leonarski_f
54c667190f
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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. * jfjoch_process: Remove pixelrefine option (replaced with ProfileIntegrate2D) * jfjoch_viewer: Some graphical improvements. * jfjoch_viewer: Simplify und unify data analysis settings. * jfjoch_writer: Add TCP keepalive to increase robustness if jfjoch_broker "dies" in the middle of data acquisition. Reviewed-on: #65
95 lines
3.6 KiB
C++
95 lines
3.6 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 "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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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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