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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
2018-07-27partialator: Report number of crystals used in residualsThomas White
2018-07-27partialator: More improvements to pr-log logicThomas White
2018-07-27partialator: Also generate logs when not doing post-refinementThomas White
2018-07-26partialator: Add --min-resThomas White
2018-06-28Merge ln of intensity rather than intensities themselvesKen Beyerlein
2018-05-17Merge branch 'tom/cmake'Thomas White
2018-05-11partialator: Don't refuse to start if pr-logs folder existsThomas White
It's a nice idea, but I'm not sure it helps.
2018-05-11Disable initial scaling if requestedThomas White
2018-05-07Preparation for adjusting B factor during post-refinementThomas White
Add --no-Bscale option to partialator, and pass down as far as needed residual() no longer does scaling: call scale_one_crystal() first if necessary scale_one() replaces old linear_scale() function to scale a pair of RefLists (but so far does the same as the old function)
2018-05-07Remove unused parameterThomas White
2018-05-02Remove scale_all_to_referenceThomas White
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