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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.
2021-04-23Add documentation about ZMQ/MsgPackThomas White
2021-04-23MsgPack: Implement peak list loadingThomas White
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.
2021-04-23MsgPack: More build system fixesThomas White
The changes in b22f6f524 were incorrect. config.h should never be included from libcrystfel headers, because that will include the main CrystFEL program config.h instead.
2021-04-23Clarify some error messagesThomas White
2021-04-23MsgPack: improve an error messageThomas White
2021-04-23Update documentation about geometry filesThomas White
2021-04-23Improve documentation about reflection data exportThomas White
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
2021-04-20MsgPack: Implement decoding numeric valuesThomas White
2021-04-20MsgPack: Improve a warning messageThomas White
2021-04-20indexamajig: Fix --no-image-data/--no-mask-dataThomas White
2021-04-20image_read_data_block: Warn user if things go wrongThomas White
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.
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