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2021-04-20Fix memory handling semantics for ZMQ dataThomas White
2021-04-20image_read_data_block: Set the correct data typeThomas White
2021-04-20Build system fixes for MsgPackThomas 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
2021-04-16Remove requirement for data path to contain "/"Thomas White
For data formats other than HDF5, the location can be anything.
2021-04-16Meson: Update and fix MsgPack/ZMQ dependenciesThomas 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
2021-04-08Fix bugs in gen-sfs-anoThomas 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
2021-04-01Implement loading of saturation mapThomas White
2021-04-01Fix authorship for stream2sol.pyThomas White
2021-04-01FromFile indexer, stream2sol.py: Remove space escapingThomas White
This isn't necessary after all, for the same reason that im-sandbox doesn't need escaping: it can count off the fields where spaces aren't allowed, and anything left is the filename. I was over-thinking things.
2021-03-31FromFile indexer, stream2sol.py: Handle spaces in filenameThomas White
2021-03-31indexamajig: Handle spaces in filename when retrieving ID from queueThomas White
2021-03-31FromFile indexer, stream2sol.py: Add/update copyright commentsThomas White
2021-03-31stream2sol.py: Remove --include-parsThomas White
These are now obsolete, and the distributed version of CrystFEL will choke on them.
2021-03-31stream2sol.py: Remove unused definitionsThomas White
2021-03-31stream2sol.py: Add lattice type, centering and unique axisThomas White
2021-03-31stream2sol.py: Strip trailing whitespaceThomas White
2021-03-31stream2sol.py: Initial importThomas 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.
2021-03-29Add documentation for --harvest-fileThomas White
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
2021-03-26Add str_integration_methodThomas 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.
2021-03-25Add detgeom_mean_camera_lengthThomas White
2021-03-25PinkIndexer: fix conversion of detector shiftThomas White
2021-03-25FussinessThomas White
The FIXMEs have both already been fixed.
2021-03-25Avoid updating detector geometry structure during prediction refinementThomas White
This makes the behaviour consistent with the prediction itself, and removes another bit of mutable state.
2021-03-23Use crystal's detector shift during predictionThomas White
Previously, this was handled by updating the detector, but this could easily lead to strange double accounting.
2021-03-23Don't automatically set --no-refine --no-check-peaks with PinkIndexerThomas White
See c876486b for rationale.
2021-03-23CMake: ensure RPATH is always set for libcrystfelThomas White
This helps with finding dependencies installed in non-system locations.
2021-03-23CMake: formatting, use pkg_check_modules instead of pkg_search_moduleThomas White
2021-03-22Allow HDF5 path substitution when there are too many placeholder valuesThomas White
This allows, for example, masks which have fewer % signs in their HDF5 locations than the main data.
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