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  • 61776a446e Scaling/Merging: Work in progress to clean-up data strctures leonarski_f 2026-05-25 12:54:13 +02:00
  • a85eb4b137 Scaling/Merging: Work in progress to improve the information that is fed to scaling. This is a mess at the moment - with redundant data structures, etc. - will clean this up, later. leonarski_f 2026-05-25 10:09:49 +02:00
  • fe19ff8ec6 ScaleOnTheFly: WIP: ScalingPostRefResidual leonarski_f 2026-05-25 09:14:15 +02:00
  • 6f3bcdd76f ScaleOnTheFly: Add (optional) regularization leonarski_f 2026-05-25 09:13:59 +02:00
  • 815080940a XtalOptimizer: Fix bugs in XtalOptimizerRotationOnly: mismatch between rotated and omega=0 coordinate system; add regularization of rotation to zero; use reciprocal cell in refinement (no need to do inverse) leonarski_f 2026-05-25 09:06:35 +02:00
  • dce6ee3d6c XtalOptimizer: Store 1/lambda (not lambda) + add check for very small lambda + set beam center as one parameter block + fix poni rotation convention (rot2 was likely wrong) leonarski_f 2026-05-24 14:27:56 +02:00
  • 6621ddb2ef BraggIntegrate2D: Keeps observed x and y positions for reflections leonarski_f 2026-05-24 12:38:54 +02:00
  • 752d3e95f1 XtalOptimizer: ChatGPT fix to monoclinic extraction logic leonarski_f 2026-05-22 21:08:02 +02:00
  • 952559d3a7 XtalOptimizer: Freeze latt_vec2 for highly regular systems leonarski_f 2026-05-22 20:44:16 +02:00
  • 65a28b2b34 XtalOptimizer: Zero initialize latt_vec0, latt_vec1, latt_vec2 leonarski_f 2026-05-22 20:43:10 +02:00
  • 41896a7ef2 CHANGELOG leonarski_f 2026-05-22 20:30:37 +02:00
  • 2e18291256 VERSION: 1.0.0-rc.146 leonarski_f 2026-05-22 20:24:11 +02:00
  • 6ad580d8c1 jfjoch_viewer: Fix shift of labels and pixels leonarski_f 2026-05-22 20:22:19 +02:00
  • 8d8e9717d0 jfjoch_scale: Align help messages leonarski_f 2026-05-21 13:40:10 +02:00
  • 65e4b2fdb9 jfjoch_scale: Fix typo leonarski_f 2026-05-21 11:44:39 +02:00
  • 8d80c64bed jfjoch_tests: Fix JFJochReader_ReadReflections_VDS leonarski_f 2026-05-20 12:36:43 +02:00
  • 805dc7d164 jfjoch_process: Select output format for scaling results leonarski_f 2026-05-20 10:33:21 +02:00
  • e59f11cb44 jfjoch_process: Simplify writing result of space group search, without Logger leonarski_f 2026-05-20 10:27:20 +02:00
  • 8b307a54ee jfjoch_scale: Improve process of reading reflections, particularly with multiple files leonarski_f 2026-05-20 09:33:09 +02:00
  • 52281bfd58 jfjoch_process/jfjoch_scale: Improve parameter handling leonarski_f 2026-05-20 08:37:19 +02:00
  • 18c0d0cf6f Merge: More printing is done directly, leonarski_f 2026-05-20 08:25:43 +02:00
  • 270e906fe7 jfjoch_process: Introduce long options + image stride leonarski_f 2026-05-20 07:58:56 +02:00
  • 39823ddb67 General function to write reflections in multiple formats (need to better integrate into jfjoch_scale and jfjoch_process) leonarski_f 2026-05-19 22:12:42 +02:00
  • 0eb0c50c66 Merge: Generate R-free flags leonarski_f 2026-05-19 21:04:55 +02:00
  • e4ff4dca9e ScalingSettings: file format and intensity settings leonarski_f 2026-05-19 17:22:13 +02:00
  • 1a70c1987a jfjoch_scale: A bit nicer handling of reflection statistics and preparation leonarski_f 2026-05-18 21:28:09 +02:00
  • a05ec050ed Merge: Merging happens in MergeOnTheFly class, not in function leonarski_f 2026-05-18 21:09:22 +02:00
  • c90e4facce CorrelationCoefficient: Separate class leonarski_f 2026-05-18 20:23:13 +02:00
  • 371a69c5b8 Merge: Fix CC calculation leonarski_f 2026-05-18 14:04:56 +02:00
  • d555042dc6 jfjoch_scale: Seems to work (though unstable) leonarski_f 2026-05-18 13:38:23 +02:00
