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CHANGES.txt
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5.0.2:
- add a test for DynaMight protocol
5.0.1: bug fix for export coordinates from subparticles (close #428)
5.0.0:
- add Relion 5.0 support, removed 3.x support
- fix gpu param value
- float16=True by default
- several fixes in the viewers
- import coordinates protocol moved to the pwem core pligin
- bugfix for finding optimiser file after gentle project cleaning
- new protocol: DynaMight flexibility
- gain estimation protocol refactored, test added
- close #391, #396
- postprocess protocol accepts a volume with associated half-maps
- scratch folder can now be custom or from Scipion config
- fix bug when saving classes from intermediate iterations
4.0.20: fix FSC viewer: Do not show empty figure when closing.
4.0.19: fix adding more coords to the output of import coords protocol
4.0.18: add ewald params to the reconstruct protocol
4.0.17: add missing CUDA_BIN env var
4.0.16: Remove direct pointer from class3d protocol
4.0.15: Extending the conversion of incompatibles formats (Yunior)
4.0.14: 2D class ranker improvements (JMRT)
- Generated outputParticles
- outputClasses now have rlnEstimatedResolution and rlnPredictedClassScore attributes
- Improved summary using summaryVar and handling when no output
- Added viewer for RelionSelect2DClasses
4.0.13: fix relion-python env for 2D class ranker, requires a specific pytorch version
4.0.12:
- remove reading optimiser file during particles import (fix #373)
4.0.11:
- fixed the bug calling system python instead of conda env's one in relion class selection protocol
4.0.10:
- allow to force assign a single optics group to a multi-group input
- in the protocol Classify2D when defining the output Classes, particles should be assigned with an indirect pointer to avoid problems when running workflows on streaming and unattended.
- in the protocol Extract particles the boxsize validator (positive) prevented the protocol from executing when an inputPointer was used to fill this parameter.
- relion 3.1 removed from the installer
- add missing _pathVars to Plugin class
4.0.9: fix output pixel size in the resize volume protocol
4.0.8: better integration with sidesplitter plugin
4.0.7: fix typo in half2 output name from multi-body protocol
4.0.6:
- add possible outputs class
- fake a mask to bypass Relion multi-body bug
- add continue mode for multi-body
- output particle set from multi-body
- subtract protocol supports mukti-body input
4.0.5.1: hotfix for multi-body protocol
4.0.5: hotfix for GPU parameters
4.0.4:
- removed RELION_PYTHON, replaced by conda env variable RELION_ENV_ACTIVATION
- update citations
- fix parsing of pixel size upon import
- fix wrong kwarg name useBaseName which caused ignoring micnames in export protocols
- fix assign optics when some mics are missing (@delarosatrevin)
4.0.3:
- allowPointers for box size related parameters
- new protocol: import coordinates from a particles star file
- remove :mrc postfix from volume names if possible
4.0.2: minor fix for auto-picking ref-based protocol
4.0.1:
- Postprocessing now supports half maps input
- emtable requirement updated
- close #325 by providing some column types to particle Tables
4.0:
- Relion 4.0 support:
- download sources from github
- all protocols updated with new args / params
- new 2D class ranker protocol (test still missing)
- new env var RELION_PYTHON for Python with Torch & Numpy modules (required for the protocol above)
- separate initial model protocol for 4.0 (3.x is incompatible)
- float16 option disabled
- EER enabled, needs more testing
- BUGFIX: wrong shifts were saved in motioncor when skipping frames
- rlnMicrographStartFrame is saved in optics for mc output movies
- Multi-body protocol improvements, viewer added
- Postprocessing now supports multi-body input
3.1.3: fix ref volume conversion for non-mrc files
3.1.2:
- allow to use Environ.setPrepend (depends on scipion-em/scipion-pyworkflow#238) to set different prepend commands (e.g when optimized CPU module is available)
- fixes for subtract no relion protocol
- fix #294, #296
3.1.1 - fixed the bug causing wrong shifts saved by init model and subtract protocols
3.1:
- initial EER support for motion correction and polishing, not available yet
- consider hot pixels from relion mc for polishing
- refactor mc protocol and viewer
- replace xmipp by eman2 for psd calculation
- add 3.1.2 binary
