4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	0c3e1462ef	merge: the completeness denominator is the declared range, not the surviving one ... CalcPossibleReflections was handed d_min/d_max derived from the reflections that came out of the merge, so a loss at either extreme took the numerator and the denominator with it. At the high end that is right: d_min is the finest d reached anywhere and the denominator is the full sphere down to it, so anisotropic loss shows. At the low end it was a tautology - d_max was the coarsest reflection that happened to survive, so anything the beam-stop shadow mask (on by default), a detector mask or the low-resolution limit itself removed left the denominator along with the data and could not be reported as missing. Both statistics paths now bin, and count, between the DECLARED low-resolution limit and the finest d reached: MergeOnTheFly::MergeStats (stills) and RotationScaleMerge::MergeAndStats (rotation). The grid and the denominator keep sharing their bounds, so no possible reflection falls outside a shell. An undeclared low limit is the whole sphere - 1/d^2 down to 0 - spelled as an infinite d_max, which ResolutionShells already handles and which gemmi's for_all_reflections special-cases; the change therefore reads correctly whether or not the 50 A default stays. The innermost shell keeps a finite d_max label, falling back to the coarsest reflection measured when the bound is infinite. This makes the shell boundaries the ones the integration document already claims: XDS lays its nine 1/d^2 bins between INCLUDE_RESOLUTION_RANGE's two values, not between the extremes of the surviving data, and counts POSSIBLE against the declared low limit - which is why its innermost shell reports the beam stop's loss. Verified against a CORRECT.LP: all nine boundaries reproduce to the printed precision from the declared 50 A, and not from the coarsest observed reflection. Measured on stored merges of seven rotation datasets, small-molecule and protein, re-scaled with --mode scale: the overall denominator moves by 0 to 2 reflections out of 70,000-100,000, because on every one of them the coarsest reflection the declared limit allows was itself measured - the corpus has no dataset whose stop eats a whole low-resolution class. What does move is the shell grid: the innermost boundary shifts by 0.1-0.4% in d (e.g. 7.21 -> 7.22 A), which changes the innermost shell's counts by up to a few per cent and its R_meas by around 0.1 percentage points. Stored battery baselines for rmeas_lo must therefore be regenerated, not compared across this commit. Two decisions read merged completeness (the two-pass wrong-cell guard, which only fires above 100.5% and only under -S); a larger denominator can only lower the figure, so the guard can fire less often, never more. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-09-02 16:39:40 +02:00
leonarski_fandClaude Opus 5	26fc4b02b3	symmetry: carry the space group as the group, not as its number ... The adopted space group travelled the pipeline as a bare int and was rebuilt downstream with find_spacegroup_by_number, which returns the reference setting. So every setting a number cannot name was destroyed one line after it was determined: P 1 1 2 came back as P 1 2 1, I 1 1 2 as C 1 2 1, R 3:R as R 3:H. DatasetSettings now holds the gemmi::SpaceGroup itself, DiffractionExperiment exposes it as GetGemmiSpaceGroup() / GetSpaceGroupOrP1(), and everything that used to take an int - HKLKeyGenerator (its int constructor is gone, so the compiler finds the callers), the merge, the R-free flags, French-Wilson, the reindexing ambiguity, the completeness enumeration, the MTZ and mmCIF exports, the model validation - takes the group. -S keeps the setting the symbol names rather than reducing it to a number. The end message carries both spellings and a reader prefers the name, since only the name keeps the setting while the number is what a reader written before the name understands. It carries them over CBOR too: the determined group was never serialised at all, so a group rugnux chose reached the master file only when the same process wrote it, and an online writer fell back to whatever the user had supplied at the start. Both keys are optional additions, so an older reader skips them and a newer one reads an older sender. On disk the master's /entry/sample/space_group carries the extended Hermann-Mauguin name and is what the reader takes the group from, so a setting survives a _process.h5 and the --mode scale that re-reads it; the number stays beside it and is the fallback for files written before. Every one of the 230 reference settings the old writer could produce reads back as itself, so older files are unaffected. Stage A and Stage B of the search still enumerate reference settings only, so this determines no group differently today - it is what the enumeration needs before it can be widened. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N	2026-08-31 07:16:43 +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
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