3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	a29edb69cf	rugnux: decide whether there is a lattice on distinct reflections, against every wrong angle ... The first pass's last gate - is the lattice this crystal's at all - compared the validation spots on the lattice with the median of five displaced-spindle-angle nulls, against the null's binomial noise floored at one spot. On the two in-house no-crystal controls it is fed a handful of genuine stray reflections from something rotating with the sample (the same detector positions, a pair symmetric about the beam 198 frames apart, in both sweeps, offset by the 15-frame start difference), plus one reflection near the spindle axis that stays in diffraction for ~46 frames. With the decisions taken from the first part of the sweep the 60 validation frames are 3 deg apart instead of 6, so that one reflection is counted on three validation frames, and the gate passed on 4 spots of 151 (null median 0) and 7 of 72, where the whole-sweep flow had seen 3 and 3. Now the evidence unit is the distinct Miller index - a reflection on several validation frames is one piece of evidence - and the test uses every displaced angle's count: with no crystal the recorded angles are one of six exchangeable arrangements, so the gate is the binomial tail of the recorded arrangement's share at p = 1/6, at the same 0.001 significance (SPOT_BUDGET_SIGNIFICANCE_Z). No threshold is added; the median and the one-spot floor go from the gate. The comparisons between lattices (ValidationEvidencePrefers) are unchanged. no-crystal control 1: 4 distinct vs 2 over 5 wrong angles, tail 0.009 -> no lattice (was P 1) no-crystal control 2: 5 distinct vs 2, tail 0.002 -> no lattice (was P 1) p.mtz md5 identical to rc175 7c9a6c7d1 (GPU) on 5nw5, 5reo, 7atg, 8v4o, 9qw8, 9rci, 5ky6, insu_I_x06da_low_isa, myob_x06da_powder_2; cytidine and myob_x06da_split pass. The weakest real lattice in the open/in-house/private battery logs has 117 spots against a null of 0. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi	2026-10-08 21:00:40 +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