[med-svn] [Git][med-team/relion][debian/master] 143 commits: EER: Started working on this project. Frame index OK.
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Oct 19 08:33:16 BST 2021
Andreas Tille pushed to branch debian/master at Debian Med / relion
Commits:
8107cc2d by Takanori Nakane at 2019-07-24T15:46:56+01:00
EER: Started working on this project. Frame index OK.
- - - - -
89e384e1 by Takanori Nakane at 2019-07-25T11:04:00+01:00
EER: RLE unpacking OK.
- - - - -
6ba8fcc4 by Takanori Nakane at 2019-07-30T14:19:07+01:00
EER: Started working on this project. Frame index OK.
- - - - -
635e7e5f by Takanori Nakane at 2019-07-30T14:19:07+01:00
EER: RLE unpacking OK.
- - - - -
5231f4dd by Takanori Nakane at 2019-07-30T14:20:16+01:00
Merge branch 'eer' of https://bitbucket.org/scheres/relion-devel-lmb into eer
- - - - -
948f9693 by Takanori Nakane at 2019-07-31T10:52:57+01:00
EER: render to 8K image. make this into a class.
- - - - -
a5987af2 by Takanori Nakane at 2019-07-31T12:08:31+01:00
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?
- - - - -
c8a31b76 by Takanori Nakane at 2019-07-31T20:49:54+01:00
EER: Use 4K gain. Get defect (cold) pixels from gain. WIP: not very efficient yet...
- - - - -
a920de70 by Takanori Nakane at 2019-08-02T13:00:37+01:00
Merge branch 'master' into eer
- - - - -
2162298e by Takanori Nakane at 2019-08-13T16:36:12+01:00
Merge branch 'master' into eer
- - - - -
089b83b4 by Takanori Nakane at 2019-09-19T10:39:38+01:00
Merge branch 'master' into eer
- - - - -
4d4bf08f by Takanori Nakane at 2019-09-19T14:41:23+01:00
EER: more verbose error messages
- - - - -
7085043d by Takanori Nakane at 2019-09-30T21:08:38+01:00
Merge branch 'master' into eer
- - - - -
4980d657 by Takanori Nakane at 2019-10-16T16:37:53+01:00
Merge branch 'master' into eer
- - - - -
5e5eba3f by Takanori Nakane at 2019-10-19T10:15:57+01:00
EER: Polish EER files with grouping
- - - - -
6211a5ef by Takanori Nakane at 2019-10-19T10:19:03+01:00
Clean clutter
- - - - -
89165e88 by Takanori Nakane at 2019-10-19T10:20:11+01:00
Merge branch 'master' into eer
- - - - -
3d8f2ed8 by Takanori Nakane at 2019-10-29T12:49:48+00:00
Merge branch 'master' into eer
Conflicts:
src/exp_model.h
- - - - -
34c1c63a by Takanori Nakane at 2019-10-30T12:49:04+00:00
EER: --eer_grouping as a command line argument
- - - - -
b74f8b37 by Takanori Nakane at 2019-11-02T21:23:03+00:00
Polish: remove debug output
- - - - -
b272ac9b by Takanori Nakane at 2019-11-02T21:23:47+00:00
Merge branch 'master' into eer
- - - - -
9eb0d5fa by Takanori Nakane at 2019-11-04T14:37:04+00:00
EER: added --eer_upsampling
- - - - -
a700e902 by Takanori Nakane at 2019-11-18T12:18:07+00:00
TIFF: made write_tiff_one_page public.
- - - - -
2ea85beb by Takanori Nakane at 2019-11-18T12:18:47+00:00
Merge branch 'master' into eer
- - - - -
5d9df9d1 by Takanori Nakane at 2019-11-18T12:31:54+00:00
EER: made renderFrames templated
- - - - -
60bc1ea5 by Takanori Nakane at 2019-11-18T17:19:44+00:00
EER: better error message
- - - - -
adc2e44d by Takanori Nakane at 2019-12-03T14:21:35+00:00
Merge branch 'master' into eer
Conflicts:
src/tiff_converter.cpp
src/tiff_converter.h
- - - - -
25ab48b2 by Takanori Nakane at 2019-12-03T15:16:52+00:00
EER: supported TIFF container. New program relion_eer_to_tiff.
