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2022-11-24GUI: Colour scale, part 2: Scrolling and zoomingThomas White
2022-11-24GUI: Colour scale, part 1: Basic image histogramThomas White
2022-11-24Remove comment about closed issueThomas White
2022-11-18GUI: Fix initialiser for 'event' during list importThomas White
Just a bug. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/72
2022-11-18CrystFELIndexingOpts: Set -nocell and -nolatt where appropriateThomas White
Without these, the algorithms assume defaults which don't necessarily match what the user intended. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/70
2022-11-18Update libCCP4 wrap to 8.0.0Thomas White
2022-11-08indexamajig: Add --cell-parameters-onlyThomas White
2022-11-08indexamajig: Remove warning when using --integration=noneThomas White
For cases where you need it (high performance online processing), it's very spammy.
2022-11-08indexamajig: Exit only once all workers received kEndOfStreamThomas White
Previously, the whole program would exit if any worker saw kEndOfStream. Unfortunately, this happens quite often, due to data starvation (too many workers for the data rate) or just general slowness. Therefore we need a more robust criterion.
2022-11-07check_hkl: Make --wilson more robust against invalid dataThomas White
2022-11-05Stream: increase maximum geometry file size to 1 megabyteThomas White
The old maximum was 64 kilobytes, and a 68k geometry file has now been seen in the wild. The limit is only needed to prevent runaway memory allocation in the case of a corrupted stream. So it's safe to increase it quite a lot.
2022-11-04Revert "ASAP::O: Report lag between timestamp and current time"Thomas White
This reverts commit 50d0043dd1177c10ba888b614c6766c5e33386e7. It spams the terminal too much, and ASAP::O-tv shows this time more comfortably via a web interface.
2022-10-28ASAP::O: Report lag between timestamp and current timeThomas White
2022-10-05data_template_get_2d_detgeom_if_possible: Avoid segfault with adu_per_eVThomas White
2022-10-05indexamajig: Improve accuracy of speed reportsThomas White
2022-10-05ASAP::O: Add timestamps to errorsThomas White
2022-10-05peakfinder8: Allocate big structures on heap instead of stackAlexandra Tolstikova
Fixes Valgrind errors and segfault with certain geometries
2022-10-05Merge branch 'pf8_faster'Thomas White
2022-09-22Add fast mode for peakfinder8Alexandra Tolstikova
2022-09-22all_panels_reference_same_clen: Handle missing unitsThomas White
2022-09-22Add missing prototypeThomas White
2022-09-22speed.rst: Add a note about static detector geometryThomas White
2022-09-22Implement data_template_get_2d_detgeom_if_possibleThomas White
It is horrible. But it's contained inside the DataTemplate module.
2022-09-21create_detgeom: Return detgeom structure rather than altering image argumentThomas White
2022-09-21Move create_detgeom to DataTemplate moduleThomas White
It seems to make more sense here, because it's all about interpreting the contents of the DataTemplate structure.
2022-09-21speed.rst: Mention --asdf-fastThomas White
2022-09-21indexamajig(1): Add --asdf-fastThomas White
2022-09-21asdf: Add fast modeAlexandra Tolstikova
This adds an optional fast mode for asdf indexing, which is around 3 times faster with only a few percent lower success rate.
2022-09-21Avoid nan/inf check unless data was given in float formatThomas White
2022-09-20load_hdf5_hyperslab: Add missing cleanupThomas White
2022-09-08Stream: don't open stream if headers aren't understoodThomas White
This avoids e.g. crashing later if the geometry is bad. This commit also removes a problematic stanza from the geometry in test.stream, since the stream reading functions are now more fussy about this.
2022-09-08speed.rst: Add more adviceThomas White
2022-09-02RefList: assert that a Reflection can only be on one listThomas White
2022-08-26GUI: Refuse to open "Index all frames" without a geometry filenameThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/73
2022-08-25INSTALL.md: Add a note about M1 MacsThomas White
2022-08-25CMake: remove unnecessary SVG installationThomas White
These are included in the GResources now
2022-08-25GUI: Get icons via a GResourceThomas White
Otherwise we have to mess around with custom paths whenever CrystFEL is installed in a non-system location.
2022-08-24GUI: Add options for detector-shift and peakogram-streamThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/63
2022-08-24scripts/peakogram-stream: Better handling of multiple streamsThomas White
This allows the "-i" option to be given multiple times, instead of having to concatenate the streams via stdin.
2022-08-24detector-shift: Better handling of multiple input streamsThomas White
Previously, the only way to process more than one stream was to concatenate them via stdin. Now, you can give '--' followed by a list of streams. The '--' is needed to distinguish from the situation where a geometry file is to be updated.
2022-08-24Install detector-shift and peakogram-stream under 'bin'Thomas White
2022-08-24GUI: Add custom task iconsThomas White
Previously, the task buttons used stock icons chosen to approximately fit the task when displayed with the icon theme on my computers. But they don't fit so well in other themes, and sometimes no icon is shown at all. So, now they have their own icons, specifically designed for CrystFEL. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/9
2022-08-23GUI: Add resolution ringsThomas White
It will refuse to draw the rings if the detector is too far from being flat (as judged by detgeom_mean_camera_length). Otherwise, the drawing is exactly the same as was done by hdfsee.
2022-08-22image_create_dp_bad_sat: Initialise saturation array to infinityThomas White
2022-08-22Update ChangeLogThomas White
2022-08-18Restructure image data array creationThomas White
This adds a central procedure (image_create_dp_bad_sat) to create all the arrays. Then it's up to the loading procedure to put the values into the arrays. This also makes the loading procedures responsible for marking NaN/inf pixels in the bad pixel map. This avoids an additional sweep through the image data, and makes it possible to skip the NaN/inf check altogether if the image data comes, as it often does, in format which can't represent NaN/inf anyway. Finally, it removes quite a lot of duplicated code.
2022-07-12Zero-weight negative intensity peaks in prediction refinementThomas White
Strongly negative peaks can occur if there are unmasked bad pixels. These cause the refinement to diverge badly. This change stabilises the refinement such that it works even in these cases. But of course, the real solution is to mask out those pixels. Negative intensity peaks are unlikely to show up "for real" in the peak search results (because we look for strong peaks!). However, if the intensity is negative, we aren't even sure that the peak exists at all and have no reason to assume it should be close to the Bragg condition.
2022-07-07indexamajig: Remove separate waitpid() calls when cleaning up last processesThomas White
2022-07-07indexamajig: --asapo-wait-for-stream doesn't require an argumentThomas White
2022-07-07indexamajig: Make sure data format is initialisedThomas White
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