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>
42 lines
1.7 KiB
C++
42 lines
1.7 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 <optional>
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// Spot-intensity extraction method. ProfileGaussian (default) profile-fits with a measured-width
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// Gaussian (ProfileIntegrate2D, Kabsch-style) - more accurate intensities than the classical uniform
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// BoxSum (BraggIntegrate2D); validated on HEWL anomalous (stronger S/Cl peaks vs box-sum). BoxSum is
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// the simpler, faster fallback. ProfileEmpirical learns the profile per resolution shell from strong
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// spots (v2) - see bragg_integration/NEXTGEN_INTEGRATOR.md.
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enum class IntegratorMode { BoxSum, ProfileGaussian, ProfileEmpirical };
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class BraggIntegrationSettings {
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IntegratorMode integrator_mode = IntegratorMode::ProfileGaussian;
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float r_1 = 4;
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float r_2 = 6;
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float r_3 = 8;
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float d_min_limit_A = 1.0;
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std::optional<float> fixed_profile_radius;
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float minimum_sigma_in_regards_to_i = 0.02;
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public:
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BraggIntegrationSettings& R1(float input);
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BraggIntegrationSettings& R2(float input);
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BraggIntegrationSettings& R3(float input);
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BraggIntegrationSettings& DMinLimit_A(float input);
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BraggIntegrationSettings& FixedProfileRadius_recipA(std::optional<float> input);
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BraggIntegrationSettings& Integrator(IntegratorMode input);
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[[nodiscard]] IntegratorMode GetIntegrator() const;
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[[nodiscard]] float GetR1() const;
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[[nodiscard]] float GetR2() const;
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[[nodiscard]] float GetR3() const;
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[[nodiscard]] std::optional<float> GetFixedProfileRadius_recipA() const;
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[[nodiscard]] float GetDMinLimit_A() const;
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[[nodiscard]] float GetMinimumSigmaInRegardsToI() const;
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};
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