leonarski_fandClaude Opus 4.8
1b91823eed
A first pass integrates and post-refines the detector geometry from the observed
diffraction, applies it to experiment_, and a second pass re-indexes and
re-integrates with it - only the second pass is written, so the _process.h5 / mtz
(and the ice-ring flags, which move with the geometry) reflect the refined values.
Default off; enable with --rotation-post-refine.
PostRefineRotationGeometry refines in two SEPARATE cross-validated steps (a joint
fit of everything is fragile - the same lesson as integration, where refining the
profile width and the scale jointly fails but separately works):
* Step A: cell scale + rotation axis from the observed rocking centroids phi_obs
(a distance-independent excitation residual, so it pins the absolute cell scale
that the positional residual leaves degenerate with distance).
* Step B: detector distance + beam centre from the observed spot positions, with
the cell fixed at step A.
Each step commits only if it lowers a held-out (deterministic split-half) residual,
else that part of the geometry is left at nominal.
Rugnux::Run wraps RunPipeline(write_output, geometry_prepass); the pre-pass runs
the first scale/merge so RotationScaleMerge fits a frame-order-smoothed mosaicity,
which is captured and fed to the second pass's Bragg prediction (via
IndexAndRefine::SetPredictionMosaicityOverride) rather than re-derived per image.
observed_x/y were plumbed through the profile integrator earlier for the positional
residual. rugnux_vs_xds.py gains --extra-args to sweep the option over the battery.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
125 lines
6.0 KiB
C++
125 lines
6.0 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <vector>
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#include <mutex>
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#include <functional>
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#include "../common/DiffractionSpot.h"
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#include "../common/DiffractionExperiment.h"
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#include "../common/AzimuthalIntegrationMapping.h"
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#include "../common/AzimuthalIntegrationProfile.h"
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#include "../common/Reflection.h"
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#include "bragg_prediction/BraggPrediction.h"
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#include "indexing/IndexerThreadPool.h"
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#include "lattice_search/LatticeSearch.h"
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#include "rotation_indexer/RotationIndexer.h"
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#include "rotation_indexer/RotationIndexerCounter.h"
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#include "scale_merge/ReindexAmbiguity.h"
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#include "scale_merge/ScaleOnTheFly.h"
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#include "scale_merge/ScalingResult.h"
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#include "IntegrationOutcome.h"
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// Integrates the predicted reflections off whatever image the caller holds: the preprocessed GPU/CPU
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// buffer on the WithoutFPGA path (GPU when available), or the assembled detector image read straight,
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// on the CPU, on the forced-CPU FPGA path. Keeps IndexAndRefine independent of the image representation.
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using BraggIntegrateFn = std::function<std::vector<Reflection>(
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const std::vector<Reflection> &predicted, size_t npredicted, int64_t image_number)>;
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class IndexAndRefine {
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const bool index_ice_rings;
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// When false, the current image's result is still returned via the outgoing message, but the
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// whole-run integration_outcome vector is not retained (viewer live/interactive use, which never
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// scales the accumulated run). rugnux/receiver keep it true so ScaleAllImages/merge have the data.
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const bool retain_outcomes_;
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const DiffractionExperiment& experiment;
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const DiffractionGeometry geom_;
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std::optional<CrystalLattice> indexed_lattice;
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std::optional<GoniometerAxis> axis_;
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IndexerThreadPool *indexer_;
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std::unique_ptr<RotationIndexer> rotation_indexer;
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RotationIndexerCounter rotation_indexer_counter;
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struct IndexingOutcome {
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std::optional<CrystalLattice> lattice_candidate;
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std::vector<CrystalLattice> extra_lattice_candidates;
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std::vector<Coord> extra_lattice_rotations;
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DiffractionExperiment experiment;
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LatticeMessage symmetry{
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.centering = 'P',
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.niggli_class = 0,
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.crystal_system = gemmi::CrystalSystem::Triclinic
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};
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bool beam_center_updated = false;
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explicit IndexingOutcome(const DiffractionExperiment& experiment_ref)
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: experiment(experiment_ref) {}
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};
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mutable std::mutex reflections_mutex;
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std::vector<IntegrationOutcome> integration_outcome;
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std::vector<float> mosaicity;
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// Optional per-frame mosaicity used for Bragg prediction, indexed by image number. When set (the
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// second pass of the rotation two-pass), it overrides the per-image spot-shape estimate so prediction
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// uses the frame-order-SMOOTHED mosaicity that RotationScaleMerge already fitted in the first pass,
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// rather than re-deriving it from scratch.
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std::vector<float> prediction_mosaicity_override_;
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std::vector<float> scale_cc;
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std::vector<std::optional<UnitCell> > unit_cells;
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IndexingOutcome DetermineLatticeAndSymmetryRotation(DataMessage &msg);
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IndexingOutcome DetermineLatticeAndSymmetry(DataMessage &msg);
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// Shared indexing path: determine the lattice/symmetry, refine geometry, and run AnalyzeIndexing.
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// Returns the outcome (ready for integration) when the frame indexes, nullopt otherwise. Both the
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// real per-image ProcessImage and the first-pass scheme validation go through this, so they cannot
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// diverge.
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std::optional<IndexingOutcome> DetermineRefineAnalyze(DataMessage &msg,
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const SpotFindingSettings &spot_finding_settings);
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void RefineGeometryIfNeeded(DataMessage &msg, IndexingOutcome &outcome);
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void QuickPredictAndIntegrate(DataMessage &msg,
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const SpotFindingSettings &spot_finding_settings,
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BraggPrediction &prediction,
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const BraggIntegrateFn &integrate,
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const IndexingOutcome &outcome);
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std::unique_ptr<ReindexAmbiguityResolver> reindex_resolver;
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void ScaleImage(DataMessage &msg, IntegrationOutcome& outcome);
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std::optional<float> RotationAngle(int64_t image) const; // mid-exposure angle for the indexer
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public:
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IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool *indexer, bool retain_outcomes = true);
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void AddImageToRotationIndexer(DataMessage &msg);
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void ForceRotationIndexerLattice(const CrystalLattice& lattice);
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void ForceRotationIndexerResult(const RotationIndexerResult& result);
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// Supply a per-frame (by image number) mosaicity for prediction, overriding the per-image estimate.
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void SetPredictionMosaicityOverride(std::vector<float> mosaicity_per_frame) {
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prediction_mosaicity_override_ = std::move(mosaicity_per_frame);
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}
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void ProcessImage(DataMessage &msg, const SpotFindingSettings &settings,
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BraggPrediction &prediction, const BraggIntegrateFn &integrate);
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// Index a single frame (no integration) with the current forced rotation lattice; used to score
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// first-pass sampling schemes on the real per-image path. Returns whether the frame indexed.
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bool IndexFrameOnly(DataMessage &msg, const SpotFindingSettings &settings);
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IndexAndRefine& ReferenceIntensities(std::vector<MergedReflection> &reference);
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ScalingResult ScaleAllImages(const std::vector<MergedReflection> &reference, size_t nthreads = 0);
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std::optional<RotationIndexerResult> FinalizeRotationIndexing();
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std::optional<UnitCell> GetConsensusUnitCell() const;
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// Not thread safe, need to be run after processing is all done
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const std::vector<float> &GetImageCC() const;
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const std::vector<std::optional<UnitCell> > &GetUnitCells() const;
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std::vector<IntegrationOutcome> &GetIntegrationOutcome();
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const std::vector<IntegrationOutcome> &GetIntegrationOutcome() const;
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};
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