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2023-07-11partialator: Add --unmerged-outputThomas White
2023-06-01indexamajig: Add --asapo-output-stream (hits only)Thomas White
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.
2023-05-02Remove pattern_sim and partial_simThomas White
Use of these programs has been following this pattern for several years: 1. Neglect 2. Once yearly attempt by someone to use either tool 3. Discovery that it's totally broken 4. Bug report and fast bug fix 5. Go to 1. For more discussion, see the issue referenced below. Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/81
2023-04-20compare_hkl: Recognise --fom=cc*, cc1/2 and cchalfThomas White
2023-04-20indexamajig(1): Mention "nproc"Thomas White
2023-03-01Remove vestigial geoptimiser stuffThomas White
2023-02-20Fix small manual problemsThomas White
2023-02-17indexamajig(1): Update text and fix untruthsThomas White
2023-02-09pattern_sim: Fix up behaviour after DataTemplateThomas White
Analogous fixes to those done for partial_sim in 0effb5f83daf0317aa97a1cd10e7708551a25201.
2023-02-09partial_sim: Fix up behaviour after DataTemplateThomas White
It's been broken for a long time. Now, at least it does what the documentation says it does. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/78
2023-02-08crystfel_geometry(5): Add missing documentation for 'bandwidth'Thomas White
2022-12-07crystfel_geometry(5): Add a missing equals signThomas White
2022-11-08indexamajig: Add --cell-parameters-onlyThomas White
2022-09-21indexamajig(1): Add --asdf-fastThomas White
2022-06-23indexamajig: Add --asapo-wait-for-streamThomas White
2022-06-02indexamajig: Add --asapo-streamThomas White
2022-06-02Seedee deserializationThomas White
2022-06-02indexamajig(1): Mention ASAP::OThomas White
2022-06-02Update indexamajig(1) to say that things also refer to --peaks=msgpackThomas White
2021-11-25partialator: Handle spaces in custom split fileThomas White
The csplit format is ambiguous when the filenames contain spaces. To make things a bit clearer, the file now requires the fields to be separated by exactly one space rather than any number of tabs/spaces. Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/55
2021-10-28Add 'mask_panel_edges' to geometry fileThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/27
2021-10-26Remove detector rail direction altogetherThomas White
This got missed out by accident in the conversion to DataTemplate, but absolutely no-one noticed. In the meantime, my views on how the geometry files should work have changed somewhat. I don't want to maintain the extra complexity here when it isn't even clear that it will eliminate the need to re-refine geometry for each camera length. This commit just takes the rail direction stuff out of the documentation and the geometry file parser. Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/50
2021-10-20Add "plain" MTZ file layout, distinct from "Bijvoet" layoutThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/52
2021-09-17indexamajig: Add --data-formatThomas White
2021-08-12Updates for manual pagesThomas White
2021-07-23partialator: Add --log-folderThomas White
2021-07-05indexamajig(1): Clarify --min-peaks default valueThomas 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.
2021-04-27Mass update of copyright dates in manpagesThomas 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
2021-04-21indexamajig: Replace --zmq-msgpack with --zmq-inputThomas White
This removes some unnecessary work (getting the address from the file) and seems cleaner.
2021-03-29Add documentation for --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.
2021-03-11indexamajig(1): Fix formatting and spellingThomas White
2021-03-11indexamajig: Add --max-indexer-threadsThomas White
This is a more general replacement for --pinkIndexer-thread-count.
2021-03-11PinkIndexer: Remove wide bandwidth stuffThomas White
This will return later in a more centralised form, if we decide to work further on wide bandwidth.
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.
2021-03-11indexamajig: Add --wavelength-estimateThomas White
This is a more sensible non-indexer-specific and non-Xray-specific replacement for --pinkIndexer-override-photon-energy
2021-03-09Add the ability to use multiple bad pixel masks at onceThomas White
2021-01-22compare_hkl: Remove --intensity-shellsThomas White
No-one uses it, it doubles the complexity of the code, and the manual even warns not to use it.
2021-01-08Update documentation about max_adu, and add a warningThomas White
2020-12-18Improve documentation about file-based peak listsThomas White
2020-12-18Add peak_list_type in geometry fileThomas White
2020-12-16Add flag_{lessthan,morethan,equal} in geometry fileThomas White
This makes handling Pilatus/Eiger files, as well as many others, much easier.
2020-10-23partialator(1): Add missing partiality modelsThomas White
2020-07-29Add detector_shift_{x,y} to geometry fileThomas White
2020-07-29Rearrange geometry manual pageThomas White
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