- - - - -
34bbef39 by Takanori Nakane at 2019-12-06T22:27:12+00:00
EER: supported lazy reading for TIFF
- - - - -
62115881 by Takanori Nakane at 2019-12-11T17:13:00+00:00
Merge branch 'master' into eer
- - - - -
45ed9433 by Takanori Nakane at 2019-12-11T21:45:00+00:00
Merge branch 'master' into eer
- - - - -
02d72a1a by Takanori Nakane at 2019-12-12T14:00:44+00:00
Merge branch 'master' into eer
- - - - -
7c3f19a3 by Takanori Nakane at 2019-12-12T14:54:42+00:00
EER: repaired gain handling (4K gain into 8K was fine)
- - - - -
58b000f9 by Takanori Nakane at 2019-12-12T17:02:44+00:00
Merge branch 'master' into eer
- - - - -
e997ec58 by Takanori Nakane at 2019-12-13T20:06:19+00:00
Merge branch 'master' into eer
- - - - -
c5eae36c by Takanori Nakane at 2019-12-16T16:48:22+00:00
Merge branch 'master' into eer
- - - - -
56b1d8dd by Takanori Nakane at 2019-12-31T12:01:27+00:00
Merge branch 'master' into eer
- - - - -
b69d089a by Takanori Nakane at 2020-01-31T12:57:04+00:00
Merge branch 'master' into eer
- - - - -
3925968d by Takanori Nakane at 2020-02-03T15:53:50+00:00
Merge branch 'master' into eer
- - - - -
65a24b63 by Takanori Nakane at 2020-02-19T11:18:08+00:00
Merge branch 'master' into eer
- - - - -
389b9412 by Takanori Nakane at 2020-02-20T11:37:42+00:00
Merge branch 'master' into eer
- - - - -
cd31c098 by Takanori Nakane at 2020-02-25T17:25:58+00:00
EER: Supported 7-bit no-waste format (not-optimised yet)
- - - - -
8f9b1cfb by Takanori Nakane at 2020-02-25T20:59:38+00:00
EER: Optimised 7bit RLE processing
- - - - -
1840ba08 by Takanori Nakane at 2020-02-25T21:26:15+00:00
EER: Unroll loop by 2
- - - - -
abac0973 by Takanori Nakane at 2020-02-25T21:26:49+00:00
Merge branch 'nv-optim-datatransfer' into eer
- - - - -
69dfddea by Takanori Nakane at 2020-02-26T14:36:35+00:00
Merge branch 'master' into eer
- - - - -
6d94aeac by Takanori Nakane at 2020-02-26T15:09:08+00:00
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).
- - - - -
05673168 by Takanori Nakane at 2020-02-26T15:45:02+00:00
relion_eer_to_tiff: repaired --eer_upsamling
- - - - -
3c61cbc8 by Takanori Nakane at 2020-02-28T23:11:25+00:00
Merge branch 'master' into eer
- - - - -
9b82601a by Takanori Nakane at 2020-02-29T18:17:10+00:00
EER: repaired many problems introduced in 6d94aeac. TODO: resampling/regrouping
- - - - -
537c8cab by Takanori Nakane at 2020-03-06T16:48:00+00:00
Merge branch 'master' into eer
- - - - -
b3e8f84c by Takanori Nakane at 2020-03-09T17:49:09+00:00
Merge branch 'master' into eer
- - - - -
35b70f0a by Alexey Romanenko at 2020-03-15T09:06:42-07:00
griddingCorrect from Projector is on GPU now
- - - - -
58e358b7 by Alexey Romanenko at 2020-03-15T09:06:42-07:00
pad translation part for Projector is on GPU now
- - - - -
6410c1e3 by Alexey Romanenko at 2020-03-15T09:06:42-07:00
centerFFTbySign for Projector is on GPU
- - - - -
6e58ec03 by Alexey Romanenko at 2020-03-15T09:06:42-07:00
calcPowerSpectrum for Projector is on GPU
- - - - -
b1c559a5 by Alexey Romanenko at 2020-03-15T09:06:42-07:00
updatePowerSpectrum for Projector is on GPU
- - - - -
22ca0ccb by Alexey Romanenko at 2020-03-15T09:06:42-07:00
Fix: use GPU only if --gpu arg was passwd
- - - - -
2da34eb8 by Takanori Nakane at 2020-03-19T17:36:54+00:00
EER: remove unused global variables.
