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2018-12-18Update ChangeLogThomas White
2018-12-18make_pixelmap: Use <input>.h5 as default output filenameThomas White
2018-12-18Update partialator manualThomas White
2018-12-18A few manual fixesThomas White
2018-12-18check_hkl: Catch NaN L-value due to two zeroed negative intensitiesThomas White
2018-12-18check_hkl: Add a note to manual pageThomas White
2018-12-11scripts/detector-shift: Click to choose different centerChun Hong Yoon
2018-12-06make_pixelmap: Fix #includeThomas White
2018-12-06Add make_pixelmap to core CrystFELThomas White
2018-12-04WhitespaceThomas White
2018-12-04partialator: Fix leaked file handleThomas White
2018-12-03indexamajig: Add --wait-for-fileThomas White
2018-11-30Merge branch 'tom/partials'Thomas 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.
2018-11-27xds: Tune indexing parametersThomas White
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
2018-11-22Typecast the data from xxdThomas White
2018-11-22Restore reflection weightingThomas White
2018-11-22Rename prediction refinement residual functionThomas White
Because there's another function with this name in merge.c
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
2018-11-15Update ChangeLogThomas White
2018-11-15indexamajig: Name and shame slow processing stagesThomas White
2018-11-14Fix error message about dimensionality of image dataThomas White
Fixes CRYS-205
2018-11-14Clean up set_dim_structure_entry() and parsing of "dimX" in geometry fileThomas White
Fixes CRYS-212
2018-11-14Remove unused variablesThomas White
2018-11-14Merge branch 'tom/logmerge'Thomas White
2018-11-13Add some new scriptsThomas 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
2018-11-09Set -Wall for files under srcThomas 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 possibly uninitialised dataf in read_cbf_data()Thomas White
2018-11-02Change a couple of important asserts to if statementsThomas White
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
2018-10-30peakfinder8: Fix some use-after-free errorsThomas White
2018-10-22fix freeing unallocated memoryYaroslav Gevorkov
2018-10-18indexamajig: Fix --spectrum-file optionThomas White
2018-10-15xgandalf: always return centered cell, if it was providedYaroslav Gevorkov
2018-10-08partialator: Add missing manual entry for --no-deltacchalfThomas White
2018-10-08geoptimiser: Fix incorrect calculation of displacement errorOleksandr Yefanov
Fixed issue with incorrect calculation of the "displacement error" for some panels. Also fixed wrong "displacement error" in case of very small amount of patterns.
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