10 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	bab52a8077	rugnux: optional decay + absorption correction surfaces for rotation scaling ... After scale-fulls, RotationScaleMerge can now fit two optional multiplicative corrections on the combined fulls (both off by default, rotation only): - -B (decay): a global Debye-Waller relative-B rate for radiation damage, ln(Iref/Iobs) = 2 (dB/dn)(n - nbar) s^2, folded into the per-full scale. Engages only above a physical floor (total relative-B > 2 A^2), so it is a no-op on low-dose data. (-B was previously rejected for rotation.) - --absorption[=iter]: a smooth factor over the diffracted-beam direction in the goniometer frame (predicted detector position de-rotated by the spindle, so a crystal-frame direction is sampled at many angles). Wires the existing ScalingSettings::absorption_iter scaffold. Negligible at hard X-rays; matters at low energy. On lyso_ref it is ISa-neutral (+0.5) but drops R-free 0.219 -> 0.212 against the deposited model: a smooth absorption error cancels among symmetry mates (small ISa effect) yet still biases the intensities (real R-free effect). Both are CROSS-VALIDATED: the surface is fit on even frames and applied only if it improves the held-out odd-frame equivalent agreement by a clear margin (and vice versa), so a fit to noise where the systematic is absent does not generalize and is discarded - the correction never adds scatter. Battery: EcwtCQ066S +2.4 ISa, lyso_ref R-free win, others neutral. Also fixes a latent bug this exposed: the GPU->host corr download before the CPU 3D-combine was gated on --dump-observations only, so any other forced-CPU-combine path (the new -B/--absorption) read a stale host corr and mis-scaled every full. The download condition now matches the CPU-combine condition. Predicted detector position (px, py) is carried on the combined fulls for the absorption surface (CPU combine only; unused by the GPU SoA path). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-12 10:14:00 +02:00
leonarski_fandClaude Opus 4.8	dee679380b	rugnux: exclude merge-rejected outliers from the error-model fit ... The rotation error-model (a,b) fit built its sample pool from all usable fulls, while the merge separately dropped symmetry outliers (> Nsigma from the per-reflection median). So the fitted sigmas were calibrated against a dirtier pool than the reflections that actually entered the merge. Refactor the intensity-binned median fit into a `fit_ab` lambda and re-run it once on the misfit-free pool (samples with dev2 <= reject_nsigma^2 * model variance), matching the merge's own rejection. It operates on the shared `samples` array, so the CPU and GPU error-model paths stay bit-identical. Neutral on lyso_ref (the median-binned fit is already robust to the few outliers) - a correctness fix that matters more on dirtier data. Gated on reject_outliers (default 6 sigma for rot3d). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-12 10:04:43 +02:00
leonarski_fandClaude Opus 4.8	6c9a22d7f3	docs: tilt-invariant solid-angle correction; brief changelog docs entry ... Update CPU_DATA_ANALYSIS.md 2.2 to document the azimuthal-integration solid-angle correction as cos^3(alpha) with alpha the incidence angle to the detector normal (cos(alpha) = D / sqrt(u^2+v^2+D^2)), tilt-invariant and matching PyFAI solidAngleArray / MAX IV azint, reducing to cos^3(2*theta) only for an untilted detector - matching the code change in acd20256. Shorten the over-detailed rc.158 "Docs" changelog bullet to a brief line. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-11 13:06:39 +02:00
leonarski_fandClaude Opus 4.8	e7fbeb527f	docs: update analysis references to match current code ... Reconcile docs/CPU_DATA_ANALYSIS.md and docs/RUGNUX.md with the current image_analysis/ and rugnux CLI (verified section-by-section against the code): unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, radial parallax/bandwidth profile with sub-pixel centring, rot3d capture-fraction handling, automatic CC1/2 resolution cutoff, and the new rugnux options; fix the section numbering and cross-references; remove the never-implemented French-Wilson and still-partiality descriptions. Delete the stale in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) and fix the two code comments that pointed at them; the BraggIntegrationEngine header no longer claims it is 'not yet wired'. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-11 10:59:15 +02:00
leonarski_f	d6389e12da	v1.0.0-rc.156 (#66) ... 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: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output. * jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling. * Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool. * jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection. * jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata. * CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-03 19:18:56 +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	2ab9deb20b	v1.0.0-rc.123 (#40) ... Documentation update Reviewed-on: #40	2026-03-12 12:17:11 +01:00
leonarski_f	64002f1e29	v1.0.0-rc.129 (#36) ... 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: Significant improvements in TCP image socket, as a viable alternative for ZeroMQ sockets (only a single port on broker side, dynamically change number of writers, acknowledgments for written files) * jfjoch_broker: Delta phi is calculated also for still data in Bragg prediction * jfjoch_broker: Image pusher statistics are accessible via the REST interface * jfjoch_writer: Supports TCP image socket and for these auto-forking option Reviewed-on: #36 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-03-05 22:13:12 +01:00
leonarski_f	061152279c	v1.0.0-rc.91	2025-10-20 20:43:44 +02:00
leonarski_f	c44a07aac2	v1.0.0-rc.90	2025-10-02 15:55:39 +02:00