)
Jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b69e8f5063b0f25b5aeaaf431540840753efe04">0b69e8f5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-10T10:01:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated command-line interface to reflect changes in ctf_refine by Jasenko
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2a109810f24e86f8238b7c2d69fdd1d82a7b578c">2a109810</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-10T10:01:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">renamed Run now button for run
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7088064737064638fa347c6883eb66e0b224e826">70880647</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-10T10:17:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added Jasenkos new eval_frac and align_frac to CL IO of motion_refine GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f44fa096283f80b3867e6d80eaaa30f883024a66">f44fa096</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-10T10:19:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed obsolete starsplit from Jasenko
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29c4b39d84503b158b44b9b3a164c8e40b5be188">29c4b39d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-10T17:17:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set version to 3.0-alpha-4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c134d67abcef0f1f13d84e8ecd8b1e71e717557f">c134d67a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-10T16:18:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #152)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a4fc33336880c2a9ceb436775f02345b3d615993">a4fc3333</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-11T14:04:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new kmin options for ctf_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60fe0dcc400672925040f33c34d87ad76d61cf97">60fe0dcc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-11T17:35:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed spurious output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3781e37ec7567b47d580478ef908b29eca1848d">b3781e37</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-11T17:35:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added --average_all_movie_frames option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f0bc66525e687121c856c19b2a8a085063f58edf">f0bc6652</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-11T17:36:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">moved warning to stderr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5f1970abd5238facc92961ef33bc0e5e8402155e">5f1970ab</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-11T17:37:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed output to logfile for nr_repeat=1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/33b5b8c52e6e4564b775d088042d4884ae200159">33b5b8c5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-11T16:37:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #153)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/07039aa1fd0cd41fef4714352dce74c7c1fda49e">07039aa1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-14T09:36:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">output directory for bayesian polishing is called Polish again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9da0646869898c223727e7a2dd8b490425c32370">9da06468</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-14T09:36:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">output to stdout instead of stderr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/064435aded82378c453044e27e2563abe61ee80c">064435ad</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-05-14T17:10:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Automatic TBB download and build.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/31aa05bf4976b4c9620709b1ad3c15c8fac5969f">31aa05bf</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-05-14T10:07:36-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'complex_projector'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b047cf06a526d87cbb1002a949618721704e4524">b047cf06</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-16T09:40:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only set ctf and beamtilt values from micrograph star file if particles input star did not contain them
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a5678ff7702b39dc97e7e8f69e3c7bd34f92f04b">a5678ff7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-16T09:40:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">explicitly mention MotionCorr input star file on motion_refine GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2eb209a99143dc613938680663767c3d45b79937">2eb209a9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-16T15:05:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">flex_analyser: clarified comment. fixed indentations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a75e79d15eabf7774d902d633dc805129cd1bb4">7a75e79d</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-05-16T17:38:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed CPU size unallocated random image pointer.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2a5c7b6cd6698f9950a3d4f2eec3e7d97b6819f">c2a5c7b6</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-05-16T09:46:32-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Various bugfixes for the ALTCPU code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/169fe61923c6d1fd9b85b7212fad3926c91b408e">169fe619</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-05-16T09:46:42-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e576a1f4011e798256d9c5138a441d6d93670549">e576a1f4</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-05-16T14:32:19-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up some things pulled back in by merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5219e97bdf058f5b6250b0bb7b4546d167e0370f">5219e97b</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-05-16T14:54:23-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More cleanup
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3bffa751fab0d2b15c16dcd239ef0b12d17c8bd5">3bffa751</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-05-16T15:09:54-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix CUDA build and isolate from ALTCPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3145e60f6950b4debc983596de06162dc4165922">3145e60f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2018-05-17T17:35:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added FOURCE_OWN_TBB for consistency.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/710c901ccd8b8c40b6ec8011e0c489e0c541df23">710c901c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-17T17:47:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">optimal motion parameters are now written to <out>/opt_params.txt and can be used by motion_refine with the --params_file argument (overrides cmd. line arguments)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/77c0f2eb3b41d278a7a2b9cd683ccf7e8e3b091d">77c0f2eb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-18T08:26:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jzivanov (pull request #14)
optimal motion parameters are now written to <out>/opt_params.txt and can be used by motion_refine with the --params_file argument (overrides cmd. line arguments)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2d92ce64a4b2b6bc81cb682c8b11b2372a397d5c">2d92ce64</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-18T16:03:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired serious bug in preprocessing when extracting rescaled particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce845915a9592bbacd8364868e9e8f65c55c9b0d">ce845915</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-18T16:35:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to randomise order in STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e9c676be4c32c030729c5b0292fcb9b8d284cee5">e9c676be</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-18T16:36:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added relion_star_handler program, modified gui for that, and for opt_params.txt input of motion_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0811ad5995f728900fc8b0b822686241fffd6425">0811ad59</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-18T17:09:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging new functionalities
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/317eda99afd5da7c5c2d87221fc645277ab41e38">317eda99</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-18T23:50:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cc-padding, cout flushing, pixel size warnings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/615c6289e0c7320f9f48c2a653ec53fecf5d0956">615c6289</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-21T15:27:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added --randomize_at_A and unhidden --random_seed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8791cabedb626cdc502151ae8705a41a4118a6dc">8791cabe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-21T15:29:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont give error for nr_split=0 when submitting Select job
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e7f7f0e0b3e91ca09263f5f8ad0f43668b3980ea">e7f7f0e0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-21T15:29:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added delete statements for all new CPlot2D statements
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/08a19f9e1285c2ce5fb6f050a051a4bda3576db2">08a19f9e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-21T16:12:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow to set both split_size and nr_split in star_handler and Select jobtypes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2ae7764c08971365ae93233637cd8f8c0561d1ab">2ae7764c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-21T16:42:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> added in pix to renceter options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/160908ed5a16121a855a0069d31a94c69c333939">160908ed</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-21T17:14:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added options to add and remove columns from STAR files in sta_handler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f3f0579c744f41ec6a63f389109904092e042adc">f3f0579c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-21T17:23:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">flex_analyser: write PCA weights and eigenvectors to files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a948447cc91a9a07506104a41a9d14b3367d580c">a948447c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-21T17:23:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3480dda3bec59ef516699b93399db5ecea41332f">3480dda3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-21T21:32:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: save angpix even when dose_weighting is not applied
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d4f6a6f34a4f9fbfc4d99f911c684ea2d884aea">8d4f6a6f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-21T21:33:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c73c96783db31f45222d01eeea8dd9dd1316bf9">7c73c967</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-22T11:23:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">always provide voltage and dose rate to motioncorr_runner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b96aa9becd3cbb5b0fea133f35c2d0553f19e02">7b96aa9b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-22T11:23:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/11e9740f8e5105390e03588149b6b16450b7b411">11e9740f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-22T12:13:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reversed change yesterday in Cplot2D: fn_eps[i] could be a linux wildcard
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ef7988f4535e51c085c936cc068fe0eb686e9e57">ef7988f4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-22T12:14:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug combine star_handler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/628cbfc6290639ce1eab55697acba06fcb5f1fd2">628cbfc6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-22T12:24:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: Made --angpix mandatory. Always writes angpix, voltage, dose and pre-exposure to STAR files.
GUI: Do not print --gpu when --use_own. Changed default Cs to 2.7 (Titan & Talos).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f0ce4bb1fac8d3adcc610492dc5224b95590324c">f0ce4bb1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-22T12:26:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added functionality for linux wildcards in test for existence of file in combineallEPSintoPDF
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9ceccdb99dab2a2188ea91bbb9d796fc7ddfe927">9ceccdb9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-22T12:31:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a41cecdddf42408a755bc5ffcf1c0c66cb6aeb9e">a41cecdd</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-22T12:34:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: removed debug output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/36f64577cd974e581b02be2464b42c16cc1309b6">36f64577</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-22T14:32:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: save angpix to the image header
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3d1678875d37d9d2561256e6d54eb4ec809c57e5">3d167887</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-22T15:20:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mask_create: implemented raised crown mask (including raised cosine) with the --denovo option.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a8828aaca1fb21d8ea00f3b4418533486702489">6a8828aa</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-22T17:29:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">flex_analyser: initialise rescale_3dmodels. This fixes SEGV in --do_map.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/295e94fbc0bf5763bde41e75071842e83e01c59b">295e94fb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-22T17:33:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jzivanov'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/606df0be2cf5072f1300fdb214962a1484d6d0c5">606df0be</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-05-22T10:23:08-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add installation instructions for accelerated kernels
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/88fbe21289f179007b2e851487c7d8bbe68bdc2d">88fbe212</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-05-22T11:28:14-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add run instructions for ALTCPU version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/72b5a18d51d1d0c7f1ff0fa605b1990a5eee634b">72b5a18d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-23T09:38:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small changes to autopicker: threshold variation opposite direction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc8a1dd2d8e1061c9d80a38abcd44bf8754601e8">fc8a1dd2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-23T11:21:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">traditional B-factor estimation implemented; \n replaced by std::endl in package motion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd37050b220942f8ab895892bed90638dce09145">dd37050b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-23T12:00:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_star_handler: Added --copy_column_from. Fixed indentations.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/055e650560259056d182cc13e8fa453d07d78bed">055e6505</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-23T15:37:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/378ea466df56ac6d7543d07be46e268b893d070f">378ea466</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-23T16:14:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_star_handler: implemented "--stat_column" to show column statistics and histogram
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f359fc8d1f2aef406b8e37557b1f531c4f246f29">f359fc8d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-24T15:05:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Flip the Y axis in PDF outputs from old and new Polish, CtfRefine and MotionCorr.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/825b5a238ca3af0bc6ef344c04be0241d907eed8">825b5a23</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-24T15:20:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove temporary comment
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ffadef71728fe2d80b812f7fb54f1666cb8a0eee">ffadef71</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-24T16:59:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/master' into jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ddc01f7116f62f111e4eb36e2768fa040dcd667">3ddc01f7</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-24T22:43:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfixes in bfactor_estimator
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/955a6b9f0bc79b4084acecae19493b5f8544cb75">955a6b9f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T10:14:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added apply_rounded_offsets_only option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ef5165245bf49c3c2f978aacbf1e46f51dee712e">ef516524</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T10:14:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f92c063fb64e06bbdc368d3feb15e3b99fce03f">3f92c063</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T10:17:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out incomplete last split starfile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bd258a48533fb3a9976d93edd609da7ea63ecf94">bd258a48</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T10:19:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed spurious spaces which GPUs to use and replaced log_diam_min and max
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3e607f5532a80cb1bda7fbbe05d1f2cbe6f4d7b4">3e607f55</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T10:20:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">log_diam min and max, as well as different default threshold
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2f7dc9ae8046592f76e8f8974a09294bff89d3fe">2f7dc9ae</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T10:20:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added log_diam min and max on GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16eeb6653587473160cf16bc0d8dde87922f87ef">16eeb665</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T10:22:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">switched back off asktraining
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dab5a18500a7a095ac3e62e18fb185f0bc60408c">dab5a185</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T12:14:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small change in warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4a00ea9537519078535ed75d824e0f3c93981b0">b4a00ea9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T12:17:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added relion_it.py for onthefly processing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b40498ff8557a7a9e18fcacb7bda0ba64a602f8">8b40498f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T14:19:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added WaitForJobs, so one can also submit to an external cluster
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/55b8589626d3411ff6ec6e6a66b2326ad318545a">55b85896</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T16:37:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added 3D classification option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/006ba5a03824927dd8433fc44c5f7d5fde87ab6d">006ba5a0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-25T16:26:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #154)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7e7c07fb7a5e8d37ac206ba90913dac851a6d41">f7e7c07f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-25T22:59:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor-estimation reconstructions written out sequentially
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/edd80936261d827668bb68afbef8eca4ab65c6b6">edd80936</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-27T19:00:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_nyquist_test app reintroduced
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a11da39f19f0e4b25bf66fcf320b3082ace1f92d">a11da39f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-27T20:43:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">frame_recombiner is now able to handle positive B-factors (supplied via the --bfactors argument)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d2b0d19bd1eed4181382fdf0bec4a9700680dd5">0d2b0d19</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-28T05:46:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">frame recombination now supports altering the box size - as long as the reference pixel size is an integral multiple of the movie pixel size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/039358e94d7f9d25ff23c01d52714d2634f29c54">039358e9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-28T10:56:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to discard images based on statstitics in Subset selection jobtype and star_handler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4865827f00c1a7580be7562479883ad4ae8f6503">4865827f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-28T10:57:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write where .lock of pipleine file comes from
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd773f47ccd6cc87c6e1cc5364617c4f0c668c0b">fd773f47</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-28T11:54:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out more informative .lock file for pipeliner#
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/40efe00e69778fca9188a13f8a82cfce1349a11e">40efe00e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-28T16:25:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add option to autopick with a 3D reference
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9400d367d68d6d317717910ce1ed3e228b1ab14d">9400d367</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-28T16:25:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only print info logfile if nr_repeat>1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58421d020f1733659660598638249668fd62fd83">58421d02</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-05-28T16:56:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">frame_recombine: boxes are now always extracted at optimal per-frame pixel-positions; this preserves the signal near the edges.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce4722cfdf4ffbbab7d2f31a1ae987a1f508bd41">ce4722cf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-28T19:13:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added inimodel and second pass with 3D reference autopicking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd4e3a15c1db56cdccadcad3ebfd098eef9faabd">dd4e3a15</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-28T19:14:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small change in IO autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb776a497acff55e4c731d8d3c3bc6e946fff3de">eb776a49</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-29T07:31:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option skip annealing in SGD and switch off do_shifts_onthefly whne do_gpu or do_cpu, as per Bjorns recommendation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4c8eafc4aa138dff6a8fb286018fab741bd2a96a">4c8eafc4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-29T07:32:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added label for optimiser skip SGD annealing of multiple classes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d11bbe4458038ec4cf96d950c25b134b78ed378">8d11bbe4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-29T07:32:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated version to 3.0-alpha-5
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/940e028ccc1bad5290ba43ef801a650d4cd95ce9">940e028c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-29T07:59:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added better functionality second pass
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0e7e4cdb197da1ffb1030ff7b54a03021f745d43">0e7e4cdb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-29T09:44:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor changes in relion_it
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/222159dddf7afb809edd25790de67188f23a990a">222159dd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-29T12:27:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use MotionCor2 by default, also repaired bug when importing micrographs instead of movies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/499d11f8460a3e92d1ae6deb9a40dcf210c237b5">499d11f8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-29T12:36:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The type of CPlot2D::SetFlipY() should have been void.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/22747240826c4d494f4f151262dca8b1bb88bc52">22747240</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-29T12:37:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61a3c95e2eccd37e6fa4c765df1a4eb1871c8bd7">61a3c95e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-30T12:47:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_project: use the pixel size in the header of the input volume when not specified.
write the pixel size to the output.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f58ec6fcec7d3d2f6feb70fe8d5cf93c4a5b288">4f58ec6f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-30T12:55:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: improved warnings for patch_x/y
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c6236096fd1ff53e9ebe30fec98bd054277e80b6">c6236096</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-30T15:58:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jzivanov (pull request #15)
Jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2351474d493a17c6573c2d8de4509c23f3466908">2351474d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-30T17:21:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added functionality to CtfFind and Autopick jobtypes to write out logfile.pdf, also changes star_handler way of doing histograms
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1e103dd79bd251fda9d9ec37f83ada539621dff5">1e103dd7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-30T17:36:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">corrected small error in autopicker logfile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e699791b41d6cf518d27c8864ab2d85fe83bc066">e699791b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-30T17:37:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired print_sym_ops and metadata labels without --i or --o
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2bb629e4e802c1c2f0aeb6e9381ecb810f2dfe62">2bb629e4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-30T18:07:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added relion_it script to generate Rosenthal and Henderson B-factor plots automatically
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e328eda70c08a4f98b966fb8730c432af812ab1b">e328eda7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-30T18:08:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small repairs in logfile for ctffind runner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c77d59db2407326a89052321a82515d38a7c15c3">c77d59db</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-30T18:12:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug when importing micrographs instead of movies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9683841ce56f62077b6c19960e43d2c4b61b7722">9683841c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-30T17:25:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #156)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2cf72e4bed91cdfbfe160b8c46167c9fe1019366">2cf72e4b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-30T19:54:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: fixed indentations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4cf11d3ea8f496010717be699860bfd35965da62">4cf11d3e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-30T19:56:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: set the pixel size in the output image header
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0843bee335bbfc8eb1a2c9188eccffce4d64a1e3">0843bee3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-30T19:56:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad4aad9321e2cbefaf7f4bff48f03df425648f71">ad4aad93</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-31T09:44:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont die if an autopick star file doesnt exist when making logfile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc2e78c312e82ad7128c22dd877fd1e24169887d">fc2e78c3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-31T09:45:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a4ca5fa1e86571f1484ae73d6ef34ab85903f67a">a4ca5fa1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-31T11:54:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">rerun logfile.pdf generation autopick
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/198f38a8aef57e309ec5c4f56edb4b1284d4fe53">198f38a8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-31T12:40:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont restart 2D classifications/inimodel in first batch upon restarting the script if the number of particles in the split_job hasn't increased meanwhile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bad6fee8fd774ed5ac1eb3b0c6910ce76bc6642">8bad6fee</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-31T12:50:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added relion_align_symmetry. Useful for aligning initial models generated in C1 to the symmetry convention.
TODO: local refinement, try multiple point group simultaneously
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2124a288e277085a17bc9f8b799e0c670dd354e1">2124a288</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-31T12:52:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/377fdef9d167b2b56fc498c0fc8553bdf938e476">377fdef9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-31T15:00:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">still debugging this nasty second pass
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d1ea66ae3fb191f9af75108ecbdf7c6912413414">d1ea66ae</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-31T15:00:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d93b3060fc352c66afdebf1518b506cd8a3ebcd5">d93b3060</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-31T15:11:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_align_symmetry: implemented local search
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/251e6dfeb5766a77e078ffdca0ba80370c8d9d8c">251e6dfe</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-31T15:12:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0839d84014b5a70d0c10ff7d4e6e223c5d861b81">0839d840</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-05-31T15:25:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> switch off debug statement in autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dde634b0272efd5d29d27a000b8f9481f0676979">dde634b0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-05-31T15:47:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mentioned relion_align_symmetry in the help message in the GUI.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6fca449f43d93e1ff9a7d565da7e2e616f5c9134">6fca449f</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-06-01T14:21:12-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try to ensure long types are not accidentally truncated to int
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/99af1cc67d631b5dc71e784c4e3635cbdaffac55">99af1cc6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-04T12:15:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add plots of total accumulated motion per micrograph to logfile.pdf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d16e1cbe200b87202104f6fc863bc61aa00774c9">d16e1cbe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-04T12:15:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more verbose generation of logfile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e5af92ca029dc93cbbd6d64464bb5028f3ced48">6e5af92c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-04T12:15:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b5558237e0d4a475bb8ba8a2c69768b57b22097">7b555823</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-06-04T14:46:30-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">README and CMakeLists.txt updates
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4acc21f5e050f6874fb5b5db60999195c1846f0e">4acc21f5</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-06-04T16:42:32-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More updates to the README.md
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe7033322afddbc2e067170f9df08fea1569fc0f">fe703332</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-06-05T03:16:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dot size increased in motion plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0057edad6e7a9293d1b0911733d7c7dfaced5916">0057edad</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-05T09:10:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired small bug in histogram EPS and in autopick logfile generation on gpu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ff1522253dcc8d5ec2dfa4db52ffe722f6267d84">ff152225</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-05T09:10:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed option to ctffind on movies from GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f896b662e3b09f16dc19f4ed80559254b064dbef">f896b662</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-05T09:11:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to ignore ctffind parameters and do EPA for gctf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/17e8e5faccc049f88eb0fc9b4323008b6d184973">17e8e5fa</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-05T09:41:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug of too large auto-diameters in sorting
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a0ba64666828e9b42afb5df5f8b551afcbf2b29b">a0ba6466</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-05T12:01:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_image_handler: Implemented --invert_hand. Made --o mandatory for safety.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ae38930b543a81167fe548f5e53ea6b2b0edfa3">7ae38930</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-05T12:05:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e5a5f19311ebbc967c25097b8ed68d7e8a5f9f4">7e5a5f19</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-05T15:32:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_image_handler: some usages do not need --o
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aabf201873aa85cc6646b36ce1e8c183a567fd78">aabf2018</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-05T17:34:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_image_handler: added power-spectrum. <cos(delta-phi)> is still work in progress, so hidden.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/942f48b88265092ef15df9e3529f5e56f5238235">942f48b8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-06-06T01:28:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Old B-factor estimation now works in single precision; Micrograph no longer returns a global component of -9999 for missing frames
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ff0a012e2904b958d6860f873f15962a8b1f04e0">ff0a012e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-06T11:11:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jzivanov'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/706f5c23e650cdf7f8e7ea1184928d62bdb846c6">706f5c23</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-06T11:53:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Micrograph Model: When not observed, return the shift of the closest observed frame.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b6563ec0e9127ecba3301a8b2b88bb9f1a0065ad">b6563ec0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-06T12:06:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: use the return value of getShiftAt()
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dc9c42ee5486db5bf7a832883ecbde14d897aaec">dc9c42ee</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-06T12:07:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41f53f0cb343c64f261f6c7581927e3274aaad09">41f53f0c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-06T12:09:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont die if cannot getShift for calculation of accumulated motion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/391e224089ad0ae0e31fca41cc5f7ffd0da8039c">391e2240</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-06T12:10:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set default sigma_offset to 10 pixels instead of 3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34760641ea132d335668600af443f01e74e861f4">34760641</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-06T12:10:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">particles can also come straight from CtfRefine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/62187108baeb2087044691c915d83e7c64479b7c">62187108</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-06T12:10:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out warning about .lock file from gui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7f7d96f1451e6ebae96dcf1470632822ff29cb51">7f7d96f1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-06T12:39:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot: Use proper Angstrom sign in the plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9170f0b0294e249f2c2c71f48c3997ad4278314d">9170f0b0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-06T12:44:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed dependency on 2 tex libraries
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/060400e26e0909d28397fcfddd07b972261752d0">060400e2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-06T12:45:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/15a688d2fa72bed09de6705a9f817db0b87aead1">15a688d2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-06T13:09:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added PDF with histogram and all values of Zscores
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61734ee84e1c8df82f54b7ef2ac0ede31bba346b">61734ee8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-06T14:15:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot: added maximum_nr_particles. skip failed Refine3D.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c326b0df8e2529cdda69bf5fab69d52472363b7c">c326b0df</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-06T14:16:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc78e78d843625da0436b8346c535b6496930ab7">fc78e78d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-06T14:57:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #157)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8caa74a7efdc648868361245eef12e02cdfda155">8caa74a7</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-06-06T09:30:39-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Change #pragma simd statements to OpenMP 4.x standard
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc3c5c2f3aba30035f3881cc95116ede620f0653">fc3c5c2f</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-06-06T11:25:35-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Work around ICC issue before 2018 update 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8e0a974e7d7ad1170ac98ef5be5c21337f71c6fd">8e0a974e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-06T21:39:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: Fixed a bug introduced this morning. In C, 0 is FALSE, all others are TRUE ...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/92f048d16c26479b92c008dc28ecf140d0be6b60">92f048d1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-07T11:47:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it.py: Use resolution instead of class distribution to find the best class.
Fixed undefined "batch_repeat_time" error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/723a11f6c19685d73b25a8f2b33644a42a8ab5a3">723a11f6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-07T13:55:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">switched ctf refinement and bayesian polishing around
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f26617dbf500be5c32076150c8106c1b72fb733c">f26617db</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-07T13:55:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">wait one minyte before dying on non-existent .lock
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/88ac883d92f45c30ec3467a3bb984e05f5c560c3">88ac883d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-07T13:55:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61db8679e597cf6713abcd1646b09673a95a3a5d">61db8679</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-08T09:47:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out star file for the new stack
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6613592f5dc011bb700e37fc46cdd3ee161fe91e">6613592f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-08T09:47:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replaced int for long in loop over vector
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9d5f224c12d4ca7fe6b7183a824e082c511ee75">d9d5f224</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-08T09:48:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added cleaning for ctfrefine, motionrefine and inimodel jobtypes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4eafda9735678ff3fbe55d452b27f2d7a4c19f4a">4eafda97</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-08T12:02:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Import: sort files by time so that incremental subset works fine in relion_it.py
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/26c97f7b39ec5ab61d8296c0495794e37935b0de">26c97f7b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-08T12:02:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">own_motioncorr: get rid of warnings about grouping
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e6fedc610f96c88a29151e373f9b9ba044a4eaf1">e6fedc61</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-08T15:20:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired before for stop_after_ctf_estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1f590e27c146f6b18c8b721cdcc276a40426e7b2">1f590e27</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-06-08T17:58:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/tcblab/relion-devel-tcblab
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4ef2968c1d7144f8470ba791883dd05bf9251a2e">4ef2968c</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-06-08T18:00:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Simplified README.md
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e486b6e973f04da6ff5b17674fb1f41cfee4023">9e486b6e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-06-09T09:53:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in FCC computation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c6a82a86210fa4e408aa343903800a24be5b7889">c6a82a86</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-10T18:05:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TIFF: supported TIFF images where the last strip is shorter than others.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/59351ce358e51dd570f460d9436949a1ef328836">59351ce3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-10T18:06:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/795d3c97786db1d8ed969ba952fdf91f5c9c3f37">795d3c97</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-10T21:14:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: Check the presence of meta data star file when --only_do_unfinished
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b6d8c06b1b20c57e0d5b9d9dc35469bc5ca70057">b6d8c06b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-10T21:15:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it.py: when the resolution is the same, take the bigger class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3107ed77acfa3eda7d84d2c920503b4f6d4a010">b3107ed7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-11T12:17:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cplot2D::joinMultipleEPSIntoSinglePDF: make this robust against the limitation of the command line length (ARG_MAX)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0db9e08ebc39e0823c2b1d235fecd6713016a837">0db9e08e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-11T15:09:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> added error for not having used relion3 for running mc2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/725dffd5750b9190ababe123146018c8e23e438b">725dffd5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-11T15:09:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ecef6167a3f7c971aee934fbf334248c8e8b479f">ecef6167</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-11T15:14:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">place error below trace not to confuse users..
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6cb20e893e9dc1c0a981d84ca3192e0bdcec7767">6cb20e89</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2018-06-11T16:45:53-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix ALTCPU build - typo in helper.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b504f4639752274b9488880d0638ec5e2df37140">b504f463</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-12T11:39:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed some testing programs from standard build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/13add67567eef9361a193f0b3bcd905a86f1bbac">13add675</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-12T11:39:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ca2547b6d5b5384c32016aa6a9132f6370479d4">3ca2547b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-12T12:03:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove remove_duplicates from extract gui as it doesnt work yet
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f2d62fef10b07eb7bbafb74eb0c2d022c16cc91e">f2d62fef</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-12T12:03:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ba20d8e41ddb0c034c3114ca07e7d8a3e38c19e9">ba20d8e4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-12T14:45:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #158)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf589ad048181a76ca0ebea0a9233ed0ce3066a8">bf589ad0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-12T16:21:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Expose the queue name and the queue submit command as environment variables. Also the maximum number of MPI and threads.
This is based on the pull request #338 from @JanneM and @jmansour on GitHub (thanks!).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4bfad023f31896fdb52a149e7ee60d2ebf0f2d1c">4bfad023</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-12T16:24:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d96013cb7a98eae1a0d612f43e9902c3e968fa6">6d96013c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-12T16:44:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed some GUI help messages. Guard against SEGV with RELION_QSUB_EXTRAs..
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41d09ce3e35ce23e2ba3ea87d75a32d17cf21824">41d09ce3</a></strong>
<div>
<span>by Lanqing Huang</span>
<i>at 2018-06-12T16:47:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed overflow bug in relion_MPI_Bcast Implement Bcast to handle larger buffer size. The definition for nzyxdim of MultidimArray is a long int type. In some cases, large boxsize makes nzyxdim overflow when broadcasting data.
Signed-off-by: Takanori Nakane <nakane.t@gmail.com>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84515654063211670b9dc28d449d9cd2f4f39613">84515654</a></strong>
<div>
<span>by Lanqing Huang</span>
<i>at 2018-06-12T16:47:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use static_cast for type conversion
Signed-off-by: Takanori Nakane <nakane.t@gmail.com>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e2de1770baf68a3069ee9a50a8db00ebe06c2c4a">e2de1770</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-13T09:20:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed defaults in header
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ed88213e7527d8d1a5155b680ebf48b8d2caeea">3ed88213</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-13T11:38:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad51ac0de09a03bf759556541a1ca54e3d0bf4c0">ad51ac0d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-13T12:01:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot.py: Print B factors from postprocess as well
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d8c4c3292c1c05bcd589bd464274966fcb7fa9c">7d8c4c32</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-13T12:02:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ef08d8feb9103219161765086b7e2bcb0a82dbe4">ef08d8fe</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-13T12:19:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: give an early error when GPU is enabled without image alignments.
Don't deactivate the Run button when the job is not submitted due to an error.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ee4e61ffdc91d74bdcf153c8ab66b09707be4283">ee4e61ff</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2018-06-14T13:06:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ALTCPU=ON sets CUDA=OFF, quits if both
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1043588e9f057f203ef70c4add45bccbe453964d">1043588e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-14T14:55:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot: Added double axes. Print the coefficients. Expolate the line.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/11bd940deb3ebd6cfde40faad906a33d08f71b2a">11bd940d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-14T16:02:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_pipeliner: added --setJobAlias option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0f3a9170dbafa0f70e79af97687cc7a889752fd6">0f3a9170</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-14T16:04:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot.py: expolation of the fit. added opts.prefix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8500ea4ea73dd56e13d97cb0b33f0c041584a28d">8500ea4e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-14T20:45:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">own_motioncorr: Detect and fix hot pixels
MicrographModel: save defect file (currently not used though)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/da5e4ef635227269bafb13468a14dcc610a737ad">da5e4ef6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-14T23:14:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot.py: Make X11 unnecessary, Tidy up aliases.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2922f18e53ad9ef8fa6eb9ca9e804680344089c6">2922f18e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-14T23:15:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">autopicker: remove unnecessary space from the file name
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1d14d04e6a66c8fb2e703ae9f86819586a895e4c">1d14d04e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-15T09:34:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it.py: set job aliases
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47babf8b77a0ab40f1af58828fe392b3988c9824">47babf8b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-15T09:48:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Improved help messages.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d68b4f6e057e418f19c642238fa111547882d3d9">d68b4f6e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-15T12:16:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it.py: described how to re-run the second pass when the automatic selection of the reference was wrong.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/80d8651fb1d2a1e6d3a19d87bf457af9c2b1a167">80d8651f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-15T12:25:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed confusing save STAR with selected images from subset selection
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/912a2d84678ea020a5cce3cec47ee8136788e185">912a2d84</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-15T12:32:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5a0cc00328838a3d77ff8eca8ee2e21a17668ec">c5a0cc00</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-15T12:34:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">made new option to reset offsets upon re-extract from data.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6647ff8397bb8609c390ef520afeb694a4b09cfa">6647ff83</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-15T12:34:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d36db560d6656ba42b142754feaf26a985411a28">d36db560</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-15T12:43:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in tcblab/relion-devel-tcblab (pull request #155)
Resolved Conflicts:
CMakeLists.txt
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4680e0870b320cedb07f4754096d44ffecd9a93">b4680e08</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-15T12:45:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5c89192bb17d574337dc782cc7548a398eb94b4c">5c89192b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-15T15:08:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Workaround for FLTK compilation error. See https://patchwork.openembedded.org/patch/112023/
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1aa0e22160ff01269695dbeaeddbf491b8710cfc">1aa0e221</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-15T15:11:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0a1d3ab40e68bed7850fc70982eee244703b352f">0a1d3ab4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-15T16:53:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add *.tiff to '2D micrograph movies'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f597285d2bd870eedeac7964050b894de222c807">f597285d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-18T10:52:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">multiple classes outputNodes in inimodel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e5a15ada0f5af821f1332e20b7ac256e9e92898d">e5a15ada</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-18T10:53:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use unmasked fsc as true if solvent correction makes things worse
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a2d2f595d24952ed681201b106245e0c7adbff2">3a2d2f59</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-18T10:53:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d2e3eb8169afc1347dd677611aa4938f4fd6f17">7d2e3eb8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-18T15:10:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bb9ab1034137adc08265a6894d56c5c31ef76b06">bb9ab103</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-19T09:38:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added modified betaGuide
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0e42f33e8bc09d50e5314b833863951f86b63305">0e42f33e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-20T11:27:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">had forgotten to set version number to beta
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9087e64e8666a5eb06ca2e31d64b0407f6d3ada">f9087e64</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-21T09:08:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor improvements by Colin
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5c10379eff62a9a7b01c225004dd3b7df6548f89">5c10379e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-21T09:10:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-3.0_beta
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/741d246201939b08d46e6d7b7521c1a74b001f10">741d2462</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-21T10:23:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2fb81c2cdf1f8aeb694028732e837ba9d0de9320">2fb81c2c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-22T11:39:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Fix crash when opening old project directories
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/96c6a21650d4b5aa2ebeb694cc385a1bdc8cdc59">96c6a216</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-22T11:39:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Fix SEGV reported by @pemsley on GitHub (#370) when double clicking the stdout/stderr box before selecting job.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/25c2ced9a79bf337bb2a8876fb5ebb070f3dc9a4">25c2ced9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-22T11:41:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: added --skip_weight and --skip_mask for Ewald sphere correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ceed10682f71d78a6ea5c605a8bba2cf6023793">6ceed106</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-25T10:50:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Fix SEGV in Import
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/97e8c6b771c232292250d353a1a15a3f6f4a5e31">97e8c6b7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-26T09:50:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better description of possible movie extensions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b0a73ffdec7a47e88c30725f9a591437517a5903">b0a73ffd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-26T09:50:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca73a0bddf74d56384db40deb9a0bc37f77168d4">ca73a0bd</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-26T13:59:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_preprocess: print the extracted pixel size.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c316b108e3fab5a7df6127845209775246b86389">c316b108</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-26T15:07:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: More accurate explanation of "Range for defocus fit"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ce89431900d14555e0dba99ae405b5134d7ee27">1ce89431</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-27T10:02:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed bug in labelling axes in C2PLot, now have to do this last
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd44b4695d381477f8a6841d238f750cd98ef861">fd44b469</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-27T10:02:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/706a30f1674d10f75b6b95015e10c37efc9750df">706a30f1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-28T13:19:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use long for split_size in star_handler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29f642b8326cf53ada568ad0061f9fd7e9f9185b">29f642b8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-28T13:49:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replaced some backslah-n for std::endl
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c10c67f274c28ae519abe89195b9aee9a05b29de">c10c67f2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-28T13:49:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replaced all std::endl for backslah-n
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a692c0a4ae256b3f15f0d663819bf51e24624e2">6a692c0a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-28T13:50:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replaced some backslah-n for std::endl
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e7a8a07b9d794bf2c25ca37807f773a98e138e28">e7a8a07b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-06-29T12:58:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use mkdir instead of touch for lock as the former is atomic and the latter is not
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/548365f3a27153951d6d80c1374d5066cde76d7d">548365f3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-29T15:04:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_star_handler: added --select_str_label, added --remove_duplicates..
