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2024-02-06Remove an unused variableThomas White
2024-02-06Fix incorrect uses of cell_freeThomas White
This also gets rid of crystal_copy_deep. From now on, all crystal_copy calls also copy the UnitCell.
2024-02-06Crystals shouldn't own RefLists (part 6)Thomas White
This fixes the remaining programs.
2024-02-06Crystals shouldn't own RefLists (part 5)Thomas White
This fixes the entire partialator/scaling/rejection part.
2024-02-06Crystals shouldn't own RefLists (part 3)Thomas White
This fixes integration.c, peaks.c and process_hkl.c.
2024-02-06Add missing image initialisersThomas White
2024-02-06Crystal: Remove reference to image structure (part 3)Thomas White
2024-02-06Crystal: Remove reference to image structure (part 2)Thomas White
2024-02-06Crystal: Remove reference to image structure (part 1)Thomas White
2024-02-06Sort-of-workaround for argp '--help' crash on MacOSThomas White
Indexamajig --help causes a segfault on MacOS due to a bug in argp-standalone. That package is unlikely to be updated any time soon. Eventually, Homebrew might switch to one of the non-crashy forks, but probably not soon. We aren't the only ones affected - see https://www.openwall.com/lists/musl/2021/02/10/1 This commit adds a warning message to state that we already know about it, and it's not "our" fault. It also removes the corresponding test, since we know it fails.
2024-01-30GUI: Remove -et-al suffix from results name, if only one streamThomas White
2024-01-12indexamajig: Implement --max-mille-levelThomas White
2024-01-12align_detector: Enumerate directory contents if necessaryThomas White
2024-01-12GUI: Fix Millepede optionsThomas White
2024-01-12GUI: Copy geometry file into indexing job folderThomas White
This could be used for indexing, but it seems more transparent to have the "real" filename in the script for auditing. The geometry copy will be used for detector alignment. The alternative - extracting the geometry from the stream - seems quite a lot more complicated.
2024-01-11GUI: Write Millepede data into folderThomas White
2024-01-11GUI: Implement align_detectorThomas White
2024-01-11GUI: Switch to GtkFileChooserDialog for detector alignmentThomas White
Rationale: the refinement is very quick, and the output geometry file name is central to the process.
2024-01-10GUI: Skeleton task for detector alignmentThomas White
2024-01-10indexamajig: Start implementing --max-mille-levelThomas White
2024-01-10GUI: Track Millepede options through projectThomas White
Note that the indexamajig option --max-mille-level isn't implemented yet.
2024-01-10CrystFELIndexingOpts: Add Millepede output optionsThomas White
2024-01-10GUI: Remove detector-shiftThomas White
The script has been replaced with align_detector --level=0.
2024-01-05get_hkl: Free symmetry and output filenameThomas White
2023-12-22FormattingThomas White
2023-12-22indexamajig: Add --asapo-consumer-timeoutThomas White
This also reduces the default timeout to 500 ms.
2023-12-22indexamajig: Add --no-data-timeoutThomas White
2023-11-07SLURM: Move all sbatch parameters into scriptThomas White
This allows the user to re-run any job, if they want, or at least easily use the GUI's work as a template.
2023-11-06SLURM: Expose reservation and QoSThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/87
2023-10-02align_detector: Try to find 'pede' next to align_detector binaryThomas White
Lots of things can go wrong here, in which case it falls back to the shell search path.
2023-09-23indexamajig: Re-use the image data arraysThomas White
We noticed that constant freeing and re-allocating the (potentially quite large) arrays resulted in much lower performance. Since we know that all images have the same data layout, we can safely re-use the arrays. This gives a large speedup.
2023-09-23indexamajig: Add profile block for free-imageThomas White
2023-09-21indexamajig: Increase buffer size for Mille filenameThomas White
With the prefix, it can get quite long.
2023-09-20indexamajig: Add --mille-dirThomas White
2023-09-18Merge branch 'millepede'Thomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/3 Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/29
2023-09-13cell_explorer: Update "about" boxThomas White
2023-09-13cell_explorer: Add "clear selection"Thomas White
2023-08-30align_detector: Don't write constraints for fixed parametersThomas White
This avoids a warning from Millepede, and means we no longer need "skipemptycons" - which will make it easier to spot future problems.
2023-08-30align_detector: Add --out-of-planeThomas White
2023-08-28align_detector: stat() portabilityThomas White
2023-08-25align_detector: Output formattingThomas White
2023-08-25align_detector: Check for mixed-up Mille filesThomas White
2023-08-24align_detector: Refine x,y position and z-rotation onlyThomas White
2023-08-24align_detector: Delete old results file before running pedeThomas White
It doesn't always return an error code.
2023-08-24Use built-in Mille writer instead of wrapping C++ versionThomas White
2023-07-28align_detector: Friendlier user outputThomas White
2023-07-28Add (undocumented) Millepede option 'skipemptycons'Thomas White
2023-07-28Add hierarchy constraintsThomas White
2023-07-28align_detector: Decode labels and apply geometry correctionsThomas White
2023-07-28align_detector: Begin parsing Pede outputThomas White
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