- - - - -
8040f82f by Sjors Scheres at 2020-03-20T15:31:01+00:00
implemented option to calculate spectra SNR of individual images
- - - - -
cdc0ad29 by Sjors Scheres at 2020-03-20T15:40:18+00:00
Merged in master (pull request #31)
Subtract job wasn't taking additional arguments
- - - - -
13098d61 by Takanori Nakane at 2020-03-20T15:51:41+00:00
Some code commenting.
- - - - -
ac497e02 by Takanori Nakane at 2020-03-30T09:50:35+01:00
Merge branch 'master' into eer
- - - - -
24c6d475 by Takanori Nakane at 2020-03-31T10:16:34+01:00
Relair --eer_upsampling in motion correction
- - - - -
f538f77b by Takanori Nakane at 2020-03-31T16:40:13+01:00
EER: show a broken file name
- - - - -
a7025168 by Takanori Nakane at 2020-04-13T17:54:59+01:00
Merge branch 'master' into eer
- - - - -
4082167d by Takanori Nakane at 2020-04-16T17:24:48+01:00
Merge branch 'master' into eer
- - - - -
d3692a44 by Takanori Nakane at 2020-04-17T11:05:32+01:00
Added relion_movie_reconstruct
- - - - -
934e5f21 by Takanori Nakane at 2020-04-17T13:03:12+01:00
movie_reconstruct: get movie file names from motioncorr STAR file
- - - - -
8a679f07 by Takanori Nakane at 2020-04-17T14:16:32+01:00
movie_reconstruct: mark as a test program; use Micrograph class to get more information
- - - - -
cebc37b4 by Takanori Nakane at 2020-04-17T17:33:01+01:00
movie_reconstruct: use threads for half sets to avoid reading movies twice. EER is still broken.
- - - - -
1187d255 by Takanori Nakane at 2020-04-17T21:47:06+01:00
EER: silence libtiff warnings for private tags
- - - - -
02b7e7fa by Takanori Nakane at 2020-04-17T22:56:32+01:00
movie_reconstructor: EER also works
- - - - -
4e6207c6 by Takanori Nakane at 2020-04-18T22:38:05+01:00
movie_reconstruct: allow changing EER grouping
- - - - -
36482787 by Takanori Nakane at 2020-04-20T11:04:22+01:00
Merge branch 'master' into eer
- - - - -
aec1835d by Takanori Nakane at 2020-04-25T21:58:31+01:00
movie_reconstruct: added --no_barcode
- - - - -
6537fb05 by biochem_fan at 2020-04-30T15:27:51+01:00
EER: Updated README
- - - - -
63effd75 by biochem_fan at 2020-05-01T09:26:54+01:00
Further updates of README for EER
- - - - -
82e4cb9e by Takanori Nakane at 2020-05-02T06:39:33+01:00
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.
- - - - -
f7b6f081 by Takanori Nakane at 2020-05-02T06:41:16+01:00
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.
