10 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	7d5fb15413	Unify still processing on one --force-still flag; scaling follows rotation indexing ... Fold the two overlapping knobs into one. Rotation-vs-stills is now a single decision (IsRotationIndexing() = goniometer && rotation-indexing) that drives BOTH indexing and scaling/merging - there is no independent scaling-model switch: - ScalingSettings: drop combine_3d and force_still_processing (and Combine3D/GetCombine3D, ForceStillProcessing/GetForceStillProcessing). The scaling stage reads experiment.IsRotationIndexing() instead - rotation indexing implies RotationScaleMerge, no rotation indexing implies per-image ScaleOnTheFly. - jfjoch_process: merge --process-as-stills and --force-still-processing into one --force-still (turns rotation processing off entirely: still indexing + still scaling). The rotation-specific scaling defaults (scale-fulls, smooth-G, capture uncertainty, outlier rejection) now key on rotation_indexing. - jfjoch_scale: replace -P fixed|rot3d with --force-still; rotation is auto-detected from the goniometer (RotationIndexing set accordingly) so it matches jfjoch_process. - jfjoch_viewer: the "process as stills" toggle already sets RotationIndexing; drop the now redundant Combine3D/ForceStillProcessing calls. Rotation path unchanged (lyso 16.4/99.6%/87.3%); --force-still routes to ScaleOnTheFly; the -R + --force-still conflict still errors. CUDA + non-CUDA + viewer all build. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-03 12:20:45 +02:00
leonarski_fandClaude Opus 4.8	b4d3d40cd8	Replace the dead PartialityModel with a force_still_processing flag ... With ScaleOnTheFly now fixed-only and rotation routed through RotationScaleMerge, the PartialityModel enum carried no information (it was always Rotation for rotation processing, Fixed otherwise, and mirrored combine_3d). Drop it: - ScalingSettings: `partiality_mode` (PartialityModel) -> `force_still_processing` (bool); SetPartialityModel/GetPartialityModel -> ForceStillProcessing/GetForceStillProcessing. Remove the enum. - DiffractionExperiment: drop GetPartialityModel(); the rotation-vs-stills decision is now just GetCombine3D() (set by the tool = rotation && !force_still). The wedge getters no longer key off the model (dead since wedge refinement was removed). - jfjoch_process: `-P/--partiality fixed|rot3d` -> `--force-still-processing` (a rotation dataset scaled as independent stills). Auto-detect sets combine_3d for rotation data unless the flag is given. - jfjoch_scale: `-P fixed|rot3d` now toggles combine_3d directly (no PartialityModel). - jfjoch_viewer: the "process as stills" toggle sets ForceStillProcessing(!rotation_mode) - UI unchanged, just wired to the new field. PartialityModel was never in the OpenAPI, so no generated clients change. Rotation path behaviour is unchanged (lyso 16.4/99.6%/87.3%); --force-still-processing correctly routes to ScaleOnTheFly. CUDA + non-CUDA + viewer all build. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-03 11:58:34 +02:00
leonarski_fandClaude Opus 4.8	9f45935fd3	Scale/merge: rotation -> RotationScaleMerge, stills -> ScaleOnTheFly (fixed) ... Consolidate the offline scaling/merging on two engines and delete the old classic rotation chain: - ScaleOnTheFly now implements ONLY the fixed-partiality model: it uses each reflection's stored partiality as-is (1 for stills, the zeta/erf rocking-curve value already set at prediction for rotation). Dropped the Rotation partiality recompute, the unity override, the ceres rotation residual, and all wedge/mosaicity refinement. - Remove Combine3D (CombineRotationObservations): its 3D-combine lives in RotationScaleMerge. - JFJochProcess / jfjoch_scale: rotation (-P rot3d) goes through RotationScaleMerge for the whole self-scale -> 3D combine -> scale-fulls -> merge; stills self-scale with ScaleOnTheFly + MergeOnTheFly. RotationScaleMerge does not support external-reference scaling, B-factor refinement, an absorption surface or wedge refinement, so those combinations now throw instead of silently falling back. Deleted the classic ScaleFulls / AbsorptionSurface / SmoothImageScaleG helpers. - CLI cleanup: drop -w/--wedge (wedge refinement) and --absorption (both tools), and the now dead -P values rot and unity (keep fixed | rot3d). Fix the -P round-trip in the reproduced command line. Behaviour on the rotation path is unchanged: the full 18-crystal battery matches the pre-cleanup metrics (SG/ISa/CC1.2/completeness) exactly on all 15 deterministic crystals. Non-CUDA build unaffected. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-03 11:41:49 +02:00
