4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	13badcfa39	Docs: battery report of the pushed rc.175, with commentary and figures ... Full open and in-house battery on 0b2dde214 (run 20261009-1447_0b2dde_rc175-0b2dde2-full) against the 10-07 battery on 9ced4c444, without the REFMAC check: the R-free figure and numbers are kept from the rc.174 battery. Report regenerated from the run with the current battery tools (verdicts scored by the current scorer, so KDP passes as an indistinguishable alternative), commentary written by hand. 5ky6 and the low-ISa cubic insulin set go from pass to fail, accepted losses of taking the pre-pass-2 decisions from the first part of the sweep; every other verdict is unchanged. The whole battery took 4898 s against 5795 s, most of it model validation now on the GPU (278 s against 1024 s); without it the HDF5 sets are at the same speed. Time, zoomed time, in-house time and resolution figures regenerated with paper_plots.py. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi	2026-10-09 16:38:23 +02:00
leonarski_fandClaude Opus 5.5	11122e4924	Docs: battery report of the rc.175 branch after phase 1, with commentary and figures ... Full open and in-house battery on 9ced4c444 (run 20261007-2139_9ced4c_rc175-p1-baseline) against the rc.173 battery, without the REFMAC check: R-free figure and numbers are kept from the rc.174 battery (20261005-2102_3770f4_rc174-final-refmac). No verdict changed from rc.174; 2ygz is new and fails. Two sets lost quality at the 50 % pre-pass default (outlier-laden outer shell on 5jk4, runaway cut on the in-house split myoglobin set); fraction 1 restores them, but nearby fractions do too and a fixed cut gives equal statistics, so the pre-pass only tips two existing weaknesses (an unmasked dead edge row; a noisy half-set CC1/2 on a multi-domain crystal). Time, zoomed time, in-house time and resolution figures regenerated with paper_plots.py. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi	2026-10-08 00:15:34 +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