3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	37a8c8e24e	Rotation merge: drop rocking events with an overloaded pixel; capture uncertainty in the merge variance ... A saturated pixel in a spot means the brightest part of the reflection was not measured. The integration used to drop the peak frame's partial (its peak pixel is unreadable) and keep the flanks, so the combine extrapolated the event from its tails by the partiality model: on a strongly diffracting small-molecule crystal the strongest low-order reflections read 2-3x low and were the largest SHELXL misfits. XDS drops such a reflection (OVERLOAD); so does rugnux now. - Integration (CPU + GPU engines): a reflection is `overloaded` when a signal-disk pixel is saturated, or unreadable on this frame but not in the run's pixel mask - EIGER/PILATUS write their error value for a pixel they could not count, which the preprocessor turns into a masked pixel like a gap's. The engines now receive the PixelMask to tell the two apart (an earlier attempt that re-classified the marker as saturation in the preprocessor broke a dataset whose gaps are not in the file's mask). An overloaded reflection is kept with its box sum, unfitted, only so its event can be recognised. - Rotation combine (CPU + GPU): an event with any overloaded partial is dropped whole; counted in the log and the report (OBSERVATIONS_REJECTED_OVERLOAD=). The unmerged MTZ export drops it too. - Everything else that reads reflections leaves an overloaded one out: AcceptReflection (stills merge, per-image scaling), the post-refinement gather, the axial-row sums. - Capture uncertainty: the merge rebuilds each full's variance at the reflection's mean (counting_variance / ModelSigma) and dropped the capture term the combine had put into sigma, so a full extrapolated from part of its rocking curve merged at the weight of a whole one. Fulls now carry it (Obs::capture) and the rebuilt variance adds (capture * <I>)^2, host and device. SHELXL R1 on rugnux's own integration (harness), median fix -> this: citric acid .0648 -> .0420 (XDS .051; 221 events dropped, EXTI 1.02 -> 0.29), HEPES .0396 -> .0381 (184), aspirin 20 keV .0387 -> .0385 (6), aspirin 25 keV .0376 -> .0375 (5); metformin/nidppe/dnba/lalanine/cytidine no overloads, unchanged. YAG .116 -> .128 (87 dropped; its scale loop does not settle either way). Proteins and private subset: see the branch report. Tests: BraggIntegrationEngineCPU_SaturatedPeakIsFlaggedNotDropped (new), BraggIntegrationEngineGPU_MatchesCPU (overloaded flag compared), AcceptReflection_ResolutionLimits, [write_reflections], [large]. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 21:01:40 +02:00
leonarski_f	84228bf8be	v1.0.0-rc.173 (#83) ... * jfjoch_broker: Optional per-dataset authentication - statistics, images and plots can require a bearer token, which jfjoch_viewer supports. * jfjoch_viewer: Dark mode and a theme-matched colour scheme, a magnifier panel, and simpler contrast and background controls. * Rugnux: Multiple performance improvements on GPU and CPU (CPU-only processing up to 40% faster, faster image decoding on ARM), with unchanged results. * Rugnux: `--model` rigid-body refinement runs on the GPU, and the model-validation check is faster and more reliable. * Rugnux: Improved scaling and merging - error model, outlier rejection, absorption correction and French-Wilson amplitudes now agree more closely with XDS and ctruncate. * Rugnux: Improved integration - radial background on powder and ice rings, crowded rotation data keep their reflections, and CPU-only builds integrate large unit cells as GPU builds do. * Rugnux: More robust detector geometry - measured beam centre, X-ray bandwidth and goniometer rate, and geometry refinement accepted only on significant evidence. * Rugnux: Merged files are written in the standard setting, or in the setting of a reference MTZ, structure-factor mmCIF or model, with its free-R flags. * Rugnux: Richer report - ice and powder rings, further lattices, superstructure candidates and mosaicity, with warnings worded as prompts to check. * Rugnux: Clear error messages when a data set needs more GPU or host memory than is available. Reviewed-on: #83 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-29 15:57:32 +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