leonarski_f
fc68a9baed
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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_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset. jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling. jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file. jfjoch_scale: Dedicated tool for rescaling/merging existing data. jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel. WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being. Reviewed-on: #56
85 lines
3.1 KiB
C++
85 lines
3.1 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 "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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#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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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<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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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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std::optional<RotationIndexerResult> Finalize();
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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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