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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.
2021-03-25FussinessThomas White
The FIXMEs have both already been fixed.
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.
2021-03-17CrystFELImageView: Fix zoom limitsThomas White
2021-03-17GUI: Show beam centre more clearly, and optionallyThomas White
2021-03-16CrystFELImageView: Avoid crash when scrolling after image load failureThomas White
2021-03-16get_hkl: Fix logic for loading unit cellThomas White
2021-03-16get_hkl: Add options to export to MTZ and XDSThomas White
2021-03-16Move MTZ and XDS export to libcrystfelThomas White
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
2021-03-12Clean up after mergeThomas White
2021-03-12Merge branch 'pascal/electrons'Thomas White
2021-03-11indexamajig: Use static wavelength from DataTemplate as estimateThomas White
If the geometry file contains a literal wavelength, then let's use it. That's better than nagging the user for a --wavelength-estimate.
2021-03-11indexamajig: Add --max-indexer-threadsThomas White
This is a more general replacement for --pinkIndexer-thread-count.
2021-03-11indexamajig: Remove misleading messageThomas White
Spectrum file is currently not supported at all. Maybe later.
2021-03-11PinkIndexer: Remove custom indexing checksThomas White
These conflict badly with CrystFEL's own checks, creating a horrible user and developer experience. Later, if we want to handle wide bandwidth beams, we will improve the central CrystFEL checks to support it.
2021-03-11detgeom_transform_coords: Take an additional detector shiftThomas White
This allows the refined detector position to be used in a lot of places.
2021-03-11setup_indexing: Remove dtemplThomas White
There is absolutely nothing useful that an indexing algorithm can do with the opaque DataTemplate object.
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: Better handling of job cancellation/crashingThomas White
2021-03-04SLURM: Cancel job by calling scancelThomas White
The API for cancelling a job seems to be Complicated. The source code for scancel is nearly a thousand lines long! The API also seems to have just changed. So, let's just run scancel and be done with it.
2021-03-04SLURM: Add one to serial offsetsThomas White
They should start from 1, not 0.
2021-03-04SLURM: Set serial offset for indexamajig jobsThomas White
2021-03-04GUI: When starting indexing, prefix relative filenames with ../Thomas White
2021-03-04read_number_processed: Only look at end of log fileThomas White
2021-03-04SLURM: Clean up some exit pathsThomas White
2021-03-04start_slurm_job: Save the real stderr filenameThomas White
2021-03-04SLURM: Implement indexing progress monitoring for job arraysThomas White
2021-03-03GUI: Submit indexing jobs as job arrays, not individual jobsThomas White
2021-03-03SLURM: Remove unused stuffThomas White
2021-03-03SLURM: Add access to account and feature constraintsThomas White
2021-03-03SLURM: Factorise common options even moreThomas White
2021-03-03Add get_text_or_nullThomas White
2021-03-03SLURM: Factorise widget creation for common backend optionsThomas White
2021-03-02GUI: Add menu item to clear logThomas White
2021-03-02CrystFELImageView: Set limits on zoomingThomas White
2021-03-02GUI: Add tooltips to navigation buttonsThomas White
2021-03-02GUI: Add tooltips for peak search parametersThomas 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: Add lots of tooltipsThomas White
2021-03-01GUI: Reject job names containing path separatorsThomas White
2021-03-01GUI: Fix some command-line options for indexamajigThomas White
2021-03-01GUI: Add history list for random image selectionThomas White
2021-02-26GUI: Automatically generate new job namesThomas White
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