6 Commits

Author	SHA1	Message	Date
leonarski_f	38ea0ec237	Remove the experimental PixelRefine integrator ... On the LysozymeJet5 serial stills the default Gaussian profile-fit integrator (ProfileIntegrate2D) + reference scaling matched or beat whole-PixelRefine on every per-shell CC1/2 (overall 95.7% vs 91.9%), ISa (1.6 vs 1.2) and R-meas (98.5% vs 175%), with CCref a tie -- so PixelRefine has no remaining advantage. Reference-based per-image scaling is integrator-agnostic (IndexAndRefine::ReferenceIntensities builds a ScaleOnTheFly(experiment, reference) applied to any integrator's output), so the reference-dataset feature (CCref + reference scaling) is kept. Delete image_analysis/pixel_refinement/, GeomRefinementAlgorithmEnum:: PixelRefine and its gates, BraggIntegrationSettings::ProfileMultiplier (PixelRefine-only; R1 is shared and kept), and the -r pixelrefine / --profile-multiplier CLI. The inherited lessons (mean background, de-biased variance, tight-profile-loses / centroid floor, R-refinement futile) are folded into NEXTGEN_INTEGRATOR.md. NOTE: this transiently breaks the viewer build -- the committed viewer still references the removed enum and ProfileMultiplier. It is fixed in the next commit (the viewer feature work), held separate while the viewer UI is being tested. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_f	e4b3064254	Scaling: reference dataset, 3D combine (-P rot3d), R-meas, profile-fit integrator ... Reference dataset (a): LoadReferenceMtz adds column selection + cell/SG/resolution + a data-vs-reference consistency check; jfjoch_process/jfjoch_scale gain --reference-column; the viewer gets a Reference section in the MX settings dock (worker-owned, independent of the loaded dataset) that flows into reprocessing jobs. 3D combine (-P rot3d): Combine3D weight-sums a reflection's per-frame partials into one counting-limited full before merging (orthogonal ScalingSettings::combine_3d flag, not a partiality model), with a de-biased Poisson variance. Crystal 2: ISa 1.7->8.4, R-meas ~67%->18.9%, intensities unchanged (CCref held). Quality metrics (b): R-meas (Diederichs-Karplus) + redundancy columns in MergeStats; ISa logged. jfjoch fulls 18.9% vs XDS 4.5% (same ASU/run). Profile-fit integrator (experimental): ProfileIntegrate2D (--integrator gaussian|empirical) is a reference-free, rot3d-compatible profile-fit extraction (the decomposed PixelRefine intensity step). Gaussian: R-meas 18.9->14.6%, ISa ->9.5. Anisotropy/per-region add nothing (the discriminating info is in the discarded rocking direction). See NEXTGEN_INTEGRATOR.md. --dump-observations exports the unmerged fulls for XDS comparison. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +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
leonarski_f	c67337cfe1	v1.0.0-rc.72	2025-09-08 20:28:59 +02:00
leonarski_f	0d1b388f4d	v1.0.0-rc.50	2025-06-20 09:52:26 +02:00