Filip Leonarski
1ab257af6c
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This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Improve logic on switching on/off spot finding * jfjoch_broker: Increase maximum spot count for FFBIDX to 65536 * jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD) * jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis * jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection * jfjoch_writer: Save more information about each reflection Reviewed-on: #32 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
717 lines
28 KiB
C++
717 lines
28 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 <catch2/catch_all.hpp>
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#include <iostream>
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#include "../image_analysis/geom_refinement/XtalOptimizer.h"
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#include "../image_analysis/bragg_prediction/BraggPrediction.h"
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TEST_CASE("XtalOptimizer") {
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DiffractionExperiment exp_i;
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exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
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.BeamX_pxl(1000)
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.BeamY_pxl(1000)
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.PoniRot1_rad(0.01)
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.PoniRot2_rad(0.02)
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.DetectorDistance_mm(200);
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CrystalLattice latt_i(40,40,80,90,90,90);
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BraggPredictionSettings prediction_settings{
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.high_res_A = 1.5,
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.ewald_dist_cutoff = 0.001};
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BraggPrediction prediction;
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auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
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std::vector<SpotToSave> spots;
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for (int i = 0; i < count; ++i) {
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auto refl = prediction.GetReflections().at(i);
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spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
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}
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XtalOptimizerData xtal_opt;
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xtal_opt.latt = CrystalLattice(40.2,39.4,80.2, 90,91, 89);
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xtal_opt.geom.BeamX_pxl(1010).BeamY_pxl(995).DetectorDistance_mm(200)
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.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
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xtal_opt.crystal_system = gemmi::CrystalSystem::Triclinic;
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auto start = std::chrono::high_resolution_clock::now();
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REQUIRE(XtalOptimizer(xtal_opt, spots));
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auto end = std::chrono::high_resolution_clock::now();
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std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
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<< " microseconds" << std::endl;
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auto uc_i = latt_i.GetUnitCell();
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auto uc_o = xtal_opt.latt.GetUnitCell();
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std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
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std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
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CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.05);
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CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.05);
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CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
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CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
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CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
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CHECK(fabsf(uc_i.alpha - uc_o.alpha) < 0.1);
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CHECK(fabsf(uc_i.beta - uc_o.beta) < 0.1);
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CHECK(fabsf(uc_i.gamma - uc_o.gamma) < 0.1);
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}
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TEST_CASE("XtalOptimizer_NoBeamCenter") {
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DiffractionExperiment exp_i;
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exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
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.BeamX_pxl(1000)
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.BeamY_pxl(1000)
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.PoniRot1_rad(0.01)
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.PoniRot2_rad(0.02)
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.DetectorDistance_mm(200);
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CrystalLattice latt_i(40,50,80,90,95,90);
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BraggPredictionSettings prediction_settings{
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.high_res_A = 1.5,
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.ewald_dist_cutoff = 0.001};
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BraggPrediction prediction;
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auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
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std::vector<SpotToSave> spots;
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for (int i = 0; i < count; ++i) {
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auto refl = prediction.GetReflections().at(i);
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spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
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}
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XtalOptimizerData xtal_opt;
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xtal_opt.latt = CrystalLattice(40.2,49.4,80.2, 90,94, 89);
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xtal_opt.geom.BeamX_pxl(999.8).BeamY_pxl(1000.2).DetectorDistance_mm(200)
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.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
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xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
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xtal_opt.refine_beam_center = false;
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auto start = std::chrono::high_resolution_clock::now();
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REQUIRE(XtalOptimizer(xtal_opt, spots));
