5 Commits

Include renames

Author	SHA1	Message	Date
leonarski_f	13113b1751	Merge branches 'rc177-no-ccp4', 'live5s-a2' and 'live5s-a5' into rc177-live	2026-10-19 11:51:37 +02:00
leonarski_fandClaude Opus 5.5	0ff6442765	Model validation: warm up on the GPU when the broker gets a model ... WarmUpModelValidation runs one throwaway validation of the uploaded model against its own calculated intensities on a background thread (holding a GPUWorkBeside), so kernels, cuFFT kernels and contexts on every card the null's replicates use are loaded before the collection's validation. ValidateAgainstModel waits for a warm-up still running, so a real validation never shares the cards with it and computes what it computes without one (test ModelValidation_WarmUpChangesNothing; CLI run with and without warm-up: identical p.mtz, p_maps.mtz, report and validation lines). The broker logs the warm-up's time at upload, which measures the first-use cost on the machine directly (local RTX 5080: 0.88 s first, 0.78 s second). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4	2026-10-19 11:23:51 +02:00
leonarski_fandClaude Opus 5.5	80ed784d1d	rugnux: no .ccp4 map files - the maps are given as coefficients in _maps.mtz only ... A model validation no longer writes <prefix>_2fofc.ccp4, _fofc.ccp4 and _anom.ccp4 (nor their _mr twins); <prefix>_maps.mtz, which Coot and PyMOL open as maps, is what is written. With the files goes everything that only existed for them: ModelMaps keeps the coefficients alone, the keep_map_grids switch is gone from the validation schedule and the rugnux config, and the mFo-DFc map is no longer transformed to real space at all (nothing read it). The 2mFo-DFc and anomalous maps are still made, for the mean atom density and the anomalous-site read-out. The anomalous difference map is now in no output file: _maps.mtz carries no anomalous columns. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4	2026-10-19 08:08:12 +02:00
leonarski_f	8261b7354e	v1.0.0-rc.176 (#86) ... * jfjoch_broker: Optional live Rugnux analysis of DECTRIS rotation collections inside the broker, with merged data, maps and the placed model written beside the master file, the rotation lattice in the scan result, and a "Rugnux live" tab and dashboard row in the web frontend. * Rugnux: Faster processing, with molecular replacement and model validation spread over several GPUs and run on the Apple GPU on macOS. * Rugnux: The polarization stated in miniCBF and d*TREK headers is used, twinned crystals' space groups are decided more reliably, and a run that finds no lattice still reports every image. Reviewed-on: #86 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-19 07:03:28 +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