4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	4979f8aa68	French-Wilson: anisotropic Wilson prior from the fitted anisotropy tensor ... The French-Wilson prior of each reflection is now epsilon * K_shell * a(h), with a(h) = exp(-1/2 s^T B s) from the deviatoric tensor AnalyzeAnisotropy already fits (the form it is fitted in) and K_shell = sum(I/eps) / sum(a), so a shell's priors still average to its measured mean. The amplitudes are made isotropically at the merge as before and made again once the tensor exists (full pipeline and --mode scale). Only F/SIGF and F(+)/F(-) change; IMEAN/I(+)/I(-) are bit-identical. Applied whenever a tensor was fitted, with no detection gate: a near-isotropic tensor gives a(h) ~ 1 and the isotropic prior back, and the prior wants the best estimate of <I> along h whatever its cause. Follows ctruncate's anisotropic prior (Ballard & Stein, CCP4); credit in ACKNOWLEDGEMENT.md, CPU_DATA_ANALYSIS.md and at the algorithm. --model scaling (ModelScaling.cpp) was checked: k_overall + symmetry-constrained anisotropic B + flat bulk solvent fitted on the working set, against the same FW F written to the MTZ - as REFMAC/phenix.refine do. No change needed. Evidence (REFMAC 10-cycle restrained refinement of the deposited model, R-free on the depositor's free reflections shared by both data sets; base = rc174 processing, same IMEAN): set base new d set base new d 9rcs 0.3475 0.3494 +0.0019 8qq7 0.4452 0.4503 +0.0051 9yzk 0.3192 0.3171 -0.0021 9hs7 0.2898 0.2465 -0.0433 6yqf 0.4642 0.4543 -0.0099 5nw5 0.3256 0.3206 -0.0050 7n2s 0.3126 0.2998 -0.0128 6z8o 0.2927 0.2892 -0.0035 6qaj 0.3390 0.3038 -0.0352 6moj 0.2756 0.2651 -0.0105 6r72 0.3826 0.3797 -0.0029 7qij 0.3239 0.3140 -0.0099 anisotropic sets: median -0.0075, mean -0.0107, 10/12 better isotropic controls: 5reo -0.0014, 7kcn +0.0003, 6fid +0.0002, 11if 0.0000 rugnux's own --model R-free moves the same way (median about -0.019; 5nw5 +0.006), R_model shell-scaled too; dep_cc_delta unchanged (intensity based). The adoption rule (median gain >= 0.005 on the anisotropic sets, no control worse than +0.002) is met. The two sets that lose are the one with a FLAT resolution signature (8qq7) and 9rcs, where the exp form drives the dead direction's prior to ~0 beyond 3.7 A. For scale: ctruncate's own anisotropic prior on the same merges moved the same REFMAC R-free by a median of only -0.0008 (9hs7 +0.026). Inhouse lyso_x06da_ref, thau_x10sa_0p1deg: every battery metric unchanged. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 14:24:14 +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	680c36c20d	v1.0.0-rc.166 (#76) ... * `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands. * `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion. * Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants. * `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing. * A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed. * `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing. * Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences. * The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to. * The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after. * The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution. * `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have. * Twinning is no longer reported when the L-test contradicts it. * The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's. * `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots. * The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area. Reviewed-on: #76 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-02 21:17:31 +02:00
leonarski_f	dd0bffb283	v1.0.0-rc.159 (#69) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-13 13:54:03 +02:00