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auto end = std::chrono::high_resolution_clock::now();
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std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
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<< " microseconds" << std::endl;
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auto uc_i = latt_i.GetUnitCell();
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auto uc_o = xtal_opt.latt.GetUnitCell();
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std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
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std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
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CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - 999.8) < 0.01);
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CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - 1000.2) < 0.01);
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CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
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CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
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CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
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CHECK(fabsf(uc_i.alpha - uc_o.alpha) < 0.1);
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CHECK(fabsf(uc_i.beta - uc_o.beta) < 0.1);
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CHECK(fabsf(uc_i.gamma - uc_o.gamma) < 0.1);
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}
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TEST_CASE("XtalOptimizer_orthorombic") {
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DiffractionExperiment exp_i;
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exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
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.BeamX_pxl(1000)
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.BeamY_pxl(1000)
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.PoniRot1_rad(0.01)
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.PoniRot2_rad(0.02)
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.DetectorDistance_mm(200);
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CrystalLattice latt_i(40,50,80,90,90,90);
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BraggPredictionSettings prediction_settings{
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.high_res_A = 1.5,
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.ewald_dist_cutoff = 0.001};
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BraggPrediction prediction;
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auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
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std::vector<SpotToSave> spots;
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for (int i = 0; i < count; ++i) {
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auto refl = prediction.GetReflections().at(i);
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spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
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}
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XtalOptimizerData xtal_opt;
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xtal_opt.latt = CrystalLattice(40.2,49.6,80.3, 90,91, 89);
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xtal_opt.geom.BeamX_pxl(1005).BeamY_pxl(997).DetectorDistance_mm(200)
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.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
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xtal_opt.crystal_system = gemmi::CrystalSystem::Orthorhombic;
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auto start = std::chrono::high_resolution_clock::now();
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REQUIRE(XtalOptimizer(xtal_opt, spots));
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auto end = std::chrono::high_resolution_clock::now();
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std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
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<< " microseconds" << std::endl;
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auto uc_i = latt_i.GetUnitCell();
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auto uc_o = xtal_opt.latt.GetUnitCell();
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std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
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std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
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CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
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CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
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CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
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CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
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CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
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CHECK(fabs(uc_o.alpha - 90) < 0.02);
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CHECK(fabs(uc_o.beta - 90) < 0.02);
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CHECK(fabs(uc_o.gamma - 90) < 0.02);
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}
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TEST_CASE("XtalOptimizer_triclinic") {
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DiffractionExperiment exp_i;
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exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
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.BeamX_pxl(1000)
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.BeamY_pxl(1000)
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.PoniRot1_rad(0.01)
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.PoniRot2_rad(0.02)
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.DetectorDistance_mm(200);
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CrystalLattice latt_i(40,55,120,95,97,100);
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BraggPredictionSettings prediction_settings{
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.high_res_A = 1.5,
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.ewald_dist_cutoff = 0.001,
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};
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BraggPrediction prediction;
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auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
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std::vector<SpotToSave> spots;
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for (int i = 0; i < count; ++i) {
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auto refl = prediction.GetReflections().at(i);
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spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
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}
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XtalOptimizerData xtal_opt;
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xtal_opt.latt = CrystalLattice(40.1,54.9,121, 95,97, 99.5);
