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<h3>
Andreas Tille pushed to branch debian/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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>
</div>
<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>
</li>
<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>
</li>
<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
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/dd8a645d73f1f4474c9f1179979e294bc98efe9d">dd8a645d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-19T09:15:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/60e463ddc58366b37c7c0480847c0d4b45dcb0c0">60e463dd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-19T09:15:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.1.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/6b67e20f4c1a4bbfb4d886ef7d57bc01f0eef67a">6b67e20f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-19T09:15:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/0ffc8a50d20036705282a3a43100028c30957265">0ffc8a50</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-19T09:15:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.1.3'
Update to upstream version '3.1.3'
with Debian dir 55ffbad5f6d2424114e72ae1cd2fa11a793da60f</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/1a1dd1d895b4c058458be64b65599445d681c41a">1a1dd1d8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-19T09:15:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/55e3a94318aa133e6fa262bb0578f5eea5ac39a1">55e3a943</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-19T09:15:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update renamed lintian tag names in lintian overrides.
Changes-By: lintian-brush
Fixes: lintian: renamed-tag
See-also: https://lintian.debian.org/tags/renamed-tag.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/5719019d822a62af7050000efda053f10969805a">5719019d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-19T09:27:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/relion/-/commit/adf20d4783e1dd46d66bb118e54d951dbf8c8231">adf20d47</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-19T09:31:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mark autopkgtest superficial
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a03585ab89eed5e0782a1875b2d8153b97865d30">
.github/ISSUE_TEMPLATE/bug_report.md
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debian/relion.lintian-overrides
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debian/tests/control
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<a href="#9f30c487d15cf5353b187b18d93b063d33818514">
scripts/star_printtable
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<a href="#704afb9f7333d43fac8dbee3524b4eb9cf64d485">
src/acc/acc_helper_functions_impl.h
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<a href="#1e4a7eaa6f598d062440e9b744df85bd731be743">
src/acc/acc_ml_optimiser_impl.h
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<a href="#21639b9a83fd6fc498123a6dfcfa73cc4b1a45bd">
src/acc/acc_projectorkernel_impl.h
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<a href="#aacfe8dc157dabf0dabcab2cd532b9fe37b3cc7f">
src/acc/cpu/cpu_backprojector.cpp
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<a href="#e423b89cdff3f9e90f4cdc3365229a935e24c5c0">
src/acc/cpu/cpu_kernels/BP.h
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<a href="#14c8758986a70989ff6b53c27b98d38afd763817">
src/acc/cpu/cpu_kernels/cpu_utils.h
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<a href="#ddfd627b733e472a04e82891632f2a65565fd380">
src/acc/cpu/cpu_kernels/diff2.h
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<a href="#6408054ff30eff344464c45cef273ce5c89f3a2b">
src/acc/cpu/cpu_kernels/helper.cpp
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<a href="#f458fff7121f4a35e72022ed5b62d2bc1ac11517">
src/acc/cpu/cpu_kernels/helper.h
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<a href="#e361044ce9ff2f651be3c90ff21c417e3073d62f">
src/acc/cpu/cpu_kernels/wavg.h
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<a href="#34b974592fc5c1c7d0a7d6b24c7ffc42645355ff">
src/acc/cpu/cpu_settings.h
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<a href="#ee02b9bcbad9b4f809b05f2939a07308be5aafc9">
src/acc/cuda/cuda_autopicker.cu
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<a href="#86f1ff8ec6ae8efaf139ffaa712788c909f5010a">
src/acc/cuda/cuda_kernels/helper.cu
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</ul>
<h5>The diff was not included because it is too large.</h5>
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