Every candidate the indexer forms is Niggli-reduced and primitive; the reference cell was
compared against them exactly as typed. For a centred lattice those are different numbers
entirely - a conventional F-cubic cell reduces to a rhombohedron with 60-degree angles, a
centred monoclinic cell to axes it shares none of - so the true candidate failed the 5% test and
the run reported that it had found no lattice. A user who supplied the cell as it is published
was worse off than one who supplied nothing.
The reference is now expanded into the primitive lattices its six numbers could stand for, one
per centring, each reduced the way a candidate is; a candidate matching any of them is kept. The
cell as typed stays in the set, so the indexer that returns the basis it was handed is
unaffected.
The cost is real and stated: a wrong cell now gets several chances to match rather than one. The
controls that hold are on data - deliberately wrong cells are still refused, and every cell that
worked before gives the same answer to the digit - but a synthetic lattice can be made to match
through a centring hypothesis it has no right to, and no volume test tightens that without
excluding a true candidate this corpus already contains.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
The score gated on 60 spots, but the seed escalation stops at the leanest seed that indexes -
30 spots on precisely the clean frames a grid scan produces - so the value was absent exactly
where beamline automation most needs it, and absence maps to "engage": the protocol would have
fired on every good frame, which degenerates the trigger into "always". The floor itself stays
where it was calibrated; what changes is what it gates. When no escalation pass could answer,
one severity-only pass runs over the full spot list - the row search alone, no reduction, no
refinement - purely to produce the number.
The same was true of the indexer choice: only the FFT family computes a row shortlist, so a
deployment configured with the known-cell indexer - the ordinary online stills path - never
produced the score at all. Where the severity-only pass has no row search to run, the severity
is read off the rows of the winning lattice instead, which any indexer produces: the lattice's
shortest few distinct directions, as many as the FFT shortlist resolves in practice, fed through
the same window and scoring with equal magnitudes. The count parity is load-bearing - a worst
case over every enumerable lattice direction fires on 100% of harmless mounts of a generic
triclinic cell against 74% for this selection at theta_max = 15 deg, and an always-firing
trigger decides nothing - while the diad-detection rate stays 1.00 on the monoclinic classes
either way, a dropped axis row being recovered by the pair normals exactly as an invisible one
is. A frame that neither indexed nor reached the spot floor still reports nothing, which is the
honest answer and maps to the recoverable error.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
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>
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: #70
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
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_broker: Improve azimuthal integration (add <I^2> calculation)
* jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated)
* jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin
Reviewed-on: #58
This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.
* jfjoch_broker: Use httplib for HTTP server instead of Pistache
* jfjoch_broker: Drop OpenSSL support
* jfjoch_broker: Base work for multi-lattice support in the future
* Update dependencies to more recent versions (spdlog, HDF5, Catch2, httplib)
Reviewed-on: #41
This is an UNSTABLE release and not recommended for production use (please use rc.11 instead).
* jfjoch_broker: Experimental rotation (3D) indexing
* jfjoch_broker: Minor fix to error in optimizer potentially returning NaN values
Reviewed-on: #18
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_fandClaude Opus 5