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2021-03-31indexamajig: Handle spaces in filename when retrieving ID from queueThomas White
2021-03-31FromFile indexer, stream2sol.py: Add/update copyright commentsThomas White
2021-03-31stream2sol.py: Remove --include-parsThomas White
These are now obsolete, and the distributed version of CrystFEL will choke on them.
2021-03-31stream2sol.py: Remove unused definitionsThomas White
2021-03-31stream2sol.py: Add lattice type, centering and unique axisThomas White
2021-03-31stream2sol.py: Strip trailing whitespaceThomas White
2021-03-31stream2sol.py: Initial importThomas White
2021-03-30GUI: Fail more gracefully if image file is not presentThomas White
With the new header cache, it's possible to operate completely from the stream.
2021-03-30Add header caching layerThomas White
This simultaneously implements --copy-header/--copy-hdf5-field and gives access to metadata (e.g. detector position or wavelength) when loading from a stream with header-specified values.
2021-03-29Add documentation for --harvest-fileThomas White
2021-03-29indexamajig: Don't write harvest file if serial start is >1Thomas White
This will avoid multiple indexamajig processes from overwriting the others' files when running a batch job.
2021-03-26partialator: Add missing comma in JSONThomas White
2021-03-26GUI: Tell indexamajig and partialator to write parameter harvest filesThomas White
2021-03-26GUI: Add missing model parameter for mergingThomas White
Whoops.
2021-03-26partialator: Add --harvest-fileThomas White
2021-03-26indexamajig: Add --harvest-fileThomas White
2021-03-26Add str_integration_methodThomas White
2021-03-26Rearrange 'struct index_args' and remove unused elementsThomas White
"cmfilter" and "integrate_saturated" were unused.
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.
2021-03-25Add detgeom_mean_camera_lengthThomas White
2021-03-25PinkIndexer: fix conversion of detector shiftThomas White
2021-03-25FussinessThomas White
The FIXMEs have both already been fixed.
2021-03-25Avoid updating detector geometry structure during prediction refinementThomas White
This makes the behaviour consistent with the prediction itself, and removes another bit of mutable state.
2021-03-23Use crystal's detector shift during predictionThomas White
Previously, this was handled by updating the detector, but this could easily lead to strange double accounting.
2021-03-23Don't automatically set --no-refine --no-check-peaks with PinkIndexerThomas White
See c876486b for rationale.
2021-03-23CMake: ensure RPATH is always set for libcrystfelThomas White
This helps with finding dependencies installed in non-system locations.
2021-03-23CMake: formatting, use pkg_check_modules instead of pkg_search_moduleThomas White
2021-03-22Allow HDF5 path substitution when there are too many placeholder valuesThomas White
This allows, for example, masks which have fewer % signs in their HDF5 locations than the main data.
2021-03-22FromFile indexer: Fix prototypeThomas White
2021-03-19Merge branch 'tom/fromfile'Thomas White
2021-03-19Update AUTHORS and README.mdThomas White
2021-03-19FromFile indexer: add copyright noticeThomas White
There is presumably an MPSD that also needs to be added.
2021-03-19FromFile indexer: Take account of working directoryThomas White
2021-03-19FromFile indexer: New parser and simplification of codeThomas White
Significant change: the solution file must now come with the lattice type, centering and (if applicable) unique axis information at the end of each line, e.g. 'cI' (cubic I), 'mAb' (monoclinic A, unique axis b).
2021-03-19Fix mode of uthash.hThomas 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
2021-03-17Add missing conversion to pixels for detector_shift_{x,y}Thomas White
2021-03-17Factorise panel in create_detgeomThomas White
2021-03-16CrystFELImageView: Avoid crash when scrolling after image load failureThomas White
2021-03-16Add CONTRIBUTING.mdThomas 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
2021-03-12FromFile indexer: Add skeleton cleanup procedureThomas White
2021-03-12Remove .gitignoreThomas White
2021-03-12FromFile indexer: Update for new event ID in image structureThomas White
2021-03-12FromFile indexer: Remove unnecessary casting/memsetThomas White
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