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2024-05-06indexamajig: Avoid is_hdf5_file("-", ...)Thomas White
With thanks to biochem-fan. Fixes: https://github.com/taw10/crystfel/issues/12
2024-02-06Sort-of-workaround for argp '--help' crash on MacOSThomas White
Indexamajig --help causes a segfault on MacOS due to a bug in argp-standalone. That package is unlikely to be updated any time soon. Eventually, Homebrew might switch to one of the non-crashy forks, but probably not soon. We aren't the only ones affected - see https://www.openwall.com/lists/musl/2021/02/10/1 This commit adds a warning message to state that we already know about it, and it's not "our" fault. It also removes the corresponding test, since we know it fails.
2024-01-12indexamajig: Implement --max-mille-levelThomas White
2024-01-10indexamajig: Start implementing --max-mille-levelThomas White
2023-12-22FormattingThomas White
2023-12-22indexamajig: Add --asapo-consumer-timeoutThomas White
This also reduces the default timeout to 500 ms.
2023-12-22indexamajig: Add --no-data-timeoutThomas White
2023-09-20indexamajig: Add --mille-dirThomas White
2023-07-28indexamajig: Hooks for MilleThomas White
2023-07-26indexamajig: Fix a few small memory leaksThomas White
2023-07-25indexamajig: Add missing initialiserThomas White
2023-06-02ASAP::O: Use input stream name as output (add _hits to data source)Thomas White
This means we don't need a stream name any more, so --asapo-output-stream became a simple flag parameter.
2023-06-01indexamajig: Add --asapo-output-stream (hits only)Thomas White
2023-06-01indexamajig: Avoid is_hdf5_file(NULL, ...)Thomas White
2023-05-05indexamajig: Catch common error '-i input.h5'Thomas White
2023-05-05Move peak search parameters into separate structureThomas White
This change takes the peak parameters structure from gui_project.h, moves it to libcrystfel/peaks.h and uses it everywhere. It should slightly reduce the hassle involved with adding a new parameter. Four parameters (noisefilter, median_filter, check_hdf5_snr, use_saturated) were previously not part of the GUI project structure. Now they are, via the new structure. However, they are not yet exposed via the GUI and just take their default values.
2023-05-02indexamajig: Add --cpu-pinThomas White
Similar code was stripped out 3.5 years ago by 4f4e5d05269eee6b192c271f2f9730a1ad3a4fbd. However, it seems there are still systems where it improves performance a lot.
2023-02-08indexamajig: Use static clen as --camera-length-estimate, if givenThomas White
This makes it work the same way as --wavelength-estimate.
2022-11-08indexamajig: Add --cell-parameters-onlyThomas White
2022-10-05Merge branch 'pf8_faster'Thomas White
2022-09-22Add fast mode for peakfinder8Alexandra Tolstikova
2022-09-21asdf: Add fast modeAlexandra Tolstikova
This adds an optional fast mode for asdf indexing, which is around 3 times faster with only a few percent lower success rate.
2022-07-07indexamajig: --asapo-wait-for-stream doesn't require an argumentThomas White
2022-07-07indexamajig: Make sure data format is initialisedThomas White
2022-06-23indexamajig: Add --asapo-wait-for-streamThomas White
2022-06-22indexamajig: Wrap ZMQ parameters into separate structureThomas White
2022-06-22indexamajig: Wrap ASAP::O parameters up inside separate structureThomas White
2022-06-02indexamajig: Make all three input options mutually exclusiveThomas White
2022-06-02indexamajig: Add --asapo-streamThomas White
2022-06-02Seedee deserializationThomas White
2022-06-02ASAP::O: Remove filesystem pathThomas White
This is only really needed for offline processing. It's an added complication for now. Maybe we'll revisit it later and re-expose this, though.
2022-06-02ASAP::O: Expose data sourceThomas White
2022-06-02indexamajig: Special cases for ASAP::O as for ZMQThomas White
2022-06-02ASAP::O: Group ID stuffThomas White
2022-06-02ASAP::O gutsThomas White
2022-06-02indexamajig: Put MsgPack peaks through validation procedure, like HDF5Thomas White
2022-05-31indexamajig: Fix JSON when not indexing/integratingThomas White
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/68
2021-09-17indexamajig: Add --data-formatThomas White
2021-07-21Reduce variable scope where possibleThomas White
2021-07-14Make all the indexer-specific option structures non-opaqueThomas White
Making them opaque seemed like a nice idea, because all the indexers could take care of their own command-line arguments. However, it doesn't work at all when indexing is run via the API.
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.
2021-05-05indexamajig: 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.
2021-04-30indexamajig: Fix an incorrect error messageThomas White
2021-04-27indexamajig: Fix an error messageThomas White
2021-04-23indexamajig: Add --zmq-subscribeThomas 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
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