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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.
2021-03-26partialator: Add missing comma in JSONThomas White
2021-03-26partialator: Add --harvest-fileThomas White
2021-03-05Mass update of copyright dates in source code commentsThomas White
2021-02-09partialator: Improve error messageThomas White
2021-01-27partialator/reflist: Propagate calloc NULL returnThomas White
This prevents an out-of-memory situation (due to ulimit) from manifesting as a segfault.
2021-01-27partialator: Fix (big) memory leaksThomas White
2021-01-06partialator: Reject crystals with obviously too large profile radiiThomas White
The criterion for "too large" is 20% of the 1/d value for the lowest reflection which is not systematically absent according to the centering. A profile radius larger than the 1/d value for a reflection will crash the xsphere partiality model, and some visualisation shows that this is a clearly non-physical situation. The profile radius shouldn't be anywhere near the inter-Bragg spacing for reasonable data. However, feedback shows that this is happening quite often in real data, probably due to bad indexing.
2020-12-04FormattingThomas White
2020-12-02partialator: Work with multiple input streamsThomas White
2020-10-27partialator: Don't copy detgeomThomas White
Detector geometry is not used for scaling/post-refinement
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.
2020-07-30partialator: Fix deep copy of image structureThomas 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.
2020-07-29partialator/process_hkl: Use geometryThomas White
2020-07-29partialator/process_hkl: Fix stream reading logicThomas White
2020-07-29Remove events.c, part 2Thomas White
New event parsing, done at the last minute in image-hdf5.c
2020-07-29Convert partialator to new Stream APIThomas White
2020-07-29Remove references to old headersThomas White
2020-07-29Convert stream to DataTemplateThomas 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
2020-01-10Mass update of copyright datesThomas White
2019-11-15Add partiality model GGPMWolfgang Brehm
2019-09-05partialator: Correct polarisation after update_predictions()Thomas White
Polarisation correction needs kpred values.
2019-09-05Allow the polarsation correction to be completely disabledThomas White
2019-09-02Don't need separate wavelength for polarisation correctionThomas White
Can use kpred
2019-09-02process_hkl,partialator: Allow arbitrary direction and degree of polarisationThomas White
2019-07-17partialator: Add "offset" model (Ewald sphere offset assuming monochromatic ↵Thomas White
beam)
2019-07-17partialator: Allow refinement of any partiality modelThomas White
2019-07-17partialator: Use Spectrum APIThomas White
2019-07-17partialator: WIP on new minimiserThomas White
2019-07-17partialator: Only strong reflections in specgraph, and remove resolution ↵Thomas White
limit for pgraph Rationale for pgraph: the viewer already has a resolution selector.
2019-07-17Allow correct_reflection() to correct anything, not just intensitiesThomas White
2019-06-21partialator: Add --force-lambdaThomas White
2019-06-21partialator: Progress bar for logs/grid scansThomas White
2019-06-19partialator: With --no-free, still show non-free residuals for crystals with ↵Thomas White
too few free reflections
2019-06-05partialator: Parallelise deltaCChalf calculationThomas White
2019-03-01partialator: Avoid double-free of stuff_from_stream and filenameThomas White
2019-01-29Fix some compiler warnings about string handlingThomas White
2019-01-28partialator: Fix incorrect free(audit_info)Thomas White
2019-01-28partialator: Fix multiple memory leaksThomas White
2019-01-28partialator: Fix a small typoThomas White
2018-11-30Factorise correction of intensity for G, B, p and LThomas White
There were no fewer than 8 different places in the code where these factors needed to be applied. They all need to agree on conventions such as whether the intensities in the pattern should be multiplied or divided by G to "correct" them. They were not. This commit reduces the number of places to three: one function (actually two functions, so that the value before partiality can also be calculated consistently), plus log_residual and scale_one_crystal, where slightly different logarithmic versions are used instead.
2018-11-22Count crystals with no reflections in various FoMsThomas White
This is the most common cause of NaN residuals, so it seems better to report that there weren't enough reflections than to report a NaN.
2018-11-14Merge branch 'tom/logmerge'Thomas White
2018-09-10Make sure reflection contribution list gets freedThomas White
2018-09-07partialator: Add option to disable deltaCChalfThomas White
2018-07-27partialator: Complain about NaN residualsThomas White
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