6 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	6468dd13be	rugnux: --mode, and detector calibration from powder rings ... --azint-only and --scale are replaced by --mode mx|azint|scale|calibration, with mx the default. The old flags are removed rather than aliased. Calibration mode fits the detector geometry - PONI x/y, the two tilts and the distance - to a calibrant's powder rings and writes a pyFAI .poni alongside a report of how far each parameter moved from the header. Bragg data constrain the beam centre worst, because it is gauge-coupled to the crystal orientation; a powder ring has no orientation to couple to. --calibrant takes lab6, agbh, ceo2, si or ice. A calibrant is a list of ring positions rather than a unit cell, because hexagonal ice is P6_3/mmc: rings enumerated from its cell would include systematically absent ones. So the crystalline standards generate their rings from a cell and ice carries the measured list, and RingsFromAzimuthalProfile, GuessGeometry and OptimizeGeometry all take ring q. The calibrant table is shared with the viewer's powder panel, which previously carried its own copy. --calibration picks how the rings are measured: rings (default) sums the (q x azimuth) profile over every processed image and fits the arcs in it; spots pools the found spots and fits those. Both use the whole run, with -s/-e/-t selecting images. rings defaults --azim-phi-bins to 32, since a profile with one azimuthal bin has averaged the ring over every direction and cannot locate it. Two fixes this exposed: The extraction window is capped at half the gap to the neighbouring ring. The background under a peak is taken from the ends of its window, so a window wider than half that gap measures the next ring's flank as this ring's background - and hexagonal ice has three rings within 0.06 1/A. Ice calibration was 3.5 px out before this and 0.29 px after; LaB6 is unaffected. RingOptimizer holds rot1/rot2 fixed when only one ring is present. A tilt and a centre offset both move a ring as cos(phi) and are separated only by the tilt's amplitude growing as the ring radius squared, so on a single ring they are exactly degenerate. Measured. LaB6 at five distances: the fitted direct beam is within 0.36 px of an independent implementation out to 300 mm, and D = -0.046 + 1.000788 dtz with an rms of 0.011 mm. At 500 mm one ring is fully on the detector and a second only clips the corners, which is not enough to constrain a tilt - restricting the q range to the resolved ring recovers 0.06 px. Ice: 5.53 -> 0.29 px on one crystal and 4.71 -> 0.80 px on another, against XDS's refined direct beam. On an ice-free crystal the fit is worse than the header, which is the correct outcome. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-07 10:00:03 +02:00
leonarski_fandClaude Opus 5	164f15c903	geom_refinement: stop committing refinements that did not converge ... Four of the seven ceres::Solve calls in image_analysis obtained a Solver::Summary and never looked at it, so a solve that failed numerically had its parameters written back and was reported as success. StillsPartialityRefine and both PostRefine solves already gated on IsSolutionUsable(); this brings the rest to the same contract. IsSolutionUsable() is the right test rather than checking for CONVERGENCE: it accepts a solve that ran out of iterations or wall-clock time but still descended, which is exactly what the real-time callers depend on when they set max_solver_time instead of max_num_iterations. Only FAILURE and USER_FAILURE are rejected. XtalOptimizer checks before the write-back, so a failed refinement now leaves the caller's geom and latt untouched instead of half-updated. GeometryRefiner folds it into result.ok, which previously reported success from spot and frame counts alone. RingOptimizer returns a geometry by value that both callers assign straight back over their input, so it hands back the unchanged reference rather than a diverged beam centre. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-31 15:02:11 +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	1ab257af6c	v1.0.0-rc.125 (#32) ... This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Improve logic on switching on/off spot finding * jfjoch_broker: Increase maximum spot count for FFBIDX to 65536 * jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD) * jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis * jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection * jfjoch_writer: Save more information about each reflection Reviewed-on: #32 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-02-18 16:17:21 +01:00
leonarski_f	c67337cfe1	v1.0.0-rc.72	2025-09-08 20:28:59 +02:00
leonarski_f	bb32f27635	v1.0.0-rc.70	2025-08-27 06:21:10 +02:00