3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	495f6a97b3	Rotation scaling: penalised per-frame scale of the fulls; fulls-only partials get flux and partiality ... Three defects in the per-frame scaling of sparse (small-molecule, weak) rotation sweeps: 1. The fulls' per-frame scale pooled sparse frames by their RAW full count, but in a high-symmetry group with many systematic absences most usable counts stayed under the minimum, so most frames were never fitted and kept corr = 1 beside pinned, fitted frames (two gauges in one reference). The release step then read the gauge offset (a constant 134x on a cubic Ia-3d small-molecule sweep) as signal and gave each frame exp(kept_f * 4.9) - the e^-5 errors on a quarter of the frames, R1 0.62. A fixed box window also cannot follow a 100x absorption ramp over a few degrees, and frames under the credible floor, exempt from the window, ran away to 1e-7. Now each round fits every frame on its own fulls (no pooling, no minimum), and the scale is a penalised second-difference smoother of log G (Whittaker/Eilers), each frame at the information of its fit, lambda by cross-validation over blocks one rocking curve wide (interleaved single frames leak through shared rocking curves and chose to follow every frame). After convergence the existing ShrinkToRestrained hands back the per-frame deviation its neighbour shares. Pooling and the box window are gone from the fulls loop; the partials loop is unchanged. 2. With partial scaling off (< 50 rocking events per frame) the partials kept the integration-time corr: no incident-flux correction and not the partiality of the ingest-smoothed geometry, because only the partial scaling loop rewrote corr. They now get corr = prescaling_corr / partiality at G = 1 (host, and a device kernel). 3. The flux meter (per-frame mean background) jumped 30x between neighbouring frames of a sparse sweep - on a few reflections it measures which reflections the frame holds. It is read through the same smoother at the precision of each frame's mean. SHELXL R1(>4sig) against the published structures, rc174-cand -> this, on the in-house small-molecule sweeps: cubic Ia-3d 0.615 -> 0.119 (XDS 0.088); four organic sweeps (monoclinic / orthorhombic) 0.0515 -> 0.0459, 0.0451 -> 0.0396, 0.0747 -> 0.0709, 0.0452 -> 0.0413; ISa up to 11.6 -> 31. Raw flux instead of smoothed costs 0.002-0.003 R1 on the first two. A weak, decaying protein sweep on the fulls-only path: ISa 6.7 -> 27.1. CPU and GPU paths agree. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 14:18:08 +02:00
leonarski_fandClaude Opus 5.5	f69339ce63	RotationScaleMerge: fulls-only per-frame scaling (prototype), pooled over sparse frames ... Prototype switch --no-scale-partials: skip the per-frame scaling of the partials and let the fulls (scale-fulls) carry the per-frame scale, as XDS does. Without partial scaling a frame whose fulls number fewer than MIN_REFLECTIONS is fitted over the nearest frames on either side that together hold enough (PoolHalfWidth), on the host and in the GPU kernel. Default path unchanged (p.mtz md5 identical on the three profiling sets). Why: on fine-sliced small-molecule sweeps the per-frame partial scale and the partiality model are degenerate within a rocking curve, and the fit swings G 0.23..1.2 with a 180 deg period (XDS's own frame scale: 0.79..0.99). That imprints an hkl-dependent bias common to all equivalents, which R_meas/CC1/2/ISa cannot see but a refinement against the known structure does. And scale-fulls never fitted a frame on such data: a full is filed under one frame, about 8 per frame, below MIN_REFLECTIONS, so every frame kept G = 1. Measured with SHELXL refining the COD structures (R1 >4sig), default -> switch: aspirin 20 keV 0.096 -> 0.062, aspirin 25 keV 0.094 -> 0.046, citric acid 0.161 -> 0.109, HEPES 0.090 -> 0.070 (XDS 0.030-0.038). Proteins lose ISa with the switch (myob 9.1 -> 7.6, cytc 25.8 -> 13.7), so it is not a default; the choice is to be made from the data. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-03 23:08:12 +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