- - - - -
6c04dd8a by Takanori Nakane at 2020-05-02T06:43:35+01:00
EER: Tentative 16K rendering support (only for debugging, not for MotionCorr or Polish)
- - - - -
425abb87 by Takanori Nakane at 2020-05-02T06:46:22+01:00
Merge remote-tracking branch 'origin/devel-eer' into eer
- - - - -
e069e159 by Takanori Nakane at 2020-05-02T06:47:11+01:00
State that relion_eer_to_tiff might be merged into relion_convert_to_tiff
- - - - -
dd89b519 by Takanori Nakane at 2020-05-02T09:40:43+01:00
EER: added disclaimer
- - - - -
92bb8af9 by Takanori Nakane at 2020-05-02T20:53:19+01:00
EER: Repair 16K rendering
- - - - -
fa3eef66 by Takanori Nakane at 2020-05-03T06:19:05+01:00
EER: Further fix for 16K rendering
- - - - -
6b66e814 by Takanori Nakane at 2020-05-06T18:37:00+01:00
Merge branch 'master' into eer
- - - - -
c1ab9cb5 by Takanori Nakane at 2020-05-24T11:36:09+01:00
Merge branch 'master' into eer
- - - - -
200e5562 by Takanori Nakane at 2020-05-29T15:13:40+01:00
Merge branch 'master' into eer
- - - - -
06ed5598 by biochem_fan at 2020-06-01T12:09:18+01:00
Merge pull request #588 from arom4github/optim3
PORT: Expectation setup to GPU
- - - - -
474e802d by Alexey Romanenko at 2020-06-01T14:30:47+01:00
FIX: add the check of Compute capability >= 6.0 to use AtomicAdd for double datatype
Signed-off-by: Takanori Nakane <nakane.t at gmail.com>
- - - - -
1fbba73c by Alexey Romanenko at 2020-06-02T10:30:01+01:00
FIX: do not use CudaCuctomAllocator if no GPU available
Signed-off-by: Takanori Nakane <nakane.t at gmail.com>
- - - - -
f1714b22 by Alexey Romanenko at 2020-06-02T22:07:10+01:00
FIX: for 2D reconstruction
Signed-off-by: Takanori Nakane <nakane.t at gmail.com>
- - - - -
a1940250 by Takanori Nakane at 2020-06-19T20:55:04+01:00
Merge branch 'master' into eer
- - - - -
d12c4f8f by Dari Kimanius at 2020-06-23T18:51:47+01:00
First attempt at support for Catch2. Configure with -DBUILD_TESTS=ON Fails at link time.
- - - - -
37f6dc7f by Takanori Nakane at 2020-06-24T21:02:53+01:00
Merge branch 'master' into eer
- - - - -
f6696979 by Takanori Nakane at 2020-06-26T12:31:43+01:00
Merge branch 'master' into eer
- - - - -
f13a91cd by Takanori Nakane at 2020-06-27T07:38:38+01:00
Merge branch 'master' into eer
- - - - -
31cbf51e by Takanori Nakane at 2020-06-30T14:34:00+01:00
Remove relion_eer_to_tiff and merge its functionalities to relion_convert_to_tiff
- - - - -
75940328 by Takanori Nakane at 2020-07-02T11:53:48+01:00
relion_estimate_gain: support the EER format
- - - - -
93a0aae8 by Takanori Nakane at 2020-07-03T14:25:04+01:00
Merge branch 'master' into eer
Conflicts:
README.md
- - - - -
f8f172d7 by Dari Kimanius at 2020-07-06T11:33:23+01:00
Merge branch 'master' into catch
- - - - -
7796d495 by Dari Kimanius at 2020-07-06T11:50:17+01:00
Tests pass
- - - - -
d50caf12 by Takanori Nakane at 2020-07-07T14:37:21+01:00
relion_convert_to_tiff: supported conversion of an EER gain reference
- - - - -
dd9ebf75 by Takanori Nakane at 2020-07-07T21:11:12+01:00
MlModel: Fixed units in the message (reported by Li Jun at CCPEM)
- - - - -
0ab9f919 by Takanori Nakane at 2020-07-09T14:55:09+01:00
Subtract: show an error when subtracting a non-existing class
- - - - -
ea89a137 by Takanori Nakane at 2020-07-10T10:39:57+01:00
Merge branch 'master' into eer
- - - - -
6c4c67cc by Takanori Nakane at 2020-07-10T10:40:35+01:00
Added eer_trajectory_handler.py
- - - - -
021ce550 by Takanori Nakane at 2020-07-10T12:40:40+01:00
Moved instructions to wiki.
