4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	677ece7b59	Post-refinement: correct a goniometer that turned further than it was told ... The angles a rotation dataset stores are the COMMANDED ones, so a stage whose travel is miscalibrated leaves no trace in the header - every angle is self-consistently wrong. No existing parameter can absorb it either: the cell scale, the axis direction, the detector distance and the beam centre are all orthogonal to an error in rotation MAGNITUDE. So fit it as what it is - one scalar k, the ratio of the travel to the commanded angle - on the rocking events the geometry post-refinement already builds, after step A so the cell scale and the axis direction are fixed and k is the only free quantity. Two details decide whether the number means anything. The angle enters measured from the CENTRE of the sweep: the reference orientation was fitted against the commanded angles and has already absorbed their mean error, so measured from the goniometer's zero instead a constant missetting about the spindle leaks into k with a gain of <phi>/<phi^2>, which depends only on where the sweep happens to sit - on a short sweep starting near zero a 0.14 deg missetting fakes 1.4 % of k. Referred to the sweep centre that leak is identically zero at any width. And the robust loss is scaled to the scatter the events actually have, which varies by more than a decade between datasets, so any fixed constant is either inert or throws away real data. A stage fault is rare and a 1 % angle correction applied to a healthy dataset would damage it silently, so the correction is committed only when every test passes: at least 30 deg of sweep and 5000 events, |k-1| over 0.5 %, a misorientation of at least 0.5 deg at each end of the sweep, and the same k from every fifth of the sweep left out. The last test is not optional. A second lattice that dominates ONE END of a sweep - exactly what happens where the primary stops indexing - fakes a k that passes the other two, and the hkl-hash split used elsewhere in this file cannot see it, because both of its folds sit at the same angles and anything structured in phi survives in both. When it commits, the second pass re-integrates against the corrected angles. The pre-pass mosaicity is dropped with it: that is a width in degrees fitted against angles the second pass has just stopped using, and since the override can only ever raise the second pass's own estimate, carrying it over would hold the second pass at the rocking width the uncorrected angles produced - the correction half-applied. --rotation-scale asserts a known stage calibration by hand and overrides the fit. On the 38-crystal rotation battery the gate fires on exactly one dataset, at k = 1.01318 with 0.74 of that k surviving every fifth left out. The largest of the other 37 is 1.00211, which fails the end-error test; 34 of them sit below 1.0006. On the one that fires: R_meas 39.2 -> 23.9 % (XDS 37.1) CC1/2 86.5 -> 96.0 % (XDS 94.3) CC1/2 outer 1.4 -> 53.4 % (XDS 42.5) unique refl 40990 -> 41540 (XDS 41322) observations 74975 -> 103858 (XDS 129322) mosaicity 0.181 -> 0.159 deg which takes it from losing to XDS on R_meas, CC1/2 and outer-shell CC1/2 to beating it on all three, and the mosaicity drop is the inflation the uncorrected angles were producing. Its low-resolution R_meas is the one number that moves the wrong way, 12.0 -> 13.9 %, still well inside XDS's 18.3. No space group moves anywhere, and every other crystal's merge is unchanged beyond the two-pass loop's own jitter - measured here as the spread of the post-refined distance across arms that do not touch post-refinement at all, which is larger than anything this commit produces. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-12 00:42:25 +02:00
leonarski_fandClaude Opus 5	d565b66916	Post-refine: drop the rocking-width diagnostic, report frames per event ... The "median rocking width -> estimated mosaicity" line took an intensity-weighted second moment of the frame-centre angles with max(0, I) weights, per event, then a median over events. For a two-frame event that moment is exactly zero whenever only one frame has I > 0 - probability 2/3 for a reflection carrying no signal - so on a noise-dominated dataset the median lands in the degenerate spike and prints 0.0000. Simulated against a known width it is wrong by 0.23x to 13x, in both directions, and on a pure-noise null it returns a plausible-looking 0.06 deg. est_mosaicity_deg was read nowhere, so nothing downstream was affected; the number only misled whoever read the log. It was built to measure a signal for a mosaicity refinement that was then abandoned, and the estimator that replaced it is the per-image one that already drives prediction. Report instead the frames per rocking event, which is what the block could honestly say: near 2.0 the reflections barely rock, so the observed angle this refinement is fitted to is under-determined. It is a geometry count, so noise cannot inflate it. Also drop phi_rms_deg, which is never assigned anywhere, and Partial::zeta, which is only written. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-09 19:10:18 +02:00
leonarski_fandClaude Opus 5	17eb6ef091	Post-refine: report the goniometer rotation scale it already fits ... A stage that turns further than commanded is invisible in the file, because the stored omega values ARE the commanded ones - both XDS and rugnux then read the discrepancy as the crystal drifting. Measured on one dataset in 37, a ~1.2 % over-rotation costs it unique 9.9k -> 29k and CC1/2 68 -> 98 % when corrected by hand. No new degree of freedom is added, because the one needed is already there and being thrown away: step A's residual rotates by -angle_rad * axis[] with axis an UNNORMALISED 3-vector, so the length it fits IS the factor by which the stage actually turned. GoniometerAxis::Axis then normalises it away (with the `increment *= len` line sitting commented out). This only reports it. Guarded by the same cross-validation that gates the cell move - a fold that merely soaked up noise cannot raise the flag - and by a 0.5 % tolerance, which is where a direct scan of this factor puts 36 of 37 datasets (all at exactly 1.0000). The known fault reads 1.00604 and warns; clean controls read 0.99958 and 0.99954. It UNDER-reads the true magnitude: the fit only sees reflections already indexed at the nominal angle, per-frame orientation refinement has absorbed part of the error, and the axis components are bounded. Treat it as a detector, not a calibration - nothing here corrects the data. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-06 16:17:23 +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