Age | Commit message (Collapse) | Author | |
---|---|---|---|
2022-03-08 | read_peaks: Simplify logic | Thomas White | |
2022-03-08 | Fix slabbiness assumptions | Thomas White | |
This adds a new routine, data_template_slabby_file_to_panel_coords, to be used (only!) in places where external forces require assumptions of slabbiness: pixel maps and MsgPack/HDF5 peak lists (including CXI-style). This also fixes the prototype of data_template_file_to_panel_coords to make the panel number strictly an input parameter. This was an oversight in the implementation of DataTemplate, and caused problems when reading non-slabby streams. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/66 | |||
2022-03-08 | stream_open_for_write: Fix documentation | Thomas White | |
2022-03-08 | Drop compatibility with old stream format versions | Thomas White | |
CrystFEL hasn't written any version other than 2.3 since before 2015. Supporting the old versions is getting difficult because of slabbiness assumptions, so it's time to get rid of it. | |||
2022-03-07 | time_accounts_init: Add a warning if timer is not available | Thomas White | |
2022-03-07 | Add image_read_with_time_accounting for fine-grained data load profiling | Thomas White | |
2022-03-07 | Move time-accounts to libcrystfel | Thomas White | |
2022-03-02 | Move file_exists() check to right before opening the HDF5 | Thomas White | |
No other code path under image_expand_frames() actually opens the file, because HDF5s are currently the only format supporting multiple frames. The aim of the existence check is to give a better error message (compared to the HDF5 backtrace splurge), but it doesn't need to be done so early. In fact, checking so early had the side-effect of breaking indexamajig --wait-for-file. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/65 | |||
2022-03-02 | Formatting and increased verbosity | Thomas White | |
2022-01-27 | correct a simple typo | Jerome Kieffer | |
2021-11-15 | pair_peaks: Use reciprocal space distance instead of pixel distance | Thomas White | |
The reciprocal space distance limit has been set as one third of the smallest inter-Bragg spacing. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/38 | |||
2021-11-15 | Ensure that crystal doesn't end up with invalid reflist after prediction ↵ | Thomas White | |
refinement | |||
2021-10-28 | Make symmetry operation parser re-entrant | Thomas White | |
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/1 | |||
2021-10-28 | Add 'mask_panel_edges' to geometry file | Thomas White | |
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/27 | |||
2021-10-28 | Add a comment | Thomas White | |
2021-10-26 | Remove detector rail direction altogether | Thomas White | |
This got missed out by accident in the conversion to DataTemplate, but absolutely no-one noticed. In the meantime, my views on how the geometry files should work have changed somewhat. I don't want to maintain the extra complexity here when it isn't even clear that it will eliminate the need to re-refine geometry for each camera length. This commit just takes the rail direction stuff out of the documentation and the geometry file parser. Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/50 | |||
2021-10-26 | create_detgeom: Factorise panel template | Thomas White | |
2021-10-22 | pair_peaks: Skip reflections if the indices are too large | Thomas White | |
2021-10-22 | reflection_new: Check indices are not too large | Thomas White | |
Previously, the combination of reflection_new and add_refl_to_list gave a way to side-step the usual check that the indices were not larger than 512. This causes corruption of the RefList, so much be avoided. | |||
2021-10-20 | Remove unused parameter | Thomas White | |
2021-10-20 | Fix column types for plain MTZ output | Thomas White | |
2021-10-20 | Add "plain" MTZ file layout, distinct from "Bijvoet" layout | Thomas White | |
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/52 | |||
2021-10-20 | Set crystal name in MTZ files | Thomas White | |
When using the GUI, it will be set to the corresponding indexing result name. | |||
2021-10-20 | Reject geometry file if wavelength isn't specified | Thomas White | |
2021-10-20 | image_hdf5_read_peaks_cxi: Make sure array is big enough | Thomas White | |
2021-10-20 | Fussiness | Thomas White | |
2021-10-20 | image_hdf5_read_header_to_cache: Make space for terminator | Thomas White | |
2021-10-20 | Add a comment | Thomas White | |
2021-10-13 | Make zlib dependency optional | Thomas White | |
2021-10-13 | Remove NCurses dependency | Thomas White | |
It's only used once, to get background colours for 'indexamajig --int-diag', itself a rarely used feature. The dependency itself seems to cause problems for some people, particularly those not using system libraries for everything. So I think it's better just to remove it, and use ANSI escape codes directly. | |||
2021-09-29 | Remove old references | Thomas White | |
2021-09-17 | Warn if in-memory CBF is attempted | Thomas White | |
2021-09-17 | Handle headers from in-memory HDF5s | Thomas White | |
2021-09-17 | Handle in-memory HDF5s | Thomas White | |
2021-09-17 | Avoid pointless passing of image/event | Thomas White | |
2021-09-07 | assplode(): Add some assertions | Thomas White | |
2021-09-07 | get_equiv: Bail out on error path | Thomas White | |
Error handling is sloppy here. | |||
2021-09-07 | check_box: Fix type used for sizeof | Thomas White | |
2021-09-07 | TakeTwo: Check for empty observed vector list | Thomas White | |
2021-09-07 | image_hdf5_read_header_to_cache: Remove double free on error path | Thomas White | |
2021-09-07 | fom_select_reflection_pairs: Keep zeroed intensities in dataset | Thomas White | |
Note the re-ordering of tasks, and the removal of 'continue'. | |||
2021-09-07 | init_fom: Clean up on error path | Thomas White | |
2021-09-07 | filter_noise_in_panel: Fix panel edge behaviour | Thomas White | |
2021-09-07 | lookup_panel: Check that panel name is not NULL | Thomas White | |
2021-09-07 | load_cell_from_file: Check fgets return value for first line | Thomas White | |
2021-09-03 | Fix typo and failing tests from previous commit | Thomas White | |
2021-09-03 | Reject geometry file if fs and ss directions are not specified | Thomas White | |
2021-08-20 | write_to_xds: Add missing 'S' (!) | Thomas White | |
2021-08-20 | Mosflm: Add -n option when probing | Thomas White | |
2021-08-13 | Increase threshold for integration warning | Thomas White | |
The warning about "XXX reflections couldn't be integrated" is tiresome - it appears for practically every indexed pattern because there are always some reflections that fall in bad regions or at panel edges. This suppresses the warning unless the number of integration failures is more than a quarter of the total number of reflections. |