- - - - -
72f7837f by Takanori Nakane at 2020-07-12T11:24:15+01:00
MotionCorr: check for a non-existing defect file
- - - - -
2cae347e by Takanori Nakane at 2020-07-12T21:07:47+01:00
Merge branch 'master' into eer
- - - - -
2f7ac4a8 by Alexey Romanenko at 2020-07-13T07:00:34+01:00
FIX: run_calcPowerSpectrum now works for 2D reconstruction
Signed-off-by: Takanori Nakane <nakane.t at gmail.com>
- - - - -
fd0190ce by Takanori Nakane at 2020-07-13T07:00:53+01:00
Merge branch 'master' into devel-nvidia-optim3
- - - - -
68b33216 by Takanori Nakane at 2020-07-13T09:52:25+01:00
Merge branch 'eer' into devel-nvidia-optim3
- - - - -
d7788499 by Sjors Scheres at 2020-07-13T09:54:53+01:00
changed save_ps and save_noDW to do_save_xxx to avoid conflict with reserved words in STAR format
- - - - -
720c6e63 by Takanori Nakane at 2020-07-13T10:03:33+01:00
Merge branch 'master' of https://github.com/3dem/relion-devel
- - - - -
4f8a1434 by Takanori Nakane at 2020-07-14T22:02:50+01:00
EER: supported a new multiplicative gain reference (.gain)
- - - - -
369d5cdb by Takanori Nakane at 2020-07-14T22:03:25+01:00
Merge branch 'master' into eer
- - - - -
814fe00f by Takanori Nakane at 2020-07-15T18:42:49+01:00
relion_movie_reconstruct: moved error checking so that command line help can be displayed.
- - - - -
bf3bc803 by Takanori Nakane at 2020-07-17T11:07:52+01:00
Catch2: repair paths
- - - - -
718f9a35 by Takanori Nakane at 2020-07-17T11:09:24+01:00
Merge branch 'catch'
- - - - -
be3c4a45 by Takanori Nakane at 2020-07-17T11:11:45+01:00
Merge branch 'eer'
- - - - -
042db62f by Takanori Nakane at 2020-07-17T11:13:57+01:00
EER: merged EER support, updated README
- - - - -
e36e5163 by Takanori Nakane at 2020-07-17T12:28:58+01:00
Merge branch 'master' into devel-nvidia-optim3
- - - - -
11739a11 by Alexey Romanenko at 2020-07-17T12:29:31+01:00
FIX: pad 1 case. redundant multiplication by variable size
Signed-off-by: Takanori Nakane <nakane.t at gmail.com>
- - - - -
51a98f10 by Takanori Nakane at 2020-07-23T10:15:47+01:00
Extract: suppress a false warning about missing columns in the first micrograph
- - - - -
7c0ddf7d by Takanori Nakane at 2020-07-23T10:19:21+01:00
Merge branch 'master' into devel-nvidia-optim3
- - - - -
9342737b by Takanori Nakane at 2020-07-27T11:06:30+01:00
MKLFFT: Use FFTW wrapper header files provided by MKL (solves issue #648. Thanks to @do-jason)
- - - - -
f0b2941a by Takanori Nakane at 2020-07-27T12:25:20+01:00
RelionIt: Supported EER movies
- - - - -
902010b0 by Takanori Nakane at 2020-07-27T14:03:00+01:00
Merge branch 'ssnr'
- - - - -
cfded31c by Charles Congdon at 2020-07-28T15:15:31-07:00
Fix assignment of xend_z - bug 646
- - - - -
05beaae2 by Takanori Nakane at 2020-07-31T11:34:11+01:00
