7 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	c3e877d5ec	bragg integration: trimmed-mean background, on by default for rotation ... The local Bragg background is the mean over the r2..r3 ring. That mean reads high because the contaminants that survive the signal-disk mask - neighbour- spot wings, tails, zingers - are one-sided (positive), so it over-subtracts. Since a weak intensity is a small difference of large numbers (I = S - nS*b), a per-pixel background bias is fractionally largest at the resolution edge, exactly where it hurts most. Replace the ring mean with a symmetric trimmed mean (sort the ring, drop the lowest and highest fraction f, average the rest), controlled by a new BraggIntegrationSettings field and the rugnux `--background-trim <f>` option (default f=0.10; 0 restores the plain mean). Default on for monochromatic (rotation) data; broadband (stills) keep their tuned high-side sigma-clip, so the base engine forces the trim to 0 there. Implemented in both the CPU engine and the GPU kernel (shared-memory bitonic sort per block, flat-mean fallback above BKG_TRIM_MAX ring pixels); the two agree. 25-crystal rotation battery (fixed SG/cell): <I/sigma> improved on every crystal (median +50%), ISa on 20/22, resolution-edge R_meas fell several-fold (e.g. lyso_ref 1.0 A 108%->43%). Last-shell CC1/2 is rescued where the plain mean had collapsed to noise (Thau_9 at ~2.0 A 3.8%->64%, ~0.5 A of resolution regained; cytC_10 0.2%->10%) at a small cost (1-3%) in already-clean shells - it flattens the CC1/2 fall-off rather than shifting it. Stills unchanged. Documented in CPU_DATA_ANALYSIS.md section 9.2. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-16 18:32:57 +02:00
leonarski_fandClaude Opus 4.8	fb399480e5	rugnux: add opt-in stills partiality (--still-partiality) ... Serial stills currently treat every reflection as a full (partiality hardcoded to 1). Add an opt-in Gaussian excitation-error partiality set at prediction time (CPU + CUDA): p = exp(-dist_ewald^2 / (2*sigma^2)), sigma^2 = profile_radius^2 + (bandwidth_sigma*|recip_z|)^2, with sigma = the per-image profile radius (ewald_dist_cutoff/2), so an edge-of-acceptance reflection keeps p ~ exp(-2). Off by default; the merge weight (~p^2) then down-weights far-from-Ewald partials instead of trusting them as fulls. Validated: helps medium/strong stills (LOV R-free 0.336->0.329, lyso8 0.433->0.410, lowers the systematic error-model b in both) but HURTS weak OCP (dividing by a small, uncertain p amplifies orientation error -> high-res noise, resolution collapse), so it is left opt-in. A static forward p explains only ~6-10% of the partiality scatter; the full win needs per-image post-refinement (future work), for which this is the prediction-side groundwork. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-14 12:03:21 +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
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