6 Commits

Include renames

Author	SHA1	Message	Date
leonarski_f	baec34685d	Rugnux live: the uploaded model is refined after placement; refined scores, model, maps and blobs in the status, the viewer and the hero ... The live run refines a placed model as `rugnux` does (ProcessConfig::refine), after every decision and before the end message; a cut before it starts leaves it out, as the model. The writer still gets the placed model; the refined one stays with the broker. API (broker/jfjoch_api.yaml): - rugnux_live_model.refinement (rugnux_live_refinement): performed, reason, on_gpu, seconds, r_work, r_free, rmsd_bonds_A, rmsd_angles_deg, blob_count, blobs (at most 50, rugnux_live_blob: kind, x, y, z, peak_sigma, volume_A3, nearest_atom, nearest_atom_distance_A) - rugnux_live_status.refined_model - /rugnux/model.cif and /rugnux/map.ccp4 take stage=placed|refined, by default the refined model where there is one; the anomalous map stays on the placed model's phases (the refined coefficients carry none). Regenerated broker/gen, frontend/src/client, redoc, and the python client docs (which also brings the hero fields and rugnux_live_model it was missing). Frontend: the model card keeps its green/red and gets "R-free 0.xx (refined)" as its context line, "refining..." while the step runs; the model section adds refined R-free and blob tiles; Mol* shows the refined model and maps, with the blobs as small spheres coloured by reading (switch, off at first). The Refinement step is in the timeline like any other. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 3b47fb9a53b7dfad1c1ed289e169094c8d3d9d3e)	2026-10-26 01:38:25 +01:00
leonarski_f	2fb4b1d015	Rugnux live page: a hero panel with resolution, ISa, space group and whether the model was placed ... Under the header of the Rugnux live page, four big-number cards in the manner of jfjoch_viewer's merge statistics window: Resolution (d_min of the merge), ISa, Space group (short symbol, screw axes subscripted) and the model. The model card shows the fit over random orientations - R-work of the placed model below its random-orientation null, in sd - which is the test rugnux places a model by, both for molecular replacement (after the TFZ/LLG-Z gate) and for a model that fits where it is. The card is green where rugnux placed the model (placement MR or RIGID_BODY), red where it did not (with MR's reason), grey where no model was uploaded; no threshold of its own. "—" while the run is going, "searching…" during the MR step. /rugnux/status gains `space_group`, `d_min` and `isa` (set with the result; absent until then, isa also where the error model did not determine it), filled from ProcessResult in RugnuxThread with the values the summary's Space group, Resolution and Signal rows print. Generated code regenerated from jfjoch_api.yaml: broker/gen (cpp-pistache-server 7.20.0), the TypeScript client (npm run openapi) and broker/redoc-static.html. Python client not regenerated. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit fcc019707751aab9d8c9f349309eeadcf364b9c2)	2026-10-25 07:20:28 +01:00
leonarski_f	128830d15e	rugnux live status: the model's scores, and whether the data carry anomalous signal ... /rugnux/status gains `model` (rugnux_live_model) - placement (RIGID_BODY/MR/NOT_PLACED), R-work and R-free of the placed, unrefined model, CC(model, data), R-work over its random-orientation null, mean 2mFo-DFc at the atoms, the rigid body's move, molecular replacement's decision, group, copies, TFZ/RFZ/LLG-Z and search resolution, and the strongest anomalous site - taken from ProcessResult::model_validation and ::model_prior (LiveModel). `anomalous_signal` says the summary's "Anomalous" row reports usable signal (CC_anom > CC_ANOM_SIGNAL, now a named constant shared with the report), so the viewer can show the anomalous map by default only then. The step that placed the model (Molecular replacement, or Model validation) now carries notes: what MR placed and its TFZ/RFZ, R-work/R-free (unrefined) and CC(model, data), the rigid-body move. Generated code regenerated from jfjoch_api.yaml: broker/gen (cpp-pistache-server), the TypeScript client (npm run openapi) and broker/redoc-static.html. Python client not regenerated. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit f602e931dc6afcccb3767b8c6df87650d9496033)	2026-10-24 19:06:04 +02:00
leonarski_f	b00c668e3a	v1.0.0-rc.179 (#90) ... * Rugnux: Stills processing needs only the unit cell and space group beyond what the file records - detector distance, beam centre, tilt, panel placement, saturation level, gain and polarisation plane are found from the images - and is up to twice as fast. * Rugnux: Stills can be indexed without a GPU, with a CPU implementation of the fast-feedback indexer (macOS, computers without a GPU). * Rugnux: Rotation and stills data are integrated in the detector's own units with one gain model, improving data from CCD detectors. * Web frontend: The Rugnux live page shows the placed model with its electron density and anomalous difference map in a Mol* viewer. Reviewed-on: #90 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-24 14:52:29 +02:00
leonarski_f	afbe844b20	v1.0.0-rc.178 (#88) ... * Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`). * Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels. * Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL. * jfjoch_viewer: Opens the same XFEL file formats. * Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL. * Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded. * jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start. Reviewed-on: #88 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-21 11:20:01 +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