7 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	0783af247c	scaling: express rot3d smooth-g as a rotation range in degrees (XDS DELPHI-like) ... --smooth-g now takes a rotation range in degrees (default 5) instead of a frame count, converted to an odd frame window from the oscillation step inside JFJochProcess. This makes the per-frame scale-G smoothing physical and independent of the frame slicing. (Note: G-smoothing is not the cure for the low-symmetry stochastic collapse - the per-image scale Cauchy loss is - but a degree-based window is the correct parameterization regardless.) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-30 20:00:53 +02:00
leonarski_fandClaude Opus 4.8	e45a1577d6	jfjoch_process: optional absorption surface for rot3d scaling (--absorption) ... Adds an opt-in smooth absorption correction for rotation scaling. After the rot3d fulls are scaled, --absorption[=num] fits a multiplicative surface A(s1_crystal) - a degree<=4 monomial basis (real spherical harmonics up to l=4, as XDS/DIALS) of the diffracted-beam direction in the crystal/goniometer frame, by ridge-regularized log-linear least-squares of I_scaled/I_ref weighted by (I/sigma)^2, over num iterations (default 3); the surface divides image_scale_corr and the fulls are re-merged. Off by default and a no-op without rot3d. On the test panel (~13 keV, thin crystals) it is metric-neutral - fitted rms(log A) ~3-4%, ISa/CC1/2 unchanged - because absorption is negligible there and the per-frame scale G(phi) already absorbs the angular part. It is kept as a lever for low-energy data (e.g. 6 keV) where absorption becomes significant. Stored as ScalingSettings::absorption_iter. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-06-30 15:23:01 +02:00
leonarski_fandClaude Opus 4.8	99b923e727	scaling: smooth per-frame scale G across frames before the rot3d combine ... ScaleOnTheFly fits each frame's scale G independently with no neighbour coupling, so the few partials of one rocking event are weight-summed in combine3D on inconsistent scales - jitter that never enters the full's counting sigma and instead surfaces as scatter between symmetry mates, inflating the error-model b (low ISa). A centered moving average of log(G) over a small frame window (default 9, on for rot3d) removes it, mirroring XDS's smooth scaling. Complementary to --scale-fulls (which rescales between fulls, after the combine): smoothing fixes within-event scale, scale-fulls fixes between-full. On the rotation lysozyme set (1.4A, merged, with --scale-fulls): ISa 11.7 -> 15.0, R_meas 10.0% -> 8.3%, CCref stable, chi2 ~0.97 (honest). Anomalous (full-res): ANODE S-peak 0.61x -> 0.80x of XDS. --smooth-g[=window] tunes/disables it (=0 off); --mosaicity <deg> is a diagnostic that fixes the scaling mosaicity for sweeps. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-29 19:02:47 +02:00
leonarski_fandClaude Opus 4.8	ed98775ba3	rot3d: capture-aware sigma for under-captured fulls + expose per-image scale ... The rot3d combine over-extrapolates fulls reconstructed from only a fraction f of their rocking curve (min_partiality admits f as low as 0.02). Against XDS on HEWL these low-capture fulls are systematically biased HIGH (+15% at f=0.8 to +100% at f=0.3), and the bias - not random scatter - is the strong-reflection floor that hurts anomalous accuracy. --capture-uncertainty <coeff> (default 0 = off, baseline bit-identical) adds a systematic uncertainty ~coeff*(1-f)*I to each full's sigma, so the merge down-weights the over-extrapolated fulls and the error model treats their scatter as expected. Unlike outlier rejection (which trades accuracy for CC1/2), this fixes a real bias, so accuracy improves: at coeff=1.0 the anomalous peak height vs XDS rises CL_CL +16%, SD_MET/SG_CYS +5-6%, ISa 10.7->11.0. Rotation- only (no-op for stills, which never combine). Also expose the per-image scale offline: Combine3D now carries the first-pass per-image scale metadata (G, B, mosaicity, wedge, CC) forward instead of dropping it, and jfjoch_process -M writes <prefix>_image.dat from it (the offline self-scaling result was otherwise unobservable - process.h5's per-image arrays are only filled on the online path). This enabled the XDS DECAY comparison (jfjoch G tracks XDS, r=0.93). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-27 19:41:20 +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