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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
2021-04-15Separate ZMQ from MessagePack, switch to pub/sub socketThomas White
Indexamajig uses only ZMQ, to receive streaming data, while libcrystfel uses only msgpack to implement another type of image format. The two of these are eventually tied together in process_image, which does this: if ( have_zmq_data ) interpret_zmq_data_as_msgpack; - however, they would be easy to split up if we wanted to do something else (CBF data over ZMQ, anyone?). This commit also switches the ZMQ connector to use a pub/sub socket instead of a request/reply one. This matches changes in OnDA. At the moment, the MessagePack image reader simply dumps the object to disk.
2021-04-14cell_tool: Fix a big memory leakThomas White
2021-04-13FussinessThomas White
2021-04-13pattern_sim: Fix incorrect argument order for detgeom_transform_coordsThomas White
2021-04-08get_hkl: Write symmetry into output fileThomas White
2021-04-08Record infinite values as 'null' in JSONThomas White
Infinity isn't allowed in JSON. 'Null' should serve equally well to indicate "the relevant feature has been switched off".
2021-04-08indexamajig: Add a missing harvest parameterThomas White
2021-04-01Local BE: Fix ownership of workdir GFileThomas White
2021-04-01GUI: Wrap filenames in job scripts in quotes, where appropriateThomas White
This makes it work when the filenames contain spaces.
2021-04-01GUI: Clean up old tasks when infobar is removedThomas White
2021-03-31indexamajig: Handle spaces in filename when retrieving ID from queueThomas White
2021-03-30GUI: Fail more gracefully if image file is not presentThomas White
With the new header cache, it's possible to operate completely from the stream.
2021-03-30Add header caching layerThomas White
This simultaneously implements --copy-header/--copy-hdf5-field and gives access to metadata (e.g. detector position or wavelength) when loading from a stream with header-specified values.
2021-03-29indexamajig: Don't write harvest file if serial start is >1Thomas White
This will avoid multiple indexamajig processes from overwriting the others' files when running a batch job.
2021-03-26partialator: Add missing comma in JSONThomas White
2021-03-26GUI: Tell indexamajig and partialator to write parameter harvest filesThomas White
2021-03-26GUI: Add missing model parameter for mergingThomas White
Whoops.
2021-03-26partialator: Add --harvest-fileThomas White
2021-03-26indexamajig: Add --harvest-fileThomas White
2021-03-26Rearrange 'struct index_args' and remove unused elementsThomas White
"cmfilter" and "integrate_saturated" were unused.
2021-03-25indexamajig: Add --camera-length-estimateThomas White
Unfortunately, PinkIndexer needs the real camera length for its centre refinement. Giving a fake value and scaling the resulting shift does not work - the indexing rate drops with even a small error. Ideally, this would work in the same way as --wavelength-estimate, by using a static value from the geometry file if it's given. However, this is rather complicated to implement because of the way all the units stuff is implemented. Therefore, this is left as an improvement for the future.
2021-03-25FussinessThomas White
The FIXMEs have both already been fixed.
2021-03-19Merge branch 'tom/fromfile'Thomas White
2021-03-19FromFile indexer: Option processingThomas White
This give FromFile its own private command-lien option processing, like the other indexers. It removes the ability to auto-generate the solution filename, but I don't think there's a way to do that without breaking abstractions.
2021-03-17CrystFELImageView: Fix zoom limitsThomas White
2021-03-17GUI: Show beam centre more clearly, and optionallyThomas White
2021-03-16CrystFELImageView: Avoid crash when scrolling after image load failureThomas White
2021-03-16get_hkl: Fix logic for loading unit cellThomas White
2021-03-16get_hkl: Add options to export to MTZ and XDSThomas White
2021-03-16Move MTZ and XDS export to libcrystfelThomas White
2021-03-15GUI: Add interface for --fix-profile-radius and --fix-divergenceThomas White
2021-03-12GUI: Add NULL filename for FromFile indexing (which isn't used here)Thomas White
2021-03-12Clean up after mergeThomas White
2021-03-12Merge branch 'pascal/electrons'Thomas White
2021-03-11indexamajig: Use static wavelength from DataTemplate as estimateThomas White
If the geometry file contains a literal wavelength, then let's use it. That's better than nagging the user for a --wavelength-estimate.
2021-03-11indexamajig: Add --max-indexer-threadsThomas White
This is a more general replacement for --pinkIndexer-thread-count.
2021-03-11indexamajig: Remove misleading messageThomas White
Spectrum file is currently not supported at all. Maybe later.
2021-03-11PinkIndexer: Remove custom indexing checksThomas White
These conflict badly with CrystFEL's own checks, creating a horrible user and developer experience. Later, if we want to handle wide bandwidth beams, we will improve the central CrystFEL checks to support it.
2021-03-11detgeom_transform_coords: Take an additional detector shiftThomas White
This allows the refined detector position to be used in a lot of places.
2021-03-11setup_indexing: Remove dtemplThomas White
There is absolutely nothing useful that an indexing algorithm can do with the opaque DataTemplate object.
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