TODO: make GUI, support down-sampled particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/efeb7ea91026562ef1bbc52bb0b52a1cb9edccbb">efeb7ea9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-29T15:04:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c4a50f8cdb3d6c321a06e4c55ce719d57303516">0c4a50f8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-06-29T15:59:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_run_ctffind, relion_run_motioncorr: implemented --do_at_most N for pipeline
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a69b7f5abce92f13f6689c3c9547edba0857eed3">a69b7f5a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-02T11:28:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it: now it can pick up results from continued jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/df3397bba17ea79d7ca8192c6506e9a93094855a">df3397bb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-03T21:20:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CPlot2D: fixed SEGV when there are no point in DataSet. This fixes SEGV on CtfFind and AutoPick.
relion_autopick: Fix average particle numbers when there is no input micrograph
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/998ec3419b24b11cb5937858f16ccbc197bbc64d">998ec341</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-04T12:36:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: make an empty PDF when there is no input. otherwise, the job never finishes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb801521d6d094d43e0377a8ce222e483b0479bd">cb801521</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-04T15:53:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">star_handler: remove_duplicate now supports down-sampled particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16d3f460f936153643ef84dc4b8d8522cdb4d192">16d3f460</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-04T16:29:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Remove duplicates
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c78ae4847a88568e80be4088e0c0ac4d056033d4">c78ae484</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-06T12:26:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">warn about lock directory rather than file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3271e9a83bdb9f461c8d32f7853f5ccee8c95d5">b3271e9a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-06T14:09:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out reference projections from 3D model for autopicking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a039a4008acafe6084e8c74a8aa2c4608a5de61">8a039a40</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-06T14:09:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/909754bbffd28a0eebb456e2b6616ae48be9bf06">909754bb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-06T14:48:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in chaeck for particle diameter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cde6d9a71e1c9f76a4e166bc9aac8f8d73c4a9a8">cde6d9a7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-06T15:08:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">warn if pixel size in reference images is not consistent with angpix_ref
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/65ccfd03d8d0ba60d99a8d004098273b1cdd1e85">65ccfd03</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-09T17:46:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only write EPS file once, was done many many times....
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d2f0dd7d2bd3fe3eeb2b4ba298c14872cc42c5ce">d2f0dd7d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-10T09:40:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">first submit queue options then add discard_job
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0d093bc812df60fb48ba7480dba7d0af35f5b97">d0d093bc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-10T12:57:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed ref-based autopicking threshold default to 0.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/769f340549e172b103b56bc8021614744c178095">769f3405</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-11T15:13:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont delete stuff from the last iteration to still allow continuation or multibody refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eeb3f7043736244cfb86c8c09ef4206414663e86">eeb3f704</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-16T09:26:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bug in reported pixel size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc8ed810d8143c1544b8a96492819859c8bc3f55">bc8ed810</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-17T12:07:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">worked towards patch from EMBL to have multiple extra fields on GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5e76a75a28fc2bc76dc4aebacc311f7e99eb5be7">5e76a75a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-17T15:32:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug maxres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a571bdba8729cace4404da854383d4c2bf87473">5a571bdb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-17T20:27:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_ctf_refine: update STAR file with user provided --angpix, --beamtilt_x, --beamtilt_y
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/32189ec1b8059257258a519176f644ce894d5577">32189ec1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-17T20:28:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4160e579577b535ebcdc99b880132c18ca9a6021">4160e579</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-18T11:52:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Alias: Prohibit use of symbols that might cause problems on (some) file systems.
Thanks to suggestion by @rbehrouzi on GitHub issues #372.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a088d7ac3d44c11f193f80f1540612f36117f876">a088d7ac</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-18T12:00:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_particle_sort: change the default output filename to sorted.star to avoid overwriting the input.
Thanks to suggestion by @daniel-s-d-larsson in Github issue #374.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f5ab3012dd4184b5c2ddd132e22608df91ac9b2">3f5ab301</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-18T15:15:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">sleep 60 seconds before checkCompleteion in pipeliner because of leeds
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3411e814e4de331461dfc8895aad3f6f63f71bb8">3411e814</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-22T22:34:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_model: Set the pixel size in the header for class averages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad5e48a957b697718f6e12b20cd6fd3f9f4b26ec">ad5e48a9</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-07-23T08:45:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/master' into jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/55f2eaa1a4b65e134af1a432db51276ebd36f1ca">55f2eaa1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-07-23T08:49:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing apps added (not for release; good to have them in the repository)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5a96fad9612a86b769ad6b2c271b3d345b16de8">d5a96fad</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-23T14:13:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI help for Cs: Most JEOL microscopes have Cs=2.7. Only some have 1.4..
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c26cc874328e05811c10c747129eed3864ec9929">c26cc874</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-24T14:14:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: check the presence of the subset column
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a0ad84c38fa952a6fff5996ae72e8da72798fc26">a0ad84c3</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-07-25T08:43:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Beam-tilt handling updated: tilt is always used via MD-table, ObservationModel no longer knows its own tilt values. If tilt values are passed through the cmd. line, they are first written into the table; Motion_fit now supports tilt (again), but only through the star-file.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/87476f20a4d3b371e59bda84c613811448de6828">87476f20</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-07-25T08:55:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ctf_refine: beam-tilt source stated on console (cmd. line, star file or neither)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/540e5699274de6e9980bfa98bd0004e328a9afe8">540e5699</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-25T10:53:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">alias: prohibits use of % and & as well
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/73d0d246244875c21a4994a3a0c8bcaef78f2363">73d0d246</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-25T11:16:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_preprocess: set the pixel size in the image header
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be495bcca7f9a039cd34a95532b0634b47ba90dc">be495bcc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-25T15:16:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont use strstream in slow writing of star files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e568c2085997dd39c1e5dfa2cb46a2c9c95ceb55">e568c208</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-25T15:17:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/35a819116f987b9e8b6966d18b6be92e481ce9e4">35a81911</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-25T15:18:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">moved to beta-2 version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5f3d17a7d06093a31f37a48e8784a46b53def475">5f3d17a7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-25T16:49:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Included MTF STAR files in the distribution.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8206e2a240c54ca181c058651c17a887ca58f5a8">8206e2a2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-25T16:50:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64cb30a40d2c1d310e509544695cb9c433fe8356">64cb30a4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-07-25T16:53:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Beamtilt classes implemented in ctf_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9911a5390260b4bcf7f70cbd7f637e5f4034c008">9911a539</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-26T10:21:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb (pull request #159)
sync relion3-beta2 to relion-devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f46fc135af9c7f211c9583ce43ce5e0c44ccd1c1">f46fc135</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-26T12:12:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only master writes out projected images from 3D reference
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e8092e905c8e3b222a8e5a1f15a753c1d01eb46b">e8092e90</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-26T12:12:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24f471d4c2efae1f4ef009b88be956757d01825e">24f471d4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-30T19:49:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_motioncorr_runner: added --max_io_threads to limit parallel disc access
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bd535a88bfd842014e5053089b141f62d64edaa5">bd535a88</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-30T19:49:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf9f35ae50e7ebc83cbe251a7d1faa11553aa484">bf9f35ae</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-07-31T11:13:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: removed debug codes (thanks to @craigyk for pointing this out)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/814940d430801fcf87a269f041e33cd61473028a">814940d4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-31T11:43:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in scheres/relion-devel-lmb/jzivanov (pull request #160)
Jzivanov
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7bb1a51bf60d70d2d2f22c770f68469a85af842">a7bb1a51</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-31T12:47:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged tcblab/relion-devel into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac6ec4c00279bfb59839ef3085f0a5741bce8a7a">ac6ec4c0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-07-31T12:49:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed temp programs from jasenko from default build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d2dd1b657da4784b6862a93131c7f6ccbbc8fa6c">d2dd1b65</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-01T15:34:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_mask_create: write the correct pixel size to the header even without low-pass filtering.
Thanks to Bonnie Murphy for the bug report.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2e0eb56ad52bf1adc6b7692540ebbc31c4f57c4">c2e0eb56</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-01T15:36:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca338c43c93cea9d8c5875337ed041f3284396e9">ca338c43</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-08-01T17:10:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated betaGuide for general beta
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3b9e3871c9daaca478b0e8d6bd7ae530a7a83a79">3b9e3871</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-08-01T17:10:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d2476f2c8a204f112ad6d3deb73a98f5899b639">8d2476f2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-08-02T11:12:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">default behaviour of EXTRA_COUNT same as before
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68ab09c048eb4e19935213464366c73b1ea49ce8">68ab09c0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-03T11:56:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">pipeliner: revert the default wait between jobs to 10 seconds and added --sec_wait_after to change this.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/616d03bb001974874f88cb1f08d3985e7f5d98b6">616d03bb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-03T12:24:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it.py: include Colin's suggestions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8c2b7743e6e8b6f10bbb78434d77ebabb034265e">8c2b7743</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-03T14:21:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">LoG picker: output dummy columns of psi and class to prevent problems in Extraction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cea11c92fda3e1bef37a4535db272da42bbee1bc">cea11c92</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-04T17:13:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">irrelevant changes to apps/CMakeLists.txt
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/527acda25a1d95f48ddc4c60a297a8750d874c31">527acda2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-04T17:15:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">irrelevant changes to apps/CMakeLists.txt (2)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/915dde90623d295fa17042e507ac636990d2a91d">915dde90</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-05T03:09:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Zernike polynomials implemented and tested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/31c5985438bd270e43cd55137c59a181cae04a32">31c59854</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-05T16:25:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">optics groups implemented (not yet supported) and conversion program written
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cf2a2b96d57295b4d4da70f69e0acc602f45b410">cf2a2b96</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-05T20:32:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_refine now uses the new data format; CTF::read renamed to CTF::readLegacy; ObservationModel renamed to LegacyObservationModel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/50c91f1f86282eb9abee126289962c6678231e17">50c91f1f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-05T23:42:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new CTF::read renamed to CTF::readByGroup to avoid confusion during merging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/416d1e956a61dfd2e7151b9709ebfb1152113a5c">416d1e95</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-06T17:26:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_star_handler: write split001.star the last. Otherwise the pipeliner can prematurely
think the job has been finished and this can kill relion_it.py
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/63970b56787f917b6e593ff2cd56186d58aff669">63970b56</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-06T21:34:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it.py: proper parsing of SUBMITTED_JOBS. Respect extract_bg_diamer.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fdd227075929904a5741db6eba22d15df2bcbd1d">fdd22707</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-06T21:42:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot.py: same improvement as relion_it.py
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/abeddb88d86837b451c0597d3dad06e7fc46f04b">abeddb88</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-06T22:03:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it.py: submit class2d_batch001 if not yet.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8cdf3dd5f4fc5fd976eb9bb626201d768b6664ec">8cdf3dd5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-07T12:54:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf.h: use SINCOS macro instead of sincos itself.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/afec33f14a7d62445edf0da9b65955343037956c">afec33f1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-07T15:08:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove jiffy test programs from distribution
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dfa94448b20db125e34b0c3416f732207ca0bf42">dfa94448</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-07T18:41:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_refine now uses optics groups instead of tilt classes and it writes the results into <out>_optics.star; handling of optics groups is more robust now (vis-à-vis undefined groups or groups given in the wrong order in the optics file)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/66503ee3bd9220c70a3bf08b1771f0d182592688">66503ee3</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-08T00:09:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tiny adaptations to tilt_estimator; anisotropic-tilt functionality removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e203e56cf0d2ca34fafbc84c964c728d117e525e">e203e56c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-08T00:32:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">yet another attempt
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b557f8255e1532b6df492146d45bfd602f1ca37e">b557f825</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-08T00:35:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">re-commit with slightly changed files to trick git into uploading the current versions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d914e4e4f6c30f6b0509b7b6c4609888dbff305a">d914e4e4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-08T01:23:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTF::readLegacy renamed back to read to make cuda code run again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f24b5b87eca7b9c6b97033a2b124d8740091c723">f24b5b87</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-08T12:48:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: give an early error message if an optimised parameter file is not specified.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f76a7a0d32b2fb70d968c3e5962f04efbf5f3a1d">f76a7a0d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-08-08T15:11:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to write out projections along eigenvectors of all particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/568a9ffb7dca215f81387ced5ecd790e4d675fec">568a9ffb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-08-08T15:57:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">modification in intel instructions suggested by Charles from intel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ab9f552dc847a92e7b41c760b527b55e8ad1fb59">ab9f552d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-09T18:43:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Odd Zernike fit implemented in tilt_estimator; coefficients written into _optics.star; MetaDataTable now supports vector<double>-typed columns
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e0190e934a9b0588c6336c11562ab8de70936a31">e0190e93</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-10T02:42:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">beam-tilt angle extracted from and inserted into Zernike coefficients; phase shift caching implemented in ObsModel; ObsModel loading streamlined
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a83cf1b52cf7953e1f289ac63c57a8c0800b51b">1a83cf1b</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-10T03:35:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">double_reconstruct adapted to new data format (incl. Zernike phase model)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f974e61fc0112d80c31343d86e224b9904388663">f974e61f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-10T03:49:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">double-template definition in metadata_container.h made CUDA compliant (> > instead of >>)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a382efa2fbc4cb7ef76ba6324b25cab2681e79d7">a382efa2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-10T13:56:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">old reconstruct updated to new format (untested)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3038be3e051949a81163f51afd7b59253fdd3fe6">3038be3e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-10T13:57:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9e4ec45430452ca8f1868297abb222fabf73031">f9e4ec45</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-14T10:31:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_postprocess: added --force_mask option to use the mask even when the resolution becomes worse
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b0be4a0a1b3f6e5d26d499df9fe3fc6af5b29988">b0be4a0a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-14T10:32:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fc3936914cb4378bc141f7f9e026512452866501">fc393691</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-14T10:34:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_motion_refine: make the warning for truncated movies clearer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e189e9060ac06b509bb04a9941845ef2b209eec7">e189e906</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-14T12:31:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MetadataTable: fixed SEGV in histogram
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d657c5b8acc3cb37670dc4a7595e428a81395a1">9d657c5b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-14T17:44:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">histogram: set ad-hoc upper limit to the bin number to avoid using too much memory
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9cc754e877906ec5e08812f3cc8647f30b5a3e81">9cc754e8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-16T14:34:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: do not add "--fast_subset" when continuing. It is read from optimiser.star.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/390afdb9d286bfa9ea1eed093896693a4769ba03">390afdb9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-16T14:44:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it: retry load_star when the file is truncated.
WIP: This is not a perfect solution, which requires a locking mechanism.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5b41293d7a1f665562b41de42e0d3e95e478bfa7">5b41293d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-16T17:12:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">non-linear aberration fit implemented in ctf_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3e9c76d0936df0650368e60eccc3c0061110c747">3e9c76d0</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-16T19:57:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">demodulate tool written; can output Relion-3.0 star files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad298041330dc26f6b867f149c6d6f6b60254af6">ad298041</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-16T20:32:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfixes in demodulate
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e65ddbe023bedc55c915a88e30b79da446e861ef">e65ddbe0</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-16T20:43:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionErrors printed on construction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/079990f02b205d7a8220259329febdc81d9cb611">079990f0</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-16T21:08:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">another bugfix in demodulate
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7bb20dde41becbbf59de71e60cf8d57333ae3203">7bb20dde</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-17T11:11:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refiner: improved a warning message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/19810adf90c041703aa079dca62aed7c50f80a99">19810adf</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-17T12:48:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_autopicker: Fixed 3D reference (had to set XmippOrigin!). Also improved a warning message.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/660d890c5a0176f0d04165d0bfea522fc68ae554">660d890c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-17T16:36:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">decomposePipelineSymlinkName: don't expand jobXXX
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ec12e5f3df1e9abcc8575a20c69aedefa936a33">6ec12e5f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-17T20:10:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">decomposePipelineSymlinkName: safer link expansion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/922ef473e2859943b1de754e4a714de8d1f53aea">922ef473</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-17T23:42:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in star conversion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47258ddb479a5dbf8f0b520cc2079f4aa6410cd8">47258ddb</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-18T00:24:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">demodulate no longer leaves an optics group id in a relion 3.0 star file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/08cd0cd699df0a7837262fb4d7b296b63977715c">08cd0cd6</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-18T00:35:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">exclusion ring implemented in tilt refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/db1f511ba90b6a9469912dfeca14290959d78eca">db1f511b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-18T22:40:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: repaied --early_binning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4be83f76c9b46bfbe7371f6fa29df361a4947764">4be83f76</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-20T14:58:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">star file version is now set to 3.0 if no version tag is present
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a88311e037e5e0bf88cf46ab95ffa594af704c8">3a88311e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-20T17:34:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">format version now written out correctly by convert_star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a025627f881dbe908f6ae4002d4df0edbebe921">9a025627</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-23T12:46:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix ResMap for multi-bodies. Do not replace 'half1' and 'half2' within directory names. Fix memory error in the default ResMap path name.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e98431944e6b02b9e3429ead3b7697fa14d2578f">e9843194</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-24T17:23:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fitting of symmetrical aberrations implemented in ctf_refine (untested)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4ce5613f46d4b6436a6a001336e9aebd93986659">4ce5613f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-24T17:36:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bugfixes in symmetric aberration fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a4f05ab51c4124e1e3b3e9d764d3601ae31f05d0">a4f05ab5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-24T23:09:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Symmetric aberration fit further developed and debugged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7204350267e8de37ccf30a5e5ff1f7bcba0c21d">a7204350</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-24T23:30:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">another bugfix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6bb94017e9ecebdd0261839d94ccb2245642cff0">6bb94017</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-25T18:57:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">effects of symmetric aberrations on the CTF implemented, including caching
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/79882c3a45de78230e194e277c286d556c252ba2">79882c3a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-25T21:17:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">distorted CTFs now used everywhere in src/jaz
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/447d8d4edb0ac350f9adab10fdf777e8b635292b">447d8d4e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-26T00:17:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">multithreaded caching issues resolved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/628013433e514350b64dca380694683090f82793">62801343</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-26T16:43:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in double-vector metadata handling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e5aada94c881a081169664ce5b6e3f1fc7f6999c">e5aada94</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-27T10:11:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Fix RELION_QSUB_EXTRA1/2 (Issue #391 on GitHub)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c728e0fc11bc6aac7c7881646b40f7b25fff3ca">9c728e0f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-27T23:20:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">pixel-weights corrected in symmetric aberration fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d578a99dc393455f8fe861d764408522c14e94c">8d578a99</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-28T14:13:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in ObservationModel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4772b013f775d952a6fa672529267ff6542bd541">4772b013</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-28T17:50:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser tentatively updated to new data model (untested)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e33c1685429a694931dc58f7c0458c5b41469276">e33c1685</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-28T18:03:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">optics_group removed from ExpOriginalParticle
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4c50458c3d09c51859dfc6901b781d13951af2f4">4c50458c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-28T18:17:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">opt. group in acc_ml_optimiser_impl.h now also obtained from Experiment
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d42b6f7186a444632da2e4bb184d3ce104792ed5">d42b6f71</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-28T19:26:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">double-template '>>' changed to the antiquated '> >' to make NVCC happy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ccb43d8324057d3edbb928c2eb39a746161a7d3">8ccb43d8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-28T19:30:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more >> changed to > >
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5bdb2d653b2f93ccb4a0b1d69270950520a619eb">5bdb2d65</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-29T00:36:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTF and pixel-size handling corrected in ml_optimiser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8dd8ca0c98b8f628203f68dde3de638ef609023c">8dd8ca0c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-29T03:16:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf handling redone in ml_optimiser: all ctfs are now created at the beginning on all nodes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/25dcb426c3ab027c2d428abaf73b63debceedf85">25dcb426</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-29T04:03:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remnants of the old approach removed from ml_optimiser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/11ccb51a3989ba5e9c462af02061886183af8359">11ccb51a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-30T15:04:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_preprocess and GUI: warn about --set_angpix as this option breaks Bayesian Polising.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6581a2b147fcf09c9cc45c70a2d58329d8682b24">6581a2b1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-30T15:09:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Changes suggested by @Fravadona (thanks!) on GitHub issues #387 for Mac OS X build.
Note that we do not officially support Mac OS X.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/340fd229a442f49442811bc00320fda307f31f5d">340fd229</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-08-30T15:11:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_helper: atomic operation is not necessary here (confirmed by Jasenko on 29 Aug 2018).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4fbd8096afb40a2e132164f72c68354234fe4f92">4fbd8096</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-30T20:07:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTF::getFftwImage now works with images smaller than the original
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/88b603a601dcc8a4becb15b0ac16ddb959f9036e">88b603a6</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-30T20:19:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bugfix by Takanori applied
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0317826aeba642cf7a291829f1b88de07bf6b8ef">0317826a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-31T03:44:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">anisotropic mag written out by mag-fit and read by ObervationModel - only used in prediction so far (untested)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/954ce066a9915737353d3833f1acaabdd9fb14f1">954ce066</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-31T04:46:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in MagnificationHelper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/783b2f6a65e7eda059d9017fdb5dd19eeb6ea8db">783b2f6a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-31T14:48:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in symmetric-aberration handling for cropped CTF-images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac09585083ca21943b069a9caf8b89d0e6d94bb9">ac095850</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-31T14:53:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">refine continuation bugfix by Takanori applied
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/20670b20d1e0335715c9739521b527bd81d67828">20670b20</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-31T19:31:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mag-matrix now transposed and multiplied from the left to A3D due to the internal transposition in Projector::get2DFourierTransform
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e76fd3bcd9dc4c4811ebce9d5ae9e90fe0418388">e76fd3bc</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-31T22:16:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">anisotropic mag support added to double_reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b90a3b7fb17766ac17ec9f188da6ee20929ba831">b90a3b7f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-08-31T23:51:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">anisotropic mag can be estimated iteratively now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ad52893ed42359c76af50d5b58cf8a54e1b123c">7ad52893</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-01T00:20:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">point-group symmetrisation can be performed in parallel now (and it is in double_reconstruct)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5b658abd9fa9c40912d5ebdd7e1f0be0094ed745">5b658abd</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-01T00:29:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in symmetrisation parallelisation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c4f6f3f90a2451ca59ea048575e83777c1a2ce74">c4f6f3f9</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-03T04:02:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTFs are now defined in coordinates undistorted by anisotropic magnification
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/95fcb400925646a32a74a0ee3713607926ac0fcc">95fcb400</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-03T11:14:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">astigmatism is now expressed as a bilinear form inside the CTF class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0aa0b0223a3954c0d3b3ec77766e681311be3706">0aa0b022</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-04T00:29:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">astigmatism is now adapted to the new coordinate system after anisotropic mag estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ea0196805c47799af16562ee470e922294b4e059">ea019680</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-04T01:05:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in particle-MDT output handling in ctf_refiner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bd838593f400e1cc0b1716c50442d06619430c4e">bd838593</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-04T01:22:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in per-micrograph constant astigmatism adaptation to anisotropic mag
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a01ea12aa9c45f33fd4f9954a2e121a883b11d3c">a01ea12a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-04T03:35:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">anisotropic mag tentatively added to CPU-refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/949d97f02310657592b3d7a6c511116b72033dea">949d97f0</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-05T08:49:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">symmetric aberration fit now uses a mag- and tilt-corrected prediction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34ffdc5cc6bcd2f018f773a16052935d69edf96f">34ffdc5c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-05T16:26:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">backprojector can no longer write outside of the data and weight volumes (relevant in the presence of a magnification matrix)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d6516a960e8a459ad6c657d80b0ce611babe46f">0d6516a9</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-05T17:19:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forward-projector (NN and Lerp) as well as NN-backprojector now also safe from out-of-bounds access
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/107f7590c153c319c3dec6be764d6e08c5596355">107f7590</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-06T07:52:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mag_fit: predicted-image gradient is now computed in 3D and projected into the 2D image in order to avoid the systematic underestimation of the gradient magnitude resulting from linear interpolation (which leads to a systematic overestimation of mag. anisotropy)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e6914cdee2a930bb6667e0025bf3353740d6b1fd">e6914cde</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-06T10:58:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix for new gradients under phase modulation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d57af2646c602a67c9111cda4e9dd7625c2d0934">d57af264</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-06T13:14:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reposition added (untested)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1f36b4db981d7fb953609e074a3f6548eef3797">f1f36b4d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-06T17:37:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: repaired --reuse_scratch, which was not doing anything before.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c15860a299c06722b6575a1a6119ef3344caef58">c15860a2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-06T20:21:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in relion_reposition
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3262f347aa31b36ce9b80826f4864589d51d5867">3262f347</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-07T07:29:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_particle_select added; --cc_pad option added to particle_reposition
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1891ab14a7018469a8d4df1720ce64b12df6c5b2">1891ab14</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-07T07:31:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_particle_select actually added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5747461c65cf858e68860442f359a1548a2702af">5747461c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-07T11:59:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to do gridding instead of using a Wiener filter to double_reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f57f57a059cf529635778840da17fc562b93ae2a">f57f57a0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-10T14:06:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">flex_analyser: --fn_keepmask is mandatory when --subtract
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/034de963226c45fbceb3a6bb1871409a76dc2221">034de963</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-10T14:22:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mask_create: repaired --and, --or, --and_not, --or_not (Bitbucket issue #24 reported by Lukas Kater)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/88101f9dfcc9a67f56d790d1da0e8bf14f58ee15">88101f9d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-11T08:00:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine: initial MotionCor2 trajectories are now being used even if only a global trajectory is known (untested)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/28e69e72c2f5491f69b2283ac4062079c8c0f5aa">28e69e72</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-11T11:52:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">LoG picker: clarified help messages.
