4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	7e47afe47f	rugnux: parallelise candidate-cell refinement, and stop repeating work in the tail ... Three independent changes to the CPU-bound parts of an offline rotation run, none of which alters a result. Candidate-cell refinement now splits across threads. RefineCandidateCells already took a (block, nblocks) partition, but the only call site passed nblocks=1, so the whole first pass of a two-pass rotation run sat on one thread per scheme - two threads, unchanged at every -N, for a third of the run. A block touches only its own scores(j) and cells rows and holds its own scratch, so the split is exact. The budget is a new IndexingSettings::RefineThreads, left at 1 by default and set only where few indexer threads exist: raising it unconditionally would oversubscribe the paths that already run one indexer per image across all workers. The mmCIF writer built a std::ostringstream per formatted number, twelve per reflection. snprintf gives the same digits for 0.535 -> 0.220 s per file. The space-group search built the same orbit mapping twice per candidate point group - once for the merge chi^2 and once for the systematic-error b, an apply_to_hkl and Canonicalize per observation per operator each time. Build it once and hand it to both. 18 Mpx rotation set 24.6 -> 18.7 s, 2.5 Mpx 13.0 -> 10.7 s, and the 37-crystal battery 13m55s -> 10m47s with no failures, the same 34/37 space groups, and statistics unchanged on 30 of 37 (the rest drift within the run-to-run spread the binary already had, which a control build with the split disabled reproduces). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-03 07:30:33 +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	cc3eb8352c	v1.0.0-rc.148 (#58) ... 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	2026-06-08 08:30:35 +02:00
leonarski_f	6133da1377	v1.0.0-rc.133 ... 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	2026-03-26 20:50:33 +01:00