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2021-05-11Add set_combo_id()Thomas White
2021-05-07Add deselect_when_active()Thomas White
2021-05-07Add has_unique_axis()Thomas White
2021-05-07GUI: Add missing initialisation/load/save for ambi.backendThomas White
2021-05-07MsgPack: Warn if dtempl->peak_list is NULLThomas White
2021-05-07MsgPack: Use the right pointer for "bin" keysThomas White
2021-05-07MsgPack: Use top-level object directly if it is a mapThomas 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
2021-04-30write_to_mtz: Fix column names and typesThomas White
2021-04-29MsgPack: Handle floating-point data, fix array readThomas White
2021-04-29MsgPack: Handle strings if they can be converted to integersThomas White
2021-04-28MsgPack: Remove warning about multiple objectsThomas White
If this happens once, it'll probably happen every frame. This makes things very noisy.
2021-04-27indexamajig: Fix an error messageThomas White
2021-04-27Complain if there are unused defaults in geometry fileThomas White
This will help to avoid mistakes when people put statements at the end of the geometry file, rather than the top. Closes https://gitlab.desy.de/thomas.white/crystfel/-/issues/20.
2021-04-27Fix #include in filters.cThomas White
2021-04-27Rename libcrystfel's config.h to libcrystfel-config.hThomas White
This removes the big potential for confusion, which has happened several times (see e.g. 095cbebaf6). It also fixes in-tree builds with CMake (but seriously, always use out-of-tree builds). Fixes #2.
2021-04-27Mass update of copyright dates in manpagesThomas White
2021-04-27Swap the order of iteration in filters.cThomas White
This code hasn't been looked at for a very long time, and can be made a bit faster by iterating in a more cache-friendly way.
2021-04-23Fix build without MsgPackThomas 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.
2021-04-23Add 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.
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