Also tested Jasenko's previous commit 88101f9.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4311d4af8a114cfe8a45db130ea367ea585b09d5">4311d4af</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-11T13:19:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_mask_test added, new way of predicting signal-delocalisation by the CTF implemented
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a59283b7af825c9d9a32cfcee78c23ea2457d44f">a59283b7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-11T17:59:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: clarified meanings of hyper-parameters for Bayesian Polish
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc5b5dc320f8d0fa30565a0ae4240646d222a958">bc5b5dc3</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-12T09:03:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">An optional spherical mask can now be multiplied with both data and weight before the division in double_reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d2fe1d1ffc8727f8685d0fcf165d09732cc25e3">5d2fe1d1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-12T09:30:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in spherical mask: radius no longer doubled
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e7f62b864f21c469dc0fb6e010b533ec2af70f7c">e7f62b86</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-12T16:46:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged master into jaz-3.1 using auto-merge
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47fe9feba91cd583859dac4d3ec1b27a7aa6633c">47fe9feb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-13T10:05:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">started removing ori_particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b7c90c7eca2351ad1e78b36f7150978200c25ef6">b7c90c7e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-13T12:45:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">per-particle B-factor fit implemented; some files moved around
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/49f147020c6883479605f01cc007f5b2b0fb7812">49f14702</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-13T12:45:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/92e56d9dca327f463e657c0e29e584985b954b97">92e56d9d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-13T13:12:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34814ea894a1e6b61baf167a9271157eb0175c49">34814ea8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-13T17:22:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">min_scale, min_B and max_B parameters added to B-factor fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a21098669cd8580bcee5314a0cb3c39fb0753c2e">a2109866</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-13T18:39:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in spherical masking in double_reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5bfcd4ce942dfc2b4f8b92aff4ae13535d4a00e7">5bfcd4ce</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-14T12:52:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">align_symmetry: added --only_rot (useful for helices)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60b44e06ff231841c1105d1da97c5fcf12b28402">60b44e06</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-14T12:59:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">align_symmetry: --only_rot respected in local search
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c66158292a3e1a80c3a55f953cd06750d91799c8">c6615829</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-14T15:01:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: clarified help strings for dose weighting
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5c42ecc9e5fdddfcaafe6fcb85f10a2f3104a8a8">5c42ecc9</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-14T15:13:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Options --window and --scale added to motion_refine and tested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7eb3ad0425160d556879f040103cda63e57ef473">7eb3ad04</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-14T15:13:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/master'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/498e6d88b6af3641df5f451d455f31a5cc60a33c">498e6d88</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-14T15:16:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/master' into jaz_3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a82234885cbda4b61cbabcb3ba56d0927f6020ef">a8223488</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-14T15:31:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine: new magnification now written into star-file when --scale is used
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c8f28cb60714318c0a17c0743bd109fab353421a">c8f28cb6</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-14T15:32:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging logs removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b21ed2e6d641c7ccf3c7ded7bb90d2205835168">2b21ed2e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-14T15:35:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merge with master #1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24a1d72a04cf0587814b9e8d770bdf781e05f60d">24a1d72a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-14T15:35:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/master' into jaz_3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2adc9f0c6c660d2b547e47a048244b60ac6a718e">2adc9f0c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-14T16:36:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">keep removing movie stuff and ori_particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c50f11617ec22f357360798989c40e25de47879">0c50f116</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-15T11:02:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_plot_delocalisation added and made user-interpretable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e2b08835a1cec9a453d082a17a1ca12a454893b8">e2b08835</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-15T11:17:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in relion_plot_delocalisation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/385928aa62fb886fd2aa6bb7c4ab021acd392e43">385928aa</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-15T13:00:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">plot_delocalisation: min_freq option added and per-particle feature implemented
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/772e8639d975cc2d2f10eeaedcc9b508c21763e6">772e8639</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-15T13:11:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">plot_delocalisation: pretty-printing in plot improved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a10f6c5a15f85098e4afd2aebb0c18ed6c39d1d">5a10f6c5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-15T13:54:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">per-particle B-factor fitting slightly improved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e5c8d7fa70201c663fd8829ec2d4af44faa26cd">7e5c8d7f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-15T17:22:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">B-factor fit debugged and accelerated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7683ed823fe165d67a96c284ef750584d3bb9bf0">7683ed82</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-15T19:36:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">B-factor fit better integrated into ctf_refine; B-factor plotting added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c9844ceb13dd0d36c493bdeac88f4c03dff6fa32">c9844ceb</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-16T14:42:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">B-factor estimation: accelerated version numerically safer now; non-accelerated version just as precise as the accelerated one now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/71429aab7ad512b18d3feaff96159ff94bd9b438">71429aab</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-16T17:11:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">B-factor estimation: added per-micrograph estimation and diagnostic plots for both estimation types
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dbce4dd65442f34f25abdc9b421785af9d142a31">dbce4dd6</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-16T17:48:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">B-factor diagnostic plots more meaningful (excessive y-range avoided)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1dd39fc0cb81fb61d6e6e1785c5464ce0fd4ef82">1dd39fc0</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-17T10:37:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ring-fits in B-factor plots no longer clipped
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/70e2c8f470a6d3081acba68852e5710d148f8fc3">70e2c8f4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-17T11:57:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed movies from refine_mpi
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/959fd50f50c99b977c5680b0c9a1935271bb5daf">959fd50f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-17T14:14:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GPL preamble added to all files in src/jaz (and all subdirectories written by JaZ)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/729452567620b39961efc7e9d9b199293abaa677">72945256</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-17T15:40:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in B-factor-estimator parallelisation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4efbc46efb1a12a8bcc5989cdf593bcd77457565">4efbc46e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-17T22:11:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">double_reconstruct can now optionally write out weight volumes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8729fe2139bd2fe53298112ffb2fd9b3d46fe43f">8729fe21</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-17T22:29:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in weight-volume downsampling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/abd833e48069dee9742258e37165ad411658ee28">abd833e4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-17T23:17:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">weight-volume value-scale now invariant under changes in padding factor
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a4f5c8d8f9c701c0a9555b451fadc03073ca2f6">1a4f5c8d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-18T10:06:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed polishing and movies from ml_optimiser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8670539d5e27e5004b1b3e1e2952236889926239">8670539d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-18T10:08:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed spurious debugging statement. now 2d_small_tagcase works fine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4dc3e921ca7f07b5777f33bc527ff70d239e5b5c">4dc3e921</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-18T12:14:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove old polishig code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4c52af1633d5149986931aaa1bedd1fb724d3af8">4c52af16</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-18T12:15:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed some indentation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/872ce3bde971990e324d1d980427c1ccaee24d84">872ce3bd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-18T12:15:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">got rid of randomised_particle order vector
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/95b21ddba06c531fd6e7f2f049cc10b56a96d40f">95b21ddb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-18T15:59:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor change to keep exactly the same
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e148d87338a594efdda10c0a582d8c65219da5e8">e148d873</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-18T15:59:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated version to 3.1-devel-scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ba33c88dc8a4885b3a7c1190d71a5d25e9f954a7">ba33c88d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-18T16:01:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed movie frames from accelerated part of the code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/69cc8f67d0dc8471a24072514d463877ae8bb005">69cc8f67</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-18T19:54:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">self-subtraction from same-halfset-prediction implemented (contains a heuristic)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e57c8c5b2230e02f26f0bf438058338e2d3dbcc7">e57c8c5b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-20T11:55:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: made the meanings of 'last_frame' clear and consistent (closes GitHub issue #400)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57c7654402f1ce5ffe1c7a72d4062f6db6be61e1">57c76544</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-20T12:00:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTF value-setting updated on line 5156 of MlOptimiser.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ec58ed04c9224e801ae9a99675d0ec0f7732a779">ec58ed04</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-20T12:14:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged master into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/00daf2ef8d35a79bf77699307287fcd0dd502b78">00daf2ef</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-20T11:15:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in origin/jaz_3.1_scheres (pull request #16)
CTF value-setting updated on line 5156 of MlOptimiser.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b530dd37e3b22c9cdbbaf395ca1caace7a7272fa">b530dd37</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-20T12:18:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">no longer need all columns to be present in loadSafely
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b0f6fae433ef1cf9968bae154bf06763dbf7f26b">b0f6fae4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-20T12:19:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b968058802b4e21761eff21f7cc9d4da5dbe8ca4">b9680588</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-20T12:24:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">introduced error when failing to read image
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7ecef50492696eba6adc80765ea7fabc8a20f43">a7ecef50</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-20T12:25:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">renamed to ori_part_id when referring to original order of particles in MDimg
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e1c6205681324d2d500f0984450ace0f020c3c33">e1c62056</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-20T12:26:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged with Jasenkos setValuesByGroup and did the same in calculateExpectedAngularError
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c40c1129930d5962705c87781f1cd15edc99f6ac">c40c1129</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-20T15:06:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">last commit before excision of self-subtraction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b24be2d17b9d9d48d3320030bbf89a40dd12634">0b24be2d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-20T15:19:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">self-subtraction removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4b57882db37b860f4d0053634a25ff3f7285874b">4b57882d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-20T15:48:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merged with jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1e9c25527393ded8a514d35913144be8dcefa1c">f1e9c255</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-20T20:21:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new particle star-file format implemented
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/91de027f155f91f300d6bed039e398b4ecb55fc5">91de027f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-20T21:13:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">All Jaz 3.1 programs adapted to work with offsets given in Angstrom
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/781e81ea67abdc904c35e1ba83e0ef0e19d47259">781e81ea</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-20T21:38:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c621f7469d475aae824997b8d942463a9052808">0c621f74</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-20T22:31:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_refine now writes the output star-file in the new combined format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/65f77f5ce5c87984b5b2e3f1add00e2a1252fc4b">65f77f5c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-20T23:02:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">metadata-table pairs written out by ObservationModel::save() are now guaranteed to have the correct names
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/480bcb25b6c719d4469552d26dfcf694c387d8f3">480bcb25</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-09-21T11:46:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Pixel size now stored in EMDL_IMAGE_PIXEL_SIZE instead of EMDL_MLMODEL_PIXEL_SIZE
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/785ffc8d792daeb697bde473a36e0ca3f2161748">785ffc8d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-21T11:12:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jaz_3.1 (pull request #17)
Jaz 3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb550b0b811c0d4f2150d2800e52d5911b6cf888">eb550b0b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-21T12:30:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">put movie frames (images) back into the Experiment after discussion with John. Better organisation than before. Still needs to be tested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be85463b617c08b1a72e4a5d3ebbd7ef4dd322fa">be85463b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-24T11:18:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctffind_runner: supported GCTF 1.18 B1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dbf36481c3b8eba1a629bb59aafdc07ee83e4af3">dbf36481</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-24T11:32:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">putting multiple images per particle back in. Only old cpu-code done.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a0bd8a638f700cd5bd4fbd1197b6fa1dea693e4a">a0bd8a63</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-24T17:00:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">put multiple images per particle back into accelerated code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8e457131973ccdf068c0c4e30b00a0b6192e1037">8e457131</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-24T17:11:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">star_handler: repaired duplicate removal of down-sampled particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f4b77c22c4b60c2ffe43f0c9b9702339790ae6c7">f4b77c22</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-25T14:50:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: fixed (global) resolution estimate in multibody
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/70d4e9f51144c53f9b34e78ffb450690cc485ffa">70d4e9f5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-25T16:40:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">decomposePipelineSymlinkName: added a warning for a corner case. This should be re-factored in future.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4c20f1d0d0983d19e477a34d1cd381a6496b3d90">4c20f1d0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-26T11:59:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">started transforming all offsets to Angstroms instead of pixels... still todo: various apps
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2c52e458b1fa09b8d269a591ce8badf9bdccb1d1">2c52e458</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-26T14:49:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in getImagePixelSize
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d7ef87438a480aa1b35382275d44a61fceee8d3">7d7ef874</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-26T14:50:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">delat with multiple optics groups and AB-matrix precalculation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4b4702ad699ab9afbc1ee472f465726c1a54e44d">4b4702ad</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-26T16:07:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">offsets are in Angstroms in stdout
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fda7c464f78eaf0e341116d512a8860c9193609">5fda7c46</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-26T16:07:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed offsets to Angsrtoms
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2071519337e4d5181c8c9a63a616889cb3d6d489">20715193</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-26T16:07:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">offsets were already in Angstroms, so only changed label
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d1658938caf633d651055afaf678cf89536f66d">9d165893</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-26T16:08:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed sort job from the GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8e7560f42d4b862925d88ccca9c83570f020186">b8e7560f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-27T11:57:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in maingui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c43456c4a4bcc04fc8b63ceda085fd133c0b35fc">c43456c4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-27T15:21:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging displayer with Angstrom offsets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/95fcf226fbc830a4a2cc6ba054317d426a793fc6">95fcf226</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-27T15:21:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make sure names of optics and particles tables are set
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ec8c5b15be3131e22d39f4b9eda1c221548c5d59">ec8c5b15</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-27T15:22:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">offsets in Angstroms
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41404c3ef1c47d78ac0f3351a65f0747c9a33d1c">41404c3e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-27T15:22:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">offsets in Angstroms
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2aff7a25b04c83894ac664a19b577c164c7f8cff">2aff7a25</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-27T16:57:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">helical track_length in Angstrom
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd48ad4793af713833539bd23dbdf44f0b1bfc1c">fd48ad47</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-28T11:06:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changes ori_particle into part_id
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/478df5df5cee3c6f5ea0d40b0b2ac8868549fb68">478df5df</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-28T11:17:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Testing lowpass-filtering mask
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d2465e7b103338f43b846d319924b02970c955c5">d2465e7b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-28T11:55:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopicker: The LoG picker does not support GPU, causing crash. Block such usage.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41d41e0accc73ed474a7b41d565f95aa09c933bd">41d41e0a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-28T15:44:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it: don't use GPU for the LoG picker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fce656abf3aeed303c61a9ae5e8ca5719fdbc48a">fce656ab</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-28T16:03:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">angstrom offsets, and first try at different image sizes for each optics_group. Still todo: test latter and adapt preprocessing, image-handler etc etc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b26fc9564bfc0491954319970ef748a7c3c15e5c">b26fc956</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-09-28T18:00:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging different image sizes, 2d small_tagcase still crashing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2bf41055a1ff329c7c11f01b6e9b063c7def4e0d">2bf41055</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-28T20:17:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">PDF generation: fixed synchronisation issue (thanks to Nicolas Coudray)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/36b8f76f93dc29aa1e8dee27c3fccaff537561fa">36b8f76f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-09-28T21:30:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">duplicate removal: fixed the sign (!)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e7bfa4bbcb0416762111d46e5fc1fb9a979997b7">e7bfa4bb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-01T16:20:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now 2d small_tagcase is running OK with different possible box sizes for images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/463ac45d4c91dd7ec1728d88d2e1489dbef0f792">463ac45d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-01T16:28:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired small bug in gpu code and removed debugging statement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d27d42b3b098fee6cb8ec2c6b6ddeff4ee1d45d7">d27d42b3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-01T17:38:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired small bug thr_wsum_sigma2_noise
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5aa7d3851c1ca27663e271c88c7e359b0f21d793">5aa7d385</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-01T21:40:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_it.py: make it more robust
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/796d1ed0f00a74bad913be36da33fe54288176b1">796d1ed0</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-03T02:41:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">optics-group support added to aniso-mag refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3e62253263652da63b2576722df01635de943c32">3e622532</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T09:41:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed spurious function
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a8689591850f7620a54c10f055846cfa3bf28c0">1a868959</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T09:42:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">be careful with rounding my_image_sizes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aca7c468885080f47d07787c370f06deacf36d8c">aca7c468</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T09:43:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired various problems, most importantly use coarse size in getsquareddifferencescoarse
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4adfc3b897a1c7f9e2631f598cd1aa937ec60210">4adfc3b8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T11:22:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed debugging statements
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ec8d86b11f98c5da509efbb5981ad2721d923bdf">ec8d86b1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T11:22:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed gui to red/pink for devel version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4139e1635bc611eba4b9a22a2b7a970c019616ec">4139e163</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T11:35:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged master into jaz_3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29eb6e0cc15c6db3b839926a6fd61e53a31f612e">29eb6e0c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T11:42:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflict with merging master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/637473f6d66a0902883f4d47052267604ddecd88">637473f6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T11:45:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">still trying to fix conflict
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7dc7e16b9f2b9fbac515b88ccf89da2b78c9570f">7dc7e16b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T14:36:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to keep CTFs from micrographs, instead of from data.star file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9da43d2707f8bb2b62845dd3f3b5c868ac01af7">d9da43d2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T14:37:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2bd84cd5b5524dfa8de7afd2886c9a1b63264eb9">2bd84cd5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-03T15:59:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">moved reading of image sizes from exp_model to star_converter, as only needed when reading old-style particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/94d1f1d51af031979e91d1d40094f7fe64bd904a">94d1f1d5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-04T11:56:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired ubg for empty groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f6fd0a93508783f0040f48a32fd0bd80622bc9ea">f6fd0a93</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-04T13:40:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">initial noise estimation: change how to handle empty groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/798e283f3ae4227e531188706c509abb5f037a23">798e283f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-05T03:17:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTF::getGamma made const and FilterHelper::raisedCosEnvCorner2DFull added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb631358d26e67393fe9ec67d0ec2619d4e0cb81">eb631358</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-05T03:19:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9b4a0b2157eb1fdebeb8122d90918353608c6c31">9b4a0b21</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-05T03:20:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/jaz_3.1_scheres' into jaz_3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/99c13f1543e743c55a9b85c7700004945ce0c565">99c13f15</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-05T03:30:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">most tomography code moved to src/jaz/tomo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57d41584f465ad3ea1b60e4d3d4c0c3aaf62b0f5">57d41584</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-05T23:26:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">first tomography test added and tomography classes partially revised
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d66bacfeafd72112f9df105fa50395786b399b5a">d66bacfe</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-06T15:26:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">presence of images now optional for conversion (a warning is issued in the case of absence)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84c205941af57598e94678a36f09845b1d024058">84c20594</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-06T18:16:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tomo_test updated and cleaned up
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b2427b6a8992bf74b55fbc94349bf89e47232f1">6b2427b6</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-07T19:32:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">different pixel and box sizes now supported throughout ObservationModel; cached values inside of it are only accessible through getters now; outside code refactored to support those changes (all untested)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c9dcc30fc26f1889f094b8ed667b0dccfdc31b25">c9dcc30f</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-07T20:49:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TiltEstimator supports varying pixel and box sizes now; optics-group handling refactored in TiltEstimator
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/81f624a5f166c767e8c40cd1e6a229d878e8b6c8">81f624a5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-07T21:18:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AberrationEstimator supports varying pixel and box sizes now; optics-group handling refactored in AberrationEstimator
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e76c5c77f041152bf5e7ef94dfd850a2b01d876a">e76c5c77</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-07T22:39:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DefocusEstimator supports varying pixel and box sizes now; optics-group handling refactored in DefocusEstimator; ReferenceMap requires a separate pixel size now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3d39b1ce274a304c90075ae141cd1ea5d3dfd743">3d39b1ce</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-07T23:23:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">BfactorRefiner supports varying pixel and box sizes now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b3a444038c785d1a93b1c35678f643e5a78208b">7b3a4440</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-08T00:37:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MagnificationEstimator supports varying pixel and box sizes now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/05886842a22e8509bb4f3b1833b3d8d55ccf3f2b">05886842</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-08T01:06:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">missing files added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/98275af25ed17a962e016b663c1843de31d85add">98275af2</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-08T03:30:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfixes in new ReferenceMap::getHollowWeight
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b3c4893f739928a504b8a17ca4a3ceb966f6a9a">8b3c4893</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-08T20:28:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Predictions made from a 3D reference now consider the differences in pixel and box size between the reference and the 2D image
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/650f5efc8a43b60feb6e1ec150102c3247f07e3c">650f5efc</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-09T00:25:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Anisotropic magnification now considered within CTFP and Ewald-weight computation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6f3cec3dfe3232374b669ad8b849e628bc082682">6f3cec3d</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-09T01:29:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ewald sphere is now still spherical even under anisotropic magnification - it was an Ewald ellipsoid until now (only in double_reconstruct)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/17cb31e98661eaddf49c84d4f2253aa5d796eaa0">17cb31e9</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-09T08:34:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTFP temporarily reverted to a version without anisotropy; Ewald sphere still spherical
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/022f9cbc04e4cc57ea4b0b7ab9ca182a46b7b1b7">022f9cbc</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-09T19:33:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in pixel size difference handling (in predictGradient)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/045f325ad99190c480df72d61a1c7aebd19b9de6">045f325a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-10T01:03:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">another bugfix in pixel size difference handling; bugfix in Ewald weights under anisotropic mag
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/647879b52ef7c849f8617f72d936d000473f546e">647879b5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-10T09:10:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added 2D-padding option to double_reconstruct; iterative L1-reconstruction code removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1519ab04175357a1ec2e6dd7294138ac9f433899">1519ab04</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-10T10:55:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">backprojector can now deal with padded 2D images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d89f32f8f6340b05a4dedae0fa7f99d736b940f8">d89f32f8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-10T10:57:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">backprojection again limited to Nyquist circle, but the one in 2D
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/79463f7bcf94281d31bc1daa52ecbd9002e0b720">79463f7b</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-10T11:36:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changes inside backprojector reverted, compatibility with padded 2D images solved on the outside (untested)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/399399270ba8415c9025a049003ee5a7e38ca087">39939927</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-10T21:22:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in r_max handling - changes are in backprojector again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/48dafb87583e15699beaf0bf9437012558f077be">48dafb87</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-11T17:23:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: check the presence of the body star file to prevent crash in getCommandsMultiBodyJob().
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e6787e0df26baaeb0ffd6bd98f2f2d53be98f3c2">e6787e0d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-11T17:25:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_project: fixed Fctf initialisation (Thanks to Dimitry Tegunov)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e32fa3b9e327c973f7b4d14daed5e08223edeae4">e32fa3b9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-11T17:33:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_refine: added --keep_scratch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/94aba04069d0b5c3693ed228dfd4a1ad4f661de9">94aba040</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-11T17:41:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_refine: fixed the final message for multi-body refinement (no run_class001.mrc)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/205aff3b235a8fd3fca0e4aa64cc7fb6d354e368">205aff3b</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-12T05:30:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">delocalisation masking implemented and added to double_reconstruct; optional support for colour images added (using libPNG); vis_delocalisation program added; bugfix in CTF::getGammaGrad()
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64ec9fa55ab96bc034e944493df686cce9f88bd1">64ec9fa5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-12T10:16:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Backprojection now correctly considers exactly those points inside the 2D ellipse that map into the 3D sphere given by r_max
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2c508250a775150869a058ba0acc7d02a7578e11">2c508250</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-13T09:35:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new Ewald weights implemented and tested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/63d39d6b5b72e6b88c8167259e65a72779395fa4">63d39d6b</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-13T11:26:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new Ewald weight now optional in double_reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0fa688bda1a25717917b3f0d78dc8cf1088cbfb">d0fa688b</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-13T13:10:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mag anisotropy implemented in both versions of MlOptimiser (untested)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/79b36a923be2af420696e7fd9670036ba87b812e">79b36a92</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-14T02:30:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in double_reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2ef6b0d8bca927293236743d23c1871a9f7e51d7">2ef6b0d8</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-14T02:48:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix in acc/acc_ml_optimiser_impl.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c106b8e62471e3c55b39c48c648b36caec21708">0c106b8e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-14T10:23:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added Ewald ellipsoid option to double_reconstruct (for comparison)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/91e45ea1a42c2e72ecf3f2d1e0cdd41433f5950f">91e45ea1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-16T16:47:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: optimised loop order. real-space interpolation is 2-3 times faster! (thanks to Jasenko)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9686b98836f978c77b5916b4f0632ee44fe02e1">d9686b98</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-17T17:31:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Infinite B-factor bug fixed: now checking for NaNs when merging FCC tables
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0ad988fdb9fc7772a9a5868e5ac72f626b7a44a9">0ad988fd</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-17T17:56:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine will now replace NaN coordinates in the estimated tracks by zero and warn the user
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/511ad437c2ac0c268ba4b31588721fda84c998dd">511ad437</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-17T20:01:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: Added GUI by Colin Palmer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a170f95b7d6e8f193e99869f8b6e8895ab8d1ec7">a170f95b</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-18T08:50:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merge_particles app added: merges datasets as different optics groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/03a8d97a7e05767296e516daeccdcf760a51d1b4">03a8d97a</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-18T09:36:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in ObsModel::c'tor, beam tilt insertion into Zernike coefficients
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/69fce15c87f5a3048323356e011b80d1e86360cc">69fce15c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-18T10:00:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Sphere condition moved from 2D to 3D in cuda kernel (lines 253 and 312 in BP.cuh)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d1cd956108f85516ec5ed2aa99dad20bc92e71f">9d1cd956</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-18T14:25:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">flowchart & layer line: respect RELION_PDFVIEWER_EXECUTABLE
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d18b4824116f669b5d05436fcedd43c0f055a101">d18b4824</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-18T14:41:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MotionCor2 wrapper: added warning for -Mag
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/294ce0d7d9b0ff0ca442ece2c074a6f01bc9a909">294ce0d7</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-18T19:23:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Hypothetical cause of NaNs removed in noise whitening (MotionHelper::noiseNormalize)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/78d216168d07160a5e21557f2b15fd850c8fc240">78d21616</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-19T16:08:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: disable AB matrix calculation for --cpu and --gpu. This solves Bitbucket issue #36 by Dimitry Tegunov. Thanks for reporting.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6f54d9c442c0a5fa23717477f1b6792a049d9a1d">6f54d9c4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-19T16:11:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/63b243180ed980ef1e46da0003335df9a99d6920">63b24318</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-19T17:12:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: define parent jobs of multi-body refinement (solves BitBucket issue #41 reported by @ncoudray.)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/877139d9dd2f254bdb475069077d8db31e80d7ba">877139d9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-19T17:23:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Image: fixed integer overflow
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e0a5317dbba0c4ef68ef02c0a0fac5a2dad8205">7e0a5317</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-22T15:48:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: Add 'Browse' buttons & Save settings with comments (by Colin Palmer)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7ade6cf8452a7456c6eebe9720527d6a936bcce">f7ade6cf</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-22T16:16:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: mask size should be in angstrom, also changed the default box size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/846cf8282f9d7d06e45299612543691e137c0982">846cf828</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-23T16:59:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_preprocess: added --use_ctf_in_mic (suggestion from Max Wilkinson)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ef44c82b0ff7a8fae639e461a838d78e7eb3a949">ef44c82b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-25T16:38:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: Improved GUI, automatic suggestion of box size by Colin Palmer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4eb9ba7015b5ed0090e8df01ceaae23a80d981ae">4eb9ba70</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-26T12:51:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: --mask_diameter is essential for Ewald sphere correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d70bb4a5abc8d3f9d9fb77cabd7798276fdc5396">d70bb4a5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-29T11:26:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix in mag estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c17ee5623ac343f586c8357a7e2cc55d8bf5c4e">1c17ee56</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-29T15:01:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">rounding when getPixelFromResolution
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1635749932618429fd42931126dbda4b49497325">16357499</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-10-29T15:03:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolved conflict upon merging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a6b96af2a448de27136656b21e9777bf70316e0">9a6b96af</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-29T16:03:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_image_handler: use the pixel size in the input map by default
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d88bb6e54d35480edd52123f2cacc545117ba04c">d88bb6e5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-29T16:04:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/008f2b14a6b93f487faa527b9a7fe554bbfaacdc">008f2b14</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-10-29T19:56:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">another bugfix in mag estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/361b281e55a0d448bfe27630f4d92146fb346a6d">361b281e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-10-30T11:02:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: Added the mask diameter to the GUI (contribution from Colin Palmer)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2a6e1002f425535fd24c8371e92b6a4944108f31">2a6e1002</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-01T15:54:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: original box size can be any even number (by Colin Palmer)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b76c4dfe9614e3262d68d0983cb72b5e090192d">8b76c4df</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-02T15:52:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">star_handler now supports star files with multiple tables (only for reading: only the selected table is written out)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7203f0e1f86fa128c4522a6e0e52e915dc2ea918">7203f0e1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-04T09:29:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bayesian polishing: duplicate particles no longer produce NaNs in the trajectories
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7222845983dd95a3626760876e38d1dcede9a6c7">72228459</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-06T09:35:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged master into jaz_3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8e2d990945b795ceaaabf0a0e556a6f1cec0e56a">8e2d9909</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-07T09:18:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged master into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/da3bbd658a76d4897b27c2e74bfdfba1efc75624">da3bbd65</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-07T09:34:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">switched off check for all same pixel sizes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d530a92af203742accedb9701748fe7183d6896c">d530a92a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-07T09:43:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jaz_3.1 (pull request #19)
Jaz 3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f0bd80904ca6f6ddc36831d98eaf2989aef54d1f">f0bd8090</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-07T09:50:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bae6e17133bd995ebce22fe12e7c182b8ecc86a3">bae6e171</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-07T09:52:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">moved loop img_id up in getAllSquaredDifferences
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f42c3c8d7c2759bcaf324b6fbd9021d4571d7069">f42c3c8d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-07T12:15:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CtfRefine: fixed NaN in RGB values when there is only one particle in a micrograph. This caused Ghostscript crash.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/94f4ea342b5c2e6aaf1441ffbfafdc975a12341d">94f4ea34</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-08T15:00:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Class2D: fixed an out-of-bound error in initial class assignment
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e1bc5e0e0ea9cb9314071be047ce5f02ccd2532">9e1bc5e0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-08T17:21:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extract: should not crash even when there is no input micrograph (to keep RelionIt running)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc5a2744703ab3957c923f70cf399d98165c6524">cc5a2744</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-12T15:28:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">all CTF-refinement programs now generate a colour PNG output incl. per-pixel residuals
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/757820d9940671e3614ef08f59733d0316a3bef3">757820d9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-12T17:41:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: improved the help message for the defect file.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/86324b2d964abe9a8ed7894b19adf282b2c95a14">86324b2d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-12T17:45:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: further workaround for numerical issue in random class assignment. Don't know why this is needed...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dfe42243f028ccc0d5ddf4dcc83d56d1097f284b">dfe42243</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-19T13:01:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TIFF: Use default values for missing tags where the TIFF specification allows
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/341ee382dee51ff503a02dd0f6e663e56494e35a">341ee382</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-19T14:00:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging combining images of different sizes and pixel sizes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51fc422733e315be736702116c374c288844235c">51fc4227</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-19T14:38:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">image_handler: allowed TIFF to MRCS conversion. TIFF to MRC does not work, though.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0dc43eb159e9e99bf6215c73329633380c3e1e03">0dc43eb1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-20T03:12:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">anisotropic pixel-weights implemented in symmetric aberration fit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e59b07e558241a51aeae403bbcbc5831832c098b">e59b07e5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-20T03:14:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">signs in aniso-mag fit now the same as in the paper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c785cf33fb396644c18f1606980027d5fa5d9862">c785cf33</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-20T12:27:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with do_simulate
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/df4caee14d49faaf5d2b3df171da429b34a014a1">df4caee1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-20T12:27:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging multi-sized image sets refinements. Still unequal results with different parallelisations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/07a53fb9ba85ea3e4f25281e91d90c7d1159cb94">07a53fb9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-21T14:51:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">flex_analyser: fixed an error message (issue #417 in GitHub)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27dd7c7d80453796756c5ea39cecfaf5ea745a29">27dd7c7d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-22T11:50:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">master shouldn't check disk space
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa02bf69ff8e0bfbc068b33e0dbe500ceb5d07c4">fa02bf69</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-22T11:50:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small tweak in array size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/277dd9597427a81b3f321cb1dfb845e5d50505e6">277dd959</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-22T11:51:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont randomise particle order when random_seed equals 0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/28476297c9ec6e58486749687a3cf5fccc239668">28476297</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-22T11:53:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in fouriertransformer with unequal size in initial noise estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61c5559a2a1fdf85899844e8476f825790ba2775">61c5559a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-22T11:54:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed suprious debug statement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41a65143389bfabf025d4685dcbd2bab67b7a867">41a65143</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-22T14:39:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">need to clear transformer if image size changes!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fb19ca2d7cbc3446eeb97926bd4ba38c8a62a527">fb19ca2d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-22T16:16:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in writing optimiser table: accuracy trans in angst, and introduced force_new_plans in fftw
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d6d55ec286fd7f4df8305dac7091155a836cbca4">d6d55ec2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-22T17:12:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replaced MDopt calls for obsModel ones in exp_model, debugged groups size in readImages of mlmodel and changed ori_size call in ml_optimiser_mpi to check for space on GPU card
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc0697b00f21046708d3cffc7743f8e6880d184e">bc0697b0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-23T15:45:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">valgrind complained about zz call to 2D offsets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/992a3c572e530f9d5d3aabbd6025d8de21c24f10">992a3c57</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-23T15:45:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired small bug avg_noise_spectra
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3478bcc63b43f9d93b096be80e1ef2169e4b2a57">3478bcc6</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-26T08:55:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/jaz_3.1_scheres' into jaz_3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d4f23bb441f8c28c60bcf1f2810f52122fe1e893">d4f23bb4</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-26T09:57:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ObsModel::getOpticsGroup() reverted to previous form because the change was based on a misunderstanding
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/684948bd33c4190e2376406bf321f9470d1c8a1e">684948bd</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-26T10:27:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cuda BP-kernel: all square/circle conditions in input space replaced by circle/sphere conditions in output space (2D, 3D and SGD) [untested]
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd0d72bde7d74a3249bf5d0ae527170f1a9a2809">dd0d72bd</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-26T10:53:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CPU BP-kernels adapted analogously
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7e4b08a67f39ba8365e6abd4ca8badb995a294e">a7e4b08a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-26T13:45:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CPlot2D histogram: improved robustness. This fixes crash of motioncorr_runner when there are no 'early' frames.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/00a96df0922bfd722b04687662bc26e3de4e4242">00a96df0</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-26T14:03:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Non-accelerated forward projection adapted and refactored
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2adaba875b7e6101f179a1c0409359f706d0e1ec">2adaba87</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-11-26T15:30:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Non-accelerated backprojection refactored analogously to forward projection (2D->3D, 2D->2D, 1D->2D and 3D->3D)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/72b814acdb9571172d97742f11c321216e6defbe">72b814ac</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-27T15:46:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">continue to debug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe3f16b40dd4511d99ab6bff30ab88dc14164437">fe3f16b4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-27T15:47:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jaz_3.1 (pull request #20)
Jaz 3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2efd5ca443581a1d1b239fae04955c7165a13b4f">2efd5ca4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-29T10:03:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed spectra from XA and AA estimates for scale correction; and started going back to ori_size spectral sizes for all groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f966199672a8e1234b71fb793ac77241293cb025">f9661996</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-29T11:44:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cpu works with mixed groups, gpu does not yet
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64df905b5f4a7e9c9d70a1ae2e450fdf578b7c42">64df905b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-29T15:46:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added applyScale Differences to GPU code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/537725fb6fe5b73f8e0a43dbc04e2f8a33e39735">537725fb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-29T17:32:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tentative support for 4-bit MRC (mode 101) from SerialEM.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d11d43a6115ec3851d15212002505ab6bdb817e5">d11d43a6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-30T09:34:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug Jasenko's BP.cuh: forgot padding factor on max_r2 (2)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/43e4178353c0868ce2813004a030d7e33fb044e8">43e41783</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-30T11:58:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">image_handler: now STAR file is processed as before
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e96ed8cb6a1090e642f4b5d8ee29eabbadee51f">7e96ed8c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-30T12:09:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">sort randomised particles on optics_group to avoid recalculating plan of cudafft all the time
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dbcdab0c45af2b417a1f025a7e2e5a2c72f69137">dbcdab0c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-30T12:09:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed superfluous bracket in timing code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8688d1e60de2a82c978b015833a4f38f4da10d0b">8688d1e6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-11-30T12:15:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GCTF wrapper: explicitly requires CUDA
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/428fc5f7d755f4eb62b8f4e1eae3acc5f650188d">428fc5f7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-30T14:42:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">enforce that model has smallest pixel size and largest box size of all optics_groups in the input particles star file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/18fa37a4414a053518c26631fee54eb0c9abe304">18fa37a4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-11-30T15:06:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try pinkfor 3.1 colours
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8085f40ceab7da1b4d2a0552329a12962cacf17d">8085f40c</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-12-02T11:28:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion estimation updated to new format (untested, parameter estimation temporarily removed, old b-factor estimation permanently removed); ObsModel::loadSafely no longer returns the optics mdt
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0e47df1f80b6297aa6fba9fb1315dafc9498113">d0e47df1</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-12-02T12:34:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion refinement: tracks stored in Angstrom now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ac2951925c051a52f9b2e71a1276fa0d43aaadc">6ac29519</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-12-02T13:09:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion refinement: star file written out in new format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51b33123b9c5646404b27ba8e6d4c032e634361a">51b33123</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-03T09:23:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small improvement stdout
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9838de0370188b8413f9964c3779e12692ec8bff">9838de03</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-03T15:42:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GCTF wrapper: complain when phase shift estimation is enabled through 'Other Gctf options' instead of --do_phaseshift.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c5fed456027612211e5808360dda6c59f4598db">3c5fed45</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-03T17:30:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: improved parameter check and help message for GCTF
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/11875c261e62879e19fd5f7b04c3a0098ab66423">11875c26</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-03T17:46:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jaz_3.1 (pull request #21)
Jaz 3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7fdd455e4caf73559544947735beb60a586761d">f7fdd455</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-04T09:08:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in jaz_3.1_scheres (pull request #22)
Merged in jaz_3.1 (pull request #21)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/389a01a985b5212131f4459e75c7b5815758f4e4">389a01a9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-04T17:00:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now import can handle optics groups for micrographs and movies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e7b40594434aa48ccfaf144b00e5310dce90d2dd">e7b40594</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-04T17:00:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f2d9a0ae6cca5df3a8513e74d0afe034debe1cff">f2d9a0ae</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-04T17:44:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set output STAR file version to current, not hard-coded 300001
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ef2c316e27aace33b4bbc409a79012ad0e63bc55">ef2c316e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-05T14:39:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> fixed bug in passing on refined helical twist and rise of half2 upon convergence
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d9157b98d995b2d52eab1fde7f2b920114ec415">9d9157b9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-05T14:45:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> fixed bug in passing on refined helical twist and rise of half2 upon convergence
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/36243a1aaa57c68358190a2f49f66e3de1fc3362">36243a1a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-05T14:46:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a737145bc44804c1575414b2d7b04d5bdb72c82">3a737145</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-05T16:31:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">first attempt at motioncor and ctffind working with optics groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c7a874339585ab1c882433c484d0cd432a39a59">7c7a8743</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-07T15:56:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">preprocess: copy rlnBeamTiltGroupName from the micrograph STAR file only when absent in the particle STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/df62c800f3c792d857e9ab606352e703ecae1c15">df62c800</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-07T15:57:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7fd21af76f9d740d8f81a9602a70689e129decaa">7fd21af7</a></strong>
<div>
<span>by Dimitry Tegunov</span>
<i>at 2018-12-07T16:29:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">3D CTF patch by Dmitry Tegunov: Adds support for 3D CTF volumes in FFTW format (no redundant half, center at 0).
