8 Commits

Include renames

Author	SHA1	Message	Date
leonarski_f	a39fd29f77	v1.0.0-rc.167 (#77) ... * `rugnux --model` reports CC(model, data) - the correlation of the merged intensities with the placed, scaled model - by resolution shell, on the same shells as CC1/2, with the reflection count and a significance for each. * `rugnux --model` fits the model's scale, anisotropic B and bulk-solvent parameters on the working reflections only, so the R-free it reports is measured against a model no free reflection helped scale. * The bulk-solvent parameters of `rugnux --model` are searched over their physically meaningful range instead of being fitted without bounds, so a model is never scaled with a solvent term that has silently switched itself off. * The rigid-body placement of `rugnux --model` uses the same bounded bulk solvent as the reported fit, so a model is no longer placed against a target carrying a solvent term with no physical meaning. * `rugnux --model` puts the model into the data's own description of the lattice before placing it, so a model whose cell is written on other axes - I-centred where the run indexed C-centred, a different unique axis, a permuted orthorhombic cell - is placed rather than scored where it was read; `MODEL_CHANGE_OF_BASIS=` and `MODEL_SETTING_AS_READ=` report it when it happens. * The rugnux results report opens with a summary - `VERDICT=` (`OK`, `WARNINGS`, `UNUSABLE`, `FAILED`), `VERDICT_TEXT=`, `PATHOLOGY_FLAGS=` with one closed-vocabulary code per condition that warned, and the `WARNING:` lines, which used to close the file - and the sections after it are renumbered 1-5 with no gaps. * `rugnux --developer` writes the full results report - the pipeline-internal keys and the long explanations the default report now leaves out - and `--finalist-ledger` adds the evidence for every space group the search considered, not only the one it adopted. * The results report warns when the merged data carry no usable signal and when too little of reciprocal space was measured inside the fitted resolution, and omits `FITTED_RESOLUTION` where the CC1/2 curve it is fitted on never falls off. * rugnux detects translational pseudo-symmetry and reports it under the `PSEUDO_TRANSLATION` flag as `TNCS_DETECTED=` and the `TNCS_*` keys - a translation the merged data are exactly invariant under is reported as `UNDECLARED_LATTICE_TRANSLATION=` under `LATTICE_TRANSLATION` instead - and a detected pseudo-translation can no longer buy a false screw axis in the space-group search or hide a twin from the L-test (`L_TEST_VS_TNCS=`). * The space-group search determines glide planes from zonal systematic absences, so a non-Sohncke space group such as P 2_1/c or Pbca is named where the run previously stopped at its Sohncke subgroup; `SOHNCKE_SPACE_GROUP=` carries the best Sohncke group beside it on every run that searched, and a centre of symmetry is never claimed. * Where the cell metric carries more rotational symmetry than the Bravais class the indexer named, the extra rotations are put to the intensities and the space-group search is asked again on the metric's own cell - adopted only where the intensities confirm the higher symmetry - so a lattice that is nearly but not exactly hexagonal, or whose reduction landed in a sub-cell, still reaches its true point group. * Systematic-absence calls rest on the evidence rather than on counts: a screw axis whose absent class the data show extinct is no longer refused because a handful of reflections in it read as present, and `SPACE_GROUP_ALTERNATIVES=` no longer drops a candidate that differs only on a zone the sweep never measured. * A reference correlation measured on too few reflections is refused instead of scored zero, so a run given a reference MTZ is no longer reindexed on an operator that mapped almost everything outside the reference's coverage. * A frame counts as indexed from 6 spots on its lattice rather than 9, so a weakly diffracting crystal whose frames cannot carry 9 is no longer refused the lattice it fits; `--min-indexed-spots` overrides it. * `-C` accepts a known cell in any equivalent description - conventional or primitive, centred or not - instead of only the reduced primitive form, so a centred cell given the way it is published no longer makes the run report that it found no lattice. * Each reflection is corrected for the sensor's quantum efficiency at the angle it meets the detector (attenuation lengths from the NIST tables, which also fixes the spot-width parallax term on CdTe) and for the attenuation of the flight path between the sample and its pixel; `--flight-path air|helium|vacuum` declares the medium - default air, since no file states it - and the report says what was assumed and what it was worth. The unmerged MTZ records the factors in new `QE` and `FLIGHT` columns beside `LP`, so raw counts are `I / LP * QE * FLIGHT`, and `_process.h5` in new optional `qe` and `flight` datasets. * Rotation geometry post-refinement fits the crystal and the detector at once, against the observed spot positions and the observed rocking angles together, so the refined distance depends far less on how wrong the file's distance was. * A coarsely sliced sweep integrates correctly: partials are joined into one rocking event by angle rather than by frame count, so two crossings of the Ewald sphere are no longer summed into one full, and at 0.5 degrees per image or coarser the per-frame geometry refinement accepts a spot whose miss the exposure's own rotation accounts for. * `rugnux --mode scale` reports the detector tilt and direct beam of the geometry it re-scaled at, instead of zeros that read as a flat detector, and no longer warns that no image was indexed on a run whose lattice came from its input file. * Every rotation run that determined a space group and merged reports what the mounting cost: `SPINDLE_LOST_UNIQUE_FRACTION=` is the fraction (0-1) of unique reflections the mounting made unmeasurable under the measured point group, also written to the master as `/entry/MX/spindleLostUniqueFraction` and what the mounting warning fires on; `SPINDLE_SYMMETRY_AXIS_ANGLE_DEG=` / `SPINDLE_SYMMETRY_AXIS_ORDER=` describe the mounting in the `--developer` report. * Stills and grid scans carry a per-image `spindle_blind_fraction` - how much of a rotation sweep's blind cone this orientation would make unrecoverable, 0.5 and above calling for a second orientation - through the CBOR stream, HDF5 (`/entry/MX/spindleBlindFraction`), the plot and scan-result APIs, and the viewer and frontend plots; an absent value means the frame could not be assessed and is not a 0. * The results report's `REPORT_VERSION` is 7. Reviewed-on: #77 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-09 07:25:13 +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	67dca388bd	v1.0.0-rc.160 (#70) ... 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>	2026-07-19 09:39:28 +02:00
leonarski_f	54c667190f	v1.0.0-rc.155 (#65) ... 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: Remove pixelrefine option (replaced with ProfileIntegrate2D) * jfjoch_viewer: Some graphical improvements. * jfjoch_viewer: Simplify und unify data analysis settings. * jfjoch_writer: Add TCP keepalive to increase robustness if jfjoch_broker "dies" in the middle of data acquisition. Reviewed-on: #65	2026-06-25 22:01:48 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... 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_broker: Add EXPERIMENTAL pixelrefine mode for image processing * jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files * jfjoch_broker: Add ROI calculation in non-FPGA workflow * jfjoch_broker: Fixes to TCP image pusher * jfjoch_broker: Remove NUMA bindings * jfjoch_broker: Improvements to indexing * jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values * jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors * jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs * jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results Reviewed-on: #63	2026-06-23 20:29:49 +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
leonarski_f	c67337cfe1	v1.0.0-rc.72	2025-09-08 20:28:59 +02:00
leonarski_f	0d1b388f4d	v1.0.0-rc.50	2025-06-20 09:52:26 +02:00