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2021-11-15pair_peaks: Use reciprocal space distance instead of pixel distanceThomas White
The reciprocal space distance limit has been set as one third of the smallest inter-Bragg spacing. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/38
2021-11-15Ensure that crystal doesn't end up with invalid reflist after prediction ↵Thomas White
refinement
2021-10-28Make symmetry operation parser re-entrantThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/1
2021-10-28Add 'mask_panel_edges' to geometry fileThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/27
2021-10-28Add a commentThomas White
2021-10-26Remove detector rail direction altogetherThomas White
This got missed out by accident in the conversion to DataTemplate, but absolutely no-one noticed. In the meantime, my views on how the geometry files should work have changed somewhat. I don't want to maintain the extra complexity here when it isn't even clear that it will eliminate the need to re-refine geometry for each camera length. This commit just takes the rail direction stuff out of the documentation and the geometry file parser. Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/50
2021-10-26create_detgeom: Factorise panel templateThomas White
2021-10-22pair_peaks: Skip reflections if the indices are too largeThomas White
2021-10-22reflection_new: Check indices are not too largeThomas White
Previously, the combination of reflection_new and add_refl_to_list gave a way to side-step the usual check that the indices were not larger than 512. This causes corruption of the RefList, so much be avoided.
2021-10-20Remove unused parameterThomas White
2021-10-20Fix column types for plain MTZ outputThomas White
2021-10-20Add "plain" MTZ file layout, distinct from "Bijvoet" layoutThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/52
2021-10-20Set crystal name in MTZ filesThomas White
When using the GUI, it will be set to the corresponding indexing result name.
2021-10-20Reject geometry file if wavelength isn't specifiedThomas White
2021-10-20image_hdf5_read_peaks_cxi: Make sure array is big enoughThomas White
2021-10-20FussinessThomas White
2021-10-20image_hdf5_read_header_to_cache: Make space for terminatorThomas White
2021-10-20Add a commentThomas White
2021-10-13Make zlib dependency optionalThomas White
2021-10-13Remove NCurses dependencyThomas White
It's only used once, to get background colours for 'indexamajig --int-diag', itself a rarely used feature. The dependency itself seems to cause problems for some people, particularly those not using system libraries for everything. So I think it's better just to remove it, and use ANSI escape codes directly.
2021-09-29Remove old referencesThomas White
2021-09-17Warn if in-memory CBF is attemptedThomas White
2021-09-17Handle headers from in-memory HDF5sThomas White
2021-09-17Handle in-memory HDF5sThomas White
2021-09-17Avoid pointless passing of image/eventThomas White
2021-09-07assplode(): Add some assertionsThomas White
2021-09-07get_equiv: Bail out on error pathThomas White
Error handling is sloppy here.
2021-09-07check_box: Fix type used for sizeofThomas White
2021-09-07TakeTwo: Check for empty observed vector listThomas White
2021-09-07image_hdf5_read_header_to_cache: Remove double free on error pathThomas White
2021-09-07fom_select_reflection_pairs: Keep zeroed intensities in datasetThomas White
Note the re-ordering of tasks, and the removal of 'continue'.
2021-09-07init_fom: Clean up on error pathThomas White
2021-09-07filter_noise_in_panel: Fix panel edge behaviourThomas White
2021-09-07lookup_panel: Check that panel name is not NULLThomas White
2021-09-07load_cell_from_file: Check fgets return value for first lineThomas White
2021-09-03Fix typo and failing tests from previous commitThomas White
2021-09-03Reject geometry file if fs and ss directions are not specifiedThomas White
2021-08-20write_to_xds: Add missing 'S' (!)Thomas White
2021-08-20Mosflm: Add -n option when probingThomas White
2021-08-13Increase threshold for integration warningThomas White
The warning about "XXX reflections couldn't be integrated" is tiresome - it appears for practically every indexed pattern because there are always some reflections that fall in bad regions or at panel edges. This suppresses the warning unless the number of integration failures is more than a quarter of the total number of reflections.
2021-07-23image_hdf5_write: Avoid weird pass-by-referenceThomas White
2021-07-23Add field widths to all sscanf("%s")Thomas White
2021-07-23TakeTwo: Remove unused variablesThomas White
2021-07-23TakeTwo: Avoid potential NULL dereference on error pathThomas White
2021-07-23rtnl_cmp: Don't use rational type for intermediate resultThomas White
See 4fbe2e349908a53032b3f23c2180a46e4f770c92.
2021-07-23FormattingThomas White
2021-07-23do_op/get_matrix_name: Rename shadow variablesThomas White
2021-07-23stream_make_index: Remove unused assignmentThomas White
2021-07-23read_crystal: Remove unused varibalesThomas White
2021-07-23spectrum_get_density_at_k: Switch order of checksThomas White
The old way could potentially read beyond the bounds of the array.
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