Fixed Conflicts:
src/apps/project.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b90d156a0391cd182b5b1b4790fc22dce23cff16">b90d156a</a></strong>
<div>
<span>by Dimitry Tegunov</span>
<i>at 2018-12-07T16:30:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More robust support for 3D CTF in FFTW format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/99d96a3ed6ef317f42aef0f94aa14b81a6356b51">99d96a3e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-11T11:42:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_preprocess: fixed handling of the beam tilt group
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0f20d5d37f18728067ec034c6802230e2a1dc55e">0f20d5d3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-11T11:44:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Image: fix indentations. MRC MODE 101 confirmed for both EPU and SerialEM
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9e7be9267de4014cc993277e85086314ebb8e0f">d9e7be92</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-11T15:06:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont need tablename as part of class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29b5623d6baa0953bbb7926c8bc67ca8e6070344">29b5623d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-11T15:06:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">magnification might not awlays be there...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58d874f896f0105f12c306e5cff33a0381c038dc">58d874f8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-11T15:07:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small adjustment to deal with v3.1 star files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b0c29f223ba77cbb16ced320460c45f07361753">7b0c29f2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-11T15:31:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">default particle is -1 for currentObject
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b946618d0219d3baf8d4c6c3f0be1ad6ec4a8bb9">b946618d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-11T15:32:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use optics group for CTFs in autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a94a71afb77199060d8f408a62beee2fb3532879">a94a71af</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-12T15:37:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make sure to use long ints for loops over particles!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e409c1e9f961dae4630fcfb484dcd6238386ca8a">e409c1e9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-12T15:48:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use long int for pc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ced57e06f4320f75d0f1da836616b2b579534d33">ced57e06</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-12T17:12:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair issue #49 on relion3.0-beta
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/98d90ed9eb9e9917f3268b3ec4a4871dac282f86">98d90ed9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-12T17:12:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/90561b4e408fd9fc22b4f7f2f598ef61a126dd93">90561b4e</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-12-12T18:36:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">astigmatism-adaptation bug for empty matrices (probably) fixed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/911f58601cbecac09c1a45e383d156ac5924d362">911f5860</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2018-12-12T18:37:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3fd8a058cfe053d041b69e07144ee5c08c1f3c70">3fd8a058</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-13T09:59:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">copied takanoris new image.h with 4-bit MRC support to avoid merging conflicts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f73705b76f86be8119e4700967cf47a8cfaad09c">f73705b7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-13T10:01:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to avoid merging conflict
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5dd0ebbc23a413f5273d16b8d3040d63f2510b3d">5dd0ebbc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-13T10:08:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts in merge with master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ebd620d1a59f3df9f636c4ae207a7a88527441e">8ebd620d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-13T10:09:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve conflicts in merge with master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6f0d208ae1966258324172cf36b8a01540df4383">6f0d208a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-13T10:13:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying to resolve merge conflict
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/edf14e49098051ff6463af0210d8ae94a48f331d">edf14e49</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-13T10:14:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in master (pull request #23)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/960a1fe42adcc5c7f9815e02470339370a068ade">960a1fe4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-13T10:48:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired errors after merging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/13f091980a4ee6be1a60b1aa6cb6563c8003c3d2">13f09198</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-13T11:50:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Get rid of rlnBeamTiltGroupName (as string). Use rlnBeamTiltClass (as int) instead.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a1a78a90acab65a206ec6a15d3d3fd94225e287">6a1a78a9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-13T11:56:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3b7de54b63db68a3739913b048c65ec3260cab40">3b7de54b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-13T15:58:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">preprocessing now with obsModel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ea30fb5c0281fd9450900d82c2984f869f5d2172">ea30fb5c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-14T12:49:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added colour display to relion_display, with Jasenkos colour scheme
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/615a6b1d87808bb647e41fb68124d829589d697d">615a6b1d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-14T15:24:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added rainbow colours too
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5dc615767eba9c4470c8c36a159903e01366dbe8">5dc61576</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-17T12:11:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">UCSF MotionCor2 wrapper: allow multiple GPUs per process
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1b3b6467fcb0a2f8fed68a9f6e4078530986a3dc">1b3b6467</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-17T16:23:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: more efficient gain correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5f152285ab9edb49772519bc46ac5b2f595ae8b8">5f152285</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-17T17:44:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed black/white to min/max on display GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2c027f2b61191c0c35763b2672487c435fce41e2">2c027f2b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-18T12:00:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTFFIND/GCTF wrapper: Don't read the pixel size from log files to avoid loss of precision
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3041a1bb77891dbd3d69c868b025e1bbd6c9f6d">b3041a1b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-18T14:11:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: make hard-coded max_iter to a command line argument, removed timing code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/31e4017bea8c8d9052b8cf08d73cb61ec5a74711">31e4017b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-18T16:37:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: improved help for duplicate removal. Also added one missing file.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/656344e6599a67b3883a465b5d1bf0d4f4b46935">656344e6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-19T11:07:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: fixed crash in Particle Extraction (reported by @kehrnal as GitHub issue #423)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/97b3a49351045cabd460f87c4c2434259a0627dc">97b3a493</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-19T12:13:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_display: save image as PNG
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/06bd9d594c6a725b754525c1cfa5dc64e1169269">06bd9d59</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T12:16:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4810be4b937ee9df9dbe8a7e9bb238c78ea51a0e">4810be4b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T12:47:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added scalebar for colours and blackred and bluewhite schemes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e446249ab7e8d415740c848d57b3ab94b268fb1">9e446249</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-19T14:56:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into jaz_3.1_scheres
Conflicts:
src/metadata_label.h
src/preprocessing.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d202ffa5915f7b35aa65b7bc5f49d0a8158a33f1">d202ffa5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-19T14:57:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5e8e3f194041501d4c963ad86624ef23db005cc">c5e8e3f1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T15:07:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> renamed colours to fire, ice etc and added fire-n-ice
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3cd2912c0fed8809d01a3c8ae12507c6890408a9">3cd2912c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T15:08:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added discover for tablename, and repaired bug jasenko in getPhaseCorrection and in getGammaOffset
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0aca3da730d25265cb724857198a1a89447c3602">0aca3da7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T15:09:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cfe4819e1890bfd9d93cc75116b744d3917de912">cfe4819e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T15:32:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow opening of 3.1 GUI in old directopries
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4d05f527ac75a449b0be9e096befc12f9c63ee2f">4d05f527</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-19T16:07:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: noise reconstruction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c58bac76f5ff010bf3bd9069b90d4209ecede7e0">c58bac76</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-19T16:19:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_toolbox: fix indentations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c0f9e9b5649c603def23579c2077d57bcc3a659">7c0f9e9b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-19T16:30:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: fix the number of menu items
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c21c0e8cc4e33d4ccb83a57e31a5fc3eff12abc">1c21c0e8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T17:05:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">greyToRGB as inline, and remove if-statement from loop over all pixels to outside the loop
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb2288cd9b24e0ecfb3b7d8d9aeebbdc4e162c22">cb2288cd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T17:09:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolving conflict
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/69d0689728718cdecc3d59960e6696e29d35229c">69d06897</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T17:12:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed argument to --colour_bar
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bed1ed00ca774a753f15a12a0081846bf21d1ff8">bed1ed00</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-19T17:39:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed test programs from standard build. (Please don't enable RELION_TEST in CMakeFile. Use cmake -DRELION_TEST=ON)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e55fe70dd061d76c766cef27ef2b29498ecf5f87">e55fe70d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-19T17:39:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_display: show label (--text_label)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a51d12dc8c5804aa574775ce27a5c922cb333cce">a51d12dc</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-19T17:40:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/93b5a5c445821a3176c7d1e59086589a36b19fcd">93b5a5c4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T17:44:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">carry through colour scheme to show original image
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ee1bd4dc0377c48d91dc3edc6e13e0e2cdec87e">8ee1bd4d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-19T17:44:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12d99575565226bbfa003e0ebc4125c24c48c86d">12d99575</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T08:36:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">change button on display window to pink
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/db3060b3c14ae689cb3e7e697960355e24340d97">db3060b3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T09:39:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make orange background image with PHF
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4a64f498e1790468b4c07dc50964f252296d61e4">4a64f498</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T09:39:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60eca62af1a92a977279a4b382b771b6238864f6">60eca62a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T11:02:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">background 3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a69b4848cf04c6709bcd5133939100897ddb027">5a69b484</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T11:42:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug downscaled multicolor images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/498047ff88ecad79cfcd5e884e4714207214168d">498047ff</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T11:42:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new background image position
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a635268fbffa289f6c0ca156c581baae8d69ad0">3a635268</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T11:42:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small bug necessary pixel sizes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5756ffdbf6908eb3304295148d75d01747c6b54b">5756ffdb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T11:50:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug to get pixel size of micrographs from obsModel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/da32e4a3a40b5d886170d76a578eb067e4286cb7">da32e4a3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T11:59:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use loadSafely of input STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bbe72b221e629a936c97e02d9300dfc1cbc8aebb">bbe72b22</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T12:00:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use obsModel.save for output STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/742a444e7fa70b2b3b0b6eb5dc200defcd51bf1a">742a444e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T12:10:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug box size of extracted particles upon rescaling or windowing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/14a376d0ef6e6841250b40d284e59e430ab13e55">14a376d0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-20T12:25:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'refine-lowpass' into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/030428f1b392cdb2bf9cea8ae457123681177e43">030428f1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T12:26:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug getting CTF info when prereading images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf2c159734c70b8db6f587ad78be70bc2662c760">bf2c1597</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-20T12:31:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_refine: fn_something.contains("None") is dangerous.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/80428b9c0eb597f7983f6f7b37397c12dc9d1c45">80428b9c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T12:32:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug image_full_size not exist yet in calculate power spectra
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/77b5b9a7618d9cdde2d6a8921728aef421b7fb0e">77b5b9a7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-20T12:32:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3483585fe356755ed6a871006ae2ce1abe8d1dad">3483585f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T12:35:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">started to change star handler for handling optics groups. not finished yet: duplicate removal
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/faea0ae718613a4d771096823a073babae033dcf">faea0ae7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2018-12-20T12:51:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">typo in option rainbow color original image
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1aff028e35656be49884a521e5ff5239419871b2">1aff028e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-23T20:52:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed compilation on GCC 6.4.0 without -fpermissive (reported by Rafael)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7251d08a96b67c578196bdb27df0164b6e6040e7">7251d08a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-24T12:01:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_import: added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ecc42d9cccae915c606dcc1e1f905204e83794e7">ecc42d9c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-25T08:20:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CtfRefine: repaired PDF output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/814a673c0e98c6a173218efb309b45a806fc012f">814a673c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-25T08:29:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ReferenceMap: Use the pixel size in the reference map by default
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7005ddb9b71f49d063f0e1dbec35e937a33bb7d2">7005ddb9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-25T11:53:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">WIP: Repairing particle re-extraction. Need careful testing!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f00119a8bfe03b4d898a05c541ec295c51f2cd82">f00119a8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2018-12-25T17:39:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_preprocess: confirmed re-extraction works. TODO: optics groups from run_data.star should be prioritized.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/560bddc0e19d0ea667f6cb903f64d25519ebe88a">560bddc0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-02T15:10:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Give an error when the gain reference is in Digital Micrograph format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce40fda273ee12c150231bbdd992415e3c37feb6">ce40fda2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-03T15:37:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">auto-refine: fixed final messages (thanks to Oliver Clarke for reporting). Removed a dead code.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de24e1d1bf7fa11ec7ea0b25fb213e7651e3bd6e">de24e1d1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-03T17:22:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: WIP: calculate power-spectrum for CTF estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/df5a0cf2ac9cf5fae0df87ea0f07d98f5d6b119a">df5a0cf2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-03T17:26:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into power-spectrum
Conflicts:
src/ml_optimiser.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4af43bbb430b9a118a019ff4f6272a1dd3a1077b">4af43bbb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-04T12:20:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cherry-picked "relion_reconstruct: noise reconstruction" to fix issue #53.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca355e1f455e2122505ca1d480ddc8f2611f6073">ca355e1f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-04T14:11:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion correction: removed UNBLUR support. fixed --only_do_unfinished
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/407a954157d5265e008413edb188e2c376cc469d">407a9541</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-04T14:14:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into power-spectrum
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc0025d68a4801d32762bc08e23b982f8e1346b4">cc0025d6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-04T14:31:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolve issue #16 Refine3D do unnecessary rewindowing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b7884cdae1fe681cfaa78c89933b4df8d42b3a8">8b7884cd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-04T14:31:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1f105469db565a71c79069b460870bdc21544789">1f105469</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-04T14:45:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolve issue #15 Refine3D should have --ref_angpix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b10110fcb695d5d15a84c3392b77bf1dd75ded48">b10110fc</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-04T17:51:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion correction writes power spectra (--grouping_for_ps > 0) and CTFFIND uses it (--use_given_ps).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9ae9b9e40c315bff5b1e36e71b2a6040b39ddea0">9ae9b9e4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-07T12:10:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">start implementation of obsmodel in manual picker, not done yet
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc082bbfaa77fe6fb069a4cff8e823914b9cf627">bc082bbf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-07T12:11:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont warn when reading pixel size from header of reference
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/193664b138a35227652085f29174f9b85141a303">193664b1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-07T13:56:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CtfFind: fixed the pixel size of power spectrum. Now this is working, but need testing.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a3fc626b99b077db795bec161e961bf9ae18404a">a3fc626b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-07T14:03:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add stochastic EM AND repair bug in maximiseOtherParam
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd8a96d40dcdc24dd3864fe2d20021a1718e8359">cd8a96d4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-07T14:04:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/230a8e7bbd8a1b0f50313dc4fd22dec144d7c21a">230a8e7b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-08T11:59:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add obsModel to manual picker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e1e995f51910d4ce7f78f541fd3c83cc2d604738">e1e995f5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-08T12:00:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add stochastic EM to GUI, and have non-negative gradients
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2c77a665d904644309983932b138844f3f44323a">2c77a665</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-08T12:10:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_display: fixed 'Show Metadata'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9d2d2070d0d42b22b0c1e7d037ce7ecd53eb60c">d9d2d207</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-08T14:05:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added obsModel to display program
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b0dbd97a1614b8281af1adb6ac43ccca380b500e">b0dbd97a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-08T14:06:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0ad5bd01eb2d1d3b01f65fad1f5c8cbbefe94704">0ad5bd01</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-08T16:47:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_pipeliner: added RELION_MPIRUN environmental variable to change hard-coded 'mpirun'. For qsub jobs, the script template is used (as before).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bfab410529843cdb5059a8f799785e03443eee25">bfab4105</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-09T11:33:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: fixed the output node name for flex_analyse. Solved issue #55 on BitBucket reported by Matt I.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f0fdd8258078265a5863481daafe78660beee7f">8f0fdd82</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-09T17:27:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch by Colin Palmer (CCPEM) to put RELION's GUI background image in-line, since otherwise it tries
to look for the pixmap file using the absolute paths of the source and install directories from the build machine, making the binary non-portable.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8229ffeda2b11043734df8c696d7ef68d1381f3d">8229ffed</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-10T13:47:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Made sure RelionError are handled correctly.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/78817717f511c60efe108753b368e0e51be4a381">78817717</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-10T14:02:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into jaz_3.1_scheres.
Conflicts:
src/apps/cs_fit.cpp
src/apps/ctf_toolbox.cpp
src/apps/free_aberration_plot.cpp
src/apps/helix_toolbox.cpp
src/apps/motion_diff.cpp
src/apps/motion_stats.cpp
src/apps/particle_polish.cpp
src/apps/particle_polish_mpi.cpp
src/apps/particle_sort.cpp
src/apps/particle_sort_mpi.cpp
src/apps/ref_aberration_plot.cpp
src/apps/refine_mpi.cpp
src/apps/split_stack.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/46d525dbb57d93a76648c67270b4f247a7f88f3c">46d525db</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-10T14:19:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">clean clutter (in my previous commit, my editor replaced ALL spaces into tabs ...)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c3e92324ebfcbf94b97bf38a82455acb317df545">c3e92324</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-10T14:30:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into jaz_3.1_scheres
Conflicts:
src/apps/free_aberration_plot.cpp
src/apps/helix_toolbox.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1de1d206f9fa4712c773e6a0d86dca7913fa4522">1de1d206</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-10T16:55:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add aberrations to the GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4c823eabd322e74fc971f0cc9fd01bb1d968848">b4c823ea</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-14T11:14:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: repaired continuation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a7ee156fdf6384e1b49c0d3cf960026b02d43a6">5a7ee156</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-14T11:57:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed a warning message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/943a876c884b1fd17a7e6e128cac19537bb71c6d">943a876c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-15T10:53:56+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: fixed crash when "images_are_movies = False" (reported by Yongchan Lee)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/da007b9791c1e7cf39eb11b25c3077ffac5debbf">da007b97</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-15T12:49:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_run_ctffind: Use the RELION_SHELL environmental variable to specify a shell other than csh
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7450afda16ead4ce5f487683760b3151d3bb713">f7450afd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-16T17:21:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove polish and movierefine windows from gui library
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9141f7a88195cdb4af1d0ccbbd589994bcccf24">d9141f7a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-16T17:21:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove polish and movierefine jobs from pipeliner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/33dd79c4cbc21aec8c2af6c6622aa6557502d4e5">33dd79c4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-18T11:04:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed polish and movierefine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/776518553a9c60a4bf4ad163c5e56c34fcde331d">77651855</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-21T17:16:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">started working on GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b5fd2685a972c4f434e7283dd19427cf1006038">2b5fd268</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2019-01-25T11:21:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Corrections/simplifications to README.md
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/48109d533bff9e1149c5779156198ea266b0125f">48109d53</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2019-01-25T11:21:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix a few more cases of data size truncation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/973480634976a3e05cabc49d9d028f416f701fe5">97348063</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2019-01-25T11:21:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Class/body-specific symmetry
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6eb57f6a5a5321ea9e9602aae93544f3f9f7a64d">6eb57f6a</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2019-01-25T11:21:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Issue in cmake variable assignment order
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c9c7c9b67f0b6405dbe312725f31b54751aeefe7">c9c7c9b6</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2019-01-25T11:21:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MPI related depricated cmake variable replaced
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac81250c4bf6aff4c03dc92c85824b2deefbec12">ac81250c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-25T11:21:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed build on cmake 2.8
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/916a49280b619067c984f5fbabed1cccc1605d5f">916a4928</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-25T11:40:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added explanation of FORCE_OWN_FFTW and FORCE_OWN_FLTK.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/855201a6597e552ee88f64ffeb5160361b86472e">855201a6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-29T09:06:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">swapped tail and awk order run.out
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bb2d5a10b565e7441558008086f14e8aacc56007">bb2d5a10</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-29T09:07:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/709b4b3c2918c89d63d92e0f394dc3e895a5cb2b">709b4b3c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-29T12:08:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MicrographHandler: use ObsModel to read corrected_micrographs.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f89d54e30612bb811af1786a67f3ef2aed116da">3f89d54e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-29T17:39:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">duplicate removal: migrated to ObsModel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f170ab5b8b86bc4bf2429a7060529e3606458c07">f170ab5b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-30T11:11:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new menu options handling for GUI, write run.job.star files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/551350ba366d9c208a8bff13b9a6039017a83637">551350ba</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-30T11:20:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolved conflict
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c7c585592cfd1ee1dc00b37a1b35853f58cd9c6a">c7c58559</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-30T11:25:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolved conflict 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a2d7905db4dcdb016e2a4436b199570115e79af">6a2d7905</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-30T17:28:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot.py: Migrated to 3.1 STAR files. Increased the number of digits.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8179ae6ace727a78ab37c9277bbb98691c6179f">b8179ae6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-01-30T17:29:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/950c7012033bc043211fd6de646029bba39065cb">950c7012</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-31T09:30:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set menu to first item if cannot find loaded value
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/963fa84cd3806d9ef85a90e8f80564d505aae5b1">963fa84c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-31T09:30:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove slash from menu, as has special meaning in fltk
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e0c3290749a666df9e334609b70b5d841565cda">9e0c3290</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-31T09:31:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow variable names in pipeliner command-line options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/56877d8496752774cf9a218cad94a148b36e84f7">56877d84</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-31T09:31:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8603a15e826034901845c0186a692d48612fc377">8603a15e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-31T09:38:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> negative twist in helical symmetry expand
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/06a0c8fbf851846c90669731c75ade4418696042">06a0c8fb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-31T09:39:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> negative twist in helical symmetry expand
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/024443c1d29b5bdff9dc28805a449a899445b191">024443c1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-31T17:22:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed comment didnt work yet
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/694bac6ed6a353b75dd7fa09ebbed3024fd175ca">694bac6e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-01-31T17:22:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow overwriting existing jobs, without continuation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2553d34d7f0ba4f282d312df90146f1eeb9572b1">2553d34d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-01T09:26:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write star files with .tmp filename first, then rename
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/46b5bacad692c3bff34da8ccd88c0a91e2797a03">46b5baca</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-01T09:27:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">die for combining: 3.1 star files not done yet
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb0c0fb74726369897e52d1eba5db1e85ba688b8">cb0c0fb7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-01T09:27:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">warn for combining: 3.1 star files not done yet
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/784536bd1f608bc4df7f101799a2bfbaa2e897f5">784536bd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-01T09:27:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added anisotropic magnification on CTF-refine GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42c5e941dc3a18b3d0ea5db74c88a47938b471d7">42c5e941</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-01T09:35:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed overwrite button and ask for confirmation to overwrite
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e12514600c84b8ac7d4393ac76d02eced53b14ba">e1251460</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-06T13:55:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to modulate instead of demodulatePhase, this is useful to apply to reference projections before subtraction from experimental images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/af0f387f44fd222ba02ad2d8cd5ececfb757f1cc">af0f387f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-06T17:35:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check for half-FFTW CTFs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5fe721aff6c93fe5e0f66db8efa96b5c54afaf94">5fe721af</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-06T20:21:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_image_handler: renumber output stack IDs when reading and writing a STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/81ce34f10374fdebe2d41c91bffcd2021aa9dcaf">81ce34f1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-11T19:33:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: fixed crashes in MlModel::pack
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6bc8f5e5cbddb7df2f8f260bec1925b662e1d246">6bc8f5e5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-11T19:33:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dc0810e70a473c75105f28b4ada81138760030a4">dc0810e7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-13T09:43:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b85ae812d013c826c7f614fa2a01d75b30f84819">b85ae812</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-13T11:26:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CtfRefine: warn when refining beam tilt in a Cs corrected scope.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/decd57193729f80cc0aeab78d26b54f2c1f8b56a">decd5719</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-13T11:43:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'beta-repo-3.0' into 3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ddca6af241ef40caae7e91acde5cf1d9532a270">6ddca6af</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-13T12:06:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Call this 3.0; Added documentation about libtiff.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ff5413de75d3051df397692b2c3b855ed855b514">ff5413de</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-13T15:04:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added libLBFGS to AUTHORS file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64ae9b2c90f799a6badc7b8927cac83a0ff0de03">64ae9b2c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-13T15:05:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/21d177425697362737c1a5b2eaa44767dca6eecb">21d17742</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-13T16:36:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">extract possibly in bigger box when doing (per-particle) CTF premultiplication
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/78dfb81299ab7f38c6b5068ab50fd267cc1d263e">78dfb812</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-13T16:37:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">option to prevent preread of images, useful for reading optimiser.star for other programs, and backwards compatibility with chnages in translations in Angstroms
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/357197066fd7dab22b3115257ce1d892bec42980">35719706</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-13T16:38:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">prepare fr v3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cda848bd1cbd64f07a487f0b0f1feb7fba34c5de">cda848bd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-13T16:44:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now works with obsModel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/984c9158b23aeebe65c83d2be9a0c625c41cb791">984c9158</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-13T17:32:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added acknowledgements to AUTHORS.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/600499f35c721e2009135ee027078e69414f7edb">600499f3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-13T17:34:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'beta-repo-3.0' into 3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4df5e5975046a93b34df4b4600798f19f9b303d9">4df5e597</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-14T14:19:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MotionCor2 wrapper: remove *_DWS.mrc produced in >= 1.2.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4629b844ba2cc1edbecc9260e8503e237f88b29d">4629b844</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-14T15:06:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CtfRefine & BayesianPolish: get file names of half maps and the mask from a postprocess STAR file. This enables scheduling of these jobs. Solves issue #435 on GitHub.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ace90405d8fef34e59e67243a18e3f5862a287c3">ace90405</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-14T15:10:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updated README
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d395e763d41dc763ffe4c24dcc3594599f6b9c3">5d395e76</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-14T15:18:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'bitbucket-3.0'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3cfa14b88391201157d1cced7201825b1523669d">3cfa14b8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-14T17:18:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">moved cropInFourierSpace to fftw.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/11ec3bbbd2d01d0cd03547ae72edec7a8f9efa4b">11ec3bbb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-15T11:34:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">used long long int for nr_directions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c750f81670173745173c96e05bfa2f4b49c3fe31">c750f816</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-15T11:34:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f853be8372fe34eb9a3590fb8e3eaf02ef5a2f1">3f853be8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-15T12:31:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added obsModel to project
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64348a26efa1a41858671b147b9fb6ebb4fe9761">64348a26</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-15T12:31:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update pixel size and image size in the optics group table if new_box or rescale_angpix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0705fa093dd74546fe3147f9f88967ea589cfdb">d0705fa0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-15T12:37:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added new particle_subtract program, both for multibodies and normal partial signal subtraction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/906beb093803b1db22a3a4ac502f3ef3e0b4f201">906beb09</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-15T12:38:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed subtraction functionality from flex_analyser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/870250894f13d5cab59830a7638ab366c59b69ac">87025089</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-15T16:59:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added relion_particle_subtract to the GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9e20d9fd43f2c4f75edcc3ee0ac4bdec7756419">d9e20d9f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-15T17:05:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1_scheres' of https://bitbucket.org/scheres/relion-devel-lmb into jaz_3.1_scheres
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d7451af96410f5d257db91b59dd2eb1ff2a6abed">d7451af9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-15T17:43:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: fixed typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/059e659da8ec8ce15064b7eb516040c7a9f8e073">059e659d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-15T20:19:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into jaz_3.1_scheres
Conflicts:
src/acc/acc_helper_functions_impl.h
src/apps/image_handler.cpp
src/jaz/ctf/ctf_refiner.cpp
src/jaz/motion/motion_refiner.cpp
src/jaz/reference_map.cpp
src/macros.h
src/pipeline_jobs.cpp
src/pipeline_jobs.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc3c11ea4bd82679c10a6648379d3e1e9fb2bf85">cc3c11ea</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2019-02-18T03:12:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion parameter estimation restored: all optics groups can be considered simultaneously for parameter hyper-optimisation if they have the same pixel and box size. Otherwise, a single group can be selected using --par_group. The output filename is now called 'opt_params_group_N.txt' or 'opt_params_all_groups.txt', respectively. For the alignment itself, --only_group can be used to only align micrographs containing particles from the indicated group.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dcd265e5427ff399aca0aa250513e7bbef2de8c6">dcd265e5</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2019-02-19T01:37:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motion_refine: images are now by default recombined at the pixel and box size indicated in the star file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/afe297be77d31b3c9e16061c701432afb073059a">afe297be</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2019-02-21T00:43:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_refine: symmetrical and antisymmetrical aberrations are now estimated after the magnification
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ed6bd9afdbbdc5bfbaab6c493a6f994f5c01936">1ed6bd9a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-21T11:59:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1'
Conflicts:
src/jaz/obs_model.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a39cf4491ad1cdf9bb8cb34b586783e90707952c">a39cf449</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-21T12:06:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: remove addition of an uninitialised magnification column
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cbcd62acb632e9f3e83caa6742f67022e75da3cb">cbcd62ac</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2019-02-21T17:56:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">the aberration fits now correctly consider the most up-to-date magnification matrix estimate
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a20aba6a3dcb6294de85e1440320d14361fa1356">a20aba6a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-21T17:37:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5360bcc22499df35cc143954ae71132ab513a4e">d5360bcc</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2019-02-22T04:39:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bugfix: magnification estimation now also updates the vector of mag. matrices in the obs. model, not only the entries in the metadata table
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a41e9683f332abe6c4b85714e6192dde254b22e6">a41e9683</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-22T07:34:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ffa62dc495483cee9a8ed84da078a8b6f75a373">3ffa62dc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-25T10:44:05+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">trying out prevention of zero CTF in ctf.h to improve code stability on GPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ddaac75e8c82d37fce93f456912fe4326995419a">ddaac75e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T10:52:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84c428b1c5d24395979a11a94b3656444dbb1808">84c428b1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-25T11:28:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adapted for obsModel and repaired bug in transformations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a715f64aca369a191e8a657a12e69d52acf7e4c4">a715f64a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-25T11:30:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in apply_transformation in stack_create
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/06b59a7e9e94ee7d8a560036b9fcd578d3866613">06b59a7e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T11:30:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Pipeliner: Forbid {, }, $ for alias. Escape special characters in flowchart TeX files. Fix the return value from flowchart generator.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fdce358ff78daff3f7e7e05b09eec70a444c2241">fdce358f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-25T11:52:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in apply_transformation in stack_create
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/632d7c834a4f913893372b65579db02f440dfb66">632d7c83</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T11:59:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_stack_create: add warning about --apply_transformation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d96df8ea629aa9f46bec9317430079c97884a4d">6d96df8e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T12:11:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'bitbucket-3.0'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/151f181a51247edc9f7bb85e5b1401743d1f08b2">151f181a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T12:19:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f73ec6eac2b3fea9dc70d0ed436e81cf74c1a95f">f73ec6ea</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T12:48:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Repaied GPU double precision build (GitHub issue #399; thanks to @miesav)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/87d87fd1af7960e0768b38074af4209704fddbc1">87d87fd1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T12:52:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: never submit to the queue for Import/SubsetSelection/ManualPick. (Github issue #445; thanks to @andschenk)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6062e4b2225977f6bb554c6f19ae84fa87000a38">6062e4b2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T12:55:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'bitbucket-3.0'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ccd88db7decc527c895fb3ae6bec5a51f1bbeafa">ccd88db7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T15:03:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: removed a confusing message (with MPI, it wrote the IDs of micrographs processed by the rank 0 only)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/09b22d06de049b3311b2fba0bfe2646f31be121c">09b22d06</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T15:09:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">run_motioncorr: removed a debug message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b819fb571add5e5dee5be9d2d2dd180e188b03be">b819fb57</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T17:46:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0'
Conflicts:
src/gui_jobwindow.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/032aac135eda2f4c847bbddbe13128b0abe399d5">032aac13</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-25T17:47:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">pipeliner: fixed continuation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5e8335bc5f1b0ec5905e178e4eae5e0c2dc7fd8a">5e8335bc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-26T12:32:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug reported by Claudio Alfiero and Takanori Nakane about multibody refinement having displaced bodies after body 0 converged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/541455618ea1e8aeb0161631dcdd8df784305a64">54145561</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-26T12:37:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'bitbucket-3.0'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5aeaca4589f462e5b427267d21a632f7a1d823e0">5aeaca45</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-26T15:54:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0'
Conflicts:
src/gui_jobwindow.cpp
src/pipeliner.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a479629a5732c510b08af9aeffffa1945e9f0a7">1a479629</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-26T15:55:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added joinSTAR with optics groups for version 3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e3056abc6fef43199c589fb4493cbc982014309f">e3056abc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-26T15:56:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added joinSTAR with optics groups for version 3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/92fc02951023705ae8020b7fa213659a08398df3">92fc0295</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-26T15:57:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
Conflicts:
src/gui_jobwindow.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3168399f144232c38acbe92c62fea33b4c75e8b7">3168399f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-27T07:35:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cache: removed the assumption about the number of digits in optics group IDs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/28adbfab75d45ab74acae0058b3871a788895ad1">28adbfab</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-27T12:16:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added unique to nr AUs for helical refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f37d8e7757d2ecab043c1546b347518beba6e23">8f37d8e7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-27T12:17:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">determine dimensionality upon initiliase and repair bug optics group
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/050171358b4a5ced941ce7997d8eee263c5856cb">05017135</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-27T12:17:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ea4dee613033e9b185829fd1c7fa467fb1a073a">7ea4dee6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-28T16:09:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">origin shifts in Angstrom for 3.1 version of do_center
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/33209f67f998d7c6481780b29dbe8462a61a1919">33209f67</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-28T16:09:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">implemented carrying on of unrecognised metadata labels
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/058edf743799412d00233b48bb1c6007e4d0b158">058edf74</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-28T16:10:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">rescale and window masks during initialiseGeneral
