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CHANGES.txt
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2.5:
- fix Falcon 4(i) EER case: parse frame rate and gain reference name from xml
- add EF-Falcon camera type
- update cryolo version
- added cmd scripts to parse metadata files
- fix microscope id parsing from mdoc
- remove skip_gridding param (#58)
- set 7x5 patches for Gatan detectors (#59)
2.4:
- upgrade to PyQt6
2.3: fix the crash due to zero wait time in prep scheme
2.2b2: Cryolo script updates:
1) cryolo 1.8+ required
2) input is a star file
3) use scratch SSD for filtered mics
4) use --skip and --write_empty to skip done mics
5) register output in .Nodes for Relion GUI
6) watch mode deprecated
2.2b1: Helical picking mode added
2.1.1:
- Fix: Falcon 4 non-EER movies case now works
2.1:
- Cryolo / LoGpicker added back as an option
- Add input picker model for crYOLO / Topaz
- Watcher mode not tested yet
- fix calculation of number of EER frames
- add 3D steps switch (not used yet)
2.0:
- Relion 4.0 support with the new scheduler, old Schedules removed, Relion 3.x is not supported!
- Topaz / 2D cls selection is now run by Relion
- tif/mrc parsers updated, add EER support
1.1: fix installer
1.0:
- separate mdoc parser, enable bigtiff header parser
- add Cryoassess for 2D cls sorting, use it by default
- create backup_selection.star so that user can see selected 2D classes
- create .gui_projectdir to automatically "start" a new project
- create .gui_manualpickjob.star so that user can visualize picking
- sortcl2d job check for accuracy
- add FEI MRC2 extended header support
- replace Ctffind & Gctf paths by shell vars
- switch off debug for release
- update Scipion template
- update documentation
0.9.10:
- cleanup filtered mics for topaz and cryolo
- add distance arg = half box size (when provided) to cryolo job
- remove wait time
- add a counter to stop preprocess schedule if no new mics after 2 hours
0.9.9:
- add different picker options: cryolo, topaz, logpicker
- add back the boxsize options to GUI
- simplified Schedules: preprocess (3 options) and class2d. No cryolo retraining is used for now.
- add parser tests
0.9.8:
- update Scipion template, fixes for SerialEM option after 0.9.7
- prints job time for external jobs
- fix "wrong" cryolo model, gpu args
- add topaz external job (not ready yet)
- fix save_noDW
- use MPIs for ctffind job
0.9.7:
- set ACL
- move more vars to config file
- major Schedules update for relion 3.1: logpicker replaced by cryolo, cinderella added
- replace symlink by copy for small files
- remove boxsizes and until_ctf options
- speed up recursive file search (replace os.walk by iglob)
- fix gain file detection
- fix wrong mask size
- update README
- add daemon mode
- fix schedules abort/stop
- new deps: emtable, watchdog
0.9.6:
- remove box sizes, replace LoGpicker by cryolo
- big schedules update
- username requirement removed (to be reimplemented)
- minor Qt5 fixes, replace Help button by a tooltip
0.9.5:
- add mrc and bigtiff parsers. Xml metadata is preferred over mrc.
- parsing functions moved to utils/
0.9.4:
- fix pixel size for super-res
0.9.3:
- first version for PyPi
0.9.2:
- Scipion 3 scheduling works, however relion 3.1 is not ready for streaming
- added more parameters to xml parser: VPP options, gun lens, spot size, beam size
- fix "do until ctf"
0.9.1:
- refactored xml parser, now it should not depend on EPU version
- launching Relion schedules in a separate subprocess, return shell immediately
- code clean up
- fix wrong ptcl diameter for preprocess schedule
- remove shell=True to increase security
- initial preparation for scipion 3 workflow
- created SCOPE_DICT, now parser is not LMB-specific
0.9:
- config reorganized
- add user id check
- create Relion project dir username_scope_date_time
- add class2d schedule
0.8:
- fix EPU xml pattern
- add particle size for LogPicker
- calculate box size params based on particle size
- create project path with links to movies
0.7:
- add extra mdoc params
- check if Images-DicsX exists in the path
- remove Help button from GUI window
- add scipion pipeline
- separate schedule setup fro mthe parser
0.6:
- add MTF dict
- add Relion Schedules
0.5:
- separate parser code from GUI
- switch to QWizard
0.4:
- add BigTiff parser
- add gain ref and counting mode detection
- guess folder name with movies