6 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	636ed1e180	space group: use merge reduced chi^2 (not R-meas) for the consistency check ... The R-meas-ratio over-symmetry guard (commit 7ade6d9) missed a near-perfect pseudo-2-fold: InsH2 (XDS R3) has a false 2-fold at operator CC 0.85 whose merged intensities still correlate well, so R-meas inflated only ~1.3x and R32 was accepted (ISa collapsing to 3.9). The reduced chi^2 (within-orbit scatter / sigma^2) is the right signal - false equivalents disagree by many sigma even when they correlate well. Measured chi^2 ratio (candidate / best subgroup) across the test set: true point groups <= 1.63 (a cubic merge of a noisy crystal, InsI3, is the worst real case), false >= 2.26 (InsH2) and 6.0 (InsH3); threshold 2.0 separates them. InsH2 now resolves to R3 (ISa 6.1 from the false R32's 3.9); InsH3/InsI2/InsI3/cytC/lysoC/MyoB/EP0210 unchanged and correct. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-30 21:54:51 +02:00
leonarski_fandClaude Opus 4.8	7ade6d9906	space group: reject over-symmetrised point groups by merge R-meas consistency ... Per-operator CC alone cannot separate a real weak symmetry operator from a false moderate one: a noisy crystal's genuine cubic 2-folds (InsI2 I23, CC ~0.51) score BELOW a pseudo-symmetric crystal's false 2-fold (InsH3, CC 0.64), so no CC threshold works. Add a self-consistency test: a candidate point group is accepted only if merging the intensities under it does not inflate R-meas past max_rmeas_ratio (1.5x) the most-consistent candidate. A false operator forces non-equivalent reflections together and blows R-meas up; a real one leaves it flat. Fixes InsH3: was over-called R32 (ISa collapsed to 2.2 from the forced merge), now correctly R3/H3 (ISa 10.2, matching XDS). InsI2 stays I23, and lysoC/InsI3/MyoB/ EP0210/cytC/lyso_ref are unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-30 20:32:03 +02:00
leonarski_fandClaude Opus 4.8	02477f1ce4	space group: determine centering from absences; jfjoch_process re-indexes from scratch ... Fixes wrong space-group assignment on cubic insulin (true I2_13, a=77.6). SearchSpaceGroup: drop the lattice-centering gate (and the now-unused lattice_centering option). The indexer often returns the conventional cell, whose geometry hides I/F/C centering - that information lives only in the systematic absences. Stage B now tests every centering of the point group and confirms it from the data, so an indexer-reported 'P' no longer excludes I2_13/I23. (I23 and I2_13 remain indistinguishable by absences and are reported as such.) jfjoch_process: discard any unit cell stored in the input HDF5 by default so the cell is re-determined from scratch. A stale/wrong stored cell otherwise resolves the indexing algorithm to FFBIDX, which trusts that cell and locks onto the wrong lattice (Ins_I_3 went from 2.7% -> 76% indexing). A user-supplied -C cell still applies. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-29 16:39:03 +02:00
leonarski_fandClaude Opus 4.8	786af96b3b	SearchSpaceGroup: POINTLESS-style rewrite, pipeline integration, twinning test ... Space-group search (image_analysis/scale_merge/SearchSpaceGroup): - Two-stage POINTLESS-style determination. Stage A scores each distinct rotation operator once (was once per candidate space group, ~34x faster on lysozyme: ~26s -> <1s) and picks the largest point group all of whose operators confirm. Stage B picks the maximal space group whose predicted absences are confirmed weak, fixing the prototype's default to the symmorphic group (it returned P422 instead of P4(3)2(1)2). Enantiomorphic / origin-ambiguous pairs (P4(1) vs P4(3), I222 vs I2(1)2(1)2(1)) are reported as indistinguishable. - Constrain candidates to subgroups of the lattice (metric) holohedry and weigh centering only P-vs-metric, fed from rotation indexing's LatticeSearch result. Integration / pipeline: - With no user-fixed space group, predict in P (IndexAndRefine) so the centering-absent reflections are integrated and the search can confirm/deny centering (catching pseudo-centering / a missed superstructure) instead of trusting the metric; a user-fixed group still rejects absences in integration. - JFJochProcess: scale+merge in P1 -> determine the space group -> set it and re-scale+merge in it (statistics then come out in the right symmetry) -> write it to /entry/sample/space_group_number (new EndMessage.space_group_number, preferred by NXmx::Sample). jfjoch_scale no longer searches; it consumes the file's space group (and no longer clobbers it with an empty -S). Twinning (new image_analysis/scale_merge/TwinningAnalysis): Padilla-Yeates L-test (<|L|>, <L^2>; acentric-only, positive intensities so L is bounded) plus a shell-normalised <I^2>/<I>^2 second moment and a twin-fraction estimate. Reported after the final merge in jfjoch_process and jfjoch_scale, and surfaced in the jfjoch_viewer merge-statistics window with a red outline when twinning is suspected. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-26 16:11:28 +02:00
leonarski_f	fc68a9baed	v1.0.0-rc.146 (#56) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. jfjoch_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset. jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling. jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file. jfjoch_scale: Dedicated tool for rescaling/merging existing data. jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel. WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being. Reviewed-on: #56	2026-05-28 18:48:35 +02:00
leonarski_f	166fcdb68f	v1.0.0-rc.131 (#39) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Fix bug in saving JUNGFRAU calibration (pedestal/pedestalRMS) * jfjoch_viewer: Fix calibration (pedestal) images being open flipped * jfjoch_process: Add space group detection (EXPERIMENTAL) Reviewed-on: #39	2026-03-07 11:34:04 +01:00