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d48edde1a806f07f98bb5ff7353efa817929b79">6d48edde</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-02-28T16:15:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in fn_mask new name for second mask
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0cb37fc2030179f1f464c5235be50569cf95714b">0cb37fc2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-02-28T21:54:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair checkMask()
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ed35a331802cf7f4dcbea806374354d9a6a38b56">ed35a331</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-01T13:53:32+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add option to import old particles.star and to rename optics groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be838e2f180f09c6aab802fc551a547d5d866dd2">be838e2f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-01T13:55:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forgot to add ../src/ml_optimiser.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d1bc38415cbb6c001e20a1699ef01ea6f705778d">d1bc3841</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-01T13:56:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/440ac10a15dd2d04d8ef86506dbefd7fce3f81d8">440ac10a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-01T13:56:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ddeade22f99f05f12244b3ea38f63acfead046e">3ddeade2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-01T14:00:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug import
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c1197d08c680d6464f0bfb54d821493c27d203e">1c1197d0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-01T15:41:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small bug in checkMask
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42c623b25ac200a82d530b419501abb77fe23e93">42c623b2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-04T13:48:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add ignore optics to displayer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/07449e41acca5f875ca358f374ba5f04bbe797cc">07449e41</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-04T13:48:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">split groups per optics_group when combining
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/75ebf486f3919ae2c77701ebda1a9773890be2ad">75ebf486</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-04T13:50:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bugs in clauclate powerSpectra
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/89e237076d1de9f4bd0e1b86e8c2a6ab2a6c59a7">89e23707</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-04T14:55:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Added RELION_QSUB_EXTRA(n)_HELP (GitHub issue #446, thanks to @Fravadona)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/89af8fa11d49ad77edddd1683f2899b5dc73b963">89af8fa1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-04T14:59:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/17c64c7bf31f2f09f076eed7d0a80585f6532860">17c64c7b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-06T12:15:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adjustments to deal with 3.1 star files in nr_uniform and others
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b6486afe43913ed3af11a7eb77c93faaab615a67">b6486afe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-06T13:35:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to ignore optics groups to stack_create
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a9c84f37ecd4fe6364e9f7457bb3428c7d3f4f4">8a9c84f3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-06T17:40:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed 3 bugs with anisotropic magnification: 1. projector and backprojector took transpose instead of inverse (in cpu code; gpu code was correct with inverse); 2. in obs_model.cpp applyAnisoMagTransp should take inverse instead of transpose, renamed it to applyAnisoMag; 3. in generateEulerMatrices of acc_helper_functios_impl.h the MAG matrix should be applied before, not after, the inverse operation. Also removed boolean for IS_NOT_INV from all set2DFourierTransform and get2DFourierTransform calls, as IS_INV was never used anyway
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7105600d468c539ba17e427759ceaf35395b4a54">7105600d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-07T11:45:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/31611d6c97c220ed1a72e83836786ba73e47bcb9">31611d6c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-07T14:30:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed comment from jasenko about anisotropic mag and inverse
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0c71f303dd98b4b16103e804493815b6a5c30be3">0c71f303</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-07T14:42:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AutoPicker: make an error message consistent with GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7714b88c7d6be8c222113587ef8de4db0cfe45c4">7714b88c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-07T15:04:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cmake: automatically add the Git commit ID to the version string (available as g_RELION_VERSION variable)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ba4b0498a511e28c7892731ae26a1bbc77a48ad2">ba4b0498</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-07T15:42:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">generateEulerMatrices is only called for Fine squared differences. Coarse squared differences uses cuda_kernel_make_eulers_3D on the GPU. This wasn't doing the anisotropic magnifications. Fixed this. Now test case with only anisotropic magnification (no CTF) goes fine both on CPU and on GPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f65ebd76d0cfffa05bec14bccc30fa62e84824f">4f65ebd7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-07T15:44:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">take inverse instead of transpose in generate euler matrices in CPU acc code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1346e18f5ed4251fb09f801fc327da17f322517d">1346e18f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-07T15:44:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/54000142b893acf8ecb7731d87a198037d8d7cc6">54000142</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-08T14:54:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug new boxsize in rescale and new_box
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7826971b63cd77de2bfec9e2d63fbcb6f235d0ef">7826971b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-11T09:42:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in project ctf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a877bdfe62f166ccf4db3e9cbf884ce47920969b">a877bdfe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-11T09:47:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in image_handler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ddfff781cfb68bd6f031b242e398b34c9aa0acc9">ddfff781</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-11T12:45:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired stupid typo bug in applyAnisoMag
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/98171da9f0a77e77dfe4fa850f7051b5619d0717">98171da9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-11T15:48:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Call this 3.0.1 because we changed (fixed) relion_refine.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b966fbbe74160a08c5a361739d4575e51e523666">b966fbbe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-12T16:27:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">do either aniso mag or CTF refinement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/03df4176f980ec9024a243239fa98f44e2a1e5ee">03df4176</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-13T10:19:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in not setting opticsGroup in CTF::setValuesByGroup, affected symmetrical aberration correction when having mroe than 1 optics group
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f87354364a702d959b5da7393c9dd432f8e8843b">f8735436</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-13T12:55:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_refine_mpi: Fix buffer overflow during initialisation (solves issue #449; thanks to @Fravadona for finding this and suggesting the fix)
Call this 3.0.2 because we touched relion_refine.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/555486c7bca6d220c8be6684323df05185533a38">555486c7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-13T15:16:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0' (MPI initialisation fix)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/055da427c67182701e473bb9d0f541141766b0fa">055da427</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-14T16:22:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">first attempt at allowing external system calls to do the reconstruction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9bc6e9d1e8e251cd349bd15edb538197087dfc32">9bc6e9d1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-14T16:22:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> test program for external reconstruct, does exactly the same as normal reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a256f2baedb33505d8b8d4e723d64db66f2bdd9">8a256f2b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-14T17:46:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">report an error if external reconstruction return an error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b988a7133c531aa0614b54f20fb596c484d889a">8b988a71</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-15T16:47:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: updated load_star for 3.1 STAR files (RelionIt itself does not support 3.1 yet)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/38dbb3a7a9ec1e713a472878cf7fa1eb38e87013">38dbb3a7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-18T12:25:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Validate the optics group name in the Import job. Also repaired 'particle optics group name'.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3330d56367b51eeb7d4d2404c4c65cf4acde8831">3330d563</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-19T10:16:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MetadataTable: fix writing of an empty DoubleArray
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/271ed1c714f18201c137fb9c93c565e6f0e169ec">271ed1c7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-19T10:16:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Antisymmetric aberration: need at least 5 elements for beam tilts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e07dc85a275c692714a6016bd3d690def46761a">7e07dc85</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-19T14:03:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed spurious function
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dbb1c9e862644a451f1257254057da848a1a99d9">dbb1c9e8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-19T14:04:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improved cerr and cout output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/171553e33073e8e600c726d75cba4a6d17ab127e">171553e3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-19T16:39:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in precalculateInvSigma2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/92eadedc310799aaa258869f91a82a4ace1b325e">92eadedc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-19T16:40:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">setXmippOrigin external reconstruction AND invtau2=0 if both invw and tau2 are zero, which may happen with different optics groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8c385ead75d383ae3c9eab977c7381d7a40b2851">8c385ead</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-19T17:40:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Aberration and Magnification fit: OpenMP parallelisation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d7258554f894f656e275def48333bc04da27c2a">9d725855</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-19T17:40:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Magnification fit: removed debug message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6172d60d9a813e9ec83cb89bd1883ed61a8d681d">6172d60d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-19T17:40:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">B/k fitting: clarified that fitting is done using FCCs from all particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b2e797b8100a19293865ceed7d6a303b59d34ab8">b2e797b8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-20T11:15:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_refine: repaired '--reuse_scratch' when there is empty optics groups. Made printed messages 1-indexed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f107911095b2d90c0b7af904b5be53b5c8812eb1">f1079110</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-20T11:55:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ObservationModel::applyScaleDifference has to be the other way aroundgit add ../src/jaz/obs_model.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bfab6818621351c0f3387ec3bfe052dfc44a469">8bfab681</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-20T12:13:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in current and coarse sizes of all optics groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6de0842b86e5962876bdfbc96ba8d4309ad9cc2f">6de0842b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-20T12:14:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in learning (pull request #24)
Learning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d557a38f5a8ae9f4b4de83f7709a78e05cc9bc6e">d557a38f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-20T12:41:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_estimate_gain: a simple gain estimation program
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/39fb1ce28dbe0be4a04618caa3d00b648e2b54a0">39fb1ce2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-21T12:58:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug applyScaleDiff in angular accuracy estimation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/65035519f3af1e9f65288bcd957e24f1fef1ce16">65035519</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-21T14:20:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">import takes MTF file and adds to optics table. postprocess takes original pixel size of micrograph for MTF correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/718438e0d48b10120879eeab2ed0eb9585fb555c">718438e0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-21T14:51:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remapped sigma2_noise onto the optics group in calculateAngularError
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c9b234b6d50f3bc833f66fe9022c90d68cf4b727">c9b234b6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-22T12:14:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AutoPick MPI: wait for all workers to finish
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a2fc30846f1e092a3c0f19e4878d5ef616a569c">8a2fc308</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-22T12:36:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in estimateAngularError
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d1ca8cfdc4018064f378d955796f58b34b4d02c3">d1ca8cfd</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-22T14:27:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0' for MPI autopick fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/15a89764313f6c49d9e8fe99a393023a44536cc5">15a89764</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-22T15:11:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">implement division by MTF during refine/reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/edb78c0bb5039b4d0a8fcab7e2adcfbe703ca1ba">edb78c0b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-22T16:26:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: fixed integer overflow at very fine angular sampling. Call this 3.0.3.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a11578584643623faa46be9192874ce903989968">a1157858</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-26T09:04:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">have option to not die upon loadSafely of obsModel, also some tweeks for divideMtf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1898d1091453bf74e8b1fec5ed804c897d5a46a4">1898d109</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-26T17:21:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont die if cannot convert for 3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/104376f83be73cb3ff4e8fd2f0e702d3f8222b90">104376f8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-26T17:22:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added writing EPS and logfile.pdf for ctf_refine with the diagnostic images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/284f3574a46ec6a97b72aeab1b937994b2cc9884">284f3574</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-27T11:37:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">get real group name
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b428396b04009733d261981b648a4a060571568">8b428396</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-27T11:38:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now allow different pixel sizes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/71432e0a7599af65db28cf7ac6b956ad515431a5">71432e0a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-27T11:52:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added functionality to simulate a CTF image
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8e83af3da1f8305310dbf7eecce6a4362131a63b">8e83af3d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-27T11:53:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/555405e3c324e10d9b097b7ffb741d68efc1e9e0">555405e3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-27T15:24:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added options to skip gridding and MAP in external reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a3f9ab6ca6029f567b572b9f5c0b985cfc5004c8">a3f9ab6c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-27T15:24:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to ignore optics groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9cf18c174da56bec496c93b50058342736544a2d">9cf18c17</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-27T15:25:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reorganised reconstruct and new implementation skip_gridding
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/35a7a7e7e5ce8201915c62c1096d00f6ba42e115">35a7a7e7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-28T11:50:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to downscale simulated CTF from larger box to simulate too-small box effect of aliasing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/448773d7dc9874e35d077ea8dd9eb85a335240a8">448773d7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-28T11:50:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">made acc kernels for premultiplied CTFs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/895ed5fd1ce066681a1f937e98649dc14179d345">895ed5fd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-28T12:04:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">option to ignore optics groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c47811d77cdcef5e02ba26fd30a8032a7d689209">c47811d7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-28T12:29:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in dLL calculation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/11cf245502c8491795e7ebd12415af07227ff547">11cf2455</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-28T15:11:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ALTCPU BackProjection kernels: Fixed a template instantiation problem with CTF_PREMULTIPLIED.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/717e0cb7d000325d776f5547db17841dae6ab372">717e0cb7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-28T17:32:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont provide --ctf_premultiplied in refine/reconstruct: get from opticsTable instead
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bee2671e14082cee16f4022622a4c8bf8525494f">bee2671e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-28T17:48:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">simplified ctf_toolbox. Also, it now sets ctfPremultiplied in the obsModel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4ef84a79501b223d7ce05bac528daab802fcb975">4ef84a79</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-28T17:48:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">made an option to use ctf-downscaling in getFftwImage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/30136dcd0e138342a3488833e78d68ba86cb9b9b">30136dcd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-28T17:48:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca2130573f006512e388aa948023c9cb063b99df">ca213057</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-29T10:19:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to use ctf padding to relion_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/47a8c39322b233aa30a1ad59fbfede0accf8984d">47a8c393</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-29T10:19:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed phase flipping options from GUI, and don't die if an undefined option is encountered upon reading run.jobstar file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0a37a0ab65acba526939f16638fe71d4a34af65c">0a37a0ab</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-29T10:20:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option for ctf padding to ctf_refine program. Also check and die/warn for ctfPremultiplied data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6201e4198b4bceecee268d1e936c5cadc74b8f24">6201e419</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-29T14:21:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: added --suffix to allow re-use of trajectories
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/63eb56ca0d9a1d79e760cd1301ec39a823e4a0d7">63eb56ca</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-03-29T15:52:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: made "Do dose-weighting?: Yes" to the default
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/04bfe0398527d0417c8fed8fef862186234171cb">04bfe039</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-03-29T16:22:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">implemented ctf_padding in ctf_refine
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/068a19d9f7496bc395aade01296a0194ccb580d8">068a19d9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-04-01T09:49:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in new implementation skip_gridding
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/249fa89bf599a82e97fd3f3b9dca85357869d3e7">249fa89b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-01T17:03:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b963b4f53bb15bb38901d6aeb9444dbd7c3756ac">b963b4f5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-01T19:29:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ObsModel: added setBoxSize to invalidate caches.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8af032341f8aaf3c8f3e561cfbd9f18a2cfde89a">8af03234</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-01T19:40:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">BayesianPolish: added CTF premultiplication and cropping after that. The order of operation is --window, --scale, CTF, --crop. Confirmed on apoferritin but NEEDS MORE ERROR CHECKS!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dc18ce2e31d3c5f046bb4c228ffc77bec984454f">dc18ce2e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-04-02T13:29:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont reconstruct when doing CTFs in reconstructor, just take data/weight
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ef684dbea8aa2b0474c6ac86cbd8ea6330551d70">ef684dbe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-04-02T13:29:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5206665c4d29d6eb00be1d145d4d7c58cc9012f1">5206665c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-03T11:28:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_flex_analyse: preserve the original image names in the rlnImageOriginalName column (reported by Sean Connell on CCPEM)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a1d5a53311ee70dec5491675d7ad4915bdec244">1a1d5a53</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2019-04-03T11:37:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix build when Intel Compiler is used
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4c10a974eea57caa4654dacdf2418b7eef3bc0c2">4c10a974</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-03T11:38:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0' of https://bitbucket.org/scheres/relion-devel-lmb into ver3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7b63f340664b4f0a627320dc92a8030dbb5f0cf">a7b63f34</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-03T11:40:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0' of https://bitbucket.org/scheres/relion-devel-lmb into bitbucket-3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e9afc9a1d52360b482e9816c6c54591165b89ac0">e9afc9a1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-03T11:47:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Multibody: fix crash during initialisation (reported by Rafael Fernández Leiro). Call this 3.0.4.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a71285c5e6e237682c3c2038fac9787de749c0d1">a71285c5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-04-08T08:59:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added openMP parallelisation and mask_diameter to helix_inimodel2d
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7f46b9f9e77784d82af53c41ecd42f720191abc2">7f46b9f9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-04-08T09:00:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added --auto_iter_max to stop auto-refinement at given nr_iter for Gustav and Jonas
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d4abe3493b17576c76686b5ec8736f578fc0ca9b">d4abe349</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2019-04-08T11:29:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix build when Intel Compiler is used
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4d5c00fbf166058997b919c0c757a0a0325d4768">4d5c00fb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-08T11:38:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extract: set rlnCtfDataAreCtfPremultiplied when --premultiply_ctf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a3c7d19448a11dab164e1cc4b51d5464df03431">7a3c7d19</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-10T15:29:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AUTHORS: Included CPlot2D (reported in GitHub issues #460; thanks for pointing this out)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a5f6579c4807086730e2200f4241356354875059">a5f6579c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-10T15:58:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0'
Conflicts:
AUTHORS
src/flex_analyser.cpp
src/macros.h
src/ml_optimiser.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8964268773804abcc86b897f5d79f1fa4cb1104">b8964268</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-11T11:36:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: fixed the path to non-dose weighted sums in a log file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c8f9fe1c4f9715ef7c085fe2eff23df6402a34a5">c8f9fe1c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-11T11:40:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6a68032a2a86fc50eba58d7ba39731382e8030dd">6a68032a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-04-11T20:09:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in writing star file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1be7c133389ec2cd2dc8a77883e386862308e508">1be7c133</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-04-11T20:09:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out optimal y-off and rotations, so output STAR files can be used as input, which allows ever finer local angular and translational searches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2c7cd922ba233ed269b4e1b4a3c2cb62469edffb">2c7cd922</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-04-11T20:10:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/28cb2db7dc758def04c6c720e5a7df27e66e8fdf">28cb2db7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-15T12:23:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Improved an error message when the directory is not writable.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/564237db1b860df6db33ae511a3511e6cf130dbc">564237db</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-16T11:51:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/381f2936d495703c048c5a6876b352aaed32c67e">381f2936</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-16T12:02:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AutoPick: Number of particles should be an integer.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eef01a82df67620cb86bfe8e2abc44409a71267b">eef01a82</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-23T14:33:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTF: implemented ignore_ctf_after_peak
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/67c1ed32c54e793439c62a501ee9b871079f9948">67c1ed32</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-04-24T14:32:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check for not too large value of ires in noise-generation outside particle mask, which went wrong with 3D data with Kino
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bd5b1443308ac6f54dcda58875edc52d74d36ca7">bd5b1443</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-04-24T14:32:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0a1471b5f68fec57d5338af1211ecc9c445bd6bd">0a1471b5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-26T11:29:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Non-void functions should always explicitly return something (GitHub issue #453 reported by @riverseow and @kmlyn).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d8fee7c46672482abe72f2510946eef81b443dd">5d8fee7c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-26T11:37:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TIFF: Report the file name upon error. Unfortunately this does not catch all errors. TIFFSetErrorHandler() cannot get the file name without using a global variable, which is not useful for multi-threaded programs ...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9caf2da0dd4aeafa492e88497e5162543fc34066">9caf2da0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-26T11:54:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0'
Conflicts:
src/displayer.cpp
src/displayer.h
src/jaz/motion/motion_param_estimator.cpp
src/metadata_table.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1887f6dcb84e3d672fff698a6fc9fd93ea73c5d6">1887f6dc</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2019-04-29T02:28:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">modular CTF refinement added; not yet functional
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/73bdb8eeaa16c1599bd9b416e38f1d96d999d188">73bdb8ee</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-04-30T14:41:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AutoPicker: removed debug output (reported by David Hoover on CCPEM)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4346e55028159ee8225ba5a0669b5ac4016ce16c">4346e550</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2019-05-02T01:14:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new modular ctf-refinement now functional
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/290308b7d76b19aca06684964f8413c8a1baec36">290308b7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-03T11:19:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Scratch: do not copy same particles (useful after symmetry expansion; suggested by Oli on Github #462)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bbd1e25c530adea02742347e72f9e224513d4171">bbd1e25c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-03T11:43:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_stack_create: added --one_by_one option to save memory
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6835b92fb469c63a9353218d4cc285e60a81f881">6835b92f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-03T11:46:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in backrotate3D
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1fc49bf29c66bb559f1a5c4cca04a6ade526d00b">1fc49bf2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-03T11:48:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'jaz_3.1' for modular CTF optimisation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64c60350efea2d8018326b388d07e2737b58751f">64c60350</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-03T14:54:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair bug backrotate3d int to rfloat
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a53aa5677859f55238b44367d7dc43b734e09d0d">a53aa567</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-03T14:54:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/15a9c813c6f57d57a5af70ae2a9326273c4ef3b0">15a9c813</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-03T15:52:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add cl_angpix to star handler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cf628050f9377d600521a6a8c1b006e475583842">cf628050</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-03T15:55:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">implementation Kent Thurbers rotational prior for helices
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d6901cbad13fdeafde07d02d8593c500728946a">6d6901cb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-04T11:45:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: fixed a bug introduced with --crop
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b9fee094b7872e02fc637d9cd842515b583cfbd9">b9fee094</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-07T11:26:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Scratch: repaired crash when 'parallel disc I/O' is no and running on multiple nodes. Call this 3.0.5.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2084dd9e2103024b0f5b12aecd0b99a8b4bde3cc">2084dd9e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-07T11:51:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adjusted GUI to work with Jasenko's new ctf_mode
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c3b33646ae0e8a8c9a19bc44dceb4cd8092699a5">c3b33646</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-07T11:53:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">This is 3.0.5.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1e1dc23a8dcc5e059cb2a0a9f80ebc0e02cae0e">f1e1dc23</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-07T12:11:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge 3.0.5 for bug fixes
Conflicts:
src/macros.h
src/ml_optimiser.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b17ffa139230b97538e6328d0549733de69d18a7">b17ffa13</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-07T14:24:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: trying to implement --strict_lowres_exp (but not working yet ...)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/add22da061650d8d9d62fef25be7c71f6fb06ef0">add22da0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-07T14:56:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">estimate_gain: added a new line to the message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2c4a49fe9a65c932155455b2161f796a3af61a0d">2c4a49fe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-07T16:56:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">strict_lowres_exp only in projector, not in images. Also store in optimiser.star for restarts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/08d6c487edafc395952f3b305e8b206ec32c72e3">08d6c487</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-08T11:57:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired small bug in subset selection with split_size AND nr_split
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/abd84a5ae8028bebbafafb5c3d8c7b49c2c87e52">abd84a5a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-08T14:05:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ctf_toolbox: --ctf_intact_after_first_peak
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/31feb245d79e9fd2f501d84625b49d47d8e390b7">31feb245</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-08T14:10:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AutoPicker: --LoG_upper_threshold
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f5f7b3090996a12fd6c6209bb9c50ce9893ea027">f5f7b309</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-09T08:02:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in E_step_max_res (pull request #25)
E step max res
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/917c9804196a39c5c6e2e5153dc206dcd869334d">917c9804</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-09T15:20:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove run.out and run.err when overwriting
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e574c19c6c7e6f4985ae4f4f0661de12502043c5">e574c19c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-10T11:25:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ObsModel: Make sure rlnMicrographOriginalPixelSize is present when applying MTF correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ae9b8e473a79f820e328cb7c786ac1b66ab2594a">ae9b8e47</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-10T12:54:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">motioncorr_runner: keep EMDL_MICROGRAPH_ORIGINAL_PIXEL_SIZE for MTF correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4d15fde66846a49393c6079ba1185c1ca26a9a94">4d15fde6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-13T14:46:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Improve stability of histogram generation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a9dff2e3b95a133b96e57844d46091d7cc394d98">a9dff2e3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-13T14:55:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0' for a histogram bug fix.
Conflicts:
src/autopicker.cpp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/81e269df9886abefe8276ce189736765c0779607">81e269df</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-14T10:33:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_star_handler --select: show the number of selected items (GitHub issue #466 suggested by @daniel-s-d-larsson)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e781ac67b0d1f8f78bd9b2ffcd9824e5c7681f4d">e781ac67</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-14T10:34:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">scratch: avoid use of wildcards to prevent too long arguments (GitHub issue #467 reported by @EMBL-Structures)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f23f1787f23f69d5554e468c19d26810d39b754">9f23f178</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-14T11:49:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">scratch: avoid use of wildcards to prevent too long arguments (GitHub issue #467 reported by @EMBL-Structures)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3057752ecdbd5505f476fca575c5b8fec44390e2">3057752e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-15T10:04:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">helical offsets restricted along x in Class2D, rot_sigma on GUI, and Fourier-mask to remove projections along helical axis from Projector
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4c0b9363d160b5738b31ead5d218d8d36187b2b0">4c0b9363</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-16T13:52:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: use a defect file (same format as UCSF MotionCor2), write local trajectories and hot pixels to metadata STAR files.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e9082074c39fd5fed84442a7d53b435dd4515279">e9082074</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-16T15:01:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MotioncorrRunner::fillDefectMask as a static function (for use in Polishing)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d63796f3d0417d1098013c53d3b3d385eeb2637b">d63796f3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-16T15:02:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">PostProcess: remove --auto_mask option (one should use 'relion_mask_create' beforehand)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d193acb1a3ad5a10aedcd4a1d8d96732e0c7403">8d193acb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-16T15:40:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hopefully repaired bug strict_highres_exp in GPU code, reported by Kino
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/edf4e2e716912f356d329bf16b6141577108dcd3">edf4e2e7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-17T09:36:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">modified apps with relion-specific exit signal to catch error or normal exit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/002151f814746485255e7fd083a33615edfcde34">002151f8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-17T09:37:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">started with a pipeline_control system (thru disk) that allows aborting jobs and catching their errors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/da1dccbf9eddcea124576b921a3a7410fd3f0a3e">da1dccbf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-17T09:54:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolving conflicts in setFouriertransforms in projector when merging rotprior into master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fdc69a1fbf8fc486b493a615d9d3aae107fd1331">fdc69a1f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-17T08:58:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in rotprior (pull request #26)
Rotprior is a modification suggested by Kent Thurber from the Tycko lab at NIH to allow priors on the rot angle in helical refinement. The branch has also accumulated some other changes, e.g. a fourier mask for helical refinement; a bug in backrotate-3d, the removal of run.out and run.err in overwriting jobs.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce8b7e7fe5e0232c8aed13f8d9c01aba01d6a739">ce8b7e7f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-17T08:59:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in master (pull request #27)
Master
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7526d602cd9b4e2373f7c92db19c9caf08267147">7526d602</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-17T11:28:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mpi_abort with relion_exit_failure
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/86ce765c15e53e314d139d039aa73e70e7ff0cfa">86ce765c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-17T11:29:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">implemented check for presence of RELION_JOB_ABORT_NOW file in output directory for pipeline_control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0cb79060c68e3da713b5c3e7e7b5620972417999">0cb79060</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-17T11:30:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">no longer move output nodes to .old copies, as pipeline_control now takes take of checking when a job has finished. Also multiple tweaks to GUI and pipeliner to make this work.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b76584fb496496b368e111fafd4fa18b38430f7e">b76584fb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-20T10:46:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: supported 100 kV
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8d34c6329075fad4fc9d0a812f5be4e3a2002326">8d34c632</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-20T10:48:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0' for 100 kV support
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f0259c526b9f6f2be59d368450628832f9e2a146">f0259c52</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-21T14:38:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">LoG picker: fixed inter-particle distance cutoff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34dc552d862e95d7323278f6ae12c7b8b5d8039b">34dc552d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-21T15:20:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polishing: removed an old code path that worked without micrograph metadata STAR files to reduce code complexity.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bdfa183abef04dea2bec73b729d2c3d3d891e1ce">bdfa183a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-21T17:12:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: use a mask of defects and hot pixels from RelionCor. WIP: need testing!!!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a38da598853914513d2112deea4461818b2e26f">1a38da59</a></strong>
<div>
<span>by Joaquin Oton</span>
<i>at 2019-05-22T14:01:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing DEBUG messages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0f9bbaf50ef8032944819e6584575d144e108d85">0f9bbaf5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-23T13:54:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_star_handler --split: removed an assumption on the number of digits
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d879c257c43d88cd699cde1e2ac37d46eca2069">5d879c25</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-26T13:51:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to average helical asymmetric units in 2D in helix_toolbox
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2852439cbb1fc88034e27a07d41f634300ebe52e">2852439c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-26T20:30:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">first version of the new scheduler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b0989420736853cdf26638c88261cfb594baf9c4">b0989420</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-26T20:57:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed some minor nuisances with sending emails
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a894be8b35a5b8b37fa809746d1a6ac713966996">a894be8b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-27T14:46:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now scheduler works with spawning new jobs and with setting joboptions with scheduler variables
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8520d9c1ec2438e5a0e928fd8861c7cf31159e63">8520d9c1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-27T15:58:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added jobtype to launch external jobs from the relion GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1056a884b309a22b93cfc5d55491a99d58873fb8">1056a884</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-28T20:31:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now with very limited version of scheduler working: can add jobs to a Scheduler, but nothing else
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6aee08b1215e276cb848d7bb58d76d4e7c0cd2ad">6aee08b1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-29T11:56:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">LoG picker: changed the default inter-particle cutoff to 100 % (pick 'touching' neighbours).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57a516c4f701441d9aab0948046b14db89cd7754">57a516c4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-29T12:23:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_model: remove debug output for --strict_lowres_exp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b0b621a154ac7c289494690bd94fb1564467436a">b0b621a1</a></strong>
<div>
<span>by Brian Bockelman</span>
<i>at 2019-05-29T14:18:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Register build byproducts for FFTW external.
If an external project is used for FFTW / FFTWF, Relion links libraries
directly against the resulting libraries (such as libfftw3f.so).
Some build generators (specifically, Ninja) require that the full dependency
graph is calculated at the beginning of the build process. Since the
file `libfftw3f.so` does not exist at the beginning of the build (the
`ExternalProject` command has not been run yet) -- and there is no
rule to generate that file -- the build fails.
With this change, we introduce a fake target that relies on the
`ExternalProject` and has as a build byproduct the resulting library.
This allows `ninja` to correctly resolve the dependency and build Relion.
Signed-off-by: Takanori Nakane <nakane.t@gmail.com>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/387089f52c4d1080541995af830a20ea9b0a06a9">387089f5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-29T14:41:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out RELION_EXIT_SUCCESS/FAILURE
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e65dbe585a2c17d245e3e79da47100d7ad23ea9c">e65dbe58</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-29T15:15:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bayesian Polish: Improve continuation. Also print out the new pixel size..
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5b30b93ed713dc1018bfa61ceb7957291b4cfcf0">5b30b93e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-29T15:49:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bayesian Polishing: removed debug code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f4ab755c5cbda33d0910fcf14230eb8d6bfce1a1">f4ab755c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-29T15:53:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: use a mask of defects and hot pixels from RelionCor. WIP: need testing!!!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/df0701f86d8ddd5e23a71402b0a0ae270c976469">df0701f8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-29T21:34:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">major change in scheduler by removing all pointers and replace by std::map, some nasty extern variables needed now...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d6f1faf97aa2954338f1ce994d35a39755621f45">d6f1faf9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-30T09:52:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">keep scope of global variables within scheduler.cpp and remove concept of SchedulerNode, now Edge just go from Operator/Jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c145c32ccb08a259afa6cebba264384d85b9c69b">c145c32c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-30T13:57:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: Patch defects frame-wise. WIP: need testing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6551b322bd4bf68e906d0318cb0b44378fa289f1">6551b322</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-05-30T14:00:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'defect-mask-in-Polish' of https://bitbucket.org/scheres/relion-devel-lmb into defect-mask-in-Polish
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cf6a3d5999d70086ad59c2181be64df3cec1c2aa">cf6a3d59</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-30T17:12:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">simplified operators and added operators for reading variables from star files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9273ebf6752378ce5cda4db5ab2faaa285857bdc">9273ebf6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-05-30T18:02:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now can add/delete operators thru the GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/db678b230079ed9e5747586cb35bf58028e2d3c2">db678b23</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-01T17:20:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">scheduler gui almost finished (delete jobs pending), now testing abort
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f81e6b56cc67049dfb61aedb4e94f43a4cb861c4">f81e6b56</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-03T12:51:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AutoPicker: --LoG_upper_threshold
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9bfb69db71ebc3d5f97bb9864f15870b7235f58">d9bfb69d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-03T12:51:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">LoG picker: fixed inter-particle distance cutoff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/418a9eb11f38860affac4e3c44451cc848fe1a5c">418a9eb1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-03T12:51:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">LoG picker: changed the default inter-particle cutoff to 100 % (pick 'touching' neighbours).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aa6f9d38be6b795205fd9c1cb53cb3e6e3fdf562">aa6f9d38</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-03T13:01:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">--LoG_use_ctf is not available in 3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/73f767f9eda7d4599d9cc9838786bffad7bb28ff">73f767f9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-03T13:03:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/198e664149b8da0a0b21855a05e7931d93d5b3e6">198e6641</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-03T15:31:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ObsModel: don't try to convert empty STAR file.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0898273e051492839ea7ee94e2415cfebd183dac">0898273e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-03T17:02:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CtfRefine: don't print defocus fitting modes unless actually refining them
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7668335f8d750ac02f96765d5f48b477aada12aa">7668335f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-03T17:48:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now with previous node button, delete jobs and complete deactivation of scheduler_run_grp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/152e4206d78e623b0e0867db3b588b82615ee5dc">152e4206</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-04T12:24:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AutoPicker: reject 3D references for filaments
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/298e7df57dadfd5c220b6b1bdd03f41d3f416cc5">298e7df5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-04T16:24:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">gui now sets jobs, operators etc when pressing next/prev/set etc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9019d5f7a6ee560660a5c490a8f4be61fbead177">9019d5f7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-04T16:55:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">start with executing the current_node, then also no longer need to gotopreviousnode upon abort/error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/10fb5b546454ec3f58de82ccf743956fbef3194d">10fb5b54</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-04T17:32:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug initialise pipeline read GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c01bdb77dfd35ab53048d4c83a9c8bfb0c472eb8">c01bdb77</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-05T15:07:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MotionCorr: Remove --movie. Fix crashes when the movie path contains "." or "_movie".
