| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 7 days | indexamajig: Avoid is_hdf5_file("-", ...) | Thomas White | |
| With thanks to biochem-fan. Fixes: https://github.com/taw10/crystfel/issues/12 | |||
| 13 days | indexamajig: Reduce ASAP::O verbosity | Thomas White | |
| 14 days | indexamajig: Send ASAP::O acknowledgement only after process_image | Thomas White | |
| Otherwise, we end up acknowledging the previous message ID after receiving something like kEndOfStream. | |||
| 14 days | indexamajig: Report ASAP::O message ID for acknowledgement | Thomas White | |
| Something strange is going on here, need to debug. | |||
| 2024-04-24 | indexamajig: Add ASAP::O acknowledgements | Thomas White | |
| 2024-04-23 | align_detector: Add missing argument in warning message | Thomas White | |
| Fixes: https://github.com/taw10/crystfel/issues/8 | |||
| 2024-04-19 | GUI: Fix buffer overflow in "delete_gui_tempdir" | Philipp Middendorf | |
| 2024-04-18 | Merge branch 'julia' | Thomas White | |
| 2024-03-07 | ASAP::O: Do not free image->data_block until we get the callback | Thomas White | |
| 2024-03-07 | ASAP::O: Add even more debug for producer | Thomas White | |
| 2024-03-07 | ASAP::O: Fix ingest flags for placeholders | Thomas White | |
| 2024-02-16 | align_detector: Add 'closeandreopen' option for Millepede | Thomas White | |
| With large indexing jobs, we generate a LOT (4000+) of Millepede files. This option is needed to prevent pede from keeping all these files open simultaneously, which runs into an operating system limit. | |||
| 2024-02-15 | GUI: Find all Mille folders for alignment task | Thomas White | |
| Depending on the backend, this could be a single "mille-data", or multiple "mille-data-X" folders. | |||
| 2024-02-15 | GUI: Use separate --mille-dir for each sub-job | Thomas White | |
| Previously, they all wrote into the same "mille-data" folder, overwriting each others' files and causing general carnage. | |||
| 2024-02-06 | Peak search algorithms should not mutate image structure | Thomas White | |
| This changes all the peak search procedures into pure functions that return a new ImageFeatureList. This takes the management of image->features out of the hands of the peak search routines, and into the calling code's responsibility. In turn, this allows a load of stuff to become const. | |||
| 2024-02-06 | Remove an unused variable | Thomas White | |
| 2024-02-06 | Fix incorrect uses of cell_free | Thomas White | |
| This also gets rid of crystal_copy_deep. From now on, all crystal_copy calls also copy the UnitCell. | |||
| 2024-02-06 | Crystals shouldn't own RefLists (part 6) | Thomas White | |
| This fixes the remaining programs. | |||
| 2024-02-06 | Crystals shouldn't own RefLists (part 5) | Thomas White | |
| This fixes the entire partialator/scaling/rejection part. | |||
| 2024-02-06 | Crystals shouldn't own RefLists (part 3) | Thomas White | |
| This fixes integration.c, peaks.c and process_hkl.c. | |||
| 2024-02-06 | Add missing image initialisers | Thomas White | |
| 2024-02-06 | Crystal: Remove reference to image structure (part 3) | Thomas White | |
| 2024-02-06 | Crystal: Remove reference to image structure (part 2) | Thomas White | |
| 2024-02-06 | Crystal: Remove reference to image structure (part 1) | Thomas White | |
| 2024-02-06 | Sort-of-workaround for argp '--help' crash on MacOS | Thomas 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. | |||
| 2024-01-30 | GUI: Remove -et-al suffix from results name, if only one stream | Thomas White | |
| 2024-01-12 | indexamajig: Implement --max-mille-level | Thomas White | |
| 2024-01-12 | align_detector: Enumerate directory contents if necessary | Thomas White | |
| 2024-01-12 | GUI: Fix Millepede options | Thomas White | |
| 2024-01-12 | GUI: Copy geometry file into indexing job folder | Thomas 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. | |||
| 2024-01-11 | GUI: Write Millepede data into folder | Thomas White | |
| 2024-01-11 | GUI: Implement align_detector | Thomas White | |
| 2024-01-11 | GUI: Switch to GtkFileChooserDialog for detector alignment | Thomas White | |
| Rationale: the refinement is very quick, and the output geometry file name is central to the process. | |||
| 2024-01-10 | GUI: Skeleton task for detector alignment | Thomas White | |
| 2024-01-10 | indexamajig: Start implementing --max-mille-level | Thomas White | |
| 2024-01-10 | GUI: Track Millepede options through project | Thomas White | |
| Note that the indexamajig option --max-mille-level isn't implemented yet. | |||
| 2024-01-10 | CrystFELIndexingOpts: Add Millepede output options | Thomas White | |
| 2024-01-10 | GUI: Remove detector-shift | Thomas White | |
| The script has been replaced with align_detector --level=0. | |||
| 2024-01-05 | get_hkl: Free symmetry and output filename | Thomas White | |
| 2023-12-22 | Formatting | Thomas White | |
| 2023-12-22 | indexamajig: Add --asapo-consumer-timeout | Thomas White | |
| This also reduces the default timeout to 500 ms. | |||
| 2023-12-22 | indexamajig: Add --no-data-timeout | Thomas White | |
| 2023-11-07 | SLURM: Move all sbatch parameters into script | Thomas 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. | |||
| 2023-11-06 | SLURM: Expose reservation and QoS | Thomas White | |
| Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/87 | |||
| 2023-10-02 | align_detector: Try to find 'pede' next to align_detector binary | Thomas White | |
| Lots of things can go wrong here, in which case it falls back to the shell search path. | |||
| 2023-09-23 | indexamajig: Re-use the image data arrays | Thomas 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. | |||
| 2023-09-23 | indexamajig: Add profile block for free-image | Thomas White | |
| 2023-09-21 | indexamajig: Increase buffer size for Mille filename | Thomas White | |
| With the prefix, it can get quite long. | |||
| 2023-09-20 | indexamajig: Add --mille-dir | Thomas White | |
| 2023-09-18 | Merge branch 'millepede' | Thomas White | |
| Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/3 Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/29 | |||
 |
index : CrystFEL | |
| Data processing for serial crystallography | Thomas White |
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