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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".
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
2021-10-27CrystFELImageView: Fix range of pixels for value display at high zoomThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/17
2021-10-25CrystFELImageView: fix scrollbar adjustment rangesThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/18
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
2021-10-12GUI: Use proper overlines for reflection indicesThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/19
2021-09-17SLURM: Add field for time limitThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/49
2021-09-17indexamajig: Add --data-formatThomas White
2021-09-07partialator write_split: Handle zero crystalsThomas White
The variable-sized array can't have zero size, so we need to check.
2021-09-07indexamajig: Avoid crash on NULL eventThomas White
2021-09-07add_stream: Fix data type for malloc sizeThomas White
2021-09-07GUI SLURM backend: Bail out if environment can't be allocatedThomas White
2021-09-07GUI remove_task: Remove from list before freeingThomas White
2021-09-07ambigator: Remove crystal list from detwin()Thomas White
It's not used anywhere, and in fact is freed before being passed in.
2021-08-20get_hkl: Complain more loudly if CCP4 libraries are not availableThomas White
2021-08-20Update AUTHORSThomas White
2021-08-16GUI: Avoid crash when trying to index no imageThomas White
2021-08-13partialator: Relax rejection criterion for profile radiusThomas White
The previous cutoff of 0.2*reflection_separation seems to have been too conservative. It cuts out over 1000 crystals from the 8000 crystals in one of the regression tests. Examining the values shows that 0.5 is better value. It's also a realistic physical limit - more than this, and the reflections should be overlapping.
2021-08-12CrystFELImageView: Fix adjustment semanticsThomas White
This changes how CrystFELImageView handles its adjustments for the GtkScrollable interface, to match the GTK examples. In particular, it adds a call to g_object_ref_sink() which prevents premature destruction of the adjustments when the GUI is closed down.
2021-08-11Add a missing includeThomas White
2021-08-10GUI: Use integer conversion for FoM minimum measurementsThomas White
2021-07-23GUI: Expose partialator --no-logsThomas White
2021-07-23GUI: Write partialator log files ("pr-logs") in working folderThomas White
2021-07-23partialator: Add --log-folderThomas White
2021-07-23indexamajig: Fix error path when worker pipe is closed mid-chunkThomas White
2021-07-23partial_sim: Fix printf format stringThomas White
2021-07-23scale_one_crystal: Remove unused exclusion totalThomas White
2021-07-23indexamajig: Fix retry if file can't be opened with --wait-for-fileThomas White
2021-07-23write_{radius,angle}_grid: Fix error pathThomas White
2021-07-23pattern_sim: Remove duplicate assignmentThomas White
2021-07-23pattern_sim: Rename shadowed variablesThomas White
2021-07-23pattern_sim: Add missing error checkThomas White
2021-07-23try_status: Remove duplicate assignmentThomas White
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