3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	7c1befd484	SearchSpaceGroup: ask the twin-immune zone of a lattice-holohedral candidate too, and do not read centring absences as screws ... RESULT-CHANGING. A tetragonal crystal in 4 twinned ~0.3 by k,h,-l (3r6o, I4_1) was merged in I4_122. Since the beam-stop fix both search arms passed 422 (H ratio 1.51 < 1.85); before it the Lorentz-filtered arm refused at 2.13x and was overridden by the all-observation arm. Either way the twin-immune zone - the one reading a twin cannot fake - was never asked: the Stage A zone gate skipped any candidate that holds every rotation of its lattice, on the argument that no twin law exists for such a group. But the subgroup's twin law is one of the candidate's own operators, so the holohedral promotion is exactly the commonest merohedral-twin case (4 -> 422, 3 -> 32 on a rhombohedral lattice, 321 -> 622), and the L-test-under-merge gate leaves such a twin in the higher group by design. The gate now runs whenever the P1 merge reads twinned (<|L|> in [0.375, 0.44)), holohedral or not. 3r6o reads 422 over 4 at -58 nats (acentric). With 422 refused, the all-observation arm took 222 over 4: the same-order tie-break credits a group's axial two-folds with the screw evidence of their rows, and on a body-centred crystal the I centring kills the odd class of every principal row (30 nats each), so a 222 of the real 2-fold plus two twin laws beat the crystal's own 4. Rows whose odd class a centring extinguishes are no longer counted where the merge reads that centring on its general reflections (the centring class at < 0.25 of the rest's mean E^2; measured 0.11-0.13 for I on 3r6o, 0.97-1.00 for the absent centrings). Changed (CPU screen of 53 sets against the kept rc175 run 20261016-0057, plus 3r6o): - 3r6o: I4_122 -> I4_1 (deposited I4_1), TWINNING INDICATED, twin law h,-k,-l ~0.32; ISa 4.15 -> 7.77, R_meas 0.218 -> 0.146, CC1/2 0.989 -> 0.993. - 8c3e: P622 -> P321 with P3_121 | P3_221 as alternatives, screw on c undetermined (deposited P3_121, twinned): 622 refused at -70.8 nats; ISa 5.69 -> 6.91. Unchanged: 3mc4, 5j23, 6toc, 6oww, 6iu5/6/9, 2wnn, 2xfw, 4bwl, 5ebi, 2wnq, 6vww, 7k1l, 6pxb, 8xte, 8xtg, 9i80, 5uth, 6h5t, 8k1g, 6moj, 7kcn, 5vml, 3p85, 7rji, 8xtf, 9h0q, 7l84, 6v2r, 7t5t, 5m17, 6p8p, 3meb, 5cc8, 9lxl, 8v4j, 6zqr, 9fcf, 5src, 11if, cuhf2, lyso_x06da_ref, lyso_x10sa_90deg_1, thau_x10sa_16keV, thau_bl1a_6p5keV, insu_H_x06da_twin/notwin, insu_I_x06da_ref, cytc_x06da_1, myob_x06da_split, kdp_x10sa_20keV (space group identical, ISa within run noise; 7l84/5src/11if differ only by the model-adopted enantiomorph label). Test: a body-centred 4 twinned at 0.45, given its cell, stays in 4 (222 without the centring rule). [SearchSpaceGroup], [twinning], [twin] pass. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4	2026-10-17 13:01:11 +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	538f3504d3	v1.0.0.rc-161 (#71) ... 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: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice. * **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster. * **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory. * **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again. **Breaking change to the rugnux command line:** * `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one. * `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride. **Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional: * `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve. * `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing. **Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional: * The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more. * `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.** Reviewed-on: #71 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-13 17:03:10 +02:00