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42017f88925812c8642319a6490fe55694a9a248">42017f88</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-05T15:54:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">In-memory TIFF decompression to reduce random disk I/O. Unfortunately, this turned out to be slower on distributed file system. So decided not to use by default.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c5f32f173da28863097b4a50d897df22a7ec75c">6c5f32f1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-05T17:11:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now can continue with has_not_started being inherited
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f9209008ac9bdb38c4b6258bc7f268dbb5eec49">4f920900</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-05T17:30:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor tweaks to scheduler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/21b956ed8dd1fdd23b612b9bab07038267b51f0f">21b956ed</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-06T11:47:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor tweaks
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ecdfc8a34bca76a579b672a93047486683bd1934">ecdfc8a3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-06T12:38:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">PostProcess: fix a bug where postprocess_masked.mrc is overwritten with --half_maps.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01ef97b2a569140abd17196f74444bbcdbed805c">01ef97b2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-06T12:40:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0' to fix the --half_maps bug in postprocess
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/67f402295bb21c6bafa2afecfd6ef8b943f32a97">67f40229</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-06T12:57:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug reported by Kino in strict_highres_exp
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e0c8a479019fcbb503fd3cbde44c77c92f84982">9e0c8a47</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-06T12:50:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in pipeliner (pull request #28)
Pipeliner
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a677f296f7038b8f479701740db729ccda3b535">8a677f29</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-07T10:51:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">This is 3.0.6.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5f72ed91d46f72163ef8a45ad0f290f77417b02d">5f72ed91</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-07T20:41:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: don't die but warn when the number of frames is too small.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc69283682cdbb2cc4c5929a1917ea795f48864d">cc692836</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-10T12:31:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">image.h: silence compiler warnings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e507479c756d815eb866b2d44c65a4b1aeb8600c">e507479c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-10T12:31:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MlModel: fix crash with empty groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0bdf72c83ea0bd80cedb93528f4c503a5bc794af">0bdf72c8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-10T12:44:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Scheduler: non-void functions must ALWAYS explictly return something
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd1d4636c4ce8fbb574ce3705cded31783c13821">fd1d4636</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-11T14:39:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">BackProjector: clean up
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3061297816bcf3c0768dc2fb823eba23a652c740">30612978</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-18T10:05:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now have option to copy a Schedule
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/00ee584b306e4eb7a8fb6cd4a89a3e5ec269c48e">00ee584b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-18T17:10:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_MPI_Bcast: fixed a bug where the MPI communicator (comm) was ignored when calculating ranks. This fixes the GitHub issue #473 and problems reported in CCPEM by Wim Hagen, Dieter Blaas and others.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc1cde7124ac66b89a74d7ce3d5185ea319af524">cc1cde71</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-18T17:13:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_star_handler --split: The GUI cannot reliably detect a finished job. A fundamental fix requires 3.1, so put a friendly message instead.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/213f032255e04aa25d80150788fd4be51b496012">213f0322</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-18T17:20:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0'
Conflicts:
src/macros.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/570f1fbff835d89c3b7a5a172ba05152ecfe56d0">570f1fbf</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-19T14:22:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: make it clear re-centering coordinate is in pixels and the origin is the center of the box.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/299bb360e1d648b8b9588a4293a2120d9b1ee4c0">299bb360</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-20T15:27:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: fixed crash in power-spectrum generation when nx > ny.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ed7bd23355cdf7bbc83950aad7ef47fdead789d5">ed7bd233</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-20T15:46:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now output nodes can also be read from a star file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aafd53c0a8ab4d38a6dfba8feb21b1814df567a7">aafd53c0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-21T16:39:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">mpi_barrier before relion_exit_success
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f20541215f94f12078fa1506feb7195d73730ffe">f2054121</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-21T16:39:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed spurious cerr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3aad2670c0305627e5138e19d093f883d5c8fe44">3aad2670</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-21T16:40:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debugging scheduler...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ae6ce1a06ac771a255201951a55558ba68b34fc4">ae6ce1a0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-21T16:40:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">button to unlock scheduler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/483efe4147f3681c477675726e1c350bbb800eb8">483efe41</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-21T16:46:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolving conflicts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42f95076142bb85ffec12d7d006ea59cc49fe1d0">42f95076</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-24T10:56:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CtfRefine: don't add unnecessary columns (e.g. Cs)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5786a0124e3fece5f61882082d988fea766ceec9">5786a012</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-24T11:08:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtract: don't make 'run' folder (reported by Madhan)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f16a92a45bac85c18bb1c2bf53c1ffd29e270d49">f16a92a4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-24T12:16:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: add "Use power spectra from MotionCorr job" option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e09d0b2adfa0db4c75694940cd177b961ce3237e">e09d0b2a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-24T12:53:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: add "Save sum of power spectra" and "Sum power spectra every e/A2"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0cfb47783e6ff19253e7d203da374c6c93076744">0cfb4778</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-24T16:15:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: remove ^J (newline) from 'Check command'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bdd13d5cd62ea80e10114fefd5bc54481be3761">8bdd13d5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-24T16:50:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: color failed or aborted jobs in the job list
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d61b1b8c30e28549baeb74698525033acb48dbd3">d61b1b8c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-24T17:49:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: repair 'overwrite' when submitting to a queue
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ed942fce82aefac79422e70d2bf56b7ceaa67fa5">ed942fce</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-25T11:50:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repair ObservationModel::setBoxSize
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/da486d63517132bef66765ace3940529f34a34c0">da486d63</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-25T12:51:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">JoinStar: don't duplicate optics group tables
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2e401de17c8a57dd6eda6da0098d29b9ea05622a">2e401de1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-25T16:37:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed deprecated programs (star_combine, star_compare, cs_fit)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c393152537693603c318911117b24845a1a2c8d">1c393152</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-25T16:54:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_star: make command line arguments RELION style. WIP: this application should support conversion of non-particle STAR files.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c478b0159eb4e61aea41a476a2fdba1b9b91d5b">7c478b01</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-26T14:13:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Repaired premature call to MPI_Finalize() in relion_particle_subtract_mpi and relion_postprocess_mpi.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f780dc4d8d8eeb58770be802d9b7f17aa6188655">f780dc4d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-27T13:43:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged CMakeFile patches from Colin Palmer.
- Ensure relion_lib is linked to libtiff and libomp, otherwise Mac (clang?) build fails
- Optionally allow shared-library build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9b7ca04e749e4bd3bae7141c9c3144024a1a7ef6">9b7ca04e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-27T14:46:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bad conflict resolve
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/106bd500dfb90e0fb528d38162b759aa69e4f7b9">106bd500</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-27T14:50:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">n_digits in split
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d050ca44bee8880b85247fd9762c077a322a4fa">7d050ca4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-27T17:53:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">continue to debug scheduler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2749b327b4d97036bcf95170c38790494eda3f9c">2749b327</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-28T15:00:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now gui can toggle between schedules and pipeline
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc5eebb704d5aaf1da3cca39df490d91425a8459">bc5eebb7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-28T15:21:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor tweaks
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/472d236fcbb924e1fe113a29e180a8d6dfa2fdbc">472d236f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-28T15:42:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now mark as failed on gui, and more debugging scheduler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4130730f1b6dfa2dbb07315befa3c2625babc95">b4130730</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-28T16:31:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further smoothened abort and GUI deactivation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f0cc2317a9a95ac93f5ddc325fd6e881b13ccb5d">f0cc2317</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-06-28T16:36:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">stopping message to out, not err
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca4acef940eb00fb4bd711228c99d571e1663fed">ca4acef9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-28T17:15:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">estimate_gain: add random sampling of movies; add normalisation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c58438c1397a7ece5cd86c21ac2ab6833f794753">c58438c1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-06-29T08:42:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor.py, relion_it.py: repaired split file names (bug reported by Shaun Rawson)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/096f9c455d72c21f3bdb5fd47f48371b66c5f01c">096f9c45</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-02T10:57:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Call this 3.0.7
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5f12461adbfaff5da79bd9ef6ed4f9b8c3b82336">5f12461a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-02T17:02:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">split: always use at least three digits; this is a very dirty workaround but necessary for RelionIt...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a1ffdc0bef7b0a4e7192bd2994d75d6c4e6afeaf">a1ffdc0b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-03T09:14:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">keep polishing the schedules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a320743c80df069d64ccbac23acf0b375abb5d5">1a320743</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-03T09:58:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">separate show_scheduler on maingui and create_cheduler_gui in gui_netries
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7ca3f33b1ea008643e587c364d89ba6c7d0ddbae">7ca3f33b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-03T11:51:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to create 3d model from 2d images straight away
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a28ff5fb52402fb3f3e307fbcd77b7ac6339e09e">a28ff5fb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-03T11:51:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small change in format of run.out
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/44ae9b4e3379160b7d5288e379325ff2b103d84f">44ae9b4e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-03T11:56:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/20ae8a083c3e03782806a1d4dd8692273bc732c3">20ae8a08</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-03T12:48:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">change only_extract_unfinished to only_do_unfinished
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5b563c834f5a2f2facd06dde47338d4abf5d3d7f">5b563c83</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-03T12:48:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in finding logfiles when using given_PS
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a4afa8dba02429ec885a23966185e9318d37de9e">a4afa8db</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-03T12:49:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better handling of choice menus in scheduler mode
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ec12d7912e4852206eabe025f925ddd6e6c32a44">ec12d791</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-03T14:20:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ManualPicker: display the end part of file names
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c455e8bf69a03486acb2b84bac165489b6115473">c455e8bf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-03T14:36:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">no make new schedule on GUI menu
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cb40264ea3160beb7c9706f4752c8ab0947d4760">cb40264e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-03T14:37:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f6529023c26bfadce167b994a6842ea4218beac">4f652902</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-04T09:07:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small things scheduler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/732396e4486ad7c266799b9b3104e83bcc66efd6">732396e4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-04T09:08:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make inimodel2d part of 3.1 release
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/888e710c4dcaa0dfbb36c1259fe66874681e4349">888e710c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-04T11:31:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added compilation flag USE_WITHOUT_STRUCTURA_LICENSE
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/96faf44f402f9052c291d62add7ac8269679be94">96faf44f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-04T11:31:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.0' of https://bitbucket.org/scheres/relion-devel-lmb into ver3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a4fce672f9c8f8028aeef009bc817f3d53b9cdd">1a4fce67</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-04T11:34:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed stochastic em option from GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/815c9010c2dd7ae5cc819ad3f10d270030acc104">815c9010</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-04T11:37:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolve conflict merging in 3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3e7953d3f7dfa85ef6ac7aa94bfa7f2cfa1279a5">3e7953d3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-04T15:37:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated messages for CTF-modulation in SGD after discussion with Francois
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ccfe5d33a8bd4930d40e1bc0df4c475b4cdcf152">ccfe5d33</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-04T15:41:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">after merge new of ver3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9212f6e40dacc0aaf04f08a5cf4416eaa5fb561">f9212f6e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-05T09:04:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added external reconstruct option to reconstructor, useful for debugging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f47827ac046eeed90609649c15ced279566aff18">f47827ac</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-05T13:44:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug translations star file helix_inimodel2d
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84b06a051419e1f2a031030af0da778fe14fd13b">84b06a05</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-05T15:36:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in filename external reocnstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3aae23246e6c9b22476f54eb3ad487c5ccb614c1">3aae2324</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-09T15:56:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">smaller letteres variables, edges etc on scheduler gui to prevent problems on osx
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2990ebebc7003f6d83075eaaa1e19eaa115c0185">2990ebeb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-10T09:48:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in not initialising do_ctf_padding
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4dd6ebed4f3fadce380dba27e61fe4f84405ee22">4dd6ebed</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-10T11:17:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: don't crash when an output file is not present.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cea2f7d28274bbe7c7dd3a12e9341de04c423840">cea2f7d2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-10T11:17:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtract job: fixed the output file name
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5ffd460f29cb04f70ca5a98e946821895780d79e">5ffd460f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-10T15:54:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">keep checking run.out in scheduler view GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/42515bb569ee68dc91ceedb063b27ff68ade8d3c">42515bb5</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-10T15:57:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/db08e96c48980f7967df079cc34bb0958290c194">db08e96c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-10T16:13:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improved RELION_EXIT__SUCCESS behavior with runGUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b273d3c97237b181065a6274240d669b61a85eb">0b273d3c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-11T12:21:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed spurious hello statement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/86f15141b11a906f93331338f94f9c8d6d8b1233">86f15141</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-12T11:54:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: don't set --angpix to CtfFind jobs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b2f3edc4cfbb6af4ad386f1e6eda70cb8948d60">7b2f3edc</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-15T10:58:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: improved check for 'save power spectra'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8fd7b74ae735d09c42c9c5b0f515a8f05624b631">8fd7b74a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-16T12:34:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MetadataTable: Removed unused 'ignoreLabels'. Check the number of columns in a loop.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/23c5a5420c7c757a2eff54d1ee12fd8ce730495a">23c5a542</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-16T12:41:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GCTF wrapper: repaired --use_noDW
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ea9425e78f5233fed2066b8c85599144ee8ab4c2">ea9425e7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-17T15:26:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: don't add --fast_subset to Class3D when continuing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bc2ec1d10748714df1013b585340d7123c852b86">bc2ec1d1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-17T15:59:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MetaDataTable: escape empty string as "".
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01848becd1667f76f51b09310916a86e6379838b">01848bec</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-19T15:19:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed bug reported by jan in relion_display when used for micrographs instead of particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/78291e5d9ada0e9a31a3525c61b5387e0927bc2b">78291e5d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-19T15:19:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7955397e88d9e1329a345d2f378899eabaa3ab0b">7955397e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-19T15:19:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">now allow 2D with helices in reading model.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b3452f1494c94a98f6ac5da8d69e9688cda9fd2">7b3452f1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-19T15:20:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">kobsmodel loadsafely for reposition
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bcc8ab381f5f9171e06718572a5e6fa29cc6cc6e">bcc8ab38</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-19T15:21:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small bnug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/65b0acd77ec1b9ef056827ccca9723eb67f28fab">65b0acd7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-19T15:21:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">return int for system call
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/455b05cf45f98b26ff7bc41d0416282f2a4d41bd">455b05cf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-22T09:38:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug helices 2d
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7fcb17f7c19cdaf44112b477d4c710a2f493f620">7fcb17f7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-24T14:09:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make RELION_EXIT file for manulapicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/78ada05ef2302c5724dc90755687621afb300b2b">78ada05e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-24T14:43:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CtfRefine: just added a comment
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c7f60860cfa727b52e42c29086bf930c8d04a901">c7f60860</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-24T14:47:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'defect-mask-in-Polish'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/87cc40c38160819c5fe49a0afbe1a480a28d0c2f">87cc40c3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-24T14:50:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8107cc2df0ffb8992fedb5c91d49d6fd22637ef3">8107cc2d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-24T15:46:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Started working on this project. Frame index OK.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3161ab50707de7916715aa92a7bef04f74a44588">3161ab50</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-25T09:21:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTF-correction of references wasn't using obsModel for autopicking on GPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/89e384e16f400fd33d17cc40f694293be28478b9">89e384e1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-25T11:04:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: RLE unpacking OK.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dbacee9ac0366365530159ccd8dc908016a08321">dbacee9a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-25T17:02:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MPI: use MPI_C_COMPLEX and MPI_C_DOUBLE_COMPLEX (GitHub issue 234)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6bcdde6c4ce2ffeab01b1169ec5f2df1c571d721">6bcdde6c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-07-26T11:44:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed GUI and ml_optimiser CL parsing: offset range and steps are in pixels, not angstroms
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/145c25ac96d9ed9a7ffae058728e68ab1210ff70">145c25ac</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-29T08:49:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Pipeliner: removed NULL characters
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d4b8877fb30f6a0d8ef1c6f1116436f3053fa1fd">d4b8877f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-29T12:09:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">IOparser: When the same argument is specified more than once, use the last one with warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3cb813a1a386966a117a8a4bfa2b35539d0401f6">3cb813a1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-29T12:24:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Import: Repaired continuation. Print the number of items.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a9504ae57eaeaa063194f71adae29e29c66b3658">a9504ae5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-30T11:46:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: make --early_binning ON by default
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6f11c59df829305fd1dce77daff4eea9997f88e7">6f11c59d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-30T12:52:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MotionCorr: supported defect maps (for both UCSF MotionCor2 and RelionCor)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4335976878eb13cf09718de59152eca98290327e">43359768</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-30T14:17:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Detect SerialEM's defect file, which is not supported
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ba8fcc4edf14e5a4d7bce20028fb6314708e23f">6ba8fcc4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-30T14:19:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Started working on this project. Frame index OK.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/635e7e5fa7c5303147e3603281aefe556fe85ad7">635e7e5f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-30T14:19:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: RLE unpacking OK.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5231f4dd40fbdae300c28ed0ab1feeb081ae03ee">5231f4dd</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-30T14:20:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'eer' of https://bitbucket.org/scheres/relion-devel-lmb into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/948f969322c33cbdc8f418ec8de95b046c3cf8bb">948f9693</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-31T10:52:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: render to 8K image. make this into a class.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a5987af291b28609b9cae394fee99f0d179144b4">a5987af2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-31T12:08:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: WIP: motion correction started to work but there are many issues.
- Gain is given in 4K x 4K; where should we apply it?
- Edges cause significant ringing artifacts.
- Design questions: where to set frame grouping? how to interact with MicrographModel?
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c8a31b76b81f1aef417f34b131bc75bfbcad9f7f">c8a31b76</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-07-31T20:49:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Use 4K gain. Get defect (cold) pixels from gain. WIP: not very efficient yet...
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4826462cb7ad292d200068138098aa9da804d737">4826462c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-01T15:33:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_image_handler: fixed "ISO C++ forbids initialization of member" error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/25c3f9e62523401599920407c1eb891c5b678157">25c3f9e6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-02T12:59:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionCor: don't "detect" hot pixels already marked in the defect map
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a920de70e499d645142e0b1ca42d882ec7658b12">a920de70</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-02T13:00:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/23f22c51d39f8783ae90f8dcd7104899d74b802e">23f22c51</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-02T15:51:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extract: use gamma offset in CTF premultiplication
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a19b6ebcb0b3915500b7e9fffdfbde50691b4c93">a19b6ebc</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-02T15:57:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: --pad_ctf is probably broken now. Disable it.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd3294ba73e9361509466a86fe59502981995f7d">cd3294ba</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-02T16:00:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: Don't die with MotionCorr STAR files from 3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4bff28a67805b4e1e57975a1095f73535cfbbff7">4bff28a6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-02T17:16:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_start: supported conversion of micrograph STAR files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61b275fc25e8654cac91b5c32f38976fce8051a1">61b275fc</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-05T14:40:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed ref_aberration_plot and RefinementProgram class.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e67d506732c5c868863722d273898d8d719d93c">9e67d506</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-05T15:04:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: allow polishing of only particles belonging to movies in the input MotionCorr STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29689a939082e26fedc928a0677da8f46485e69c">29689a93</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-05T17:32:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Added --window and --scale for Polishing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9e2bf4a05f8f6f011e08eae15561e37db6d3402f">9e2bf4a0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-06T11:00:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subset selection: judge datablock type properly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/93638b6761284daea91977a46d2e08cd19ba0a73">93638b67</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-06T11:54:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Import: fixed import of coordinates. WIP: the content of suffix STAR file is still not right.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0be9ba5066a1b42a0802c6dd6ecc7b8ff878cfa1">0be9ba50</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2019-08-06T13:40:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">FSC added to external reconstruct star-file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16add052891b3251601367b6148314efba2c2041">16add052</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2019-08-06T14:33:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subsets fixed for half sets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cc0702379fb02466957bdaea70f9928703207337">cc070237</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-07T20:29:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refine3D: don't allow Refine3D on even number of MPI processes.
This caused 'loss' of some particles in half1 and resulted in empty groups
due to a bug in "if ((node->size - 1)/nr_halfsets > 1)" logic.
Don't know how to fix the logic yet, so disable such operation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/853ca84bcd1df53f3a7033a90828905c0790a1ad">853ca84b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-07T20:38:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refine3D: don't allow Refine3D on even number of MPI processes.
This caused 'loss' of some particles in half1 and resulted in empty groups
due to a bug in "if ((node->size - 1)/nr_halfsets > 1)" logic.
Don't know how to fix the logic yet, so disable such operation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/451976b524188e075c2765fc49852b46a29934df">451976b5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-08T10:34:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_mask_create: fixed --and, --or, --and_not, --or_not. (GitHub issue #495)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51121a0531e54ff5b760805a85fb063eadd1490c">51121a05</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-08T10:38:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_mask_create: fixed --and, --or, --and_not, --or_not. (GitHub issue #495)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ebc3ad600c3a76043a3d5ffbc58fac626396a7bd">ebc3ad60</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-08T16:29:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extract: make sure rlnMicrographPixelSize is present
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ecdbfa5c68fd7c7b03cc75890df377cf20a8d700">ecdbfa5c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-12T16:45:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">pipeliner: make sure rlnPipeLineJobCounter to be positive
(some tempted to make it negative to avoid JobID overlaps in RelionIt...)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5a3d3a009ba208f8169b62c247037a3e8358233">c5a3d3a0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-13T15:20:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refactored histogram
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e944e174223c251c19b00dea9adc343629e8b89e">e944e174</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-13T15:21:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">LocalRes: histogram of local resolution
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2162298e1f972bb3aea17a1ac4bdca4567ba5b06">2162298e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-13T16:36:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5432f7c86cafedb89f463cd787cea32451f0865c">5432f7c8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-14T17:26:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TIFF: Detect SerialEM's 4-bit packed TIFFs and raise an error.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/76c64d31d1647737dc051cfe18b9f9e3a58f104a">76c64d31</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-14T20:12:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TIFF: Support SerialEM's 4-bit packed TIFFs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6bb61d1d2fbe0e67d66c3eb0965a6794297c9bc1">6bb61d1d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-14T20:48:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_pipeliner: Add --gentle_clean (Yang Lee's request)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/abcb9850e5afa619c958f74161361bb04ff3961d">abcb9850</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-19T20:45:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_preprocess: removed unused --fn_list and repaired continuation in the MPI version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ec3d10123d0c2064cf87dc77460b4437176063d">8ec3d101</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-19T21:54:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Fixed a crash in scheduler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b53114b6228dd4c7eff160232105da82fc427503">b53114b6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-19T23:04:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">PostProcess: Make sure the pixel size is positive.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f4b0bf0dbf58e5f06d66f4752d11dd0b704cfdaf">f4b0bf0d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-20T10:27:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">PostProcess: Rather than stopping, use the pixel size in the header when --angpix is not specified.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd39b15bdbe8ba287e37cfd0b29f795290863b96">cd39b15b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-20T10:52:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">PostProcess: don't low pass filter by default when FSC weighting is enabled. (rationale: local resolutions can be higher)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f2012dea7b02a9142895825a50ea35d7a658acc">4f2012de</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-20T14:36:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Fixed a GUI crach (the patch 8ec3d101 caused side effects)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f14183dac04966183b7f0198764a1b2a8ab15e43">f14183da</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-20T17:19:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CtfFind: don't die on an empty STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/250dbbabd49a4a5150d4a35efc4723c392f2f7f6">250dbbab</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-25T20:43:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: change the default angpix for PostProcess to -1 (use the header value)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f3dc213d95a2d32c78fabcd00ca164e8705369a">3f3dc213</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-25T20:44:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: repair polishing only micrographs present in the specified MotionCorr job
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/945cff5b06bfe503ca432b49004721ba5e3a5831">945cff5b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-26T10:00:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: fix typo in GCTF's PMID
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7996c59c7cbecfaa78bc9a9fa1f6b8729ea5234f">7996c59c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-08-26T10:04:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: respect "reconstruct subtracted bodies" in continuation of MultiBody (reported by Sean Connell)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e9d8fd7a791ece9e2f8e48f596a505aa86b18c46">e9d8fd7a</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2019-08-27T11:34:10+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Relax sym option has been added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8c763e289fe8bc57cb0b252d6e4c5671b075ee3b">8c763e28</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-02T09:25:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">when importing micrographs, use micrograph_pixel_size and not original_micrograph_pixel_size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/98d46edf223c57ec38443d8863f4d7d305a3cb72">98d46edf</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-02T09:28:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added log_upper_thr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8efc93f05d563fb7ea60e6573abb07e2271f9736">8efc93f0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-02T09:51:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added log_upper_thr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad7b9141c5076d15bdbe28d51f3d8c6baa7591f1">ad7b9141</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-02T09:52:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small changes?
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8213780a8220d969446f5ee62a46ee52c87736d6">8213780a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-02T12:15:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">for micrographs set both orginal and micrograph pixel size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27e6a69e1df315f5b26fb27f88cbbbd3ffa45cb0">27e6a69e</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2019-09-02T15:40:01+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">prints have been removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fb64c9071e330e20beafbc6b22f2565f45a72f16">fb64c907</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2019-09-04T10:00:32+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">some prints has been removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/966c00d7f7cc5013dcedec5d817b9dd95bf32904">966c00d7</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2019-09-04T10:24:57+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relax_sym now can be continued
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ea666246b283721af41ab2ccb223a2ed8d1620f">1ea66624</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-04T12:53:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update the start up screen for 3.1.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/713e6653259a1c0683f9c9bc3b6121a1547035df">713e6653</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-05T11:41:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7074d77182c79ef594b86cface9592ded30f8de5">7074d771</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-05T12:34:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: remove un-processed particles and optics groups (for easier joining)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3696d0e6d9f0560959b5b28d04337d01892157cd">3696d0e6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-05T12:47:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">deactived --mics and set interpolator to 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d0f09adfa6fb584ab185ac0fdb79d0d6813eab7">7d0f09ad</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-05T12:47:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/447b15826bf89af9342f709be781aee7a16d4182">447b1582</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-05T14:49:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: improved explanation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dcff62393b397a09df0917f85305a3f7863e1e25">dcff6239</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-05T14:49:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Split: respect BOTH subset size and number of subsets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/542ee9c1244ae26d46645d30b39aad79e8de339f">542ee9c1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-05T15:53:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Repaired access to member functions on a NULL pointer
(this might have been working but very dangerous: https://stackoverflow.com/questions/2533476/what-will-happen-when-i-call-a-member-function-on-a-null-object-pointer)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/532bc3c238723ca4267418f4c491fcc984a39ed0">532bc3c2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-05T16:21:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot.py: updated for RELION 3.1 and supported Python 3.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1486db3b93e018aced6695ce22f1eab43be0d3ea">1486db3b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-05T17:21:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: supported Python 3 (WIP: only syntax change; RELION 3.1 not supported yet)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3f106b38995223b64589ff5b0f777b9a8d99877b">3f106b38</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-06T11:25:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont let the GUI die when textToInteger/Float goes wrong
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b2d9df9b43e1c843e8dff347900ef1efd3383de">0b2d9df9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-06T11:25:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51bb4d34ba9118371cf960b52bf2fa506b5917cd">51bb4d34</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-06T12:15:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: add help messages to --maxsig and --skip_griding, and make --maxsig's default to -1, not 0, for consistency.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/848092ff16d65449759a7fe3c346443ad3b1b4e9">848092ff</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-06T14:19:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: added "Skip gridding" except for Class2D.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b19554b6db3d310cfbeb314c39757e58436ec01">2b19554b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-06T15:36:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AutoPick; change the default shrink factor to 0.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d164502f381411e17bacdd4e339faf93cfed1b6a">d164502f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-06T17:38:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: support RELION 3.1 up to CTFFIND.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e8083f67aec4fb40475f0fba67df020842c8b881">e8083f67</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-10T19:53:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Escape strings in a STAR file.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f83a42463a9888dc90abfebd0fd2a695cd5d7459">f83a4246</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-10T19:54:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">STAR: fixed an offset bug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e0485a10e11d130bd4df5e7765f0e73c4aed3056">e0485a10</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-10T20:32:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">STAR: repair quoting condition
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24de06cc02069c804320807bfcdd174164a96e58">24de06cc</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2019-09-11T10:44:28+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing redundant symmetry in relax mode has been removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3258bf3b3e1f3723e4465bd2e43ff8ba57660dbb">3258bf3b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-11T17:01:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: support RELION 3.1 up to Class2D (i.e. first pass is now OK)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27b99e526a1031371abbec5a3637846f2411a117">27b99e52</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-11T17:29:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: fixed IniModel task
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fce0ac3701695d5d37117fadde78ecbf23c98c7a">fce0ac37</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-12T10:24:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Print --version before asking for a new project directory. Solves GitHub issue #505 from @rubyFeedback and @delarosatrevin.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4d0979093605cb2906e40da5f3269c81d6615ead">4d097909</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-12T10:28:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Escape strings in a STAR file.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2799df346ac0d236ded859b91e0cfcc009d4ced8">2799df34</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-12T10:28:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">STAR: fixed an offset bug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3604d6fc003e72ef257e25360bcb13fc5e868405">3604d6fc</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-12T10:28:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">STAR: repair quoting condition
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/11d61457b9e9ec53b8a926b64a4f331736cabac8">11d61457</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-12T10:29:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'escape_string_in_STAR' of https://bitbucket.org/scheres/relion-devel-lmb into escape_string_in_STAR
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/408bccef350cc5216a8683e2cc44cd47ed4af218">408bccef</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-12T12:42:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unused beamtilt functions from StackHelper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ed22a4567f0c4b0900e675e547d891ae21ffe92e">ed22a456</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-12T12:43:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move FrameMerge class to jaz/archive
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/911c62e89f774c3fbd07b5ed111dc9c409f909a3">911c62e8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-12T14:37:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: 2nd pass works now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dfc4de86b56c12163ed116c0e50d158b62996c25">dfc4de86</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-12T14:42:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">order for displayer of images: micrographname above power spectrum
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/33574c47e51546baa91dd93e3a570d9b644f23e3">33574c47</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-12T15:09:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use FLTK 1.3.5. (GitHub issue #500)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c6e162511b1a984bd3e96797ec9473c4e1b94505">c6e16251</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-12T15:32:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hardcore Schedules/ directory for output schedules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a1cf4ab72287836a058346842d52b772ed5b7703">a1cf4ab7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-12T15:33:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed scroll bars from GUI window in Scheduler mode
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24eb73095c9ddcd52403d2a4dcfcf562dae65245">24eb7309</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-12T17:41:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: add recentering
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a67cbc508f1e218d7bd38dbe7605b6c3f3310298">a67cbc50</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-13T17:28:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">be able to work with empty string variables
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0785e1af03fe4a5b78b7643de601e6b5d4453d66">0785e1af</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-16T12:28:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">introduced i/o and jobs view on maingui
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b68c3c30823a98a69af782d44822be686a4be4d">0b68c3c3</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-16T12:30:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into HEAD
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/17edd5e4dab5e7c76478e1abe1753fb752d92dfc">17edd5e4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-16T14:31:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug readStarList Takanori
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/022f33fe73ebd8372fb2a584f7892e2663a9cb18">022f33fe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-16T14:34:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">prevent reuse of global variable name in read
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2bccba42ee7907f81df12dc70849ee687c523607">2bccba42</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-16T15:45:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">no longer use __ and && for spaces and EOLs, still use restore for __ for backwards compatibility
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d89bca92a777612735b0232a320563e3805027b">7d89bca9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-16T16:29:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">moving buttons around for scheduler/pipeliner1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/66b55baa7c3c0fafe85af98fe0ac9441a47d4f24">66b55baa</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-16T16:31:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with non-integer paddings in cuda BP kernels
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad170cc1e60dc8d1cde737a2c4cf82c3f81e9758">ad170cc1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-16T16:35:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug with non-integer paddings in cuda projector kernels
