4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	a609f6ba1c	rugnux two-pass: the integration radius decided on the pre-pass frames, before the canonical pass ... Where the measured spot width widened the integration radius, the canonical pass integrated the whole sweep at the widened radius, and only then did the starvation guard read how many background rings the neighbouring predictions crowd; over the bound (1.13%) the pass was thrown away and run again at the fixed radius. The geometry pre-pass now counts that same quantity at the widened radii without integrating there (BraggIntegrationEngineCPU::CountNeighbourCrowding: the neighbour mask and the ring pixels the run's mask leaves readable, no image) on 20 frames spread over the pre-pass, with the standard error of the ratio over those frames. Over the bound, the canonical pass integrates at the fixed radius from the outset. A count within NEAR_TIE_SIGMA of the bound is a near tie in the part-B sense: the canonical pass counts the widened radii again on 20 frames over the whole sweep, and where that puts them under the bound the run is made again deciding late. A run deciding late counts nothing early and decides as before. Under the bound the canonical pass integrates at the widened radius and the measured guard stays as it was, so a pre-pass count that is too low (its prediction holds fewer tails than the canonical pass's, or it stood on another lattice class) costs only the pass it cost before. No new threshold. Battery against 46be3f647 (the 14 open sets that re-ran at the fixed radius, the 9 open/in-house sets closest under the bound, the ci tier, 2 private sets): - p.hkl and MTZ data identical on all 51 open/in-house sets and on one private set. - The 14 re-running sets: rugnux wall 534 -> 447 s (7qij -27, 4nwv -12, 7yzx -10, 9fhc -9, 5src -6 s, on a shared machine). 8sqq and 8xtf count under the bound on the pre-pass and re-run as before. 4nwv (1.69 +- 0.28%) and one other set were near ties, re-checked on the whole sweep (1.72%, 1.61%), ending where they did. - One private, densely crowded set: same space group and d_min, R_meas 28.6 -> 39.3%. Its old re-run re-indexed starting from the spot budget the thrown-away pass had measured (152 of 1000). With that budget given (--max-spots 152), the new run gives 30.6%. The difference comes from that path, not from the radius. - The count costs ~13 CPU-s on the heaviest set (65k predictions a frame). Over the 22 ci sets that count, pre-pass integration took 45.2 -> 45.8 s. - A build forcing the near tie and its overturn on 4nwv re-checks on the whole sweep (1.80% against the engine's 1.81%) and makes the run again deciding late. It ends with the same p.hkl. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3	2026-10-11 13:01:23 +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
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