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xtal_opt.geom.BeamX_pxl(997).BeamY_pxl(1005).DetectorDistance_mm(200)
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.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
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xtal_opt.crystal_system = gemmi::CrystalSystem::Triclinic;
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auto start = std::chrono::high_resolution_clock::now();
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REQUIRE(XtalOptimizer(xtal_opt, spots));
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auto end = std::chrono::high_resolution_clock::now();
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std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
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<< " microseconds" << std::endl;
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auto uc_i = latt_i.GetUnitCell();
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auto uc_o = xtal_opt.latt.GetUnitCell();
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std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
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std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
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CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2);
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CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2);
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CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
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CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
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CHECK(fabsf(uc_i.c - uc_o.c) < 0.5);
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CHECK(fabsf(uc_i.alpha - uc_o.alpha) < 0.1);
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CHECK(fabsf(uc_i.beta - uc_o.beta) < 0.1);
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CHECK(fabsf(uc_i.gamma - uc_o.gamma) < 0.1);
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}
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TEST_CASE("XtalOptimizer_tetragonal") {
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DiffractionExperiment exp_i;
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exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
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.BeamX_pxl(1000)
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.BeamY_pxl(1000)
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.PoniRot1_rad(0.01)
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.PoniRot2_rad(0.02)
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.DetectorDistance_mm(200);
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CrystalLattice latt_i(40,40,80,90,90,90);
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BraggPredictionSettings prediction_settings{
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.high_res_A = 1.5,
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.ewald_dist_cutoff = 0.001};
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BraggPrediction prediction;
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auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
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std::vector<SpotToSave> spots;
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for (int i = 0; i < count; ++i) {
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auto refl = prediction.GetReflections().at(i);
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spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
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}
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XtalOptimizerData xtal_opt;
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xtal_opt.latt = CrystalLattice(40.6,39.3,80.5, 90,91, 89);
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xtal_opt.geom.BeamX_pxl(1010).BeamY_pxl(995).DetectorDistance_mm(200)
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.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
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xtal_opt.crystal_system = gemmi::CrystalSystem::Tetragonal;
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auto start = std::chrono::high_resolution_clock::now();
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REQUIRE(XtalOptimizer(xtal_opt, spots));
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auto end = std::chrono::high_resolution_clock::now();
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std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
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<< " microseconds" << std::endl;
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auto uc_i = latt_i.GetUnitCell();
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auto uc_o = xtal_opt.latt.GetUnitCell();
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std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
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std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
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CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
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CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
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CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
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CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
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CHECK(fabsf(uc_i.c - uc_o.c) < 0.5);
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CHECK(fabs(uc_o.alpha - 90) < 0.02);
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CHECK(fabs(uc_o.beta - 90) < 0.02);
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CHECK(fabs(uc_o.gamma - 90) < 0.02);
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}
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TEST_CASE("XtalOptimizer_hexagonal") {
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DiffractionExperiment exp_i;
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exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
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.BeamX_pxl(1000)
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.BeamY_pxl(1000)
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.PoniRot1_rad(0.01)
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.PoniRot2_rad(0.02)
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.DetectorDistance_mm(200);
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CrystalLattice latt_i(40,40,70,90,90,120);
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BraggPredictionSettings prediction_settings{
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.high_res_A = 1.5,
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.ewald_dist_cutoff = 0.001};
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BraggPrediction prediction;
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auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
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std::vector<SpotToSave> spots;
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for (int i = 0; i < count; ++i) {
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auto refl = prediction.GetReflections().at(i);
