leonarski_f
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>
99 lines
3.2 KiB
C++
99 lines
3.2 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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#include <cmath>
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#include "BraggIntegrationSettings.h"
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#include "JFJochException.h"
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#define check_max(param, val, max) if ((val) > (max)) throw JFJochException(JFJochExceptionCategory::InputParameterAboveMax, param)
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#define check_min(param, val, min) if ((val) < (min)) throw JFJochException(JFJochExceptionCategory::InputParameterBelowMin, param)
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#define check_finite(param, val) if (!std::isfinite(val)) throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, param)
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BraggIntegrationSettings &BraggIntegrationSettings::R1(float input) {
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check_finite("Integration radius R1", input);
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check_min("Integration radius R1", input, 0.1);
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check_max("Integration radius R1", input, 20.0);
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r_1 = input;
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return *this;
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}
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BraggIntegrationSettings &BraggIntegrationSettings::R2(float input) {
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check_finite("Background inner radius R2", input);
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check_min("Background inner radius R2", input, 0.1);
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check_max("Background inner radius R2", input, 30.0);
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if (input <= r_1)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Background inner radius (R2) must be larger than integration radius (R1)");
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r_2 = input;
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return *this;
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}
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BraggIntegrationSettings &BraggIntegrationSettings::R3(float input) {
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check_finite("Background outer radius R3", input);
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check_min("Background outer radius R3", input, 0.1);
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check_max("Background outer radius R3", input, 40.0);
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if (input <= r_2)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Background outer radius (R3) must be larger than background inner radius (R2)");
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r_3 = input;
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return *this;
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}
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BraggIntegrationSettings &BraggIntegrationSettings::DMinLimit_A(float input) {
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check_finite("Minimum d-spacing", input);
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check_min("Minimum d-spacing", input, 0.5);
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check_max("Minimum d-spacing", input, 100.0);
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d_min_limit_A = input;
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return *this;
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}
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BraggIntegrationSettings & BraggIntegrationSettings::FixedProfileRadius_recipA(std::optional<float> input) {
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if (input) {
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check_finite("Profile radius", input.value());
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check_min("Profile radius [A^-1]", input.value(), 0.000001);
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check_max("Profile radius [A^-1]", input.value(), 0.01);
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}
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fixed_profile_radius = input;
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return *this;
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}
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std::optional<float> BraggIntegrationSettings::GetFixedProfileRadius_recipA() const {
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return fixed_profile_radius;
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}
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BraggIntegrationSettings &BraggIntegrationSettings::Integrator(IntegratorMode input) {
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integrator_mode = input;
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return *this;
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}
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IntegratorMode BraggIntegrationSettings::GetIntegrator() const {
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return integrator_mode;
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}
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float BraggIntegrationSettings::GetR1() const {
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return r_1;
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}
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float BraggIntegrationSettings::GetR2() const {
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return r_2;
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}
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float BraggIntegrationSettings::GetR3() const {
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return r_3;
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}
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float BraggIntegrationSettings::GetDMinLimit_A() const {
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return d_min_limit_A;
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}
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float BraggIntegrationSettings::GetMinimumSigmaInRegardsToI() const {
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return minimum_sigma_in_regards_to_i;
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}
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