3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	b7e4ea23a3	Pre-scan masks a pixel at the saturation limit on most frames, as one holding the error value ... A pixel stuck at the saturation limit was never masked: the defective-pixel scan counted only the error value as "invalid on most frames", and a saturated pixel merely as lit, which the hot rule does not judge on stills. A Rayonix stills set has 3,627 pixels at 65535 on every frame, at high resolution; each flagged every reflection whose disk it fell in as overloaded, and the spot finder found them on every frame. The saturation limit now counts with the error value (CPU and CUDA), so such a pixel is masked like one holding the error value. On that set the indexed fraction rises from 10% to 33% (and 7% to 30% on the second lattice of the same run), R_split 0.120 -> 0.106 and the unrefined R-free against the deposition -0.001 / -0.024. Rotation merges checked bit-identical (three in-house sets with overloads). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu	2026-10-22 17:27:43 +02:00
leonarski_fandClaude Opus 5.5	dcad4104ce	Dense per-pixel maps through the panel table (panel layout stage 1) ... Every dense map that needs geometry now evaluates each image pixel at its place on the detector plane (DetectorModules), so it is right for a stacked panel layout and picks up refined module placements: - AzimuthalIntegrationMapping: bins, resolution, solid-angle/polarisation corrections built per pixel through the table; a pixel on no panel is left as a masked one. The geometry cache key now includes the panel table, so a mapping built after the stills module placement is rebuilt rather than served from the cache. ResolutionMaskBits follows (it is a lookup). - ROIMap / ExportROIMap: azimuthal ROIs on the plane (box and circle ROIs stay in image pixels). - ROIIntegration CPU+GPU: the weighted sums are taken per ROI and panel in image pixels and placed on the plane at the end (exact; the affine commutes with a weighted mean). - HotPixelFinder: ring/sector keys and the zeta of the persistence rule on the plane. - Background beam-centre walk CPU+GPU: pixels binned at their plane position; host and device share BackgroundPlanePoint so they stay bit-identical. New common/PanelRows.h: ForEachPixelInRows, ForEachPixel cut to a band of rows in index order, for the row-parallel builders. An empty table takes the old arithmetic in the old order: rotation sets and every single-panel input are unchanged. [PanelLayout] AzintMapping and ResolutionMask enabled (+ azimuthal ROI map and ROI centroid on the plane); new BeamCenterFromBackground_BinsOnThePlane and ROIIntegrationGPU_MatchesCPU_Panels. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu	2026-10-21 10:26:30 +02:00
leonarski_fandFilip Leonarski	19b135186d	v1.0.0-rc.175 (#85) ... * Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`). * Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection. * Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS). * Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead. * Rugnux: On macOS, Bragg integration runs on the Apple GPU. * Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand. * Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`. * Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit. * Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed. * Rugnux: The beam-stop shadow is found correctly on tilted detectors. * Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement. * jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps. * jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection. * jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images. * Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges. --------- Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home> Reviewed-on: #85 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-16 15:34:43 +02:00