5 Commits

Author	SHA1	Message	Date
leonarski_f	383072ac80	Consolidate viewer settings into the panel + add the merge-stats window ... Make the inline settings dock the single home for processing settings and retire the separate Processing-settings window (and the dock<->window sync): - "Analyze image" / "Analyze dataset" move to the top of the panel; the MX/AzInt toggle decides the dataset-job kind, so the job dialog drops its mode combo. - The panel gains the most-used spot-finding (max spots, high-resolution, min pixels), Bragg (Gaussian profile-fit, r1/r2/r3) and scaling (partiality, "3D rotation scaling" = rot3d combine + scale-fulls, merge Friedel, refine B, resolution limit) handles, a live indexing-algorithm description line, and now owns the Bragg/Scaling settings. The now-unused window tab classes are deleted. - Complete the PixelRefine removal on the viewer side (the "Pixel refinement" option + profile-multiplier widget), fixing the transient HEAD breakage. New JFJochMergeStatsWindow: an analysis pop-up for a finished merge (hero numbers over a per-resolution plot / per-shell table), auto-opened on completion and reopenable from the processing-jobs dock. Fixes: disable tear-off dock floating (a floated dock is a dead off-screen window under WSLg, which has no window manager); version the saved dock layout so a stale arrangement is discarded instead of restoring a broken one; keep the Analyze-button icons; right-align and equal-width the stats table; line-plot / table toggle icons (ToolbarIcons gains linePlot + table). Add ScalingSettings::HighResolutionLimit_A(optional) so the panel can clear the resolution limit. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-25 20:43:04 +02:00
leonarski_f	c84d581d3e	Remove the global (joint) scaling path ... Profiling showed the joint Ceres solve took ~120 s versus ~3.5 s for the alternating per-image scaling loop (~35x) for no quality gain (HEWL anomalous 0.54x vs 0.53x), so it is not worth keeping. Drop GlobalScale.{h,cpp}, the jfjoch_process --global-scale flag, and ScalingSettings::GlobalScaling. While here, in the same scaling/process area: fold scale_fulls into ScalingSettings (alongside combine_3d) so the CLI and experiment carry it uniformly, add per-substep [timing] logging to the scaling/merge post-pass (including the serial MergeAll vs parallel ScaleAllImages split), and carry structured MergeStatistics + ISa in ProcessResult. 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