- remove Relion 3.0 protocols and code, but users can still import old star files
- fix #278, #274, #277, #257
- add a test to read old star format
- fix shifts conversion for pre-3.1 (origins are in px already)
- fix accuracy label, use Angstroms by default
- add a warning about polishing gain bug
- subtract protocol supports non-Relion input (thanks @rmarabini)
- add a protocol to "gentle clean" all Relion jobs
3.0.4: bugfix for the missing option "Consider alignment as priors" (reported by Serban Ilca)
3.0.3: another bugfix in assign optics: abs paths are not allowed by Relion
3.0.2: bugfix for the wrong gain transform parameters in assign optics protocol
3.0.1:
- quick fixes for issues from PR #282, #283 (thanks to @rmarabini)
3.0.0:
- Scipion 3.0.0 support, migration to python 3
- GPLv2 to v3
- Add Relion 3.1 support, remove relion 2.x support
- New STAR file parser (emtable package)
- New protocol to assign optics groups
- Sort protocol will be deleted soon (gone in relion 3.1)
- Extract particle movies is gone
- Updated drift plot for motioncor, added new plot for drift per frame
- convertMask changed so that it uses relion_image_handler to change box/pix size/threshold
- movie refinement is gone and fully replaced by bayesian polishing
- picker protocols code cleanup
- get rid of shell=true in subprocess
- refactor viewers code
- xmipp metadata is gradually replaced by the Table class from new star file parser
- new protocol to export coordinates to star format
- new protocol to remove preferential views
- new protocol to compress movies
- new protocol to resize / rescale volume
- add new Falcon 4 MTFs
- updated extra labels list for particles
- set PARTICLE_EXTRA_LABELS inside ClassesLoader and refine3d _updateParticle
- fill random subset by default
- Autoscale input vol refs with relion not xmipp
- Add missing ProtRelionExportParticles to protocol tree
- Fix default values for missing extra ctf attrs
- Use abs paths when creating symlinks
- Add warning about dm4 gain flip by xmipp
- Optimize imports
- Assign gain and defects file from input or star file, transform gain if required
- use getVar for cuda vars
- update optics from image set upon conversion
- fix wrong MicrographOriginalPixelSize
- update priors help
- add PSD calculation for mc
- add missing frame grouping param for mc
- picking wizards removed
- optimize mode removed in relion reference-based picker
- fix --odir param for pickers
- add min_avg_noise to picker
- add skip_gridding to 3d jobs (True by default)
- add missing flatten_solvent to init3d
- remove unrequired params from polishing
- add RELION_CUDA_LIB var
- Hide Allow coarser sampling if doing no alignments
- Hide some args in continue mode for classification/refinement/init model protocols
- Fix healpix arg for autopicking, add missing ctf param
- Fixed matching between particles and movies by using micName in polishing
- Fixed generation of the local motion table when needed (e.g when only some movies failed to align)
- Allowed to display ctf-refinement results with matplotlib (still need to find the proper color map)
- Fixed function splitCTFGroups, now replaced with class DefocusGroups and not using Xmipp metadata
- Now use proper pixelSize label depending on input set
- Remove failing reconstruct rot-shift-flip test as we don't support flip in 3D
- add the colorScale wizard to the LocalRes viewer
- chimeraX support
1.0.9: Fixed multibody output bug. Added a test for it.
1.0.8:
- Fixed bug when creating symbolic links from binaries with different root
- Fixed a few visualization issues from Relion - initial volume viewer
- Fixed dose-weighting bug when no dose was provided
- Fixed wrong pixsize in particle extraction
- Fixed polishing bug to ignore particles from missing movies
1.0.7: Add missing MTF files to the pypi plugin
1.0.6: Fix reconstruction and extract ptcls tests
1.0.5:
- wizard for MTF files in post-processing
- fix mask scaling in several protocols
- fix multi-body protocol bugs
- remove unnecessary symlinks
- fix motioncor output
- new test for relion3 protocols
- many small fixes
1.0.4: Fix post-processing test, improvements in ctf refine viewer
1.0.3: Big update for relion3.0 support
1.0.2: Include protocol.conf to create the source distribution
1.0.1:
- add missing protocol for movie ptcl extraction, other small bugfixes
- updated viewers import, added protocols.conf
- remove xmipp3 dependencies
- updated citations
- remove relion 1.4 support
11-September-2018 - Add pip module file