5 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	5984bf467f	rugnux: the no-crystal near-tie line prints the exact log10 tail against log10 significance ... The line put the distinct-reflection count against a normal-approximation bar, which at a handful of reflections reads the wrong way: a control the exact test rejected (5 vs 2 by chance, tail 10^-2.70 against 10^-3) was printed 0.59 above the bar. It now prints the exact binomial tail and the significance, both as log10, with the margin in decades and the noise as the tail's change over one binomial standard deviation of the count. The tail is summed in logs (ValidationEvidenceLog10Tail), so it stays finite for a real lattice; the decisions compare the same tail in log10. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi	2026-10-10 09:33:34 +02:00
leonarski_fandClaude Opus 5.5	cd20c2c378	rugnux: the no-crystal test asks its own significance, 1e-9 ... The final no-crystal test (RejectChanceLattice) used the 0.001 binomial level of the comparisons between candidate lattices. The lattice it tests is the winner of some fifty indexing attempts, each fitted to an accumulated cloud that already holds the long-lived reflections it then re-finds on the validation frames, so that null is optimistic by roughly the number of attempts. The two in-house no-crystal controls passed it by one or two distinct reflections (tails 10^-2.06 and 10^-2.70 against 10^-3). The test now asks 1e-9 (Z ~ 6); the rescue comparisons keep 0.001. With two reflections by chance the controls would now need 15 distinct reflections instead of 4-5. Real lattices are tens of decades past either level (weakest seen: 10^-83). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi	2026-10-10 09:27:50 +02:00
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