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>
78 lines
3.3 KiB
C++
78 lines
3.3 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 <cstdint>
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enum class IndexingAlgorithmEnum {FFBIDX, FFT, FFTW, Auto, None};
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enum class GeomRefinementAlgorithmEnum {None, OrientationOnly, BeamCenter};
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class IndexingSettings {
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IndexingAlgorithmEnum algorithm;
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int64_t fft_num_vectors = 16*1024;
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float fft_max_unit_cell_A = 500.0;
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float fft_min_unit_cell_A = 10.0;
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float fft_max_angle_deg = 150.0;
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float fft_min_angle_deg = 30.0;
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float fft_high_resolution_A = 2.0;
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float indexing_tolerance = 0.1;
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float max_angle_from_ewald_deg = 2.0;
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float unit_cell_dist_tolerance_vs_reference = 0.05; // relative
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static constexpr float unit_cell_angle_tolerance_deg = 5.0; // degree
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int64_t indexing_threads = 4;
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int64_t viable_cell_min_spots = 9;
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int64_t max_extra_lattices = 2;
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bool blocking_behavior = true;
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bool index_ice_rings = false;
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bool enable_rotation_indexing = false;
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float rotation_indexing_min_angular_range_deg = 20.0;
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float rotation_indexing_angular_stride_deg = 0.5;
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GeomRefinementAlgorithmEnum refinement = GeomRefinementAlgorithmEnum::BeamCenter;
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public:
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IndexingSettings();
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IndexingSettings& ViableCellMinSpots(int64_t input);
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IndexingSettings& Algorithm(IndexingAlgorithmEnum input);
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IndexingSettings& FFT_MaxUnitCell_A(float input);
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IndexingSettings& FFT_MinUnitCell_A(float input);
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IndexingSettings& FFT_MaxAngle_deg(float input);
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IndexingSettings& FFT_MinAngle_deg(float input);
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IndexingSettings& FFT_NumVectors(int64_t input);
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IndexingSettings& FFT_HighResolution_A(float input);
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IndexingSettings& Tolerance(float input);
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IndexingSettings& IndexingThreads(int64_t input);
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IndexingSettings& UnitCellDistTolerance(float input);
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IndexingSettings& GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum input);
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IndexingSettings& IndexIceRings(bool input);
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IndexingSettings& RotationIndexing(bool input);
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IndexingSettings& RotationIndexingMinAngularRange_deg(float input);
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IndexingSettings& RotationIndexingAngularStride_deg(float input);
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IndexingSettings& BlockingBehavior(bool input);
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IndexingSettings& MaxExtraLattices(int64_t input);
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[[nodiscard]] int64_t GetViableCellMinSpots() const;
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[[nodiscard]] IndexingAlgorithmEnum GetAlgorithm() const;
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[[nodiscard]] GeomRefinementAlgorithmEnum GetGeomRefinementAlgorithm() const;
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[[nodiscard]] float GetFFT_MaxUnitCell_A() const;
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[[nodiscard]] float GetFFT_MinUnitCell_A() const;
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[[nodiscard]] int64_t GetFFT_NumVectors() const;
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[[nodiscard]] float GetFFT_HighResolution_A() const;
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[[nodiscard]] float GetTolerance() const;
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[[nodiscard]] float GetFFT_MinAngle_deg() const;
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[[nodiscard]] float GetFFT_MaxAngle_deg() const;
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[[nodiscard]] int64_t GetIndexingThreads() const;
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[[nodiscard]] float GetUnitCellDistTolerance() const;
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[[nodiscard]] float GetUnitCellAngleTolerance_deg() const;
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[[nodiscard]] bool GetIndexIceRings() const;
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[[nodiscard]] bool GetRotationIndexing() const;
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[[nodiscard]] float GetRotationIndexingMinAngularRange_deg() const;
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[[nodiscard]] float GetRotationIndexingAngularStride_deg() const;
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[[nodiscard]] bool GetBlockingBehavior() const;
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[[nodiscard]] int64_t GetMaxExtraLattices() const;
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};
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