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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
2021-03-12GUI: Add NULL filename for FromFile indexing (which isn't used here)Thomas White
2021-03-12FromFile indexer: Remove getcwd()Thomas White
It's only used for some error messages, and it doesn't compile anyway.
2021-03-12FromFile indexer: Remove update_detectorThomas White
Everything should use the per-crystal detector shift now.
2021-03-12FromFile indexer: Add missing semicolonsThomas White
2021-03-12FromFile indexer: Strip trailing whitespace and sort out formattingThomas White
2021-03-12Clean up after mergeThomas White
2021-03-12FromFile indexer: Move to libcrystfel/src/indexersThomas White
Also adds to meson.build
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.
2021-03-11Add some warningsThomas White
2021-03-11indexamajig(1): Fix formatting and spellingThomas White
2021-03-11indexamajig: Add --max-indexer-threadsThomas White
This is a more general replacement for --pinkIndexer-thread-count.
2021-03-11PinkIndexer: Allocate peak lists when indexingThomas White
There doesn't seem to be any point in allocating them earlier, except to make space for some nice bugs.
2021-03-11PinkIndexer: Remove unnecessary castThomas White
2021-03-11indexamajig: Remove misleading messageThomas White
Spectrum file is currently not supported at all. Maybe later.
2021-03-11PinkIndexer: Remove wide bandwidth stuffThomas White
This will return later in a more centralised form, if we decide to work further on wide bandwidth.
2021-03-11PinkIndexer: Use fake camera length for detector refinementThomas White
... and calculate the real value afterwards, checking that the detector is really flat enough for it to work.
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.
2021-03-11Re-enable PinkIndexerThomas White
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.
2021-03-11Update copyright dates in libcrystfel/src/indexersThomas White
2021-03-11PinkIndexer: Don't use ImageFeature->rx,ry,rzThomas White
This brings it up to date after e7cf3911104f.
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