5 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	6d39a4e1ab	Space-group search: decide a screw from the evidence, not from a count of absences ... A screw's predicted-absent class was required to hold min_absent_observed = 8 reflections before the screw could be claimed. That count is the wrong measure of evidence, and it is wrong in both directions. A screw extinguishes one row of reciprocal space, and that row is often the one a rotation sweep records least: it lies near the spindle, where the blind cusp maps onto itself and symmetry cannot fill it in. Counting it measures the geometry of the sweep. A monoclinic crystal whose 2-fold sits 7.6 deg from the spindle contributed six 0k0-odd reflections, every one of them measured between -0.013 and 4e-5 of the shell mean with zero violations, against a 0k0 row averaging 1.44x the shell mean - and was refused its 2_1 for being six rather than eight. XDS's own integration of the same images finds seventeen of those reflections and every one of them is likewise dead. The count is equally wrong the other way: a uniformly weak axial row produces no violations at all, so with enough reflections on it a screw is claimed from no evidence whatsoever. The second new test section demonstrates exactly that on the old gate. Judge the class by how unlikely it would be if the screw did not exist. Under "no screw" the absent class and the rest of its row are both Wilson-distributed with the same mean, so with each absent intensity taken in units of its row's control mean, sum_u/(sum_u + n_control) follows Beta(n_absent, n_control) exactly; the reported evidence is -log of that lower tail. The row's own strength cancels, which is the property the count lacks, and the scale is set by the number of reflections, so few-but-decisive and many-but-marginal are told apart. It is sigma-free by design: the merged sigma carries the error model's intensity-proportional term and so shrinks with I, reading much the same on an absent reflection as on a present one. This follows POINTLESS (Evans, Acta Cryst D67, 282-292 (2011), Appendix A3), which likewise scores an absence against the rest of its own axial row rather than against a global mean or a fixed cut, and likewise lets confidence fall away with the number of axial reflections instead of refusing outright below a count. POINTLESS calibrates its null width from control transforms of non-axial reflections; the Beta tail here is an analytic null in its place. XDS is not a reference for this: it "deliberately avoids any test for the presence of screw axes as these tests would depend strongly on the completeness of the data" (Kabsch, Acta Cryst D66, 133-144 (2010), section 6), so a screw axis in a CORRECT.LP was supplied to it, not determined by it. Measured over five probe crystals, genuine screw conditions read 34-800 nats and false ones - the 4_1/4_3 conditions of a cubic crystal that has no screw, whose predicted-absent class is STRONGER than its control row - read -7 to -8.5. The bound is set at 20, in the gap, at p <= 2e-9: three well-measured dead axial reflections clear it and two do not. min_absent_observed keeps its job for CENTERING, where a count is a fair measure - that class is a third to a half of every reflection in the data set and the bound is never binding on a centering that exists. The candidate table now prints the screw-absent count and this evidence in place of the two E^2 medians that were its raw ingredients, so a refusal can be read off the log. Measured on the five probes: the monoclinic crystal above returns to P2_1 with every merge statistic unchanged (R_meas 58.8 -> 58.7%, CC1/2 49.1 -> 49.3%, ISa 6.61 -> 6.59 - P2 and P2_1 share a point group, so only the symbol and the absent reflections differ). The other four are untouched, space group included, and the two-pass branch fingerprint (indexed frames, distance, mosaicity) is identical on all five. The full battery has not been run. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-11 16:15:56 +02:00
leonarski_fandClaude Opus 5	d28db19ab1	Space-group search: judge a screw axis against its own axial row ... A reflection the group predicts absent counted as a violation when I/sigma > 3 AND E^2 = I/<I>(shell) > 0.3. Neither half survives contact with real data: * merged sigma is floored at b|I|, so merged I/sigma saturates at ISa for nearly every reflection - the I/sigma half is an on/off switch keyed on ISa vs 3, not a per-reflection test. On one crystal the absent class read <I/s> 4.10 against 3.73 for the present class while being genuinely extinct; * <I>(shell) decays with resolution while a systematically-absent reflection keeps a small NON-decaying residual (background / profile leakage), so absent reflections drift over an absolute E^2 cut at high resolution. That cost a tetragonal 42_12 crystal its 4_1: 18 of its 47 absent 00l crossed the cut, all beyond 3.7 A, at absolute intensities identical to the low-resolution ones correctly judged absent, while their l=4n row-mates sat 20-60x higher at the same resolution. A screw extinguishes only the reflections that lie ON its axis, so the fair yardstick is the rest of that same row. The threshold is now 0.3 * max(1, median E^2 of the reflection's own row), the row being the gcd-reduced reciprocal-space direction and the control class the same-row reflections the group predicts present. Floored at 1, so it only ever relaxes: a screw can be recovered by it, never lost. Per row, not pooled. A 4_1 along c and a 2_1 along a are separate conditions with separate controls; pooling let the weak a/b rows (median E^2 ~0.5) set the threshold for a strong c row (8.4) and the rescue never fired. The candidate table now reports the screw evidence (median E^2 of the absent class and of its rows) - the <I/s> columns are the centering evidence and say nothing about screws, for the sigma-floor reason above. Rotation battery, 33 crystals: 31 decisions bit-identical, the 42_12 crystal recovers its 4_1 (0 violations, row E^2 8.4 vs absent 0.12), and one crystal with a long axis and heavy 00l overlap moves to a 4_1 group at exactly 10.0% violations - marginal, and its sister crystal of the same form sits at 13.3% and does not move. Real screws now span 0-9.3% violations, so max_absent_violation_fraction cannot be tightened below 0.10 without risking a genuine one. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-07-29 08:27:34 +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	d6389e12da	v1.0.0-rc.156 (#66) ... 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: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output. * jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling. * Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool. * jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection. * jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata. * CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-03 19:18:56 +02:00
leonarski_f	166fcdb68f	v1.0.0-rc.131 (#39) ... 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.124. * jfjoch_broker: Fix bug in saving JUNGFRAU calibration (pedestal/pedestalRMS) * jfjoch_viewer: Fix calibration (pedestal) images being open flipped * jfjoch_process: Add space group detection (EXPERIMENTAL) Reviewed-on: #39	2026-03-07 11:34:04 +01:00