3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	d6166f6fa5	Panel layout stage 2: prediction and Bragg integration through the panel table ... Everything sparse that took a radial quantity from an image coordinate now takes it from the reflection's (or spot's) position on the detector plane, through its panel (DetectorModules). With an empty module table every changed expression reduces to the old one in the same floating-point order, so flat detectors - every rotation set, EIGER, CCDs, assembled JUNGFRAU - integrate bit for bit as before. - Prediction (CPU, GPU, rotation CPU and GPU): bounds test against PlaneBounds instead of the image rectangle. - IntegrateOnImage: a prediction in a gap or off every panel is dropped (PlaneToPanel), no longer passed through onto an unrelated stored pixel. The panel id stays local: the engine and the way back find it from the image position (the panel boxes tile the image), and a prediction that rounding to float put on another panel's edge is dropped so the two agree. Nothing is added to Reflection. - Bragg engines (CPU, CUDA, Metal) take a BraggPanel per reflection (BraggStencil.h): its plane position, the panel's pixel axes on the plane and its box. The stencil's radial direction is taken on the plane and expressed in the panel's pixel axes; r0, the radial background curve, the Gaussian's elongation, the learned moments, tan(2theta) and Finalize's polarisation use the plane position; r_max / n_rad come from PlaneBounds. The neighbour mask and the owner map are clamped to the reflection's own panel; inside the walked box a pixel off the reflection's panel is read as a gap (unreadable, statically masked - not an overload), which is what the assembled image has there, so a disk cut by a panel edge is partial rather than silently "full". - Risk R4: the ProfileEmpirical grid is learned and applied in the plane's axes (the panel axes taken to the nearest quarter turn, BraggProfileCell), so turned panels pool one shape. Without it the stacked layout read up to 0.3 % off the assembled one in the harness. - SpotWidth / SpotFootprint: aperture bounds against the spot's panel box, beam distance, resolution and the shape's 2theta Jacobian on the plane, moments read in the panel's axes. - GetDetectorMaxQ_recipA, the far-corner radii (first-pass tilt report, metric-symmetry arm, footprint table range) from PlaneBounds; pre-scan spot resolution on the plane; LogHeaderBeamCenter: geometric centre of the panels' plane box, and the masked-pixel check on the panel the beam lands on (none when it is in a gap). Harness: PanelLayout_BraggIntegration is now a real [PanelLayout] check, over six settings (default, bandwidth-elongated ring, radial background, overlap exclude, box sum, empirical profile, all with polarisation), stacked vs assembled to 1e-5; PanelLayout_BraggIntegrationGPU runs the same on the CUDA engine. Its spots avoid exact half pixels: the grid centres on the rounded position, and a half rounds to the other neighbour on a turned panel. The Metal engine (.metal/.mm) mirrors the CPU change exactly but is UNCOMPILED here (no macOS): it needs a build and BraggIntegrationEngineMetal_BitIdenticalToCPU on a Mac. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu	2026-10-21 10:40:20 +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
leonarski_f	a395f358ef	1.0.0-rc.174 (#84) ... * Rugnux: Performance improvements on GPU and CPU (more of the pre-scan and of scaling on the GPU, faster CPU spot finding and crystal refinement), with unchanged results. * Rugnux: More robust processing - patches of persistently hot pixels are masked, an inconsistent merge triggers a retry at the measured beam centre, and builds targeting different CPU levels give the same results. * Rugnux: Improved scaling and merging - reflections with an overloaded pixel are dropped, as in XDS, sparse rotation sweeps are scaled more reliably, and French-Wilson amplitudes use an anisotropic Wilson prior. * Rugnux: Improved space-group determination - glide planes in groups without a centre of symmetry, screw axes from short or weak axial rows kept when a higher group is adopted, and more reliable decisions on twinned and pseudo-symmetric crystals. * Rugnux: Improved small-molecule processing - spots that grow wider than the integration disk and split spots are integrated over their measured footprint, sparse lattices are integrated on every frame, and the `.hkl` file holds unmerged scaled reflections (SHELX HKLF 4). * Rugnux: Reads Rigaku d*TREK SMV images (Saturn CCD), including detector 2theta and encoded pixel overflows; home-source (rotating-anode) datasets were added to the validation battery. * jfjoch_viewer: Fixed processing failing at the end with "Wrong JPEG library version" on Linux; the merge window shows the space group with proper subscripts and a checklist of crystal pathologies. Reviewed-on: #84 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-06 14:03:18 +02:00