6 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	2c97e654ed	Battery: add two L-cystine sweeps (in-house arm); say which open sets are pink beam ... lcystine_x10sa_20keV and lcystine_x10sa_25keV are scored against the literature structure only (hexagonal L-cystine, P 61 2 2, COD 5000005, Oughton & Harrison 1959): XDS indexes under 10% of the spots of either sweep, with the cell supplied and with the spot range cut to 150 frames, so there is no CORRECT.LP to take a reference from. On the current build the 25 keV sweep passes (P 61 2 2, cell within 0.5%) and the 20 keV sweep finds no lattice. EXTERNAL_TEST_DATA.md: none of the open-arm datasets is pink beam; every PDB record is single-wavelength (9Q41 used a multilayer monochromator). The pink-beam sets are the in-house ones. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-02 16:27:52 +02:00
leonarski_fandClaude Opus 5.5	f06780bd91	Battery: record each set's wavelength; add the rc173 battery report to docs ... Every open and in-house manifest row now carries `wavelength` (A), taken from WAVELENGTH in rugnux's own p_report.txt of the latest run of that set (the full rc173 run 20260929-2003 plus the two 10-02 runs for the sets added since). Descriptive only; the scorer ignores it. docs/BATTERY_REPORT.md is report.md of the full rc173 open + in-house run (210 sets), verbatim, to be polished. The private arm runs separately and has its own report, so nothing from it appears here. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-02 16:06:13 +02:00
leonarski_fandClaude Opus 5.5	dcc710a226	Battery: eight more home-source sets (open arm), five small molecules (in-house arm) ... Open arm, all IRRMC, single Cu K-alpha sweeps on Rigaku Saturn CCDs read through the d*TREK SMV path: 3mc4 (H 3), 3meb (P 1 21 1, Saturn 944, overflow ratio 32), 3p85 (P 63 2 2), 3r6o (I 41), 5uth (P 31 2 1), 5vml (P 42 21 2), 6cee and 6v2r (P 21 21 21 / P 41 21 2, Saturn A200, unbinned 2048x2048, 0.1 mm pixels). Detector 2theta spans -10 to +10 deg. Run 20261002-1326_84228b_home-source-12: all pass except 3r6o, called I 4 2 2 against the deposited I 41 with twinning suspected (<|L|> 0.32). Two further candidates (3r6h, 3sgw) were dropped: what the repository lists as one dataset is two sweeps under one file template, split by a phi change, which the reader refuses. In-house arm: aspirin (20 and 25 keV), anhydrous citric acid, HEPES and YAG, measured at X10SA. The reference is XDS's CORRECT.LP (refs --write) with the space group taken from the literature as ref_override, because XDS reports only Sohncke groups; each override cites its COD entry and paper. Run 20261002-1354_84228b_small-molecules-inhouse: four pass, including HEPES as P b c a where XDS has P 21 21 21; YAG is called I 41 3 2 against I a -3 d (both programs merge it poorly, rugnux CC1/2 0.40, XDS ISa 3.2). EXTERNAL_TEST_DATA.md gains the eight depositions (DOIs checked on DataCite) and updated counts; the battery README lists the small-molecule standards and has the current count of symlinked open-arm directories (42). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-02 13:57:30 +02:00
leonarski_fandClaude Opus 5.5	ac7c6af5a8	Read Rigaku d*TREK SMV images; add two home-source sets to the open battery ... The SMV reader only knew the ADSC vocabulary, so a Rigaku Saturn frame was recognised as SMV and then refused for want of PIXEL_SIZE. A header naming DETECTOR_NAMES is now read as d*TREK: - pixel size and the point of normal incidence from <det>SPATIAL_DISTORTION_INFO; - image directions from <det>DETECTOR_VECTORS combined by <det>SPATIAL_DISTORTION_VECTORS, matched to a DetectorOrientation (a Saturn 944+ image is mirrored and turned a quarter, so the hand is preserved); - distance and the detector circles (2theta etc.) from <det>GONIO_*, composed into PONI angles; spindle from ROTATION_VECTOR, angles from ROTATION; - wavelength from SCAN_WAVELENGTH, or the second number of SOURCE_WAVELENGTH (the first is a count - the old NumAny fallback would have read 1.0 A); - pixels above 32767 decoded as (v - 32768) * RAXIS_COMPRESSION_RATIO. dxtbx's FormatSMVRigakuSaturnNoTS, which claims headers without DTREK_DATE_TIME, ignores the distortion vectors; on a Saturn 944+ sweep that puts the spindle 90 degrees off (DIALS: 12% indexed vs 98% with the vectors applied, at the deposited cell). The arm geometry is confirmed by the data: the refined direct beam of a 2theta = 10 deg sweep lands at x = 621.1 against 621.6 predicted. The anomalous map peaks at 11.5 sigma on the two K+ and 6-7 sigma on S and P, so the hand is right. Battery, open arm: 5cc8 (rotating anode, Saturn 944+ SMV, 2theta = 10 deg sweep) and 9jq9 (Ga K-alpha liquid-metal jet, PILATUS3 1M miniCBF, single 450 deg sweep), both IRRMC. Run 20261001-2132_84228b_dtrek-home-source: 9jq9 passes (P 21 21 21, 1.65 A); 5cc8 merges to 1.53 A at the deposited cell but is called P 21 21 21 against the deposited P 21 21 2 (screw evidence on 00l 68-78 nats, tNCS at (1/2,1/2,0.11)) - left failing, not yet adjudicated. The Saturn gain (~5 ADU/photon) is not in the header and is not modelled. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-01 21:44:44 +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	6dfe065365	v1.0.0-rc.172 (#82) ... * Fixed `jfjoch_broker` cancelling every data collection with a CUDA "out of memory" error after long operation: GPU memory no longer leaks with each collection. * Rugnux scales a rotation sweep until the per-frame scales settle instead of for a fixed three rounds, and says so when they did not - merged intensities, and the space group, resolution cut and frame rejection read off them, change accordingly; `--scaling-iterations` is now the cap on that loop (default 100). * Rugnux places every frame of a marCCD, SMV or miniCBF series at the spindle angle its own header states, so a series with missing frames, or with angles written modulo 360, is no longer read at the wrong geometry or refused. * Every rotation run writes two diagnostic files beside its reflections: `<prefix>_detector.jpg`, the detector projection with the pixel mask and the detected beam-stop shadow drawn on it, and `<prefix>_plot.txt`, one row per image. Reviewed-on: #82 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-22 06:48:37 +02:00