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2022-09-21asdf: Add fast modeAlexandra Tolstikova
This adds an optional fast mode for asdf indexing, which is around 3 times faster with only a few percent lower success rate.
2022-08-26GUI: Refuse to open "Index all frames" without a geometry filenameThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/73
2022-07-06GUI: Invoke programs without pathThomas White
Including the path wasn't working very well. One of the problems is that it prevents the use of a wrapper script for the programs, which is needed for certain environments. This commit just removes the path prefixes altogether.
2022-03-03GUI: Better handling of error-filled indexamajig logsThomas White
If there are lots of error messages (e.g. a missing mask file), looking at the last 4k of the log file is not always enough. Now it will go back to 16k, in steps of 4k. It will stop early if it finds the start of the file, and it will complain if it still doesn't find what it's looking for.
2022-03-03GUI: Use fixed profile radius for indexing onceThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/61
2021-08-16GUI: Avoid crash when trying to index no imageThomas White
2021-07-22GUI: Really use temporary folder for single-shot indexingThomas White
Somehow, I missed out the actual "chdir" call!
2021-07-21Add missing cleanup on error pathsThomas White
2021-07-15pinkindexer_used: Handle methods=NULLThomas White
In this case, return false because PinkIndexer is never in the list of automatically-chosen indexers.
2021-07-15GUI: Run all jobs with same CWD as GUI itselfThomas White
This requires changing all the paths to relative ones. Previously, the jobs ran with their CWDs set to the corresponding "result" folder. The trouble is, this breaks everything that uses a relative location: image filenames, mask/satmap files referenced by the geometry, etc. Note that this change also means that the temporary folders ("indexamajig.XXX") are now produced in the top-level working directory. Eventually, a GUI option should be added to allow these folders to be put somewhere better (i.e. somewhere fast). Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/44
2021-07-14GUI: Add PinkIndexer options to command lineThomas White
2021-07-14GUI: Get/set PinkIndexer optionsThomas White
2021-07-14Make all the indexer-specific option structures non-opaqueThomas White
Making them opaque seemed like a nice idea, because all the indexers could take care of their own command-line arguments. However, it doesn't work at all when indexing is run via the API.
2021-07-12GUI: Add --wavelength-estimate and --camera-length-estimateThomas White
Only when using PinkIndexer. Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/25
2021-04-30GUI: When indexing one frame, don't force results selector or repeat peak searchThomas White
The logic behind forcing the results selector (to "Calculations within GUI") was that anything calculated in the GUI should appear under that selection only. Unfortunately, when loading a stream without images, there is nothing at all to be seen under this selection, not even an image. Forcing the selector resulted in proj->cur_image = NULL and therefore a crash when trying to index based on that. Similarly, the call to update_peaks expected image data, but there is none. In reality, we have a perfectly good image structure with peaks from the stream already. This allows a non-image stream to be "re-indexed" based on the peaks. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/33
2021-04-01GUI: Wrap filenames in job scripts in quotes, where appropriateThomas White
This makes it work when the filenames contain spaces.
2021-03-26GUI: Tell indexamajig and partialator to write parameter harvest filesThomas White
2021-03-25indexamajig: Add --camera-length-estimateThomas White
Unfortunately, PinkIndexer needs the real camera length for its centre refinement. Giving a fake value and scaling the resulting shift does not work - the indexing rate drops with even a small error. Ideally, this would work in the same way as --wavelength-estimate, by using a static value from the geometry file if it's given. However, this is rather complicated to implement because of the way all the units stuff is implemented. Therefore, this is left as an improvement for the future.
2021-03-19Merge branch 'tom/fromfile'Thomas White
2021-03-19FromFile indexer: Option processingThomas White
This give FromFile its own private command-lien option processing, like the other indexers. It removes the ability to auto-generate the solution filename, but I don't think there's a way to do that without breaking abstractions.
2021-03-15GUI: Add interface for --fix-profile-radius and --fix-divergenceThomas White
2021-03-12GUI: Add NULL filename for FromFile indexing (which isn't used here)Thomas White
2021-03-11indexamajig: Add --max-indexer-threadsThomas White
This is a more general replacement for --pinkIndexer-thread-count.
2021-03-11indexamajig: Add --wavelength-estimateThomas White
This is a more sensible non-indexer-specific and non-Xray-specific replacement for --pinkIndexer-override-photon-energy
2021-03-05Mass update of copyright dates in source code commentsThomas White
2021-03-04SLURM: Set serial offset for indexamajig jobsThomas White
2021-03-04read_number_processed: Only look at end of log fileThomas White
2021-03-03GUI: Submit indexing jobs as job arrays, not individual jobsThomas White
2021-03-01GUI: Fix counting of processed frames during indexingThomas White
2021-03-01Local BE: Write a script and run itThomas White
This easily gives us the stdout.log and stderr.log needed for monitoring the job.
2021-03-01GUI: Pass --peak-radius to indexamajigThomas White
Another one missed out before.
2021-03-01GUI: Pass --int-radius to indexamajigThomas White
Whoops - this was missed out before. This also reduces the precision displayed in the dialog box to reflect what is actually passed to indexamajig.
2021-03-01GUI: Fix some command-line options for indexamajigThomas White
2021-02-26GUI: Automatically generate new job namesThomas White
2021-02-26Remove unused variablesThomas White
2021-02-25GUI: Factorise force_{peaks,refls}_onThomas White
This should help avoid them getting out of sync. Again.
2021-02-22Set peak and reflection radii after indexing one patternThomas White
This ensures that the display matches the parameters that were last used.
2021-02-22Fussiness (extreme)Thomas White
2021-02-22Read job progress from written log files, even for local BEThomas White
This simplifies the backends somewhat, and makes them look more similar - e.g. there is now only one routine to find out how far along a merging job is. It has the added bonus of adding a log file for local jobs, which we would've had to add soon anyway.
2021-02-17GUI: Use unified job notes routine for indexingThomas White
Like with merging, this makes the required job name more prominent.
2020-12-11result -> indexing_resultThomas White
Because shortly we will have merging_result as well
2020-12-04GUI: Set wrap mode for "notes" boxThomas White
2020-11-30Move get_crystfel_exe and get_crystfel_path_str to crystfel_gui.cThomas White
2020-11-20Move indexing option tabs to side, and rearrangeThomas White
This seems to give a more compact and logical layout
2020-11-20GUI: Add stream output options including metadata to copyThomas White
2020-10-30Bring common GTK routines into separate fileThomas White
2020-10-26Fix tolerance units in GUIThomas White
2020-10-23new_job -> new_index_jobThomas White
Because we now have new_merge_job as well.
2020-10-07FussinessThomas White
Commented out debug message is no longer relevant
2020-09-24GUI: Pass the real streams for the result to cell_explorerThomas White
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