| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-05-14 | data_template_write_to_fh: Fix output of mask filename | Thomas White | |
| 2024-05-14 | compare_reindexed_cell_parameters: Don't automatically select identity matrix | Thomas White | |
| The previous behaviour gave biased cell distributions in some situations, because it preferred not to overrule the indexing algorithm. Some indexing algorithms (xgandalf) always return a certain cell variant, e.g. gamma > 90. To make the histograms interpretable, we have to randomise our choice of reduced cell in all cases. However, we need to be careful that the cells we randomise between are really equivalent. The previous behaviour here was to look only at the axis lengths. We must look at the angles as well. But that's not the end of the story. We would have to choose some weighting factor between axis lengths and angles when deciding if a new cell is "better". That would be hard. Instead, compare_rcp now compares the G6 vectors directly, which consider lengths and angles on an even footing. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/95 | |||
| 2024-05-13 | Julia: Add basic wrapper for compare_reindexed_cell_parameters | Thomas White | |
| 2024-05-06 | data_template_write_to_fh: Don't try to write coffset at top level | Thomas White | |
| Previously, there was a bad bug here. We would still try to write a top-level coffset even if panels have moved such that the coffset is no longer a single value. One possibility is to unset panel->cnz_offset_default when moving a panel. This works, but we have to do it on every translation, or accept a floating-point comparison with zero and associated non-determinism. It's very likely that if we move one panel, we'll be moving all panels, even if only by a small amount. So, a more stable way seems to just write separate coffset values all the time. The coffset values aren't really meant to be used at the top level anyway (that's what clen is for!), so this fits pretty well. | |||
| 2024-05-06 | indexamajig: Avoid is_hdf5_file("-", ...) | Thomas White | |
| With thanks to biochem-fan. Fixes: https://github.com/taw10/crystfel/issues/12 | |||
| 2024-05-02 | data_template_write_to_fh: Fix bad region output | Thomas White | |
| Two problems: 1. Didn't take into account that bad->name already includes the prefix "bad". 2. Didn't convert the panel-relative coordinates back to slab-relative. Fixes: https://github.com/taw10/crystfel/issues/11 | |||
| 2024-05-02 | tests/geom_roundtrip: Check bad regions | Thomas White | |
| 2024-04-30 | indexamajig: Reduce ASAP::O verbosity | Thomas White | |
| 2024-04-29 | 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. | |||
| 2024-04-29 | indexamajig: Report ASAP::O message ID for acknowledgement | Thomas White | |
| Something strange is going on here, need to debug. | |||
| 2024-04-26 | Further clarification about ordering of panel group directives | Thomas White | |
| See 79bda19687e425818888ce17cc6e2239744ee640 | |||
| 2024-04-26 | DataTemplate: Add an "all" group if no panel definitions are given | Thomas White | |
| Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/96 | |||
| 2024-04-26 | Whitespace | Thomas White | |
| 2024-04-26 | crystfel_geometry(5): Mention that group definitions must come after panels | Thomas White | |
| Also mention this when complaining about the geometry file. Fixes: https://github.com/taw10/crystfel/issues/10 | |||
| 2024-04-25 | indexamajig: Avoid writing empty Mille records | Thomas White | |
| Fixes: https://github.com/taw10/crystfel/issues/9 | |||
| 2024-04-24 | Julia: Add 'setreflections!' to add a RefList for a Crystal in an image | Thomas White | |
| 2024-04-24 | Julia: Avoid making a list of Nothing | Thomas White | |
| The type of the list needs to be correct, otherwise we can't push to it later. | |||
| 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 | |||
| 2024-04-22 | asdf: Force cell to be right-handed after refinement | Thomas White | |
| In some rare cases, the cell changes from right to left handed during the vector refinement stage of asdf, while ending up at an apparently correct indexing solution. This commit just flips the axis round when necessary, in the same way that asdf already does in an earlier stage. I haven't done a proper survey, but I can say that the image I used to isolate and test this issue had very low resolution while still being what we would call "indexable". The left-handed cells appeared for six out of the 12173 hits in that run, or slightly below 0.05%. So, it's rare but not totally impossible. | |||
| 2024-04-22 | asdf: Don't store cell volume | Thomas White | |
| It's hardly needed for re-use, and invites problems with the volume going out of sync with the vectors. Better just to calculate it when needed. | |||
| 2024-04-22 | Minor documentation tweaks | Thomas White | |
| 2024-04-19 | GUI: Fix buffer overflow in "delete_gui_tempdir" | Philipp Middendorf | |
| 2024-04-19 | CI: Better way of restricting build-centos7 to mainline only | Thomas White | |
| 2024-04-19 | CI: Run build-centos7 only for "main" project (not for e.g. MRs) | Thomas White | |
| 2024-04-18 | Merge branch 'julia' | Thomas White | |
| 2024-04-18 | Address pipeline performance improvement changes which Tom requested. | Parthasarathy Tirumalai | |
| 1) Remove MacOS native build job and build-brew-macos the only job for MacOS. 2) Make container builds manual. | |||
| 2024-04-18 | Reorder job stages so that maxwell deployment can start as soon as centos7 ↵ | Parthasarathy Tirumalai | |
| build is done. | |||
| 2024-04-17 | CONTRIBUTING.md: Fix DOI link | Thomas White | |
| 2024-04-17 | Update Homebrew formula to 0.11.0 | Thomas White | |
| 2024-04-17 | This is CrystFEL 0.11.00.11.0 | Thomas White | |
| 2024-04-17 | Add -f option to brew upgrade commands in the MacOS jobs. | Parthasarathy Tirumalai | |
| 2024-04-17 | INSTALL.md: Fix link to crystfel.rb | Thomas White | |
| Needs to be a raw download. | |||
| 2024-04-17 | Update crystfel(7) | Thomas White | |
| 2024-04-17 | Update INSTALL.md | Thomas White | |
| 2024-04-17 | Update README.md | Thomas White | |
| 2024-04-16 | Update INSTALL.md | Thomas White | |
| 2024-04-16 | Update AUTHORS | Thomas White | |
| 2024-04-16 | Tweak prediction refinement weightings | Thomas White | |
| 2024-04-16 | alignment-test.jl: Plot shift/sigma (pull value) | Thomas White | |
| 2024-04-16 | alignment-test.jl: Round peak coordinates to one pixel, to get realistic errors | 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 | |
| 2024-02-27 | alignment_test.jl: Break plotting routine into 3 | Thomas White | |
| 2024-02-27 | Julia: Do polarisation correction via CrystFEL function | Thomas White | |
| The Julia-native correction was 50% slower. | |||
| 2024-02-27 | Julia: Move merging utils to separate module | Thomas White | |
| 2024-02-26 | process_hkl.jl: Add polarisation correction | Thomas White | |
| 2024-02-26 | Julia: RefList: Return indices as vectors, not tuples | Thomas White | |
| We're going to be doing a lot of linear algebra with these numbers, so this makes more sense. | |||
| 2024-02-26 | Julia: UnitCell: Add accessors for cell parameters and basis vectors | Thomas White | |
 |
index : CrystFEL | |
| Data processing for serial crystallography | Thomas White |
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