9 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	7fe12773de	rugnux: report anomalous signal-to-noise SigAno (stats table + mmCIF) ... Compute SigAno = <|I(+)-I(-)|>/<sigma(I(+)-I(-))> per report shell and overall from the full-multiplicity I(+)/I(-) Bijvoet split, store it on MergeStatisticsShell, and surface it in the console merge-statistics table (new SigAno column) and the mmCIF via the standard wwPDB PDBx items _reflns.pdbx_absDiff_over_sigma_anomalous (overall) and _reflns_shell.pdbx_absDiff_over_sigma_anomalous (per shell) - the dictionary's home for this quantity, so no jfjoch_ local item is needed (unlike ISa). SigAno approaches ~0.8 for pure noise and rises above 1 with real anomalous signal. A half-set anomalous CC is deliberately not used: its two half estimates are complementary partitions of one observation pool (dI0 + dI1 = 2*dI_full), so differencing the two Bijvoet hands cancels the large common intensity that keeps CC1/2 non-negative and, once the anomalous SNR per half drops below 1, drives the correlation towards -1 rather than 0 - misrepresenting a weak-but-real signal. Emitted only when an anomalous split was made (has_anom guard), so a non-anomalous merge keeps its stats block and shell-loop columns byte-for-byte. Export-neutral: the I(+)/I(-)/IMEAN accumulation is unchanged. On low-energy S-SAD test data SigAno tracks XDS (13 keV null ~0.89, 6 keV ~1.44, 5 keV ~1.5-1.7) and never goes spuriously negative. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-17 20:54:03 +02:00
leonarski_fandClaude Opus 4.8	b647cf454c	rugnux: write I(+)/I(-) and F(+)/F(-) by default (rotation) ... A rotation merge now keeps each acentric reflection's Bijvoet split - the inverse-variance I(+)/I(-) from the same scaled fulls - even when the merge is Friedel-averaged (the default, no -A). IMEAN stays the primary intensity and is bit-identical to before; the split is purely additive and scaled non-anomalously, so a weak anomalous signal is preserved in the output without having to reprocess with -A. French-Wilson now also fills F(+)/F(-) from the two hands (one pass, shared Wilson prior). Writers: the default (Friedel-merged) MTZ and mmCIF now carry IMEAN plus I(+)/I(-) and F/F(+)/F(-) whenever a reflection has an anomalous split (the stills path, which computes none, keeps the previous columns). A missing mate or a centric is emitted as the CCP4 missing-value flag (NaN). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-17 11:52:31 +02:00
leonarski_fandClaude Opus 4.8	85cf826d2e	rugnux: dataset Wilson B-factor estimate + robust per-image Wilson B ... Add a dataset-wide isotropic Wilson B-factor estimate, the analogue of XDS's "WILSON LINE ... B=" which we did not export. CalcGlobalWilsonB fits ln<I> vs 1/d^2 over the merged reflections (B = -2*slope), skipping the low-resolution non-linear region (d > 4 A) and shells past the signal limit (<I/sigma> < 1) so the estimate is insensitive to how far the merged data were carried. It is diagnostic only - not fed back into scaling - and is written to the mmCIF (_reflns.B_iso_Wilson_estimate), the printed merge statistics, and the log. Also harden the per-image Wilson B (CalcWilsonBFactor): accept the fit only when it is well-correlated and physically plausible (0 < B < 200 A^2), else leave b_factor unset. A bad frame (an indexing glitch, too few reflections) otherwise produced a wildly steep Wilson line and a B of several hundred A^2 that polluted the per-image plot; NaN is preferable to garbage. Diagnostic-only: the merged intensities and every merge statistic are byte-identical (verified baseline vs modified on the rotation battery). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-17 08:58:17 +02:00
leonarski_fandClaude Opus 4.8	eae7ea90dc	rugnux: always write both MTZ and CIF; drop --scaling-output ... The merged reflections were written in one of mtz/cif/txt selected by --scaling-output. Write both an MTZ and an mmCIF unconditionally instead - each has its uses downstream (MTZ for the CCP4/phenix tools, mmCIF for deposition) - and remove the format selector, the plain-text .hkl writer, and the now-unused IntensityFormat enum / ScalingSettings::FileFormat plumbing. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-16 10:45:08 +02:00
leonarski_fandClaude Opus 4.8	ce12d69751	rugnux: write standard CCP4 anomalous MTZ (IMEAN + I(+)/I(-)) ... In anomalous mode the merge keeps the two Friedel mates as separate rows, which WriteMtzReflections emitted verbatim - two IMEAN rows per Bijvoet pair that downstream tools had to re-collapse. Pair the mates into one row per reflection with the standard CCP4 anomalous layout: IMEAN + I(+)/I(-) and the matching F/F(+)/F(-) amplitudes. A single HKLKeyGenerator(merge_friedel=false) yields both the shared ASU group key and which mate a row is (.plus); IMEAN/F are the inverse-variance Friedel mean, centrics/unpaired keep one hand with the other missing. aimless/mtz2sca/ANODE now read the file directly. The non-anomalous MTZ path is unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-16 10:37:56 +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
leonarski_f	54c0100e8e	v1.0.0-rc.157 (#67) ... 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: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`. * rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling. * rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics. * rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1. * rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group. * rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix. * jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation. * jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning. * jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint. * jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed). * jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types. * jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails. * jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak. * Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation. * CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-11 07:19:11 +02:00
leonarski_f	d6389e12da	v1.0.0-rc.156 (#66) ... 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. * jfjoch_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output. * jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling. * Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool. * jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection. * jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata. * CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-03 19:18:56 +02:00
leonarski_f	fc68a9baed	v1.0.0-rc.146 (#56) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. jfjoch_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset. jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling. jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file. jfjoch_scale: Dedicated tool for rescaling/merging existing data. jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel. WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being. Reviewed-on: #56	2026-05-28 18:48:35 +02:00