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ba38b830cf55b59eba9839d9300cf5a633c2711">6ba38b83</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-16T16:37:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/52c45536210e546926f9f05bfcbcd6a5269e3ebe">52c45536</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-16T17:14:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed --skip_gridding with non integer padding
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c3379ed59feb7cb777eec9b3739b7daec866792">9c3379ed</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-16T17:33:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dont restoreString with __ for input options as gainref may have __. Now always write job.star, but read run.job to maintain backwards compatibility
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bb98cd4ec8fc57e434a7adea2a388c31093a2ee6">bb98cd4e</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2019-09-17T10:13:01+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Problem with searching in a sigma has been solved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d86263db3e6f8369dc6fd4c8e61c826242f4a436">d86263db</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-17T09:50:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">return false if no run.job or job.star file is present
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a13b48df430b3e7d9271b5e941b805976a3cdef4">a13b48df</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-18T09:17:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better error message for half-sets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5097d0aebc345fb45793a15cf10e43c7687a4946">5097d0ae</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-18T12:25:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prevent divide by zero in skip gridding.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3ac296e1cf771f63bb71b439c589dcad56cc101c">3ac296e1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-18T16:17:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">keep tilt prior fixed debugged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a59c3f420fa75bccaaee2bd14085541fd210f435">a59c3f42</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-18T16:18:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2297c520dd910fc7bbdcd136a05e8828a531907e">2297c520</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-18T17:48:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Repaired single precision build (WARNING: accuracy of CtfRefine in single precision is not throughfully tested!)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/089b83b4c066a3062664829e62376fc02bd3f48d">089b83b4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-19T10:39:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8fd3a52d8a3069dc227cbb05c2278deb3ed31d9f">8fd3a52d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-19T14:38:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in event handler, now shortcut keys work again
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3360c2444203d70966608808c11066d93dd1396b">3360c244</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-19T14:38:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4d4bf08f3f24fd21042445d4b9c0e33ff770557d">4d4bf08f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-19T14:41:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: more verbose error messages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/27f8a3017cc38fbe74b5a0fc0d762935d57252b7">27f8a301</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-23T17:25:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug reprted by Tj from Leicester about manualpickrun.job, now being job.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/396cab4592913be54026ecde03753fd0fb2e8f5b">396cab45</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-23T17:25:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">port for 3.1 star files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/acb90f6364b8b8feaf483ea5c13b1613e32ab8ff">acb90f63</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2019-09-26T15:05:11+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://github.com/3dem/relion into HEAD
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dcf451ad887de5cd6cd5381eaa3f9477a69de831">dcf451ad</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-27T16:41:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove spaces from name of new job in scheduler
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/695b2d5c7e2bd717c38288dfa23922234d0f5bae">695b2d5c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-27T17:00:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug reported by TJ from Leicester when RELION_QSUB_EXTRA_COUNT < 4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a52cccdf98240c40fca07398dcf602a3126060a">9a52cccd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-09-27T17:04:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to harsh clean a job
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fab92a6194886ecddce82f50514ffb32b6ac5cc7">fab92a61</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-30T21:08:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_project: improve the help message (suggestion from @evanseitz on GitHub issue #510)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/693b93bedf557a8d8150e6437ca6345a020ecf94">693b93be</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-30T21:08:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">external_reconstruct: repair a critical bug that ignored padding_factor
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7085043d9d008bd84d71105b42305d5f9bd860f0">7085043d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-09-30T21:08:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/64c94c3606d9edf706cdf281e3db826a3bbb0c3a">64c94c36</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-01T11:59:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extract: repair uninitialised variables
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7290d2cdb5008c833a36b3ce81207075eac4de6e">7290d2cd</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-01T12:29:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Add local resolution histogram
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a28e92e90c3eaa3726fb280bd9e06aabb60598f9">a28e92e9</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-08T17:00:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">print warnings to stderr if the reference in on different scale/box size as the data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bd925fec080932773f50c9fc76f30161ede77ce2">bd925fec</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-09T10:08:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">spell out inside SGD
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34a9ee6d6323120e7ea24b07cc800397a25efd86">34a9ee6d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-09T10:20:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set default CTF_IN_SGD to OFF and explain how to switch on on the GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ba935b4b5df0e6808b23e3d8cef6b1b077326e1">6ba935b4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-09T12:54:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTFRefine: report anisotropy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/646db9823a894c150b3e265de025d3b133efdb04">646db982</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-09T14:56:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tweaked cmake message ctf i sgd
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/79162cb4dbeb33df97c40324b4a4a9119ee17241">79162cb4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-09T14:56:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d1464cb88f79975b6c2bce11eb103d9784e651cd">d1464cb8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-09T15:13:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed warnings of pixel and box size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/92aaf5a357a7fd9ca65ae071df6db27d75fb7304">92aaf5a3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-09T16:13:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: add --class as requested by Oliver Clarke (GitHub issue #513)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dab3bd4183a0db528fd9f9cc779bb34b81a1139e">dab3bd41</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2019-10-10T11:40:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create a bug-report template</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d0a301235b1844c2118c59186e6eff871dcea9ee">d0a30123</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-14T15:24:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">made search helical symmetry netter organised, less push_backs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60f263ac2aac689cef249c7941c4a7e7c344d4fc">60f263ac</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-14T15:24:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5a8f82785e53bc8ed271b096c3f7afff09e5e82f">5a8f8278</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-14T17:04:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: use "--reconstruct_subtracted_bodies" in continuation as well (as reported by Dr. Yanagisawa)
Call this 3.0.8 (hopefully final version in 3.0.x)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8b2510280dad951d5f0d8846a10994cae3b48203">8b251028</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-14T17:15:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Final preparation for 3.1 public beta
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d341435ebe7cad300096a574edfbd428b6c3e9d">5d341435</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2019-10-14T17:26:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create a bug-report template
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d5a160bbd4e12dfccbe7f10ee301ab1efb07a087">d5a160bb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-14T20:36:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: use formatted strings for safety
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a6aaa580b995337c7d67eb96365e1444eaf103f5">a6aaa580</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-14T21:41:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">README: fix installation instructions as pointed out by Rui Zhang
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2ebd8861a5184038d1caba086b03eb237b1b3ed3">2ebd8861</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-16T09:33:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added anisomag and scaling to particle_subtractor and to multibody inside ml_optimiser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f0406999ad7d45d3f3c7025a9384fd186d69543">8f040699</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-16T09:33:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/263d5954c94c8ae6378788144ad07315973bf68a">263d5954</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-16T11:02:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_particle_symmetry_expand: use EMDL_ORIENT_ORIGIN_X/Y_ANGSTROM not EMDL_ORIENT_ORIGIN_X/Y.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bdbc7491a0ded1fc8723a8ef32e60b162e598f7">8bdbc749</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-16T11:35:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">README: further update on installation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6110eaca704fbf4c8808c2cb21fe6655dce4a27a">6110eaca</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2019-10-16T13:43:53+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://github.com/3dem/relion into HEAD
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9b4ce5e3354fa291410e833f5fb0771cbd95063b">9b4ce5e3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-16T11:44:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">README: more updates
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ce28d249ecb06db7a2a121f2e784accb8c99ff2c">ce28d249</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-16T11:46:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">README: make it clear this is 3.0 repository
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/767dc597e495b36553f24ba3d712ecf77766ad9d">767dc597</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2019-10-16T13:52:06+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://github.com/3dem/relion into HEAD
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8fe742e84597558909e384d053a95ac6b15da6c7">8fe742e8</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2019-10-16T14:18:08+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Code cleaning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ff6c2066f4d646bac9269a3627df1fb072fcd9d7">ff6c2066</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-16T16:20:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extract: Remove particles not present in the input micrographs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e09586fd54be4648fdba3300e30a2b9a805d8852">e09586fd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-16T16:23:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">starting to take out operate_on star files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d069339f1f7634a1ac88636c82f6440e67f2d47">0d069339</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-16T16:23:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b86482c458d88425594a7b1eab0709ca21f487c1">b86482c4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-16T16:26:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed STAR file option for operate_on in preprocess
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4980d657cf6b121df36f386bb754f6157660acfa">4980d657</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-16T16:37:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de05e4d680e0a6629b7f72a3f2656beced0278cf">de05e4d6</a></strong>
<div>
<span>by Joaquin Oton</span>
<i>at 2019-10-18T12:16:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bug fixed. Pixelsize in reference map is checked
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d4966576ccb12dbb1b17875f6873be5bb918ade">6d496657</a></strong>
<div>
<span>by Joaquin Oton</span>
<i>at 2019-10-18T12:17:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of bitbucket.org:scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5e5eba3ff886c0a31223d7a0330cc6a0444e9d77">5e5eba3f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-19T10:15:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Polish EER files with grouping
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6211a5efb869f2a653e7adc93e46bc4a89963a32">6211a5ef</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-19T10:19:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean clutter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/89165e88f9998b27af24b893726b032dcf00996e">89165e88</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-19T10:20:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0ac9f4f6c106d29c7c390a04cf529a959e0f44b2">0ac9f4f6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-21T12:28:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean clutter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/145b0b1360d8bfbc38a27cac5e0807d265b34570">145b0b13</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-21T12:28:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">loadSafely: assign a correct table name after conversion (GitHub issue #521)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/69a4dd4a285cd437b91938ec948c478ad36f5562">69a4dd4a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-21T13:42:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_display: repair --lowpass (GitHub issue #523)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f0b8b48a7ac5a3fbbec2437597901bc8adca08e7">f0b8b48a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-21T17:16:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Improve CtfRefine GUI (GitHub issue #517)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3600ede5bea38cfbf6903fe1442bb93246c8f91a">3600ede5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-21T17:18:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">STAR conversion: stronger warning when box size cannot be determined
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a01ec785664ace739d1267179538dd0032f5749e">a01ec785</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-21T17:23:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Import: Make sure voltage and angpix is positive
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6903cc46e7b29c73ac71e5edf10e24c8510e22ac">6903cc46</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T10:28:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">STAR conversion: make the default optics group name to OpticsGroup1, not OpticsGroup0.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/151f15bc767c9e664bb64323f88a038013718b57">151f15bc</a></strong>
<div>
<span>by Joaquin Oton</span>
<i>at 2019-10-22T11:17:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autodetect data_dim in case --3d_rot is not provided
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1f054fc13894cc5e838e24a6af0af9279426a3b">f1f054fc</a></strong>
<div>
<span>by Joaquin Oton</span>
<i>at 2019-10-22T11:17:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of bitbucket.org:scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6f8ddb70262bedb87e1ffce18faac50e5658b18f">6f8ddb70</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T11:53:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Repaired the output file name for training
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b4f84cf63a518b638a3ddf445aa23665cae9548">0b4f84cf</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T12:22:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: Repaired false warnings about pixel size.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/296f75192a4dbd461a2a11afeb5b204207e7f959">296f7519</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T12:24:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Repaired the output file name for training
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa2ea304c2bfd5a217e16454b21a2acb5d39db2d">fa2ea304</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T12:24:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: Repaired false warnings about pixel size.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0f91b47b20bc35d1d54cbded4a7124228ef1f114">0f91b47b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T12:31:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e22c93f2f84c5cd4662843f80dcaec0006761f01">e22c93f2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-22T12:49:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added warning if data dimensionality was missing from particles STAR
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9babce43227a600addbfd6904268969896dd708f">9babce43</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-22T12:50:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">write out reprojections and summed classes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a97ac093b2e2e438f6c19292023772303e2dcaaf">a97ac093</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-22T12:50:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7f17498b156c38ff31cd21bd50fe8024bdc740b1">7f17498b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T12:51:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Repaired the output file name for training
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d43db7177f2fba7b7ae6affbf924df6ef968d824">d43db717</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T12:51:08+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: Repaired false warnings about pixel size.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd833470104412a3538655d8bb4ff2fb71abd5f1">dd833470</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T12:51:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7b0bd5214975c344b3d9e7b6d1480b058f4e8ae">a7b0bd52</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T13:57:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: repair crash when deleting operators with missing arguments
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f13e1800e2b2b55dc24388abeffb0e9381a96a18">f13e1800</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T17:05:36+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ObsModel: Clearer messages when the box size is not available.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/41c4ad14705e6d1227ca546d5811001af1f261c4">41c4ad14</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-22T17:07:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ObsModel: more warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/780dd7baad7bac9463603b95257b0db6ac3e48e1">780dd7ba</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-23T17:13:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_refine: clearer error message when rlnModelStarFile2 is empty.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1f2188891791f3a3f64907953534e50947cf43f">f1f21888</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-24T15:00:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: repaired --recenter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1f22d6a7d50860d72791806334ebd1eea346ba2c">1f22d6a7</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-25T11:26:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug reported by Clinton Lau
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/13869ee424985ca5b52dc458be1be7bf0f8821f5">13869ee4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-25T11:26:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f8a215df6f69fca73f774bb9e7da778a93426cd9">f8a215df</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-28T15:03:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">scratch with MPI: repair crash when the disk is full (Github issue #529)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e023ce55d3e96253268439c6a43c17360c16acd7">e023ce55</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-10-28T15:08:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">not ori_size but image_size in exp_imagedata array when not doing parallel disc i/o; die if multiple image sizes in input star file with not parallel disc i/o
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d3d5419ee3e86aea7375d9ae02f6703608063f66">d3d5419e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-28T15:10:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ef36c564b8fe40d6a6f296a1780b24400152ab71">ef36c564</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-28T15:26:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Improved help messages for parallel disc I/O.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/95dfc62cc1764ef5429595b9ebfcf063c6ffd22a">95dfc62c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-29T11:33:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtract: restore box sizes when reverting to original particles (GitHub issue #531).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3d8f2ed89ed678abab8d03546935fad5e93cae4e">3d8f2ed8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-29T12:49:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
Conflicts:
src/exp_model.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34c1c63a24979c62351d1a65454bd731cc70b5e8">34c1c63a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-30T12:49:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: --eer_grouping as a command line argument
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/198bddeaaeb1f0b3d437513494866fe7023f0ad1">198bddea</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-30T16:54:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: minor tweak for Polish parameter files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9efbe650fafb6c15ac10b3004ce98deca0e88258">9efbe650</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-30T17:49:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">STAR conversion: Do not set EMDL_MICROGRAPH_ORIGINAL_PIXEL_SIZE for particles, because particles might have been down-sampled.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/16ba44ade5b7cafe7be26e7d01e48922c936a3c0">16ba44ad</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-31T11:17:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">STAR conversion: Do not set EMDL_MICROGRAPH_ORIGINAL_PIXEL_SIZE for particles, because particles might have been down-sampled.
(the last commit was a wrong file ...)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/024605311249a39a4b877b9f7bc77df6494e0bcb">02460531</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-31T15:45:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ExpModel: more efficient sorting (hopefully related to GitHub issue #514)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7f8d1d640fcad685bba828ccdf6eaa569b27e067">7f8d1d64</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-10-31T19:14:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ExpModel: remove debug message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/76fa3d2811301afb76c34e3e99f5e721f113af3b">76fa3d28</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-01T17:23:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ExpModel: particle shuffling and sorting in place to save memory
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b74f8b37d105a6f983a55462761c9bf064b00543">b74f8b37</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-02T21:23:03+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: remove debug output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/82aff6f0aa8f531c205049bf8994fad96023fa38">82aff6f0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-02T21:23:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: remove debug output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b272ac9b6dcf2ea958c0ead4487da5dfdabda0d1">b272ac9b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-02T21:23:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9eb0d5fae8ca0c94cd87eba879b8b4d6ddb79bdc">9eb0d5fa</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-04T14:37:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: added --eer_upsampling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0841d0688e1183decdcb23504d5cb84b27d10e4d">0841d068</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-04T14:49:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Fixed help message for External job (GitHub issue #534)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/72574efe0d653f672e705f69a05707047d5daac3">72574efe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-11-06T16:10:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">multiple by average MTF in divideByMtf function to prevent oversharpening of 2D and 3D classes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a8e935cde4bcb014ae5c8bbd4b213376b50c032d">a8e935cd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-11-06T16:51:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove do_mtf from postprocess GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c0ecf2f191d8805201e741894acbcc176816971">6c0ecf2f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-11T11:54:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MultidimArray: added const to some functions (although not sure if this helps optimizations)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/87a80ded006d2e71d4a93c0805861e0023769711">87a80ded</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-11T12:47:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/414b04ef1cf73da3f3377a69f86a3c6de303ada5">414b04ef</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-11T21:20:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: repair a false warning introduced in e023ce55d
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ee1f5913709fb54459dd73d32e5cd9dfad29f671">ee1f5913</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-11T21:30:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtraction: Write the pixel size to the header
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e14169496407af7f7e06fb0463269c64eae471ee">e1416949</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-11-12T12:02:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> fixed issue #535: apply orientations in particles assigned to a class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/885dff3a129bce033e62904597f86fcb7f7908c1">885dff3a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-12T14:37:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtract: Fix 3D tomo (GitHub issue #532) and fix particles with different box sizes (GitHub issue #538)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f10a9a889463e398157e43b2a2c5a2ca8307fc2f">f10a9a88</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-12T15:39:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtraction: repair compiler warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/63ec0029d5128dfef1cd6bd30fd8f3ec3b200f1e">63ec0029</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-12T17:52:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Image: supported writing integer MRCs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/62f7d2c31bd059d621a969ab429619f8238b480d">62f7d2c3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-12T21:55:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtract: fixed an indexing bug (thanks to Bojian Ding)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d75256d6f053b408a0c060dabb49ddbca631e89">9d75256d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-12T22:04:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert accidental addition of relion_convert_to_tiff, which is not yet ready.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aa8daa6a98f9420cefc64c44524d04b4095819eb">aa8daa6a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-12T22:06:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into tiff_converter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9696c6381e56357b2f25754b3ca0910d4ce91ba">d9696c63</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-12T22:12:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: simple conversion and gain estimation done. gain unnormalization work in progress.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c75996598bbd422e984671572a1422d151f3550c">c7599659</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-12T23:44:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: implemented lossless strategy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d29a2d3cdf2515aaccca006663b5c37420878aa4">d29a2d3c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-13T14:46:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: implemented unnormalisation, tidied up I/O.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4c18b2de4aa2b9896f9a1c1a09119f27e49f12df">4c18b2de</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-13T15:06:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: repair --estimate_gain
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/48bc8332021501a8a074b9ff60e9f7662675d253">48bc8332</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-13T15:58:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: fix SEGV and preparing for MPI version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9a299847eb3d7e51d4f72f64bd2c0be07f682851">9a299847</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-13T20:14:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: MPI version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7db848305b3707191e6e41e5f6bffd3d8d2eb89b">7db84830</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-13T21:43:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: use temporary files in simple conversion, fix message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1c53280fec044ea4bb254ebdc4af43ede0e68a71">1c53280f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-14T15:01:17+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: differentiate unsigned and signed short (mode 6 and 1)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/62c59153049aa6aae6cf3d38858103522586165b">62c59153</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-11-14T16:04:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug reported by Wim Hagen in getAverageMtf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3493645a6eb535c1863f732dc2d617e1d40567f5">3493645a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-11-14T16:04:31+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f29379eed570d9f1c7a98c688e19ec3d0c5e5aaf">f29379ee</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-14T17:09:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'tiff_converter'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d928eb13a9b1be8b6c868d47f8a44bc351be05ce">d928eb13</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-15T21:35:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: make frame number 1-indexed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f2c3d8d8d7cad27c2259f2053819f817d890b631">f2c3d8d8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-15T22:34:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: supported cases where the number of frames is not uniform
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a700e902fccec963e6c86159fab99c61a5e55eed">a700e902</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-18T12:18:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TIFF: made write_tiff_one_page public.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2ea85beb09f660c291793367fce83d731ec4259c">2ea85beb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-18T12:18:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d9df9d19caeeb4e792c86c3575d186a33ff9a20">5d9df9d1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-18T12:31:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: made renderFrames templated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f045222ced54fbd19959f4ad79f28c1eff00ba6f">f045222c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-18T12:42:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: allow an empty MTF file name to skip MTF correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60bc1ea50c50ecdedd1d0b975fee99250f3e9762">60bc1ea5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-18T17:19:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: better error message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/74beeb58b04752133ae75001f8c7fc3f6b81e590">74beeb58</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-18T17:20:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added MPI version of TIFF converter (pointed out by Vish)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/da823c1fa87839d84bad3edf348b391bdf54223b">da823c1f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-19T11:20:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MRC: Treat mode 0 as SIGNED char to be compatible with the official speficifation and SerialEM. (It was treated as unsigned before)
TIFF: Support both signed and unsigned char
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb89fc97291bbae9185571abffa59187fdc7e458">eb89fc97</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-21T11:41:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TIFF: read and write a pixel size in the header
relion_convert_to_tiff: more checks
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c9fadd8102499e5e498ee0d0dc691db0a6db9306">c9fadd81</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-21T13:44:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: accept a simple list (.lst)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f2335a489635cd2df1e71fcd83b65ef833227dcb">f2335a48</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-21T17:45:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">JoinStar: Removed false warning reported by John Heumann
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8bdeba8577838e380e125f272dc3cca591901692">8bdeba85</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-22T15:44:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: write at the final iteration regardless of --sgd_write_iter.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7b3195ec046a88e7c3aed52eefb6f0ed5d1c980d">7b3195ec</a></strong>
<div>
<span>by Jeffrey Salmond</span>
<i>at 2019-11-22T16:46:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix typo in tiff_converter
currently preventing ver3.1 from building with TIFF support</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b8b4faf02041d177907ba285b2cd957e4fb0afcc">b8b4faf0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-22T16:47:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: don't free return values from fl_input(). Fixes GitHub issue #545.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/76b9772ecb9ba166a7032a7eb12d78a9c684d802">76b9772e</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2019-11-22T16:48:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #546 from js947/patch-1
Fix typo in tiff_converter</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0babfbec6099b7db66c8aac6c9704f74f7f5813e">0babfbec</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-22T16:49:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/55e57fcaa5a915a7c32f1c470092a0ee76207f58">55e57fca</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-22T17:09:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">star_handler: fixed the output node type (solves #544)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/932818d15ac6ead42129f7a0784d892cdc971b51">932818d1</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-25T12:13:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_project: make it clear that --ang accepts only particle STAR files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6dddc66643be7e3157ec43892244933eddeede61">6dddc666</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-25T12:17:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ManualPicker: added --coord_scale. This is only for display. CoordinateX/Y should nonetheless refer to the original micrograph pixels, otherwise Extract and Polish will fail.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/afe75e89fbc7908d94ab1095da0e435ada4b6233">afe75e89</a></strong>
<div>
<span>by TJ Ragan</span>
<i>at 2019-11-25T16:49:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add environment variable for default scratch directory.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/94d5d64fe62f0765b24d94826a3e1d89fd9e34c1">94d5d64f</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2019-11-25T16:57:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #550 from LISCB/ver3.1
Add environment variable for default scratch directory.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6997e2dfbbd2f4619c75a4ffdb4587456ee398d8">6997e2df</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-25T17:40:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_star_handler: make minumum and maximum inclusive
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a76cf5e43b165eed9fb317f51c6b5d08e6005317">a76cf5e4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-25T17:41:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6503c00b9740d81e01555b1d23e30251521a98a6">6503c00b</a></strong>
<div>
<span>by Bjoern Forsberg</span>
<i>at 2019-11-26T17:45:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">display of model.star rot 3D-helix recon by 90 deg
but only when "apply orient" is ticked
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f511addaa5961e8f378bafcbe204f66c70d981b6">f511adda</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-27T11:58:07+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_flex_analyse: write the optics group table (pointed out by Rafael Leiro)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b6f9fe93240e399b3a12411424c31d278cc334a">6b6f9fe9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-28T17:24:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">JoinSTAR: fixed a type error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3bfef2bd680046ea3bfebcfb454e40a9a683a800">3bfef2bd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-11-29T12:20:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug reported by Sean Connell about refinement hanging with multiple different MTFs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/734866cea21f7e240c5e0f3d4215920317294e75">734866ce</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-29T14:25:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MetaDataTable: added MDT_TYPE_CHECK flag to cmake (only for developers). This checks type compatibility on every call to setValue and getValue.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd7dc1a2f9f1bf7c988d2c0e4bf50b4d5f8fcab5">fd7dc1a2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-11-29T14:36:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ObsModel: make critical sections independent
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/699f3dabde158c47565b5b9b6752c599ca75784b">699f3dab</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-03T11:56:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EPS colorimage: limit the number of elements in string / array literals for compatibility with earlier Ghostscript and Preview in Mac OS.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f6ce7a7ce52cd4a2ebf6d30aee0121d5fe61469d">f6ce7a7c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-03T12:24:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TIFF: made write_tiff_one_page public.
Resolved Conflicts:
src/tiff_converter.cpp
src/tiff_converter.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/adc2e44d23f8e2419526884426e37bf52bd09925">adc2e44d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-03T14:21:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
Conflicts:
src/tiff_converter.cpp
src/tiff_converter.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/25ab48b2c86ebb79347ed77dd3cdddf0bf53c7cb">25ab48b2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-03T15:16:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: supported TIFF container. New program relion_eer_to_tiff.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d0b093a060aa1dbda344992e73a9e2cf3d45c2f">7d0b093a</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T09:07:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to debug split_random_half and repaired bug in subtracting COMs with different vdims
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f981a5ece559bccee8ec9fb8dc7c9c5c9c3ecd80">f981a5ec</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T09:07:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in subtracting COMs with different vdims
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29f1b42dc28a9e7cced485638b9a9e7789b2389f">29f1b42d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T09:08:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added cisTEM-like FSC-part calculation to postprocessing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e01882af0ddc03d6ff9057ed2d51ecf931309562">e01882af</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T09:08:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">built in protection against operations of unequal vdim
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a06d9cdb5da582aba77c7fe2facd511fbc39e209">a06d9cdb</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T12:27:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in inverseFFT in multibody refinement on CPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ffe049a8a27a0e44ee9d70e03bb0fa05ed7f9926">ffe049a8</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T13:54:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed strange initialisation of Faux in acc ml_optimiser
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c2d7a46ce5aefa59aa5e85edc584a5a41bf69759">c2d7a46c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T13:54:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check whether fFourier is expected size when deciding whether to recompute the plan
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a75ef3623ce2fc609d8f66273a06702a274a313">7a75ef36</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T14:10:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2fc87bf0f1c18c66015461240c8818afdab68521">2fc87bf0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T14:11:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">for now disable FSC plot with cisTEM comparison
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d47c40172a827e2e9cfa9a3d63084bdf1a07b2e">0d47c401</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-04T14:17:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: fix crash when choosing "job options" without any selected job (GitHub issue #552)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c75aba4c421f50af0aaf08d1eb5baa840eeaae6a">c75aba4c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-04T14:18:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01cf0b355771858c624d727bf30068b5f199151f">01cf0b35</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T14:41:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">made CL option to pipeliner to add a job from STAR file, and change some options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9f499d2f7e7527d5e7f228a54f0ab0ba58e39d7a">9f499d2f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T14:42:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fe4a2efa2494541cd3540f5c4b1dc6f3450b43e3">fe4a2efa</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-04T17:18:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only count pixels in mask>0.5 for cisTEM fraction f
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/db787df494d0ac5adcb7a81775f647da63ae11b8">db787df4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-05T11:03:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_display: working toward colorful manual picker. Refactored the color selection dialog.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ee065021634c8835d7d6753bb3e90b0c999f0aba">ee065021</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-05T11:03:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_display: initialise color
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/39664d8562adbbb4eafe23965203d6100933999f">39664d85</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-05T11:03:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_display: display and save color particles.
TODO: BUG: somehow I cannot unpick particles now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aab11976b77b089621274ebbdadbb3975bc5dc6b">aab11976</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-05T11:03:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ManualPicker: repair particle deletion with --coord_scale
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8af52e32ff1c75f10b47379b9475f54244eafc30">8af52e32</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-05T11:03:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_pipeliner: make --addJobFromStar working
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9ff7c7ba80977afbcdf327c7559bab81fd51ad42">9ff7c7ba</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-05T11:03:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot.py: supported job.star
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ad3cd69cdb781602a6318e79fb2be868179a32be">ad3cd69c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-05T11:54:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bfactor_plot.py: repair twin X axes for old matplotlib
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9c2ab9219dc1b2f4a9d0de840dee8844a3814c03">9c2ab921</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2019-12-06T15:54:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added define flag for cisTEM plot FSC
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/34bbef39527ee65dba2af618497ded3a9b2eabc2">34bbef39</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-06T22:27:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: supported lazy reading for TIFF
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/62115881eb3ebdabbc1f8d16f9ac896f481618eb">62115881</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-11T17:13:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2085051ed7ca31f6583223482217d17bc3ebbea7">2085051e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-11T21:43:59+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Repaired opening of coordinate suffix STAR files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/45ed9433ecdad8d5fab1d6c8e7612a1792134ac5">45ed9433</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-11T21:45:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7a05f1c3cfc25f3660f514cec7f0e51f2e367620">7a05f1c3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-12T14:00:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ManualPicker: removed a debug message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02d72a1a5041761a2b79674092f88566fd295da0">02d72a1a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-12T14:00:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c3f19a3152c517b7ae2f3ba45ec6b3ee02012a0">7c3f19a3</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-12T14:54:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: repaired gain handling (4K gain into 8K was fine)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c49f8450c3e9152df1c0cba593bb3c5a44bdb26">6c49f845</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-12T15:57:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: fixed JobOptions::read (again!)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58b000f90035f407f24b0c1dcc383112a50b57ee">58b000f9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-12T17:02:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4854bbafcb53e2d32e7ce2d71f471fc5c074813e">4854bbaf</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-13T13:59:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: don't use string::back() for compatibility with older compilers
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e997ec587c1d7d0ed475e8bca863036140aa67f7">e997ec58</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-13T20:06:19+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/914542ea84d32b7f924344914a5dde53c046f921">914542ea</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-16T11:02:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">JoinStar: repaired a bug introduced in f2335a48, where optics group numbers are not renamed when rlnGroupName is missing (reported by Giuseppe)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c5eae36c3f338ea45d095aca666906d497f5cff0">c5eae36c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-16T16:48:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f5721ee7f740aa244d4d6b98c18b2c162ce5868f">f5721ee7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-22T21:58:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: repaired support for RELION 3.1 movie STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/96bef33889c6747c7a0ab635660be871bcc501ff">96bef338</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-22T22:37:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">STAR parser: trim trailing spaces
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a451e833d67125ac81e1bcce9769576102311da6">a451e833</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-28T11:15:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: removed compiler warnings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/56b1d8ddb01de1b88d0de33a676612d594918b95">56b1d8dd</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2019-12-31T12:01:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7d4fc2e65da907649466171592ca1bb1bf008cf4">7d4fc2e6</a></strong>
<div>
<span>by Kiyo Tsunezumi</span>
<i>at 2020-01-10T18:16:49+09:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixed a bug that "Browse" button was not displayed in "Raw input files".
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5e744e41c4328fe79c0602abac3e2c0d42bfd985">5e744e41</a></strong>
<div>
<span>by Kiyo Tsunezumi</span>
<i>at 2020-01-11T10:02:19+09:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added support for tiff files and others.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2bd3ad1bb2b62ea3678dc5b343c7bc59ec5aa37d">2bd3ad1b</a></strong>
<div>
<span>by Joaquin Oton</span>
<i>at 2020-01-13T14:47:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bug fixed when --sigma parameter is provided. Number of images per group is now calculated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e6949ab53b39b13cb3808a25cd7762007f099819">e6949ab5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-01-14T12:56:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: fixed timing code
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0b35ccca0d48855119ba7955d834186daa8a02a1">0b35ccca</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-01-14T12:57:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">inserted statement about SAGD patent from Structura to section 8
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8144d6fc75974aa33cec8cf7994b84cabcd882ba">8144d6fc</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-01-14T12:57:44+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/408f51a57f9b01f85235b2c06da54050de66d19f">408f51a5</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2020-01-14T12:58:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #564 from kiyotune/ver3.1
Fixed a bug that "Browse" button was not displayed in "Raw input files".</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/09b7e6a5d724d09abb70c4bd5f539d99ca22f62e">09b7e6a5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-01-14T12:59:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4203926e15e0017be4cd997c88df0256ebe2be5">b4203926</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-01-14T14:03:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired typos and changed SGD into SAGD
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/06afb9fe634d32265ce9e305e655e30812057683">06afb9fe</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-01-14T14:04:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7da6711db131ce639673ec377b4c83d31ce1c0af">7da6711d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-01-27T12:37:13+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Converted micrograph STAR files should use rlnMicrographPixelSize not rlnImagePixelSize.
