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2019-03-07Remove old debug messageThomas White
2019-03-06indexamajig: Rename --min-gradient to --min-squared-gradientThomas White
The eventual aim of this is to deprecate the "--min-gradient" option, resolving the long-standing confusion about whether this option is the gradient or the squared gradient.
2019-03-01partialator: Fix two small memory leaksThomas White
2019-03-01partialator: Check for failed minimiser setup in write_grid()Thomas White
2019-03-01partialator: Fix string overruns in write_grid()Thomas White
2019-03-01partialator: Avoid double-free of stuff_from_stream and filenameThomas White
2019-01-30Simplify fill_queue()Thomas White
2019-01-30Fixes for get_pattern()Thomas White
2019-01-30Fix read_prefixed_filename()Thomas White
2019-01-29Remove debugging messageThomas White
2019-01-29Fix some compiler warnings about string handlingThomas White
2019-01-29Tidy up no_moreThomas White
2019-01-29Improvements to get_pattern()Thomas White
2019-01-29Add multi_event_geometry() functionThomas White
2019-01-29hdfsee: Fix possible string truncationThomas White
2019-01-28partialator: Display error message if minimiser can't be set upThomas White
2019-01-28partialator: Fix incorrect free(audit_info)Thomas White
2019-01-28partialator: Catch failure to set up post-refinement minimiserThomas White
2019-01-28partialator: Fix multiple memory leaksThomas White
2019-01-28partialator: Fix a small typoThomas White
2019-01-22Fix some small memory leaksThomas White
2019-01-03indexamajig: Return non-zero exit status if no patterns were processedThomas White
2018-12-18make_pixelmap: Use <input>.h5 as default output filenameThomas White
2018-12-18check_hkl: Catch NaN L-value due to two zeroed negative intensitiesThomas White
2018-12-06make_pixelmap: Fix #includeThomas White
2018-12-06Add make_pixelmap to core CrystFELThomas White
2018-12-04partialator: Fix leaked file handleThomas White
2018-12-03indexamajig: Add --wait-for-fileThomas 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.
2018-11-22Don't weight reflections by partiality in residualThomas White
Because we want under-prediction to be penalised just as much as over-prediction
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.
2018-11-22log_residual: Actually set n_usedThomas White
2018-11-22Restore reflection weightingThomas White
2018-11-22Typecast the data from xxdThomas White
2018-11-22Don't do deltaCChalf with reference data setThomas White
2018-11-16partialator: Handle partial reflections properly in deltaCChalfThomas White
2018-11-16Require deltaCChalf to actually be negative before rejectingThomas White
2018-11-15indexamajig: Name and shame slow processing stagesThomas White
2018-11-14Remove unused variablesThomas White
2018-11-14Merge branch 'tom/logmerge'Thomas White
2018-11-09Fix prototype for calculate_refl_mean_varThomas White
2018-11-09geoptimiser: Fix ifdefsThomas White
2018-11-09Time account fussinessThomas White
2018-11-09Remove ununused variableThomas White
2018-11-06Exclude flagged crystals from deltaCChalf calculationThomas White
2018-11-06Separate variable for excluded reflectionThomas White
It was actually fine, becuase "refl" isn't used again until it's re-set at the start of the next loop iteration. However, it was confusing.
2018-11-02Remove some residual debugging stuffThomas White
2018-11-02partialator: Speed up deltaCChalf calculationThomas White
I'd been lazy with the first implementation, and it's turned out to be too slow. Instead of calculating the entire CChalf each time removing a different crystal, this makes it store some intermediate values so that a crystal can easily be subtracted afterwards.
2018-11-02Fix some warnings from static analyserThomas White
2018-10-30compare_hkl: Check for Bijvoet partners only once all other rejection tests ↵Thomas White
have passed
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