leonarski_fandClaude Fable 5	7e3ad84a5b	jfjoch_process/scale: default to mmCIF, auto-detect rotation, rot3d partiality ... - Default reflection format is now mmCIF (ScalingSettings.h, the single source of truth). jfjoch_process and jfjoch_scale no longer hard-code a local MTZ default; they override only when --scaling-output is given. jfjoch_viewer inherits this. - A dataset with a rotation goniometer axis is processed as rotation data (two-pass indexing) by default; add --process-as-stills to force per-frame stills. -R still tunes the first-pass image count. - rot3d is the default partiality model for rotation processing (fixed for stills) when no explicit -P is given. - Update docs/JFJOCH_PROCESS.md: new de-novo rotation/stills examples, corrected -R/-P/--scaling-output defaults, --process-as-stills, and a real Integration table. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 08:34:50 +02:00
leonarski_fandClaude Opus 4.8	35607057d9	CC1/2 merge: assign half-sets by deterministic per-image hash ... MergeOnTheFly::AddImage picked each image's CC1/2 half from a shared mt19937 drawn in call order (and before Mask), so the split depended on iteration/thread order and on how many images were masked. The class is mutex-guarded for concurrent "on-the-fly" use, so any parallel merge would make CC1/2 non-reproducible - a latent race. Assign the half as a splitmix64 hash of the image's stable index instead, computed after Mask. The split is now reproducible run-to-run, independent of AddImage order, parallel-safe, and decoupled from masking. Callers pass the outcome's vector index as the image id. Verified: lyso_ref two-pass -M -P rot3d gives identical CC1/2 across runs (overall 99.6%, P41212); hash split is balanced ~50/50. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-01 07:25:34 +02:00
leonarski_fandClaude Opus 4.8	a773aaa6a9	WriteReflections: write merging statistics + ISa to the mmCIF output ... The .cif (--scaling-output cif) now carries the per-shell and overall merging statistics in the standard _reflns / _reflns_shell categories (resolution, redundancy, completeness, <I/sigma>, R-rim/R-meas, CC1/2) plus the Diederichs asymptotic I/sigma (ISa) as a free-text _reflns.pdbx_diffrn_ISa item (no standard CIF tag exists). The MergeStatistics and the ISa string are threaded through WriteReflections to the mmCIF writer; jfjoch_process and jfjoch_scale pass them. Values match the text statistics table. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-30 22:29:45 +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	54c667190f	v1.0.0-rc.155 (#65) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_process: Remove pixelrefine option (replaced with ProfileIntegrate2D) * jfjoch_viewer: Some graphical improvements. * jfjoch_viewer: Simplify und unify data analysis settings. * jfjoch_writer: Add TCP keepalive to increase robustness if jfjoch_broker "dies" in the middle of data acquisition. Reviewed-on: #65	2026-06-25 22:01:48 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing * jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files * jfjoch_broker: Add ROI calculation in non-FPGA workflow * jfjoch_broker: Fixes to TCP image pusher * jfjoch_broker: Remove NUMA bindings * jfjoch_broker: Improvements to indexing * jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values * jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors * jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs * jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results Reviewed-on: #63	2026-06-23 20:29:49 +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