7 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	df9a9c2a2c	Fix the defects found reviewing the branch before merge ... Image buffer: the per-image CBOR metadata headroom had been re-derived from the online reflection cap alone, which cut it from 4 MiB to 2.55 MB while the measured worst case - reflections plus the capped spot list plus the three azimuthal arrays - is 2.9 MB, so the receiver dropped the frames with the most to say. Restore it and give it a name that both the code and its guard test read: written down twice, the two had drifted and the test kept passing against the value the code had left. Spot finding: an unset low_resolution_limit means no limit at that end, as an unset high_resolution_limit already did. An optional rather than a zero sentinel, because zero is not a natural "no limit" here - every pixel lies above it, so the plain comparison masked the whole image instead of none of it, and nothing validated the zero. The API field is no longer required; a zero is folded into the unset case at the boundary, where older clients still send it, so one spelling reaches the analysis code. The FPGA takes its fixed-point ceiling instead, since ap_ufixed<16,9> wraps above 512 A and would have masked everything. image_preprocessing: check the CUDA calls on the fused decode path - the one new GPU file with none, and the path fed by bytes we did not produce. An unchecked synchronise returned the host-written sentinel as if it were a measurement, so the decode looked successful and the fallback to the host decoder never fired. rugnux: --stride no longer writes one past the end of the per-image arrays, whose count floored where the worker loop ceils, and the written process file links the images actually processed rather than the first N - each frame's picture now sits next to its own analysis. Powder calibration: the face-centred calibrants no longer list their systematically absent rings, so the distance fit starts from a reflection that exists rather than an extinct one; the triclinic calibrant covers both signs of h and k instead of a single octant, which is only valid for a diagonal metric. The test asserted the old behaviour - one ring formula for every cubic standard - and is rewritten. CBOR: skip an unknown tagged value in the end block, as the other four blocks already do. One advance lands on the tagged item rather than past it, so an older reader fed a newer end message threw and never finalized its file. Viewer: a settings value the setter rejects no longer escapes as an uncaught throw from a worker slot, and the field offers only what the setter accepts. Space-group search: judge stage B on the same "present" cut stage A already computes. Merged sigma is floored so no reflection reads above ISa, so on a low-ISa merge the fixed cut left both stage B tests unsatisfiable - every screw axis passed unchallenged and the centering rescue switched itself off on exactly the weak data it exists for. Where the fixed cut is the smaller of the two they are equal and this is inert: over the 37-crystal rotation battery every crystal reports the identical space group and identical merge statistics, so it is a no-op there and the low-ISa case it targets remains unmeasured. rugnux: --polarization reaches --mode azint, which parsed the flag and then dropped it; that mode also applies the same polarization default as every other mode. Acknowledge the ACTS/traccc project, whose sparse connected-component labelling both spot extractors take their algorithm from, with its citation and its license. The rc.161 change list is brought back to one line per entry, and the user-visible changes that were missing from it added. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-08 18:18:46 +02:00
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_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	bb9f5c715f	v1.0.0-rc.135 (#44) ... 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.132. * Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4) * jfjoch_viewer: Improve image render performance Reviewed-on: #44 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-16 11:59:59 +02:00
leonarski_f	8b356a7001	v1.0.0-rc.96 (#1) ... This is an UNSTABLE release. * Fixes in CI pipeline * jfjoch_broker: Remove PNG preview, no dependency on libpng * jfjoch_writer: Fix UTC timestamp being generated wrong (mix between milli- and microseconds) * jfjoch_viewer: Show data collection time in dataset tooltip * jfjoch_viewer: Allow to choose the calibrant (presets for LaB6 and silver behenate) * jfjoch_viewer: Auto foreground value * Use external libjpeg-turbo and libtiff: simpler build stack, these are built and linked statically in automated Docker builds * Remove OpenBLAS dependency Reviewed-on: #1 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2025-11-02 13:45:57 +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