  • 7c0cc22e47 HDF5: Save per reflection scaling factor leonarski_f 2026-05-18 13:37:55 +02:00
  • 8371743cbb Merge: Add CCref leonarski_f 2026-05-18 13:13:51 +02:00
  • 4e2043ec4b jfjoch_viewer: Add Image B-factor leonarski_f 2026-05-18 12:54:24 +02:00
  • ac907e8aef jfjoch_viewer: Fix displaying per image CC leonarski_f 2026-05-18 12:23:22 +02:00
  • 68047ef787 ScaleOnTheFly: Make scale factor always positive leonarski_f 2026-05-18 12:18:38 +02:00
  • 1bc96d0f17 jfjoch_test: Add test for systematic absences leonarski_f 2026-05-17 21:10:03 +02:00
  • 980074baf9 UnitCell: Use direct path to gemmi unitcell leonarski_f 2026-05-17 21:02:46 +02:00
  • be341e4cce Merge: Apply systematic absences to merging/merging statistics leonarski_f 2026-05-17 20:56:20 +02:00
  • 1d3ccdaa00 Add possible reflection and completeness to MergeStatistics leonarski_f 2026-05-17 20:00:32 +02:00
  • 39fef1bcef UpdateReflectionResolution: Separate file + clear bug leonarski_f 2026-05-17 17:11:45 +02:00
  • f5447b3478 Update resolution of reflections based on consensus unit cell leonarski_f 2026-05-17 16:23:49 +02:00
  • 4ca6684252 Merge: Fix ambiguity in names leonarski_f 2026-05-17 16:13:48 +02:00
  • 8b7bd4c8b6 jfjoch_process: remove printing final rotation lattice leonarski_f 2026-05-17 16:10:33 +02:00
  • 023e08e80d Integrate consensus unit cell handling leonarski_f 2026-05-17 16:08:48 +02:00
  • 6185b870cf Merge.h: Clean-up leonarski_f 2026-05-17 14:54:50 +02:00
  • 079d85628b jfjoch_scale: Clean-up leonarski_f 2026-05-17 14:54:20 +02:00
  • bb40c9518b Improve handling/calculating merge mask leonarski_f 2026-05-17 14:44:33 +02:00
  • 1bf70dcae7 Merge: Some clean-up of CC merge mask + add unit cell handling in IndexAndRefine leonarski_f 2026-05-17 14:32:39 +02:00
  • 25d3f660be HDF5NXmx: Fix leonarski_f 2026-05-17 14:07:35 +02:00
  • 19f8d5e776 IndexAndRefine: Keep unit cell dimensions constant when using rotation indexing leonarski_f 2026-05-17 13:15:22 +02:00
  • bed03840ea Merge: Mark TODO leonarski_f 2026-05-17 12:35:39 +02:00
  • 0ceff6e91b HDF5NXmx: Save unit cell after rotation indexing as main one + lattice (in UB-matrix format) + input unit cell as extra information leonarski_f 2026-05-17 12:33:10 +02:00
  • 68e3cbf1b4 Merge: Make table a bit prettier leonarski_f 2026-05-17 12:16:07 +02:00
  • b8e770e424 jfjoch_test: Fix scaling tests leonarski_f 2026-05-17 12:06:13 +02:00
  • 3e9c9c3f9b Merge: Use random number generator with fixed seed to assign half-datasets. Also make it per image, not per reflection leonarski_f 2026-05-17 11:01:00 +02:00
  • 674ac4afa2 Merge: For anomalous signal, treat Friedel pairs separate, but add half-datasets leonarski_f 2026-05-17 10:27:19 +02:00
  • 7e656ae1f9 IndexAndRefine: Fix pragma once leonarski_f 2026-05-17 10:03:48 +02:00
  • 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?) leonarski_f 2026-05-17 09:29:13 +02:00
  • 6dd9997610 jfjoch_scale: Minor improvements leonarski_f 2026-05-17 09:17:02 +02:00
  • 83ae1f0ced ScaleOnTheFly: mosaicity input is float, for consistence with other code leonarski_f 2026-05-17 09:14:32 +02:00
  • 6852908dff IndexAndRefine: Use pragma once leonarski_f 2026-05-17 09:12:16 +02:00
  • b0a64fb254 ScaleOnTheFly: DiffractionExperiment is first argument to constructor, as this is convention used elsewhere leonarski_f 2026-05-17 09:12:05 +02:00
  • 7212f5a628 jfjoch_scale: Add scaling iteration count leonarski_f 2026-05-17 09:09:50 +02:00
  • 65ff3a2b68 jfjoch_scale: Add tool, work in progress leonarski_f 2026-05-17 09:06:48 +02:00
  • de36a8c421 jfjoch_process: Add CC-based merging limit leonarski_f 2026-05-16 22:02:47 +02:00
  • ac769ea930 jfjoch_process: Display metrics in millisecond and cut one digit of precision - down to 10 us leonarski_f 2026-05-16 21:34:13 +02:00
