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2019-03-11Change horribly confusing names of unit cell comparison functionsThomas White
cells_are_similar -> compare_cell_parameters_and_orientation compare_cells -> compare_reindexed_cell_parameters_and_orientation cell_tool.c:cells_the_same -> cellutils.c:compare_cell_parameters All comparisons now done in real space, checking that centering is the same, and without uncentering anything.
2019-03-11Remove cells_are_similar() from APIThomas White
There are two functions with this name. Avoid confusion.
2019-03-11cell_tool: Use libcrystfel cells_are_similar() functionThomas White
2019-03-06indexamajig: Rename --min-gradient to --min-squared-gradientThomas White
The eventual aim of this is to deprecate the "--min-gradient" option, resolving the long-standing confusion about whether this option is the gradient or the squared gradient.
2019-03-01crystal_copy(): Make new copy of notes if non-NULLThomas White
2019-03-01Don't mask out entire image if bad pixel map can't be loadedThomas White
2019-02-08Add a comment to CMakeLists.txtThomas White
2019-01-30Make sure of string length in get_event_string()Thomas White
2019-01-30Re-write get_event_string()Thomas White
2019-01-29Fix some compiler warnings about string handlingThomas White
2019-01-29Fix a couple of memory leaksThomas White
2019-01-29DS9K compatibilityThomas White
2019-01-29Add multi_event_geometry() functionThomas White
2019-01-29Strip out CPU affinity stuffThomas White
This was from an early experiment when we were having performance problems on a big NUMA machine. It didn't help very much back then, and it certainly doesn't help much now. It's not worth maintaining the code or build system needed for this.
2019-01-28Remove #define _GNU_SOURCEThomas White
2019-01-28partialator: Fix multiple memory leaksThomas White
2019-01-24Say what path was being opened when event enumeration failsThomas White
2019-01-22TakeTwo: fix various memory leaksThomas White
2019-01-22Fix some small memory leaksThomas White
2019-01-14clock_gettime isn't needed for libcrystfelThomas White
2019-01-03Use gzclose() instead of gzclose_r()Thomas White
The only downside to this is that the zlib library will be twice the size if statically linked into libcrystfel. Since we don't anticipate much use for static linking, and since the extra space is unlikely to be a serious problem anyway, this seems fine.
2018-12-18make_pixelmap: Use <input>.h5 as default output filenameThomas White
2018-12-04WhitespaceThomas White
2018-11-27xds: Tune indexing parametersThomas White
2018-11-22Rename prediction refinement residual functionThomas White
Because there's another function with this name in merge.c
2018-11-15indexamajig: Name and shame slow processing stagesThomas White
2018-11-14Fix error message about dimensionality of image dataThomas White
Fixes CRYS-205
2018-11-14Clean up set_dim_structure_entry() and parsing of "dimX" in geometry fileThomas White
Fixes CRYS-212
2018-11-02Fix possibly uninitialised dataf in read_cbf_data()Thomas White
2018-11-02Change a couple of important asserts to if statementsThomas White
2018-10-30peakfinder8: Fix some use-after-free errorsThomas White
2018-10-22fix freeing unallocated memoryYaroslav Gevorkov
2018-10-15xgandalf: always return centered cell, if it was providedYaroslav Gevorkov
2018-09-28mosflm: Check for existence of unit cell before checking centeringThomas White
2018-09-27Write in stream whether crystal was selected as a "hit" or notThomas White
2018-09-27xds: Also set unique axisThomas White
2018-09-27xds: Increase INDEX_ERROR to 0.2Thomas White
As recommended on the XDSwiki for indexing individual frames
2018-09-27xds: Read final unit cell, i.e. after refinementThomas White
Previously, we were reading the very first cell to pop out of the indexing, which didn't even follow the requested lattice type or centering. The result was that XDS couldn't index any centered lattices without cell combinations.
2018-09-27xds: Fix space groups for latticesThomas White
2018-09-26parse_symmetry_operations(): Handle numbers, e.g. k-2hThomas White
2018-09-25Add warning about monoclinic I cells when using MosflmThomas White
2018-09-20Don't give P centering to Mosflm when not providing cell parametersThomas White
It's supposed to ignore it, but apparently it doesn't.
2018-09-20Allow cbf.gz buffer to grow if the file is largeThomas White
2018-09-20Handle gzipped CBF filesThomas White
2018-09-20Stop reading "simply" if file type is unknownThomas White
2018-09-20Factorise CBF data readThomas White
2018-09-19Stop opening file if it's not recognisedThomas White
2018-09-19Handle 16bpp CBFs (as well as 32bpp)Thomas White
2018-09-11Fix header dependencies between reflist.h and crystal.hThomas White
2018-09-10Merge branch 'tom/deltacchalf'Thomas White
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