leonarski_fandClaude Opus 4.8
38ea0ec237
On the LysozymeJet5 serial stills the default Gaussian profile-fit integrator (ProfileIntegrate2D) + reference scaling matched or beat whole-PixelRefine on every per-shell CC1/2 (overall 95.7% vs 91.9%), ISa (1.6 vs 1.2) and R-meas (98.5% vs 175%), with CCref a tie -- so PixelRefine has no remaining advantage. Reference-based per-image scaling is integrator-agnostic (IndexAndRefine::ReferenceIntensities builds a ScaleOnTheFly(experiment, reference) applied to any integrator's output), so the reference-dataset feature (CCref + reference scaling) is kept. Delete image_analysis/pixel_refinement/, GeomRefinementAlgorithmEnum:: PixelRefine and its gates, BraggIntegrationSettings::ProfileMultiplier (PixelRefine-only; R1 is shared and kept), and the -r pixelrefine / --profile-multiplier CLI. The inherited lessons (mean background, de-biased variance, tight-profile-loses / centroid floor, R-refinement futile) are folded into NEXTGEN_INTEGRATOR.md. NOTE: this transiently breaks the viewer build -- the committed viewer still references the removed enum and ProfileMultiplier. It is fixed in the next commit (the viewer feature work), held separate while the viewer UI is being tested. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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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