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2022-01-14This is CrystFEL 0.10.10.10.1Thomas White
2022-01-13INSTALL.md: Add 'cd /home/user/downloads/crystfel'Thomas White
This makes it explicit that the Meson and Ninja steps should be run from the CrystFEL folder, not (e.g.) the Meson folder.
2022-01-12SLURM: Fix a silly mistake counting the environment entriesThomas White
2022-01-12SLURM: Get rid of path_addThomas White
This is no longer needed after 48c02e71e5bf. Simply set the correct PATH before starting the GUI, and it will be propagated to the SLURM jobs. Astute readers will notice that the feature has been silently broken since last March (65a1afdce2da5cd), anyway. Whoops.
2022-01-12GUI: Try to get geometry from result (stream), if not explicitly providedThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/56
2022-01-12SLURM: Copy environment from parent processThomas White
Unfortunately, several environments rely on "magic" environment variables to make things work. These need to be propagated. The path to the GUI will no longer be added to the PATH. This was intended to help when the indexing executables (mosflm, dirax etc) were found alongside the CrystFEL executables. However, it's highly likely that the path to the CrystFEL executables will be in PATH anyway. This way, running the SLURM jobs in the same environment as the GUI itself, also seems more compliant with the "principle of least surprise".
2022-01-10Meson: Switch to libccp4c from WrapDBThomas White
2021-12-17indexamajig: Set file read time account for unpacking frame dataThomas White
2021-12-17indexamajig: Avoid fclose(NULL)Thomas White
When running online, there's no input file handle to close.
2021-12-17indexamajig: Send sandbox ping while waiting for next frameThomas White
This avoids the process getting killed while waiting e.g. between runs in an online context.
2021-12-07indexamajig: Generate per-frame profiling numbersThomas White
2021-12-07indexamajig: Shut down cleanly on SIGUSR1Thomas White
2021-12-02GUI: Add a checkbox for automatically rescanning streamsThomas White
Usually, one will want this option enabled. However, sometimes it speeds things up a lot to disable it. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/54
2021-12-02GUI: Always set toggle actions at startupThomas White
Otherwise, setting the defaults won't work properly.
2021-11-29GUI: Allow selection of multiple streamsThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/51
2021-11-29Add GtkMultiFileChooserButtonThomas White
2021-11-26GUI: Don't store stream filename in projectThomas White
There's already some confusion between "loading a stream into the GUI" and "adding a stream as a result". This should help resolve it, as well as simplifying multi-stream results (coming up).
2021-11-25partialator: Use image_free() to avoid memory leaksThomas White
Requires that the array of crystals isn't allocated on the stack.
2021-11-25partialator: Handle spaces in custom split fileThomas White
The csplit format is ambiguous when the filenames contain spaces. To make things a bit clearer, the file now requires the fields to be separated by exactly one space rather than any number of tabs/spaces. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/55
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
2021-10-27CrystFELImageView: Fix range of pixels for value display at high zoomThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/17
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
2021-10-25CrystFELImageView: fix scrollbar adjustment rangesThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/18
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
2021-10-20GUI: Set project name in MTZ filesThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/28
2021-10-20Set crystal name in MTZ filesThomas White
When using the GUI, it will be set to the corresponding indexing result name.
2021-10-20GUI: Track the indexing result from which each merge result cameThomas White
2021-10-20Add photon_energy to ev_enum test filesThomas White
Also fixes newline at end of files
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
2021-10-15Update INSTALL.mdThomas White
2021-10-13Tweak INSTALL.mdThomas White
2021-10-13CI: Remove ncursesThomas 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.
2021-10-12GUI: Use proper overlines for reflection indicesThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/19
2021-10-08INSTALL.md: Remove extra bracketThomas White
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