6 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Fable 5.1	61afff891b	Rotation scaling: the per-frame scale loop runs to convergence, gauge pinned, plain fit ... The alternating per-frame scaling used to run a fixed three rounds of a Cauchy-reweighted fit against a reference that included half a sweep's rocking-curve tails. Three rounds left a short sweep merged in P1 far from its answer (a 90 deg tetragonal sweep refused its 422 with the P1 scales anti-correlated with the converged ones), and more rounds did not help: the fit had no fixed point. Two things made it walk. The objective is invariant under G -> cG with the reference -> reference/c, so every round moved every scale by a constant factor; and the robust loss, iterated against a reference refitted each round, drops the strong reflections of a frame whose scale is off by a third (ten-sigma residuals) and lets the weak ones carry it further off - measured on a 360 deg sweep the scales shrank 10-30% per round for thirty rounds and the H ratio of a genuine 222 read 21x. Now the loop pins its gauge every iteration (G divided by the precision-weighted typical frame scale G_ref = sum G^3 / sum G^2, one definition shared with the CC1/2 weight), fits the plain weighted least-squares slope with the weights the reference uses and only on the observations the reference is built from (the partiality floor), and stops when the rms |log(G_new/G_old)| over the frames falls below 1e-3. With the same weights on both sides the alternating fit is exact coordinate descent on one objective and cannot climb; measured, the 360 deg sweep settles in 19 rounds and the 90 deg one in 30-50, each pass's partials and fulls loops alike. --scaling-iterations is now the cap (default 100). A loop that reaches it is logged, the report prints SCALING_ITERATIONS and raises SCALING_NOT_CONVERGED, and the correction surfaces run to the same tolerance under their own cap. On the GPU the loop runs one iteration per call so the pin and the step test read the same numbers as on the host; the fulls' reset is split out of ScaleFulls. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT	2026-09-20 18:45:17 +02:00
leonarski_fandClaude Opus 5	3d7891c347	rugnux: weight every CC1/2 by the information a reflection carries ... The resolution cutoff, the shell table and the overall CC1/2 counted every unique reflection equally. The merge itself is inverse-variance weighted, so an observation from a frame the crystal barely diffracted on enters it at 1/G^2 of a good one - honestly, with its sigma - but a reflection measured only on such frames is scaled-up noise that then counts as much as a well-measured pair in every Pearson CC1/2 read off the merge. On a sweep where half the frames are weak the curve collapses at every resolution: the cut lands at 3.7 A on a P1 crystal whose good frames reach 1.5 A, and the UNUSABLE verdict fires (CC1/2 0.40 beside I/sigma 10). Each merged reflection now carries cc_weight: the precision its half-sets would have had with every observation at the run's typical frame scale, over the precision they have. G_ref = sum G^3 / sum G^2 over the usable observations is the precision-weighted typical scale, which the dead frames cannot drag down however many there are; the factor per observation is max(1, (G_ref/G)^2), with G the frame's total scale (partial scale, flux and the fulls' own G) taken before the correction surfaces and before collapsed frames are dropped, so nothing intensity- or resolution-dependent enters it. On a sweep without a weak stretch every weight is 1 and the CC1/2 is the plain Pearson it was. The cutoff fit, the shell table and the overall CC1/2 (and so the UNUSABLE verdict and the report's shell checks) all read the same weighted statistic. The two extra per-group sums are accumulated on both merge paths, the host loop and MergeAccumKernel, from one per-frame factor array; a host recompute of the device sums agrees to 1e-15 relative on every merge after the corrected corr is uploaded, and a host-merge run gives the same cut, space group, CC1/2 and ISa on five sets. Weighting by the half-set error variance alone (1/(v0+v1)) is not this: v grows with the intensity, so it weights the weak end of the intensity distribution and biases homogeneous data coarser. Measured (written resolution, together with the weighted outlier median): a P1 sweep with a long weak stretch 3.73 -> 1.40 A against a 1.63 A XDS reference, UNUSABLE withdrawn (overall CC1/2 0.40 -> 0.97); a second 3.61 -> 3.00 A; one with most of the sweep out of beam 7.35 -> 5.20 A. Lysozyme, thaumatin and two insulin sets unchanged to 0.01 A (one lysozyme sweep with a weak wedge 1.13 -> 1.16 A, from the median), same space groups throughout. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-09-20 18:45:03 +02:00
leonarski_f	9aae0c2ba7	v1.0.0-rc.169 (#79) ... * Building Jungfraujoch no longer needs zlib or Eigen installed on the machine, and the dependencies the build fetches are pinned and updated to current releases. * rugnux: improvements in indexing, lattice selection and geometry post-refinement, which index crystals that previously returned no lattice and keep the better of the two geometries a run measures. * rugnux: improvements in beam-centre measurement, beam-stop detection and space-group determination. * rugnux: the unit cell reported with a determined space group now obeys that group - a cell whose symmetry was confirmed from the intensities is re-refined under it, and a cell the group cannot describe is reported with a warning rather than as it stands. * rugnux drops the stretches of a rotation sweep whose removal measurably improves the merged intensities and reports what became of every frame, and decides the resolution cut on the crystal's own diffraction rather than on its ice rings. * The rugnux results report is machine-readable - every line that is not `KEY= value` data starts with `#` - and states the build it was written by, its authorship and its terms of use (`REPORT_VERSION= 8`). * `jfjoch_viewer`: improvements in the file manager (CBF frames beside HDF5 datasets, a remembered root), the dataset plots, the inspector and the image statistics, plus a settable font size, a view of the rugnux results report, usable performance over a remote display (`ssh -X`) and a reset of all settings to defaults; the reciprocal-space window is removed. * Broker fixes around DECTRIS collections and dark-mask calibration: re-initialising after a run that never started no longer freezes the broker, a cancelled calibration is abandoned instead of reported as done, and a collection whose start message never arrives ends by itself. Reviewed-on: #79 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-15 17:09:31 +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	451310f43d	v1.0.0-rc.158 (#68) ... 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. * Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation. * jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window. * rugnux: Accept an absolute `-o` output prefix in offline processing. * Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed). * Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-12 19:42:29 +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