  • cd492db2eb jfjoch_process: Display scaling time in per image metrics leonarski_f 2026-05-16 21:30:19 +02:00
  • 1b781660c9 jfjoch_process: Minor refactor leonarski_f 2026-05-16 21:27:55 +02:00
  • a39a751670 jfjoch_process: Remove French & Wilson - let's leave it to Phenix to figure out leonarski_f 2026-05-16 20:59:41 +02:00
  • ffc5c1f561 IndexAndRefine: Save scaled reflections leonarski_f 2026-05-14 20:11:27 +02:00
  • 0e9f7cc956 Save/transfer/read/display image scale results leonarski_f 2026-05-14 15:45:58 +02:00
  • 1bccbda370 JFJochMessages: Need to include gemmi via exact path leonarski_f 2026-05-13 21:31:05 +02:00
  • 1afbaf6f11 CrystalLattice: Need to include gemmi via exact path leonarski_f 2026-05-13 21:21:14 +02:00
  • 2397a108dd ScaleOnTheFly: Add CC image/ref leonarski_f 2026-05-13 15:23:32 +02:00
  • e70d71912b Merge: Add partiality limit leonarski_f 2026-05-13 14:36:41 +02:00
  • 6aa6890a8b Enable reading MTZ files with reference Fcalc leonarski_f 2026-05-13 14:22:39 +02:00
  • 08bf186766 Gemmi: Add more functionality from gemmi 0.7.5 leonarski_f 2026-05-13 13:44:02 +02:00
  • b27b140bf0 JFJochHDF5Reader: read pixel_mask defined under /detectorSpecific takaba_k 2026-05-13 15:25:52 +02:00
  • e1c661e48d Revert "Gemmi: Include through FetchContent full gemmi library (not limited cpp/hpp files)" leonarski_f 2026-05-13 13:32:25 +02:00
  • b06dfc8357 Gemmi: Include through FetchContent full gemmi library (not limited cpp/hpp files) leonarski_f 2026-05-13 13:13:17 +02:00
  • d5b928fa73 Merge: Simplify code for merging, make it more efficient leonarski_f 2026-05-13 12:27:43 +02:00
  • 02327bf610 BraggIntegrate2D: For very large sigma's, use 2% of I as sigma (if larger than sqrt(I)) leonarski_f 2026-05-13 12:20:10 +02:00
  • 8a9d1d39ec Merge branch '2605-scaling-bugfix' into 2605-scaling takaba_k 2026-05-13 11:33:55 +02:00
  • f0601289d9 Report merge time leonarski_f 2026-05-13 07:49:59 +02:00
  • c55e91ccfa Merge: Simplify (but not yet gaining performance) leonarski_f 2026-05-13 07:48:17 +02:00
  • 078c871ec1 jfjoch_process: Fix reading missing metadata takaba_k 2026-05-12 21:44:12 +02:00
  • 2fa9293fda HKLKeyGenerator: Make HKLKeyGenerator having already prebuilt gemmi data structures leonarski_f 2026-05-12 19:38:15 +02:00
  • e45d1ff4d3 jfjoch_process: removed geometry restriction option takaba_k 2026-05-12 16:04:45 +02:00
  • b7627b5a11 jfjoch_process: Multiple scaling iterations leonarski_f 2026-05-11 13:59:16 +02:00
  • a468e46222 Merge: Remove scaling correction for now (need to think about it) leonarski_f 2026-05-11 13:56:05 +02:00
  • b1fe201047 Clean-up leonarski_f 2026-05-11 13:25:02 +02:00
  • 0cf801c2d2 Merge: Remove old statistics leonarski_f 2026-05-11 13:18:49 +02:00
  • cecb3024e0 ScaleOnTheFly: Fix B term leonarski_f 2026-05-11 13:17:10 +02:00
  • c92d01222c ScaleOnTheFly: Calculate rotation partiality correctly leonarski_f 2026-05-11 13:15:52 +02:00
  • aa347096d2 Merge: Remove unused statistics values (for now) leonarski_f 2026-05-11 13:12:02 +02:00
  • 4e6a6e2aa2 jfjoch_process: Fixes to parameter logic leonarski_f 2026-05-11 13:11:42 +02:00
  • 9ec8ebcde8 jfjoch_process: Add space group number handling leonarski_f 2026-05-11 13:06:28 +02:00
  • b53f0d6474 jfjoch_process: Print statistics moved to Merge.h/Merge.cpp and ScalingResult.cpp/ScalingResult.h leonarski_f 2026-05-11 10:37:39 +02:00
  • 486310fd87 jfjoch_process: Optimize design choices for scaling integration leonarski_f 2026-05-11 10:10:11 +02:00
  • e70b21f6de HKLKey: Test properly, fix bug with merging Friedel pairs when no SG given leonarski_f 2026-05-11 08:29:41 +02:00