relion_star_handler --compare: use the right optics group table (issue #651 reported by @frozenfas)
- - - - -
a96ba957 by Joaquin Oton at 2020-08-03T11:13:19+01:00
Merge pull request #649 from 3dem/bug646_fixes
Fix assignment of xend_z - bug 646
- - - - -
861e9d09 by Takanori Nakane at 2020-08-16T21:11:47+01:00
Use HTTP instead of FTP for FFTW download (GitHub issue #659)
- - - - -
87c294c2 by Takanori Nakane at 2020-08-16T21:19:27+01:00
Merge branch 'ver3.1' of https://github.com/3dem/relion
- - - - -
dd8a645d by Andreas Tille at 2021-10-19T09:15:38+02:00
Fix watchfile to detect new versions on github
- - - - -
60e463dd by Andreas Tille at 2021-10-19T09:15:41+02:00
New upstream version 3.1.3
- - - - -
6b67e20f by Andreas Tille at 2021-10-19T09:15:41+02:00
routine-update: New upstream version
- - - - -
0ffc8a50 by Andreas Tille at 2021-10-19T09:15:50+02:00
Update upstream source from tag 'upstream/3.1.3'
Update to upstream version '3.1.3'
with Debian dir 55ffbad5f6d2424114e72ae1cd2fa11a793da60f
- - - - -
1a1dd1d8 by Andreas Tille at 2021-10-19T09:15:51+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
55e3a943 by Andreas Tille at 2021-10-19T09:15:59+02:00
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
- - - - -
5719019d by Andreas Tille at 2021-10-19T09:27:02+02:00
routine-update: Ready to upload to unstable
- - - - -
adf20d47 by Andreas Tille at 2021-10-19T09:31:32+02:00
Mark autopkgtest superficial
- - - - -
30 changed files:
- .github/ISSUE_TEMPLATE/bug_report.md
- .gitignore
- CMakeLists.txt
- README.md
- cmake/BuildFFTW.cmake
- cmake/FindTBB.cmake
- + data/mtf_falcon4EC_200kV.star
- + data/mtf_falcon4EC_300kV.star
- debian/changelog
- debian/control
- debian/relion-gui.lintian-overrides
- debian/relion.lintian-overrides
- debian/tests/control
- debian/watch
- + scripts/eer_trajectory_handler.py
- scripts/relion_it.py
- scripts/star_printtable
- src/acc/acc_helper_functions_impl.h
- src/acc/acc_ml_optimiser_impl.h
- src/acc/acc_projectorkernel_impl.h
- src/acc/cpu/cpu_backprojector.cpp
- src/acc/cpu/cpu_kernels/BP.h
- src/acc/cpu/cpu_kernels/cpu_utils.h
- src/acc/cpu/cpu_kernels/diff2.h
- src/acc/cpu/cpu_kernels/helper.cpp
- src/acc/cpu/cpu_kernels/helper.h
- src/acc/cpu/cpu_kernels/wavg.h
- src/acc/cpu/cpu_settings.h
- src/acc/cuda/cuda_autopicker.cu
- src/acc/cuda/cuda_kernels/helper.cu
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/1ad57bcedfa2eeb945cb9fa59ff62084ab6dd375...adf20d4783e1dd46d66bb118e54d951dbf8c8231
--
View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/1ad57bcedfa2eeb945cb9fa59ff62084ab6dd375...adf20d4783e1dd46d66bb118e54d951dbf8c8231
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20211019/aadc4d36/attachment-0001.htm>
More information about the debian-med-commit
mailing list