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2024-01-05get_hkl: Read MTZ filesThomas White
There are still some rough edges, e.g. it only works with a simple I/SIGI column (not I+/I-), and can't yet interpret the symmetry information in the file. However, it's still better than the old mtz2hkl script. Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/7
2024-01-05get_hkl: Free symmetry and output filenameThomas White
2024-01-04Use prebuilt containers for CI pipelineParthasarathy Tirumalai
The containers have all the development package dependencies and tools preinstalled to save time and network bandwidth in the Fedora 32 & 37 and Centos7 jobs.
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
2023-12-19Check for duplicate member in panel groupThomas White
Example: group_all = q0,q1,q2,q2
2023-12-19Meson: Move crystfel_geometry.5 inside check for PandocThomas White
2023-12-19index_pattern: Gracefully handle image with no peaksThomas White
2023-12-19Meson: Fix installation location for crystfel_geometry.5Thomas White
Previously, this file ended up in man1, where it couldn't be found.
2023-12-18Pin Millepede version to V04-13-06Thomas White
Unfortunately, V04-14-00 cannot be compiled with older Meson versions (which we otherwise support) - they apparent confuse the old version of the Fortran dependency scanner with use of #ifdef. There's not currently much for us to gain from a more recent Millepede version, so this is the easiest solution.
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
2023-10-16indexamajig(1): Correct an untruth about --peakfinder8-fastThomas White
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.
2023-09-23image_create_dp_bad_sat: Don't worry about "sat"Thomas White
The saturation array is created by create_satmap when needed, which takes care that all panels get an array (so we only have to check image->sat != NULL). The array created by image_create_dp_bad_sat was actually leaked! In any case, saturation maps are rarely used. We can do without the extra allocations. The routine name has been changed accordingly, to prevent future confusion.
2023-09-23indexamajig: Add profile block for free-imageThomas White
2023-09-23Fix a couple of profiling memory errorsThomas White
The "children" array was the wrong size, and not freed. Also, some formatting fussiness.
2023-09-22Don't complain about missing 'all' group until it's actually neededThomas White
2023-09-21indexamajig: Increase buffer size for Mille filenameThomas White
With the prefix, it can get quite long.
2023-09-21Update manual pagesThomas White
2023-09-20crystfel_geometry(5): Convert to Markdown and re-structureThomas White
Still some work to be done here, but it's already an improvement.
2023-09-20CI: Add Pandoc to build-centos7Thomas White
We'd like the manual pages to be built for the central deployment.
2023-09-20indexamajig: Add --mille-dirThomas White
2023-09-20Update INSTALL.mdThomas White
2023-09-20Add manual page for align_detectorThomas White
2023-09-20Examples: Remove rigid groupsThomas White
These are now ignored, but shouldn't be in the examples.
2023-09-20Fix inappropriate use of r_devThomas White
These should be get_exerr. Following 1ae9a4582, the r_dev values are no longer useful physical quantities, only a refinement target function. This was causing the last few Git versions to not predict any reflections at all!
2023-09-19CI: Download only the required artifacts for each jobThomas White
2023-09-19Meson: Remove unnecessary subproject pokingThomas White
The variable isn't needed, and just serves to break the build when Fortran isn't available.
2023-09-19Prediction refinement: Weaken restraint and reduce number of iterationsThomas White
The restraint was way too strong, after the last round of tweaking. With a weaker restraint, the algorithm converges very quickly - it's practically linear - so ten iterations is way too much.
2023-09-19CI: Remove gfortran from minimal build testThomas White
2023-09-18Use a*a instead of pow(a, 2)Thomas White
2023-09-18Meson: Make Millepede subproject optionalThomas White
This should help avoid confusion when people find they need a Fortran compiler.
2023-09-18Build EXC_WEIGHT into r_devThomas White
This avoids weird weighting factors everywhere and much confusion. Since Millepede doesn't have an easy way of weighting measurements (only via altering the ESD values), treating it as a units conversion seems to be easier.
2023-09-18pred_residual: Remove vestigial conversion to metresThomas White
We want the residual in pixels, as described in the comment for EXC_WEIGHT. This routine is only used for displaying the total residuals, not for the real minimisation maths. However, we need to be clear.
2023-09-18tests/gradient_*: Use r_dev instead of get_exerrThomas White
We explicitly want the gradient of the residual, nothing else.
2023-09-18Prediction refinement: Record excitation error and distance residuals separatelyThomas White
2023-09-18Add gfortran to DockerfileThomas White
Needed for Millepede
2023-09-18Prediction refinement: Record initial residual and total shiftsThomas 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
2023-09-18indexamajig: Add documentation for --milleThomas White
2023-09-18indexamajig: Add missing documentation for --indexing=fileThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/85
2023-09-18Convert indexamajig(1) manual page to MarkdownThomas White
2023-09-13cell_explorer: Update "about" boxThomas White
2023-09-13cell_explorer: Add "clear selection"Thomas White
2023-09-12Fix nominal space group when exporting MTZ in PG 2Thomas White
2023-09-12Fix sense of panel rotationsThomas White
Should always be a right-hand grip rotation around positive axis direction.
2023-09-12Seedee: Handle format i4<Thomas White
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