leonarski_f
c86beeb393
Running rotation indexing on a sub-range (e.g. images 60-120) segfaulted: the first pass passed the *global* image number to RotationIndexer::ProcessImage, which indexes v_ (sized to the run's image count) -> out-of-bounds write. - ProcessImage now takes an explicit mid-exposure angle (optional; falls back to the goniometer at the image index), so the indexer no longer assumes its slot index equals the goniometer image index. IndexAndRefine supplies it via RotationAngle(), matching the angle used for prediction. Added a bounds guard in ProcessImage so a bad index can never corrupt memory. - JFJochProcess feeds the rotation indexer the local ordinal (not the global index), and shifts the goniometer (start += start_image*incr, incr *= stride, per-image wedge preserved) so local index i maps to the angle of original image start+i*stride - fixing rotation angles for the whole sub-range pipeline (prediction, refinement, output), not just the indexer. - Expose "Rotation images" (number used for the first pass) in the job dialog, enabled when rotation indexing is on. (Count > available is already clamped by select_equally_spaced_image_ordinals.) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
108 lines
4.4 KiB
C++
108 lines
4.4 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 "../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 "bragg_prediction/BraggPrediction.h"
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#include "pixel_refinement/PixelRefine.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 "RotationParameters.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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class IndexAndRefine {
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const bool index_ice_rings;
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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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RotationParameters rotation_parameters;
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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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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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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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const CompressedImage &image,
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BraggPrediction &prediction,
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const IndexingOutcome &outcome);
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std::unique_ptr<ScaleOnTheFly> scaling_engine;
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void ScaleImage(DataMessage &msg, IntegrationOutcome& outcome);
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// Experimental PixelRefine integration path (selected via
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// GeomRefinementAlgorithmEnum::PixelRefine). Needs reference intensities; the
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// engine is built lazily on first use (when the azimuthal mapping is known)
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// and is safe to share across threads (prediction is supplied per call).
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std::vector<MergedReflection> pixel_reference_;
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std::unique_ptr<PixelRefine> pixel_refine_;
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std::once_flag pixel_refine_once_;
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bool PixelRefineIntegrate(DataMessage &msg,
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const CompressedImage &image,
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BraggPrediction &prediction,
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const IndexingOutcome &outcome,
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IntegrationOutcome &i_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);
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void AddImageToRotationIndexer(DataMessage &msg);
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void ForceRotationIndexerLattice(const CrystalLattice& lattice);
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void ProcessImage(DataMessage &msg, const SpotFindingSettings &settings, const CompressedImage &image, BraggPrediction &prediction);
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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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