Commit Graph

1185 Commits

Author SHA1 Message Date
leonarski_f 68047ef787 ScaleOnTheFly: Make scale factor always positive 2026-05-18 12:18:38 +02:00
leonarski_f 1bc96d0f17 jfjoch_test: Add test for systematic absences
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2026-05-17 21:10:03 +02:00
leonarski_f 980074baf9 UnitCell: Use direct path to gemmi unitcell
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2026-05-17 21:02:46 +02:00
leonarski_f be341e4cce Merge: Apply systematic absences to merging/merging statistics
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2026-05-17 20:56:20 +02:00
leonarski_f 1d3ccdaa00 Add possible reflection and completeness to MergeStatistics
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2026-05-17 20:05:28 +02:00
leonarski_f 39fef1bcef UpdateReflectionResolution: Separate file + clear bug
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2026-05-17 17:11:45 +02:00
leonarski_f f5447b3478 Update resolution of reflections based on consensus unit cell
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2026-05-17 16:23:49 +02:00
leonarski_f 4ca6684252 Merge: Fix ambiguity in names 2026-05-17 16:14:04 +02:00
leonarski_f 8b7bd4c8b6 jfjoch_process: remove printing final rotation lattice 2026-05-17 16:10:33 +02:00
leonarski_f 023e08e80d Integrate consensus unit cell handling 2026-05-17 16:08:48 +02:00
leonarski_f 6185b870cf Merge.h: Clean-up 2026-05-17 14:55:13 +02:00
leonarski_f 079d85628b jfjoch_scale: Clean-up 2026-05-17 14:54:20 +02:00
leonarski_f bb40c9518b Improve handling/calculating merge mask 2026-05-17 14:44:33 +02:00
leonarski_f 1bf70dcae7 Merge: Some clean-up of CC merge mask + add unit cell handling in IndexAndRefine 2026-05-17 14:32:39 +02:00
leonarski_f 25d3f660be HDF5NXmx: Fix
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2026-05-17 14:07:35 +02:00
leonarski_f 19f8d5e776 IndexAndRefine: Keep unit cell dimensions constant when using rotation indexing
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2026-05-17 13:15:22 +02:00
leonarski_f bed03840ea Merge: Mark TODO 2026-05-17 12:35:39 +02:00
leonarski_f 0ceff6e91b HDF5NXmx: Save unit cell after rotation indexing as main one + lattice (in UB-matrix format) + input unit cell as extra information 2026-05-17 12:33:10 +02:00
leonarski_f 68e3cbf1b4 Merge: Make table a bit prettier 2026-05-17 12:16:07 +02:00
leonarski_f b8e770e424 jfjoch_test: Fix scaling tests 2026-05-17 12:06:13 +02:00
leonarski_f 3e9c9c3f9b Merge: Use random number generator with fixed seed to assign half-datasets. Also make it per image, not per reflection
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2026-05-17 11:01:00 +02:00
leonarski_f 674ac4afa2 Merge: For anomalous signal, treat Friedel pairs separate, but add half-datasets
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2026-05-17 10:27:19 +02:00
leonarski_f 7e656ae1f9 IndexAndRefine: Fix pragma once 2026-05-17 10:04:03 +02:00
leonarski_f 43d8c93bd1 Merge: Add CC1/2 - I don't like it though, as there is big overlap between merge and merge statistics (better to calculate 1/2 datasets in merge separately?)
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2026-05-17 09:29:13 +02:00
leonarski_f 6dd9997610 jfjoch_scale: Minor improvements 2026-05-17 09:18:24 +02:00
leonarski_f 83ae1f0ced ScaleOnTheFly: mosaicity input is float, for consistence with other code 2026-05-17 09:14:32 +02:00
leonarski_f 6852908dff IndexAndRefine: Use pragma once 2026-05-17 09:12:16 +02:00
leonarski_f b0a64fb254 ScaleOnTheFly: DiffractionExperiment is first argument to constructor, as this is convention used elsewhere 2026-05-17 09:12:05 +02:00
leonarski_f 7212f5a628 jfjoch_scale: Add scaling iteration count 2026-05-17 09:09:50 +02:00
leonarski_f 65ff3a2b68 jfjoch_scale: Add tool, work in progress 2026-05-17 09:06:48 +02:00
leonarski_f de36a8c421 jfjoch_process: Add CC-based merging limit
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2026-05-16 22:02:47 +02:00
leonarski_f ac769ea930 jfjoch_process: Display metrics in millisecond and cut one digit of precision - down to 10 us 2026-05-16 21:34:13 +02:00
leonarski_f cd492db2eb jfjoch_process: Display scaling time in per image metrics 2026-05-16 21:30:19 +02:00
leonarski_f 1b781660c9 jfjoch_process: Minor refactor 2026-05-16 21:27:55 +02:00
leonarski_f a39a751670 jfjoch_process: Remove French & Wilson - let's leave it to Phenix to figure out 2026-05-16 21:25:28 +02:00
leonarski_f ffc5c1f561 IndexAndRefine: Save scaled reflections
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2026-05-14 20:11:27 +02:00
leonarski_f 0e9f7cc956 Save/transfer/read/display image scale results
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2026-05-14 16:37:21 +02:00
leonarski_f 1bccbda370 JFJochMessages: Need to include gemmi via exact path
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2026-05-13 21:31:05 +02:00
leonarski_f 1afbaf6f11 CrystalLattice: Need to include gemmi via exact path
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2026-05-13 21:21:14 +02:00
leonarski_f 2397a108dd ScaleOnTheFly: Add CC image/ref
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2026-05-13 17:26:51 +02:00
leonarski_f e70d71912b Merge: Add partiality limit 2026-05-13 17:26:51 +02:00
leonarski_f 6aa6890a8b Enable reading MTZ files with reference Fcalc 2026-05-13 17:26:51 +02:00
leonarski_f 08bf186766 Gemmi: Add more functionality from gemmi 0.7.5 2026-05-13 17:26:51 +02:00
takaba_k b27b140bf0 JFJochHDF5Reader: read pixel_mask defined under /detectorSpecific
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2026-05-13 15:25:52 +02:00
leonarski_f e1c661e48d Revert "Gemmi: Include through FetchContent full gemmi library (not limited cpp/hpp files)"
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This reverts commit b06dfc8357.
2026-05-13 13:32:25 +02:00
leonarski_f b06dfc8357 Gemmi: Include through FetchContent full gemmi library (not limited cpp/hpp files)
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2026-05-13 13:13:49 +02:00
leonarski_f d5b928fa73 Merge: Simplify code for merging, make it more efficient
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2026-05-13 12:27:50 +02:00
leonarski_f 02327bf610 BraggIntegrate2D: For very large sigma's, use 2% of I as sigma (if larger than sqrt(I)) 2026-05-13 12:27:50 +02:00
takaba_k 8a9d1d39ec Merge branch '2605-scaling-bugfix' into 2605-scaling
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2026-05-13 11:33:55 +02:00
leonarski_f f0601289d9 Report merge time
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2026-05-13 07:49:59 +02:00