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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
2022-03-07Add new time accounts (preparation for finer-grained profiling)Thomas White
2022-03-07indexamajig: Remove pointless time account/last task/pingThomas White
This doesn't do anything. The very next lines override all the settings.
2022-03-04GUI: Fix stream rescan logicThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/64
2022-03-03GUI: Better handling of error-filled indexamajig logsThomas White
If there are lots of error messages (e.g. a missing mask file), looking at the last 4k of the log file is not always enough. Now it will go back to 16k, in steps of 4k. It will stop early if it finds the start of the file, and it will complain if it still doesn't find what it's looking for.
2022-03-03GUI: Use fixed profile radius for indexing onceThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/61
2022-03-02Add tests/indexamajig-missing-fileThomas White
This checks that indexamajig correctly recognises when no files could be processed.
2022-03-02indexamajig: Return a specific error code (5) if no files could be processedThomas 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
2022-03-02Add tests/file-waitThomas White
This tests that indexamajig --wait-for-file works
2022-03-01Add section about syminfo.lib to INSTALL.mdThomas White
2022-03-01Add scripts/install-indexersThomas White
2022-03-01Add new tutorialThomas White
2022-02-21cell_explorer: Handle smooth scrolling eventsThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/59
2022-02-10CrystFELImageView: Handle smooth scrolling eventsThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/58
2022-02-09Update dependencies for FedoraThomas White
2022-01-27Merge pull request #5 from kif/typoThomas White
correct a simple typo
2022-01-27correct a simple typoJerome Kieffer
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
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