Up to now, rlnImagePixelSize was used, leading to (1) failure to open ManualPicker and (2) Autopick using a wrong pixel size.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7e0a5d2d01684381fb77320223bbc14c0cef5bf8">7e0a5d2d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-01-27T12:43:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ObsModel: repair a loop variable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c11be6a66b6dfa71f9a761030c8b8606667576a5">c11be6a6</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-01-27T15:11:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option to read tau2 or FSC back in from external reconstruct programme
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4b08d038c7d15564c381b3af16709d6dc0b3cee">b4b08d03</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-01-28T10:38:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extract: "Manually set pixel size" (--set_angpix) has been non-functional since 3b7de54. Remove it from the GUI and the command-line option.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4e60d1ffdb0ca5917ba4db61ef430d12272f49c0">4e60d1ff</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-01-28T16:29:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Don't regroup particles from different optics groups into a same (noise-estimation) group
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a5d691e8a9507c1efcce2810ba74f5fac6d2a098">a5d691e8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-01-31T12:38:30+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">AutoPicker: Repair a bug where non rank-0 MPI processes failed to read the reference pixel size from the header (solves #572)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b69d089ae8bfb4800e5b5a4d3cf60018f17c62ea">b69d089a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-01-31T12:57:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0d19adf07bfe23f22f59957b53a8e467bd79aeea">0d19adf0</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2020-02-03T15:29:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Conflict has been removed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9231b1875b3f31840c6c611632204ae5be7143a0">9231b187</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-03T15:53:21+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: clean clutter (preparing for per-frame reconstruction)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3925968d9c9946d8402e21c2677dde188271a023">3925968d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-03T15:53:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9575df8e089cfa5902b3a7282873251ffed1205c">9575df8e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-04T12:17:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Don't allow padding factor less than 1.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/07586c3b1bb7a45d93d6dd1ba3b20a0a618513cc">07586c3b</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2020-02-06T13:15:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion into va_relion_relax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f9d266bdca2f9e600211de09f422e17f4ecc3ea6">f9d266bd</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-10T09:31:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired critical bug in subtraction with auto-refine results
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/40a21f2402e1d830f82e5f40e925a43d1108cc47">40a21f24</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-10T13:47:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">also replaced part_id to ori_img_id for ctf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f92c60f28305c5a090da72ee6580ee02a5148f4a">f92c60f2</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-10T17:45:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further debugging subtractor
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1645d183897f9fbd4ef6925239cf30e2a0f1dc6c">1645d183</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-11T15:03:04+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">no longer pass orients around, instead modify output MDt and combine those in the end
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57bac07adcbcfa2cfcfec7655103f15d4d1acc02">57bac07a</a></strong>
<div>
<span>by Alexey Romaneko</span>
<i>at 2020-02-11T21:50:08-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">OPTIM: merge data transfers. part 1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9eff2a3b1338bc2a999480e4d1025715df46be77">9eff2a3b</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-12T14:22:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bu in plotting phase differences for beam tilt estimation in logfile.pdf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3112c488dc02b0d4c8cd3a924dd21b08399cda62">3112c488</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-12T14:32:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Micrograph: more friendly error messages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/257ec0945af8938a4333fbc7cbddb0937e01dfeb">257ec094</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-12T14:33:06+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">README: add explanation about "make install" and MPI version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/237a506fbc4453ccbb80f48ba9909064fdaf9dd0">237a506f</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-02-12T22:41:34-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">OPTIM: merge data transfers. part 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2b1f5aba2dd534515e9631f8ff366a2dd6c94362">2b1f5aba</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-02-12T22:42:14-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">OPTIM: merge data transfers. part 3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/eb55b063ae0d0a0f8e9a45e219e5a81f4255f172">eb55b063</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-02-12T22:42:59-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">OPTIM: merge data transfers. part 4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/245c441d2112e01d2a92501d8f619dace3e9f514">245c441d</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2020-02-14T10:45:28+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #575 from arom4github/optim
OPTIM: merge data transfers</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c17c89673dbba6230b14ca265058f54f5a1c1e00">c17c8967</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-14T11:59:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in reconstruct when dealing with multiple optics groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/de27462ff0d0138b6361845de94c1891677faeef">de27462f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-14T16:09:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into nv-optim-datatransfer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0de3f2d5090463f332ae00ca314955f9da4fb051">0de3f2d5</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-02-17T00:40:44-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">move init_pdf_orientation on GPU
by this commit, we eliminate one data transfer and move calculation of init_pdf_orientation on GPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7f1ec1c3af1b0523274940c79e94fd0bf9726585">7f1ec1c3</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2020-02-17T11:36:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion into va_relion_relax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/65a24b6337fb228212204981b88d0e3580906bec">65a24b63</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-19T11:18:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/baea39fd3d90e3a2ac33652c2ec1616b0852f902">baea39fd</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-20T11:20:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removed dependency on libjpeg (JPEG is never used in RELION).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f8693be7c8251b20e96a265cbe542a1a2f727adf">f8693be7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-20T11:21:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'nv-optim-datatransfer'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2784a5f52dd82311e770bebeba59959bfcb888c4">2784a5f5</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2020-02-20T11:24:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #578 from arom4github/optim1
move init_pdf_orientation on GPU</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/389b9412e3bb433a141455a9e8c9c074d399a457">389b9412</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-20T11:37:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1ca266fc2a4a777ccecf94dc25ec087edfbec413">1ca266fc</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2020-02-25T15:56:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion into va_relion_relax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/98676205cebe521989d09a08066cb5beb1c2a30c">98676205</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2020-02-25T16:13:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New flag added to check for relax option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd31c098e0e0dd10a9245f51d3aebc1cce76c48b">cd31c098</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-25T17:25:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Supported 7-bit no-waste format (not-optimised yet)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8f9b1cfb2b1fde6d1fa2ee1a5f88fb588073a7b9">8f9b1cfb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-25T20:59:38+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Optimised 7bit RLE processing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1840ba08244ee8178d71729651aae42f41782c60">1840ba08</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-25T21:26:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Unroll loop by 2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/abac0973b61d2b9674e467e6cbdbc687c7290ebe">abac0973</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-25T21:26:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'nv-optim-datatransfer' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7fb53e5f1398b5c5a4f7223aea300b4759a24276">7fb53e5f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-26T09:35:42+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">set default skip_gridding to true. In future perhaps remove from GUI and make a --gridding instead of a --skip_gridding refine CL option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a8382367de0b1f9bd89b66a272aa9e2c701b9c75">a8382367</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-26T09:36:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed some debug statements in skip_gridding
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ff549659e3cc3a3d30878704636ef0577026657a">ff549659</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-26T09:37:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">also changed wording of help text
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa896427d80ffa9448f6ffa6f76ea625dc8f16eb">fa896427</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-26T13:01:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug #580 reported by JoeBeton
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8ba188c02d9ed2ee3cdeb7643a30ceda0eb28366">8ba188c0</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-26T14:08:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">implemented faster convergence in auto-refine and put it on GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1618311441921d8592735f1f0899bf9184fa80e7">16183114</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-26T14:13:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use finer angular sampling faster instead of converge faster on auto-refine GUI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a0af57dfad778474f234f82428ccd15d85431090">a0af57df</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-26T14:30:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'nv-optim-datatransfer'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/69dfddeaf5cdb17e54b195c4166d40967021863c">69dfddea</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-26T14:36:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d94aeac132e816f9cfd0d9cf53f67b455e0025c">6d94aeac</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-26T15:09:08+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Removed global variables, EER_grouping and EER_upsampling. Save these in movie metadata STAR file. This is work in progress; Polish cannot change the values (yet).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/05673168e75d9d0c717aaaa8dff1c36096bbef91">05673168</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-26T15:45:02+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_eer_to_tiff: repaired --eer_upsamling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/12d9d527a1c4fecb49fe8ee57555f22c18f88800">12d9d527</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-02-26T08:12:48-08:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix timers, optimize two kernels, fixed issue with pixel coordinate calcuation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/29de8077a7fbb5fb8c54a111890a68ed14de570d">29de8077</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-27T14:32:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">allow saving coordinates with CTRL-S in the manual picker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4463657ee1339f02beb9cfefed5946c3a0dc2d3f">4463657e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-27T17:37:55+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add also CTRL-Q to close picker window
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b94876883fb743dfab5bc459dcf7b993c5e5700">6b948768</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-27T17:38:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add option to CTRL-click a Pick button to open multiple micrographs simultaneously
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/04b252585d5120cede20e509ba8d3ddb81f62b4e">04b25258</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-27T17:39:33+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2399ef4da2067a4aa0b6bf02eb8e03ccb0dfafed">2399ef4d</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2020-02-28T12:35:26+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #581 from arom4github/optim2
Fix timers, optimize two kernels, fixed issue with pixel coordinate calculation</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4a17fbea4081feaf660f540a6988a8a121db351f">4a17fbea</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-28T14:11:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">faster 2D/3D classifications by allowing coarser angular and translational samplings in initial iterations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0053ba19c809bda087cf6829bc72157e2993c609">0053ba19</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-02-28T17:44:52+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">first phase of replacing centerfft with centerfftbysign
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a4163b43357693c8a6b33a85b4d4e0b811849f2">1a4163b4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-28T23:10:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Nelder-Mead: Repaired memory leak
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c61cbc8981d6c2b5ddf4dde0594d12ce173e3a7">3c61cbc8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-28T23:11:25+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9b82601a4f10047580e4248032e906c35a12dc93">9b82601a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-02-29T18:17:10+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: repaired many problems introduced in 6d94aeac. TODO: resampling/regrouping
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2d1a6e49e7bbbaab1821fa21c078fd7c130de6f8">2d1a6e49</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-02T10:09:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">centerfftbysign in autopicker
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/25c642d43dcfbf5b642219039a3440c0b312b603">25c642d4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-02T10:51:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/18abf519b1f1db762a34379655e19d94115a817a">18abf519</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-02T14:35:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'nvidia-optim2'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7893c91893f0ede1d4be643b22f31e98690b686b">7893c918</a></strong>
<div>
<span>by Joaquin Oton</span>
<i>at 2020-03-03T12:33:43+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of bitbucket.org:scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6ee9bdefc45907d48f6b19d6552ecfb7588a2c21">6ee9bdef</a></strong>
<div>
<span>by Joaquin Oton</span>
<i>at 2020-03-03T14:03:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bugfixed: removeDuplicatedParticles in metadata_table.cpp won't consider Z coordinate #584
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/069719809bde709a5729280061cb06c8cf50d9a5">06971980</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-04T15:09:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">centerfftbysign for reconstructor and subtractor; ewald sphere tested now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/284137ba33317ab9cba614627a9b4979630618cc">284137ba</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-04T15:09:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Takanori suggested further optimisation of centerfftbysign
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c3cb32b12439303799d72086af7c38e09698c46d">c3cb32b1</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-04T17:34:14+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">go back to without sorted_idx
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f57bd847f2a320fff4f068e5102dc70e6b0737b8">f57bd847</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-04T17:50:53+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ManualPicker: added Ctrl+1 to Ctrl+6 for color selection. TODO: synchronize this with the pop up window. prevent multiple pop up windows.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68bbeea9f2ba6f838e48af47d80ddcc00aa38a0b">68bbeea9</a></strong>
<div>
<span>by Joaquin Oton</span>
<i>at 2020-03-05T12:30:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bug fixed when --sigma parameter is provided. Number of images per group is now calculated in MPI version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/296321970bf1bcca9542b7ccac46512b478cf92d">29632197</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-06T11:38:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7f66ca02215ad0ffdabbcccdbba717d56348ec73">7f66ca02</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-06T12:17:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">sort particles indices instead of whole particle vector; calls to getFT, getDelta2 etc inside expectationOneParticle still work on original part_id, but above that, use the index from the sorted vector
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/01abbf86b80ea125f8ce3ef7e0482092aed86339">01abbf86</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-06T12:45:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: we cannot perform Ewald sphere correction on CTF premultiplied particles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/57dd801183c4e3e16dd86d6a5cf437c092d85a60">57dd8011</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-06T12:45:57+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b6c9f439bd58f6114842d9d7886ba6eada4f6f55">b6c9f439</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-06T16:09:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bug in half-set division
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/537c8cabd71233a94b7d488a954dfd95674d99fb">537c8cab</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-06T16:48:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3eef41f66edc590762b0df01216956b34af61a25">3eef41f6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-07T22:08:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">obs_model: repaired a false warning about rlnImagePixelSize reported by John M. Heumann in CCPEM.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6d9a0da7fe71419539e836ea0f021d6e1ebbe1e0">6d9a0da7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-09T14:11:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'newsort'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b3e8f84cf570aa37b351bacd194336b0d0afe2fa">b3e8f84c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-09T17:49:09+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/35b70f0a12e30dd36324281e7a5edae7c84d1a04">35b70f0a</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-03-15T09:06:42-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">griddingCorrect from Projector is on GPU now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/58e358b7203e7690b36a97bff3566a010433f29c">58e358b7</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-03-15T09:06:42-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">pad translation part for Projector is on GPU now
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6410c1e308bc5c7e02e0fd628e81221831b4aea2">6410c1e3</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-03-15T09:06:42-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">centerFFTbySign for Projector is on GPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6e58ec0363320ab29fac428809b180ea734c98ac">6e58ec03</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-03-15T09:06:42-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">calcPowerSpectrum for Projector is on GPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b1c559a5a47bf4a8a82228eefa8cb7e01a92885f">b1c559a5</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-03-15T09:06:42-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updatePowerSpectrum for Projector is on GPU
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/22ca0ccbb93ef01d15d24c3e86eeea54fdf52d15">22ca0ccb</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-03-15T09:06:42-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix: use GPU only if --gpu arg was passwd
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/016bc040ca3bf6f56d52d7b440795f075c22e2ca">016bc040</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2020-03-16T12:53:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Confflict solved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2da34eb8e282165e04e7ce81e660753b4372eb34">2da34eb8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-19T17:36:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: remove unused global variables.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8040f82f5464112818076e3157f77f8ed95b5bdd">8040f82f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-20T15:31:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">implemented option to calculate spectra SNR of individual images
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d86d3c947729251c40b820484f3796d688a1192f">d86d3c94</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-20T15:32:54+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtract job wasn't taking additional arguments
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cdc0ad29c6d5991e4e9f06263cf1453469b2ebf4">cdc0ad29</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-03-20T15:40:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in master (pull request #31)
Subtract job wasn't taking additional arguments
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/13098d6102e057a0b724eddd3864d1aa9b7df2b5">13098d61</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-20T15:51:41+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some code commenting.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/50fd10de28d497e149be4808e5795ae97738cfa0">50fd10de</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-27T09:58:51+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_star_handler: added --random_seed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/164b0f0296632f43c28177494af2757afaa58626">164b0f02</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-27T10:00:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ac497e02173eac98c207a95d870139299e81ad24">ac497e02</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-30T09:50:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/24c6d475b95a6f72fcc769c0af695119eafbecdf">24c6d475</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-31T10:16:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Relair --eer_upsampling in motion correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5d1eaca49d0b6bf32db8957d5a69fb3e674382a5">5d1eaca4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-31T15:58:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Write a pixel size to the header of shiny particles (solves GitHub issue #597)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f538f77b95592de9f21ac0ec8fc94fd2fa11ef4b">f538f77b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-03-31T16:40:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: show a broken file name
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d92f3f281941b3fd88136f10c522a420f878d73b">d92f3f28</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-01T14:23:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TBB: Updated URL and MD5SUM for TBB 2018 U3 (GitHub issue #594)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ca101fab137eba76ae7f29071265cac7a929a936">ca101fab</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-02T21:26:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_display: repaired training set contribution (applies to LMB only)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f6b9e2ed6a99f4f311efd44f611995b7a5c33db7">f6b9e2ed</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-13T17:53:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ml_optimiser: repaired a bug reported by James Conway on CCPEM
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a7025168f1eb40cb31dbc6969d3e9d145b1a3580">a7025168</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-13T17:54:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3533f637234dc5a89d54ba07ff90980a4d44a168">3533f637</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-16T14:58:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repiared bug reported by Max wilkinson in subtraction with different image sizes in optics groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/94e2802f5f8c7fb2f3fc849021c7a83f7f189e60">94e2802f</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-16T14:59:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2bed2f63c2f0573739e62ba8be07c11a17496841">2bed2f63</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-16T17:17:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct_mpi: fixed the class name in error message
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e3fa664c066875e3c9925dbad4036f5f7162438b">e3fa664c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-16T17:17:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4082167df44aee4dae671468c08ca10f025e2ee7">4082167d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-16T17:24:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d3692a445ea41381b7b57367e23310ea1a75a629">d3692a44</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-17T11:05:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added relion_movie_reconstruct
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/934e5f21fabf08ea3812c218e15c4b7ed7e403d6">934e5f21</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-17T13:03:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">movie_reconstruct: get movie file names from motioncorr STAR file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a679f07b35ae7f8aa6937f75262ec1fef9ba5ca">8a679f07</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-17T14:16:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">movie_reconstruct: mark as a test program; use Micrograph class to get more information
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cebc37b43cde7f24416734c909fa6fb1896af4e5">cebc37b4</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-17T17:33:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">movie_reconstruct: use threads for half sets to avoid reading movies twice. EER is still broken.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1187d2554410b538843303a2842a9e4bb8ba5dee">1187d255</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-17T21:47:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: silence libtiff warnings for private tags
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/02b7e7faf9efb8c9657ee12656cbc0a5452a6c8c">02b7e7fa</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-17T22:56:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">movie_reconstructor: EER also works
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4e6207c6b8475ac8477f4d53ee860a6edf304349">4e6207c6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-18T22:38:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">movie_reconstruct: allow changing EER grouping
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/84d160fc2e3d866d87d97823e47f34153908ecd3">84d160fc</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-20T11:03:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">flex_analyser: don't allow MPI when performing PCA
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/36482787f8b4234d5397536c03b8d95cabf97556">36482787</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-20T11:04:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cd096c0c078c481e516c9894e008a447fdd06f92">cd096c0c</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-21T13:20:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bugs by KThurber2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/649aa3891f78b6a2b66cb36217b773d843e5b4ae">649aa389</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-21T13:21:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9d4609b4da4d4074db1e6ac0e60c0ec02ef50f5d">9d4609b4</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-21T14:12:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed orientational_prior_mode from the sampling object
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2258321dd8f8546adadda12221e497e2ec8bad77">2258321d</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-21T14:18:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed orientational_prior_mode in sampling object in GPU code too
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/75dfe143f09b7cbb158b45389c6d5c92f6d160e5">75dfe143</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-21T14:55:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">renamed do_local_search to include _helical for improved clarity
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4e274013ee0705136dcc6373b7caaf60be56fd6e">4e274013</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-21T16:22:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further simplified the handling of helical priors, still to be tested
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b741ab5b2480ef857e0d1a88398d15029fa5eb09">b741ab5b</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2020-04-21T21:47:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Relion now compiles if libTIFF was not found.
Also, cmake messages regarding system occurrence of libPNG, libopenMP and libTIFF are outputted only once in proper cmake format.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d7a588118e97636b0a514262bb344d31f38e6e9d">d7a58811</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-24T10:42:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">revsered sign rot prior in code by KThurber
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d9309ddcb0bffaf1e887b3664ce8e71b0a6687b7">d9309ddc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-24T13:29:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">only write out number of opposites if psi or rot prior is used
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aec1835d4288dcc49754220d5daef5817c294cb8">aec1835d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-25T21:58:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">movie_reconstruct: added --no_barcode
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6427ef6300465308f0742aca0b2d711f6286b27f">6427ef63</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-27T08:49:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added helical_nstart to helical prior calculation to go back the N-start twist and rise to avoid very large fluctuations in predicted rot priors for small errors in twist and rise
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d28fb9f5947ace92ec21fd930cd7353825c79db4">d28fb9f5</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2020-04-27T11:44:48+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion into va_relion_relax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/911bdc55283f714af0504d35c34888341486ce5d">911bdc55</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-04-27T18:04:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">introduced search for both directions of distance along helix for rot prior, reverse direction if needed by making distances negative
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ae50cb7772836ab95707b58e20546220a99339a0">ae50cb77</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-27T20:59:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Removed harmful spaces from the help message of MultiBody body STAR file.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c6c5c7c24ffeb3320d5bd339ed4beb387717f998">c6c5c7c2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-04-27T21:00:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://bitbucket.org/scheres/relion-devel-lmb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6537fb055b92956ac4e16a210c1304d75a925a39">6537fb05</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2020-04-30T15:27:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Updated README</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/63effd75783e4d3275355b05f21552b33fc981ae">63effd75</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2020-05-01T09:26:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Further updates of README for EER</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/82e4cb9ee7f06ad8d4c9ff190c30f10a381f5608">82e4cb9e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-02T06:39:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Polish: Use the pixel size in data star file when calculating particle centers. Now OriginX/Y should be valid even after changing the pixel size and/or box size. But the warning message was kept just in case.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f7b6f0813c399b21945fbf72591be15546cd6eec">f7b6f081</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-02T06:41:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTF::getFftwImage can be dangerous because gammaOffset calculation does not respect orixdim, oriydim, angpix. The box size and pixel size must be set in ObsModel before using it. Added this check. This is better than silently returning wrong results.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c04dd8a4135edf371e93aa9df6d8fc5d1efcc69">6c04dd8a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-02T06:43:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Tentative 16K rendering support (only for debugging, not for MotionCorr or Polish)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/425abb8788943b94dad20175cd7cbf5fbe62e416">425abb87</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-02T06:46:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote-tracking branch 'origin/devel-eer' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e069e15902b6a2f77f3e97cd6b6f2be6702a9561">e069e159</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-02T06:47:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">State that relion_eer_to_tiff might be merged into relion_convert_to_tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd89b51957dd12af0ae0c3c638dbc8aea663f363">dd89b519</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-02T09:40:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: added disclaimer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/92bb8af92c9252abf375018d9ffdb38f9b686512">92bb8af9</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-02T20:53:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Repair 16K rendering
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fa3eef668d7f9bd9f39bb8d9f5fb0fa9b92388c0">fa3eef66</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-03T06:19:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: Further fix for 16K rendering
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/23bbe42e38afe80683fb5552fb3b9121fcaeff98">23bbe42e</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-05-06T12:31:23+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merged in kthurber2 (pull request #33)
Kthurber2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b66e81421123f95b5e5105220b1079de15008a5">6b66e814</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-06T18:37:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/40c8d214945ef8a7012ea49e4886dd19a600fdd5">40c8d214</a></strong>
<div>
<span>by Björn Forsberg</span>
<i>at 2020-05-08T09:09:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #1 from 3dem/ver3.1
Ver3.1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6782e81bd1349552ea398a0cf73453e37fd75856">6782e81b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-12T12:43:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Allow Intel MKLFFT for GNU compilers
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a67564a7383e2005ba22d682e085226162576d97">a67564a7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-12T14:28:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MultidimArray: always use aligned malloc for better FFTW performance. This should fix an unexpected crash when an FFTW plan is re-used illegaly with different memory alignment.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5cebbd53f75d79f0c7fbd65a8ef17fc936ed80d6">5cebbd53</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-13T23:05:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Regrouping: Fixed issue #621 reported by Huw Jenkins.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/307c8766fde5ca9d192dcdab081bae2aeed451ec">307c8766</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-13T23:10:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into devel-fft-improvement
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/335f2d5cdc1911566e7930d5f9a6507c3a48eb81">335f2d5c</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2020-05-20T11:36:02+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge with ver3.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c1ab9cb540e0767113f94c6353bcaca21c04c712">c1ab9cb5</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-24T11:36:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8a7eb11182e4372d09d65472dae0d8e7e684dde1">8a7eb111</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-24T22:11:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_ctf_toolbox: repair defV
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3a49598ce500ce08e2e5533af774ce526aebe064">3a49598c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-24T22:11:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Check either Polish or Tune is selected.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b4a3aa5aa042d8847c775686ebcee10af1c5f2ea">b4a3aa5a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-27T15:41:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_image_handler: supported writing a PNG file (only single image per call; e.g. "--i 1@stack.mrcs --o 1.png")
Colouring functions were moved from displayer.h/cpp to image.h/cpp because displayer.cpp is not compiled without GUI.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4268a182880fae7dd357f5d982a344732863ecf5">4268a182</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2020-05-27T15:47:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #620 from bforsbe/ver3.1
rotate helical display from model.star</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e176a91de37f8059065332f601a8d4a56eaa184d">e176a91d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-27T16:43:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extract: make the program robust to absent columns
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8275ac6154ba08688dcb4c675e70752fc8167198">8275ac61</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-29T15:11:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_image_handler: write the REAL pixel size when the box size is rounded by --rescale_angpix. --force_header_angpix can overwrite the header pixel size. --stats shows the header pixel size.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/200e55629cea96a5023c56efbc522c7cc5d2507d">200e5562</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-05-29T15:13:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/50bfe7197d021d03d6444520d54548fc6f42216e">50bfe719</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-01T12:05:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CMake: clean clutter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5997001f75abd0f1fa135ee25e04f92c855e5e29">5997001f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-01T12:06:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_refine: --print_symmetry_ops also shows Euler angles
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/06ed5598559829f6574385fa7a5115ed886374c1">06ed5598</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2020-06-01T12:09:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #588 from arom4github/optim3
PORT: Expectation setup to GPU</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/b781fe80dfcdc5f93fd3e3ae94f770401d8dcf40">b781fe80</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2020-06-01T14:11:19+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion into ver3.1-relax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/474e802d3c886070dd9d9c5a6654ee5e9c89c0a0">474e802d</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-06-01T14:30:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">FIX: add the check of Compute capability >= 6.0 to use AtomicAdd for double datatype
Signed-off-by: Takanori Nakane <nakane.t@gmail.com>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1fbba73cb1ec9a9b4895693f3dffa9d6cc334576">1fbba73c</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-06-02T10:30:01+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">FIX: do not use CudaCuctomAllocator if no GPU available
Signed-off-by: Takanori Nakane <nakane.t@gmail.com>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f1714b22babd39958cb27c3c1a221b24d6db80be">f1714b22</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-06-02T22:07:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">FIX: for 2D reconstruction
Signed-off-by: Takanori Nakane <nakane.t@gmail.com>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9090fdebd668b7e0c0439f2987a8226321dd1a78">9090fdeb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-09T11:47:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">regrouping: repaired a bug reported by @huwjenkins (GitHub issue #629)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/35b22622414b2a8837121818cf3c127f0e27e12e">35b22622</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-12T12:26:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MetadataTable: repaired the label index when skipping rlnSortedIndex (Reported by Kailu Yang on CCPEM)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3dbc26358a7a6eca3934bd8e6ec0a1f2e1279a54">3dbc2635</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-12T16:41:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_pipeliner: supported External job type as suggested by Colin Palmer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/c619a1a75445dee1ce0433789ec175163f680118">c619a1a7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-13T21:44:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CTF: Respect gammaOffset in CTFP
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/aa088f119aee7a5d4ae0fe6b05eb25d42b653815">aa088f11</a></strong>
<div>
<span>by Jasenko Zivanov</span>
<i>at 2020-06-13T22:56:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">aberrations are now interpreted as given in undistorted coordinates when they are applied
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5857e17fd9f1c530c6a426103cb688db4efaf863">5857e17f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-13T22:22:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'aniso_aberrations_fix'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a72dcc25af0b5a7f2a16635dfe7b0bca7213af91">a72dcc25</a></strong>
<div>
<span>by Vahid Abrishami</span>
<i>at 2020-06-15T11:12:50+03:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion into ver3.1-relax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bea738fe092c919623d182ea30502659807ed65d">bea738fe</a></strong>
<div>
<span>by biochem_fan</span>
<i>at 2020-06-15T21:11:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #632 from LSB-Helsinki/ver3.1-relax
Symmetry relaxation contributed by Vahid Abrishami.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a01b0800b391805a891a39bced7ba7b69b29fd9d">a01b0800</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-16T16:11:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added contributors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1bc958fa0089c3d73ebcb6e0471ef69faa4d1bc8">1bc958fa</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-06-17T10:55:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">automatically rescale the reference to the smallest pixel size of the input optics groups
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cfbffbbc5ebc93ac6b0971dd2ea8df5eb7637e4f">cfbffbbc</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-06-17T10:57:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">included fabs in pixel size check: dont use smaller pixels than smallest input optics group either!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/226d3e41a0a2cb4d337d8a996238f123a2b3fa96">226d3e41</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-06-17T13:37:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added functionality to opitmise scale and bfactor prior to subtraction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/61cf47ba556a90dfc8047b1d82ad2cd7a02018a9">61cf47ba</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-17T14:49:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI and pipeliner: Fixed illegal memory access in HealPix order choice. Made the code more robust against illegal inputs.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e771648326767a10ad17e8f1b2550492a11a33f4">e7716483</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-17T15:18:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://github.com/3dem/relion-devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/49c5a5835de3ad0346482fcd55a5bcc7db221e42">49c5a583</a></strong>
<div>
<span>by scheres</span>
<i>at 2020-06-17T16:26:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">die if reference size incompatible with data, unless --trust_ref_size is given
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/885321f316f0e9d1aaae42a78a2aa3bacecbbcab">885321f3</a></strong>
<div>
<span>by scheres</span>
<i>at 2020-06-17T16:27:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://github.com/3dem/relion-devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7be1eb757b40fe458ff982a135cf23efdbe4c662">7be1eb75</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-17T17:11:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MlModel: tidy up messages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8eecda3b7c32c71def553881597cb5e494d679a6">8eecda3b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-17T17:13:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into devel-sym-relax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d366c3600a12d3327e3812de3a006c5ffdac0811">d366c360</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-19T20:50:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MetadataTable: Column numbers should count from 1 (a bug introduced in 35b2262)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/3c824b420d4f875845d08a0cc4ea969b7c62e552">3c824b42</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-19T20:54:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into devel-sym-relax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a194025036e6a59411479e4c10b8bce700015a6e">a1940250</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-19T20:55:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d12c4f8fdc58ed76391b75758fe1a2e98a284c46">d12c4f8f</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2020-06-23T18:51:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">First attempt at support for Catch2. Configure with -DBUILD_TESTS=ON Fails at link time.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8476f0eb08a85e24c8b5d61e4df234b6be08b391">8476f0eb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-24T20:57:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Made FileName.decompose more robust to fix a problem with new SerialEM movie names (reported by Dr. Shigematsu). Nonetheless we are against the use of @ in the filename; it might break other programs/scripts using RELION STAR files.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f1acaf7a7ef8df1387ee730f19ffe6ffe7568c6">4f1acaf7</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-24T20:57:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtract and MultiBody now respect CTF premultiplication (reported by Sean Connell).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/37f6dc7f5366b396da6e788ac378210132c97084">37f6dc7f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-24T21:02:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e1bcf0aeac3f15ebfe85098864d60a5eceebe3a2">e1bcf0ae</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-26T10:57:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: removed '=' from arguments help (Reported by Juha Huiskonen in GitHub issue #636)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f669697958551e15907105da21325ec3ed079ca2">f6696979</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-26T12:31:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/17889467781a3416c5ecc22c7f9c07f7232688b9">17889467</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-27T07:00:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtract: Repair recentering when the input has anisomag, multiple pixel sizes or boxsizes (reported and analyzed by Max Wilkinson)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f13a91cd262dab9a2c3fabb0c50b731b4f85e1ce">f13a91cd</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-27T07:38:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9dec2988036506a60cffe27f5bb4dfac2db94e40">9dec2988</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-29T12:22:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Code clarifications suggested by @do-jason in #637 and #638.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/8724745935129b9cb8b628c0cb6780d510b59867">87247459</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-29T15:13:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extract: added --ref_angpix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/31cbf51e8d390c4dec6a48588548602895bcf03c">31cbf51e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-06-30T14:34:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove relion_eer_to_tiff and merge its functionalities to relion_convert_to_tiff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d8f7e6c7fef0a03b644c8d8aedf7f2e4a6bf2a9e">d8f7e6c7</a></strong>
<div>
<span>by scheres</span>
<i>at 2020-07-02T10:41:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">repaired bugs in autopicker and local symmetry
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/759403287740b62ae50405dbf65f366e5fea3433">75940328</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-02T11:53:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_estimate_gain: support the EER format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/53514d7cef5ac596bd6f5a2788b72e2191aa1e42">53514d7c</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-03T12:44:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_reconstruct: renamed a confusing variable name (pointed out by Jasenko)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7607fcb686300e0e8b89ed92a38ad8cb94b0be34">7607fcb6</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-03T14:18:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">GUI: Update citations
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1e738ecbb7191b76e0bd64ed36c4a91850a640eb">1e738ecb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-03T14:18:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">This is version 3.1.0.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/93a0aae8c65bd5934a816c3aa949706d8ad596cf">93a0aae8</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-03T14:25:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
Conflicts:
README.md
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f8f172d7b72736779c9a2f9964c0cedb1072583b">f8f172d7</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2020-07-06T11:33:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into catch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7796d49530b6ade81901a2aff5cc56ab12651767">7796d495</a></strong>
<div>
<span>by Dari Kimanius</span>
<i>at 2020-07-06T11:50:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tests pass
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d50caf12895c3cbc861097fd0e95b21ca8ba63e8">d50caf12</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-07T14:37:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_convert_to_tiff: supported conversion of an EER gain reference
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd9ebf7553af484be2bf1b49cfc8cb1e616ae432">dd9ebf75</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-07T21:11:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MlModel: Fixed units in the message (reported by Li Jun at CCPEM)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0ab9f91949ca70bd52f25f0c5f8034787d31d758">0ab9f919</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-09T14:55:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Subtract: show an error when subtracting a non-existing class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/ea89a137cb52a09bc25605ad1f8b7f324a611f0d">ea89a137</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-10T10:39:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6c4c67cc1358bcd8a51607cc21be9f766c91c09e">6c4c67cc</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-10T10:40:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added eer_trajectory_handler.py
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/021ce55006b78ce61e9180ece517e3359bcb646e">021ce550</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-10T12:40:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Moved instructions to wiki.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/72f7837f5343f100cc09fb66d5eab3b43639a7a4">72f7837f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-12T11:24:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MotionCorr: check for a non-existing defect file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2cae347e2c59e262424fd5edceb9c16752d34b3e">2cae347e</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-12T21:07:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/2f7ac4a82498d539d87738d3a4c7f8b94b113e30">2f7ac4a8</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-07-13T07:00:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">FIX: run_calcPowerSpectrum now works for 2D reconstruction
Signed-off-by: Takanori Nakane <nakane.t@gmail.com>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/fd0190ce3ba1deed89e30687d34f34632af7d671">fd0190ce</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-13T07:00:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into devel-nvidia-optim3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/68b332162f73960bf4df3a12f93871f0de5c1630">68b33216</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-13T09:52:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'eer' into devel-nvidia-optim3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/d7788499a5a804ad7bfcda6abd912a5b19d2a90a">d7788499</a></strong>
<div>
<span>by Sjors Scheres</span>
<i>at 2020-07-13T09:54:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed save_ps and save_noDW to do_save_xxx to avoid conflict with reserved words in STAR format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/720c6e63dc2728cfc38a20373bd348b02dd473da">720c6e63</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-13T10:03:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of https://github.com/3dem/relion-devel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/4f8a14346062f010e02f35e320621d2024117ca7">4f8a1434</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-14T22:02:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: supported a new multiplicative gain reference (.gain)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/369d5cdb1a96f44b572161d16c9144e3ccc42361">369d5cdb</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-14T22:03:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into eer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/814fe00f1f374733815078d4faa4ec342ab80a60">814fe00f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-15T18:42:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_movie_reconstruct: moved error checking so that command line help can be displayed.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/bf3bc803996750784fa2f2ebe9e83583714cfbd2">bf3bc803</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-17T11:07:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Catch2: repair paths
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/718f9a3536474c16e11dd8270f4a521e7036f533">718f9a35</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-17T11:09:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'catch'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/be3c4a45ee1b33aca13dcac45120ecf9c84c6cb1">be3c4a45</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-17T11:11:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'eer'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/042db62fb4aebd14b0ba25aded924e30936f0573">042db62f</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-17T11:13:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">EER: merged EER support, updated README
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/e36e5163ee3debcbd65160663998301f0b9c15b6">e36e5163</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-17T12:28:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into devel-nvidia-optim3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/11739a115efbf3df12cb791a790a760408811296">11739a11</a></strong>
<div>
<span>by Alexey Romanenko</span>
<i>at 2020-07-17T12:29:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">FIX: pad 1 case. redundant multiplication by variable size
Signed-off-by: Takanori Nakane <nakane.t@gmail.com>
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/51a98f10a0f4cd870f86d9f65ae94d66370e946b">51a98f10</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-23T10:15:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extract: suppress a false warning about missing columns in the first micrograph
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/7c0ddf7d663c9725a55eb97d4e36dd902e9eeb0a">7c0ddf7d</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-23T10:19:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into devel-nvidia-optim3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/9342737b7318cd4402b60d36f77d9f8b742f3c58">9342737b</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-27T11:06:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">MKLFFT: Use FFTW wrapper header files provided by MKL (solves issue #648. Thanks to @do-jason)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/f0b2941a908e0d3848e2d9808bb36770c601c089">f0b2941a</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-27T12:25:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">RelionIt: Supported EER movies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/902010b02fc3be3bb907d2b755f8e8a91741c093">902010b0</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-27T14:03:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ssnr'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/cfded31c1b911c2b001f9dd61bdb09c8d6f1545c">cfded31c</a></strong>
<div>
<span>by Charles Congdon</span>
<i>at 2020-07-28T15:15:31-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix assignment of xend_z - bug 646
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/05beaae2e20bc91f47299ecdd7cf1f67c7560ae0">05beaae2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-07-31T11:34:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">relion_star_handler --compare: use the right optics group table (issue #651 reported by @frozenfas)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/a96ba957a4cb4783e68203cd40f4149670ea09b6">a96ba957</a></strong>
<div>
<span>by Joaquin Oton</span>
<i>at 2020-08-03T11:13:19+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #649 from 3dem/bug646_fixes
Fix assignment of xend_z - bug 646</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/861e9d092b4fa79ee9c1873588e5d225802f3950">861e9d09</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-08-16T21:11:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use HTTP instead of FTP for FFTW download (GitHub issue #659)
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/87c294c2783afeb6fd2791449aefcefd3b4ea355">87c294c2</a></strong>
<div>
<span>by Takanori Nakane</span>
<i>at 2020-08-16T21:19:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'ver3.1' of https://github.com/3dem/relion
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