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path: root/src/indexamajig.c
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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
2021-04-20indexamajig: Fix --no-image-data/--no-mask-dataThomas White
2021-04-08indexamajig: Add a missing harvest parameterThomas 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.
2021-03-26indexamajig: Add --harvest-fileThomas White
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.
2021-03-19FromFile 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.
2021-03-12Clean 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.
2021-03-11setup_indexing: Remove dtemplThomas White
There is absolutely nothing useful that an indexing algorithm can do with the opaque DataTemplate object.
2021-03-11indexamajig: Add --wavelength-estimateThomas White
This is a more sensible non-indexer-specific and non-Xray-specific replacement for --pinkIndexer-override-photon-energy
2021-03-05Mass update of copyright dates in source code commentsThomas White
2020-10-26Label all uses of cell tolerancesThomas White
I'm sick of fixing this same issue over and over again. New rule: any code handling unit cell tolerances MUST be labelled with details of units.
2020-08-27indexamajig: Hide --hdf5-peaksThomas White
This option is no longer used, and generates a warning. The peak location comes in the geometry file instead.
2020-08-19Remove STREAM_UNITCELL and STREAM_CRYSTALSThomas White
These flags weren't orthogonal at all, which was turning some routines into spaghetti-code. It's still possible to avoid read/write of peak lists, reflection data or image data. But that's it.
2020-08-19Make Stream responsible for its own DataTemplateThomas White
It makes no sense for a different DataTemplate to be used for every frame in a stream. And this way makes everything much easier for users ot the API.
2020-08-07Move indexers out of APIThomas White
2020-07-31Move spectrum loading out of indexamajig/process_imageThomas White
2020-07-29New way of injecting version informationThomas White
Also, this fixes some incorrect headers and adds --version flags to programs which didn't yet have them.
2020-07-29Add --no-image-data and --no-mask-dataThomas White
2020-07-29Remove unused includesThomas White
2020-07-29Convert indexamajig to new Stream APIThomas White
2020-07-29Remove references to old headersThomas White
2020-07-29Get rid of imagefile_field_list and stuff_from_streamThomas White
The only place this is used is in geoptimiser, to get the average_camera_length, itself a very bad solution.
2020-07-29Port indexamajig to new API, part IThomas White
2020-07-29Split off parse_peaksearch()Thomas White
2020-07-29Add DataTemplate to iargsThomas White
2020-07-09unit cell vectors are correct, space group missingPascal Hogan-Lamarre
2020-02-11indexamajig: Fix incorrect units of default cell toleranceThomas White
2020-02-05indexamajig: Hide --spectrum-file and add a warningThomas White
2020-01-10Mass update of copyright datesThomas White
2019-10-29bug fix: rename peakFinder9 argumentYaroslav Gevorkov
2019-10-18indexamajig: Fix incorrect timeout logicThomas White
2019-10-17indexamajig: Shut down gracefully after failed image loadThomas White
2019-09-23Add missing initialisationThomas White
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