leonarski_f
de36a8c421
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78 lines
2.8 KiB
C++
78 lines
2.8 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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#ifndef JFJOCH_INDEXANDREFINE_H
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#define JFJOCH_INDEXANDREFINE_H
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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 "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 "scale_merge/Merge.h"
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#include "RotationIndexer.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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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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RotationParameters rotation_parameters;
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struct IndexingOutcome {
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std::optional<CrystalLattice> lattice_candidate;
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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<std::vector<Reflection>> reflections;
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std::vector<double> mosaicity;
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std::vector<uint8_t> merge_mask;
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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);
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public:
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IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool *indexer);
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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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MergeResult Merge(bool statistics, bool apply_cc_limit) const;
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std::optional<RotationIndexerResult> Finalize();
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};
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#endif //JFJOCH_INDEXANDREFINE_H
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