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2022-06-02Refuse to overwrite an existing streamThomas White
With online processing, we might end up with a very long stream. It should not be so easily deleted if indexamajig is restarted!
2022-06-02Profiling: Increase debugging informationThomas White
2022-06-02Profiling: Increase MAX_PROFILE_CHILDRENThomas White
This number has to be at least 2x as high as the number of detector panels because, when using HDF5 and a bad pixel map, each panel will have an H5Dopen2 and H5Dread block inside create-badmap.
2022-06-02Merge branch 'better-profiling'Thomas White
2022-06-02Meson: Replace '1' with 'true' inside conf_data.set10Thomas White
Use of numbers (rather than booleans) in this routine is deprecated in recent meson versions.
2022-05-04Write profile information in one call to write()Thomas White
Unfortunately, the complicated series of nested printf()s doesn't work well from multiple processes.
2022-05-04Add improved profilingThomas White
Improvements: - Recursive, so we can see how things are working at different levels - Everything is profiled, even if not explicitly labelled - No possibility of losing time - Detects mistakes if routines aren't wrapped correctly
2022-05-03Strip out time-accountsThomas White
2022-04-20Recognise .nx5 as HDF5Thomas White
2022-04-20Install time-accounts.hThomas White
2022-04-05indexamajig: Fix profiling when using streamed dataThomas White
2022-04-05Time accounts: make sure that last account is loggedThomas White
2022-03-18FormattingThomas White
2022-03-09Meson: enable building without HDF5Thomas White
2022-03-08read_peaks: Simplify logicThomas White
2022-03-08Fix slabbiness assumptionsThomas White
This adds a new routine, data_template_slabby_file_to_panel_coords, to be used (only!) in places where external forces require assumptions of slabbiness: pixel maps and MsgPack/HDF5 peak lists (including CXI-style). This also fixes the prototype of data_template_file_to_panel_coords to make the panel number strictly an input parameter. This was an oversight in the implementation of DataTemplate, and caused problems when reading non-slabby streams. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/66
2022-03-08stream_open_for_write: Fix documentationThomas White
2022-03-08Drop compatibility with old stream format versionsThomas White
CrystFEL hasn't written any version other than 2.3 since before 2015. Supporting the old versions is getting difficult because of slabbiness assumptions, so it's time to get rid of it.
2022-03-07time_accounts_init: Add a warning if timer is not availableThomas White
2022-03-07Add image_read_with_time_accounting for fine-grained data load profilingThomas White
2022-03-07Move time-accounts to libcrystfelThomas White
2022-03-02Move file_exists() check to right before opening the HDF5Thomas White
No other code path under image_expand_frames() actually opens the file, because HDF5s are currently the only format supporting multiple frames. The aim of the existence check is to give a better error message (compared to the HDF5 backtrace splurge), but it doesn't need to be done so early. In fact, checking so early had the side-effect of breaking indexamajig --wait-for-file. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/65
2022-03-02Formatting and increased verbosityThomas White
2022-01-27correct a simple typoJerome Kieffer
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
2021-10-13Meson: Get zlib via wrapThomas 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.
2021-10-07Meson: Get PinkIndexer via wrapThomas White
2021-10-07Meson: Get Xgandalf via wrapThomas White
2021-09-30Doxygen: More improvementsThomas White
2021-09-29Add missing Doxyfile-version.inThomas White
2021-09-29Doxygen: Exclude datatemplate_priv.h and uthash.hThomas White
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