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2021-07-12GUI: Add Tools->Jump to frameThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/41
2021-07-12GUI: Update the "About" boxThomas White
2021-07-12GUI: Add --wavelength-estimate and --camera-length-estimateThomas White
Only when using PinkIndexer. Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/25
2021-07-09pattern_sim: Fix typo in --helpThomas White
2021-07-06SLURM: Show the real error message if job can't be submittedThomas White
2021-06-23GUI: Avoid writing '(null)' to project fileThomas White
The problem is, '(null)' is not NULL.
2021-06-23CrystFELSymmetrySelector: Set have_pg when PG is set via APIThomas White
2021-06-23GUI: Swap Close/Calculate buttons in FoM windowThomas White
This makes it consistent with all the other windows.
2021-06-23GUI: Fix a tooltipThomas White
2021-06-22GUI: Fix paths to streams for merging and ambigatorThomas White
They need to be prefixed with "../" because they are in a different folder.
2021-06-22CrystFELImageView: Adjust threshold for showing box centresThomas White
I find that starting to show centres at a higher magnification level makes it easier to distinguish the centre markers from bright pixels.
2021-06-22GUI: Remove old debugging watchpointThomas White
2021-06-22CrystFELImageView: Rearrange reflection coloursThomas White
Smaller numbers of crystals are more common, so it's better for the second crystal to be something very distinct from the peak search colour.
2021-06-17GUI: Add a tooltipThomas White
2021-06-16GUI: Warn if chunk can't be loaded from streamThomas White
2021-05-28GUI: Store relative paths of resultsThomas White
This allows project folders to be relocated more easily. At the same time, I fixed the weird ownership semantics of add_indexing_result and add_merge_result. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/31
2021-05-28Pass errors back when retrieving values for wavelength etcThomas White
Big improvement on just sending NAN back. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/37
2021-05-25Fix dummy prototype for im_zmq_connectThomas White
2021-05-19GUI: Add button to reset FoM resolution range to entire dataThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/11
2021-05-19GUI: Increase size of FoM min resolution boxThomas White
2021-05-17Resolve FIXMEs and TODOsThomas White
Prompted by the article linked below, for each FIXME/TODO I've either referenced an issue in the tracker, or removed it if it's not worth fixing. https://schleiss.io/plotting-source-code-todos-for-open-source-projects
2021-05-17GUI: Improve error handling for default_projectThomas White
2021-05-11indexamajig: Put cell tolerances and pk/int radii into separate objectsThomas White
Rationale: it makes the JSON structure a bit more logical, and enables things like the following: set_of_params_1.integration.radii == set_of_params_2.integration.radii params.peaksearch.radii == params.integration.radii Previously, these would have required multiple comparisons.
2021-05-11GUI: Fix loading of merging parameters from project fileThomas White
Apparently, I can't count.
2021-05-11GUI: Fix checkbox logic in CrystFELMergeOptsThomas White
2021-05-11GUI: Ensure that streams get re-scanned after job terminationThomas White
Previously, they would not get scanned because no job was running. We need one more scan after a job exits to make sure everything is up to date.
2021-05-11Add the 'real' implementation of CrystFELSymmetrySelectorThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/13
2021-05-11Add set_combo_id()Thomas White
2021-05-07Add deselect_when_active()Thomas White
2021-05-07GUI: Add missing initialisation/load/save for ambi.backendThomas White
2021-05-05indexamajig: Add --zmq-requestThomas White
This (re-)adds the ability to get data via a request/reply socket. See afcb7b568947c for when it was removed.
2021-05-05indexamajig: Add a missing breakThomas White
This fixes --threshold when --zmq-subscribe is used.
2021-04-30GUI: Take optional stream on command lineThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/12
2021-04-30GUI: Force results selector to "from GUI" when peak search window is openedThomas White
2021-04-30GUI: Fix force_refls_onThomas White
A silly cut+paste error.
2021-04-30GUI: When indexing one frame, don't force results selector or repeat peak searchThomas White
The logic behind forcing the results selector (to "Calculations within GUI") was that anything calculated in the GUI should appear under that selection only. Unfortunately, when loading a stream without images, there is nothing at all to be seen under this selection, not even an image. Forcing the selector resulted in proj->cur_image = NULL and therefore a crash when trying to index based on that. Similarly, the call to update_peaks expected image data, but there is none. In reality, we have a perfectly good image structure with peaks from the stream already. This allows a non-image stream to be "re-indexed" based on the peaks. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/33
2021-04-30indexamajig: Fix an incorrect error messageThomas White
2021-04-27indexamajig: Fix an error messageThomas White
2021-04-23indexamajig: Generate a unique filename for ZMQ dataThomas White
The unique filename is needed by the GUI for looking up results in a stream. Otherwise, the filename is "(null)" for everything and the lookup just returns the first chunk in the stream. The filename is generated based on the unique serial number for each chunk, and is therefore unique across one run of indexamajig regardless of the number of worker processes (-j). This might have to change in future to accommodate jobs run across multiple nodes, if there is any demand for looking at results in one big concatenated stream. This also changes the condition for deciding when to look for a 'real' file, to take into account that there is always a non-NULL filename.
2021-04-23indexamajig: Mercilessly ignore short ZMQ messagesThomas White
This is a hack to filter out what seems like "keepalive" messages. It's nasty, but better than contaminating the stream with spurious chunks.
2021-04-23indexamajig: Add --zmq-subscribeThomas White
2021-04-23MsgPack: Implement extraction of image dataThomas White
2021-04-21indexamajig: Replace --zmq-msgpack with --zmq-inputThomas White
This removes some unnecessary work (getting the address from the file) and seems cleaner.
2021-04-21indexamajig: Set indexing,integration=null if we are not indexing at allThomas White
2021-04-21Remove index_args->max_n_peaksThomas White
It's not used anywhere.
2021-04-21indexamajig --harvest-file: Handle no cell or no indexing methodsThomas White
2021-04-20indexamajig: Fix --no-image-data/--no-mask-dataThomas White
2021-04-20Fix memory handling semantics for ZMQ dataThomas White
2021-04-19Unify loading of image data and header valuesThomas White
This moves the entry point for loading MsgPack data to a new function, image_read_data_block. Inside image.c, the image structure can be created using exactly the same functions as for data files.
2021-04-19Move file_exists to utils (and eliminate several duplicates)Thomas White
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