3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	3d62388467	Twin-immune zone evidence for the operators a promotion adds (report-only) ... Under a twin law T a reflection whose twin mate is itself (up to the true group and Friedel) is untouched at every twin fraction. For each index-2 subgroup H of the adopted point group, those are the reflections centric in the group and acentric in H: centric if the operators the group adds over H are real, acentric if they are a twin law or a pseudo-symmetry - the one intensity statistic that still separates the two at fraction 0.5, where every operator statistic reads "real". Read on the P1 cross-check merge: epsilon-1 reflections in shells with <I/sigma> >= 5 (noise inflates every class towards centric), each class normalised against its own mean in bins of ~100 reflections and within the two phase classes of a detected pseudo-translation, Wilson outliers above E^2 = 20 dropped. Reported per subgroup: the added operators, n, <|E^2-1|> +- SE read absolutely against 0.968 / 0.736, and the centric-over- acentric Wilson log-likelihood in nats with both densities convolved with each reflection's error (flooring E^2 at its sigma instead read a genuine 1.2 A lysozyme zone as acentric), with the acentric control beside it. Log, report prose and TWIN_ZONE_n keys. Nothing reads it back; no decision changes. On the reference sets: 6toc P4222, all three subgroups centric (1.04-1.07, +253 to +534 nats); 6iu9 P3121 over P31 acentric (0.789, -294 nats); 5j23 R32 over R3 acentric (0.805, -304 nats, tNCS-class normalised); lysozyme P41212 centric (0.90, +476 to +1297); a P21 myoglobin centric (0.930, +135). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-09-20 18:45:03 +02:00
leonarski_fandClaude Opus 5	99123f33df	Twinning: normalised L-test, and one verdict read in every Laue class ... The L-test now divides each intensity by its resolution-shell mean before forming pairs, over the shells whose <I/sigma> reaches 1 (the floor the second moment already used). Two index steps are not the same resolution, and on a small cell with a steep fall-off the raw pairs read <|L|> up to 0.08 high: an untwinned crystal 0.568 and a partial twin 0.427 where phenix.xtriage reads 0.486 and 0.360. Normalised, the four reference merges (6toc, 6iu9, 5j23, a lysozyme) agree with xtriage within 0.02 (0.487, 0.376, 0.374, 0.480). Selection stays by shell, never by the reflection's own I/sigma, which biases <|L|> down. Equal-count shells were tried for the second moment and widen its gap to xtriage, so the shells are kept. The L-test is no longer switched off in holohedral Laue classes. Merging I(h) with I(Th) under a false operator gives (I(h)+I(Th))/2 for every twin fraction, the perfect-twin distribution, so <|L|> < 0.42 there is reported as an adopted operator averaging unequal intensities (promotion suspect, or a twin law absorbed into the point group) - a warning, not a veto. Over 42 holohedral merges of the corpus the genuine ones read 0.436-0.513, the over-promoted H3 twin 0.374, and one ~490 A-axis crystal 0.365. The verdict is one line (TwinningVerdictLine) used by the stats text, the report prose, the summary row, the warning and the viewer; a new TWINNING_VERDICT key names it. The twin fraction comes from the statistic that carries the verdict (the L-test unless the call rests on the second moment alone), is not quoted from a second moment under a detected pseudo-translation, and is not quoted at all on a merge under a suspect operator. The pre-search numbers (measured on the P1 search merge) are user-visible, are measured with that merge's own pseudo-translation declared, and leave out the reflections the lattice centring extinguishes - an R lattice in its hexagonal cell otherwise pairs present with absent reflections (5j23: 0.633 with them, 0.40 without). Report-only: no space-group decision, merge or intensity changes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-09-20 18:45:03 +02:00
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