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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
2020-09-24Generalise get_indexamajig_exe to get_crystfel_exeThomas White
2020-09-24Use cell_print in index_onceThomas White
2020-09-24Use integration radii in GUI indexingThomas White
2020-09-09Show job title in progress barThomas White
2020-09-09GUI: Do "Index this frame" in a temporary folderThomas White
2020-09-08Add integration radii to CrystFELIndexingOptsThomas White
2020-09-08Just use project structure in backendsThomas White
We have to pass the crystfelproject anyway, to add the new results to the list. It seems messy to pass everything else separately, when at this moment the values must be exactly what is in the project structure anyway.
2020-09-07Show cell parameters after "Index this frame"Thomas White
2020-09-07Fix update_peaks logicThomas White
2020-09-04Omit some more arguments if NULLThomas White
2020-09-04Add results from new indexing jobThomas White
2020-09-04Set results selector to "internal" when indexing one patternThomas White
2020-08-31Split up job for submission via SLURMThomas White
2020-08-31GUI: Fix units of tolerancesThomas White
2020-08-31SLURM: Give full path to indexamajig, and set up pathThomas White
2020-08-28Insist on a job nameThomas White
2020-08-27Construct complete command line for indexamajigThomas White
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