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spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
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}
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XtalOptimizerData xtal_opt;
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xtal_opt.latt = CrystalLattice(39.5,39.8,70.1, 90,90, 119.5);
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xtal_opt.geom.BeamX_pxl(1007).BeamY_pxl(990).DetectorDistance_mm(200)
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.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
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xtal_opt.crystal_system = gemmi::CrystalSystem::Hexagonal;
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auto start = std::chrono::high_resolution_clock::now();
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REQUIRE(XtalOptimizer(xtal_opt, spots));
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auto end = std::chrono::high_resolution_clock::now();
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std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
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<< " microseconds" << std::endl;
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auto uc_i = latt_i.GetUnitCell();
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auto uc_o = xtal_opt.latt.GetUnitCell();
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std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
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std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << " " << uc_o.alpha << " " << uc_o.beta
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<< " " << uc_o.gamma << std::endl;
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CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
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CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
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CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
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CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
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CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
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CHECK(fabs(uc_o.alpha - 90) < 0.02);
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CHECK(fabs(uc_o.beta - 90) < 0.01);
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CHECK(fabs(uc_o.gamma - 120) < 0.01);
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}
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TEST_CASE("XtalOptimizer_hexagonal_unconstrained") {
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DiffractionExperiment exp_i;
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exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
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.BeamX_pxl(1000)
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.BeamY_pxl(1000)
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.PoniRot1_rad(0.01)
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.PoniRot2_rad(0.02)
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.DetectorDistance_mm(200);
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CrystalLattice latt_i(40,40,70,90,90,120);
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BraggPredictionSettings prediction_settings{
|
|
.high_res_A = 1.5,
|
|
.ewald_dist_cutoff = 0.001};
|
|
BraggPrediction prediction;
|
|
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
|
|
|
|
std::vector<SpotToSave> spots;
|
|
|
|
for (int i = 0; i < count; ++i) {
|
|
auto refl = prediction.GetReflections().at(i);
|
|
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
|
|
}
|
|
|
|
XtalOptimizerData xtal_opt;
|
|
xtal_opt.latt = CrystalLattice(39.9,39.8,70.1, 90,90, 120);
|
|
xtal_opt.geom.BeamX_pxl(1002).BeamY_pxl(998).DetectorDistance_mm(200)
|
|
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
|
|
xtal_opt.crystal_system = gemmi::CrystalSystem::Triclinic;
|
|
auto start = std::chrono::high_resolution_clock::now();
|
|
REQUIRE(XtalOptimizer(xtal_opt, spots));
|
|
auto end = std::chrono::high_resolution_clock::now();
|
|
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
|
|
<< " microseconds" << std::endl;
|
|
|
|
auto uc_i = latt_i.GetUnitCell();
|
|
auto uc_o = xtal_opt.latt.GetUnitCell();
|
|
|
|
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
|
|
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << " " << uc_o.alpha << " " << uc_o.beta
|
|
<< " " << uc_o.gamma << std::endl;
|
|
|
|
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.3);
|
|
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.3);
|
|
|
|
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
|
|
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
|
|
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
|
|
CHECK(fabs(uc_o.alpha - 90) < 0.1);
|
|
CHECK(fabs(uc_o.beta - 90) < 0.1);
|
|
CHECK(fabs(uc_o.gamma - 120) < 0.1);
|
|
}
|
|
|
|
TEST_CASE("XtalOptimizer_cubic") {
|
|
DiffractionExperiment exp_i;
|
|
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
|
|
.BeamX_pxl(1000)
|
|
.BeamY_pxl(1000)
|
|
.PoniRot1_rad(0.01)
|
|
.PoniRot2_rad(0.02)
|
|
.DetectorDistance_mm(200);
|
|
|
|
CrystalLattice latt_i(Coord(40,0,0),
|
|
Coord(0, 40 / sqrt(2), -40 / sqrt(2)),
|
|
Coord(0, 40 / sqrt(2), 40 / sqrt(2)));
|
|
auto uc_i = latt_i.GetUnitCell();
|
|
|
|
BraggPredictionSettings prediction_settings{
|
|
.high_res_A = 1.5,
|
|
.ewald_dist_cutoff = 0.001};
|
|
BraggPrediction prediction;
|
|
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
|
|
|
|
std::vector<SpotToSave> spots;
|
|
|
|
for (int i = 0; i < count; ++i) {
|
|
auto refl = prediction.GetReflections().at(i);
|
|
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
|
|
}
|
|
|
|
XtalOptimizerData xtal_opt;
|
|
xtal_opt.latt = CrystalLattice(Coord(39,0,0),
|
|
Coord(0, 39.5 / sqrt(2), -40.5 / sqrt(2)),
|
|
Coord(0, 39.2 / sqrt(2), 39.7 / sqrt(2)));
|
|
xtal_opt.geom.BeamX_pxl(1007).BeamY_pxl(990).DetectorDistance_mm(200)
|
|
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
|
|
xtal_opt.crystal_system = gemmi::CrystalSystem::Cubic;
|
|
auto start = std::chrono::high_resolution_clock::now();
|
|
REQUIRE(XtalOptimizer(xtal_opt, spots));
|
|
auto end = std::chrono::high_resolution_clock::now();
|
|
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
|
|
<< " microseconds" << std::endl;
|
|
|
|
auto uc_o = xtal_opt.latt.GetUnitCell();
|
|
|
|
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
|
|
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << std::endl;
|
|
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.1);
|
|
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.1);
|
|
|
|
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
|
|
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
|
|
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
|
|
CHECK(fabs(uc_o.alpha - 90) < 0.02);
|
|
CHECK(fabs(uc_o.beta - 90) < 0.02);
|
|
CHECK(fabs(uc_o.gamma - 90) < 0.02);
|
|
}
|
|
|
|
TEST_CASE("XtalOptimizer_monoclinic") {
|
|
DiffractionExperiment exp_i;
|
|
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
|
|
.BeamX_pxl(1000)
|
|
.BeamY_pxl(1000)
|
|
.PoniRot1_rad(0.01)
|
|
.PoniRot2_rad(0.02)
|
|
.DetectorDistance_mm(200);
|
|
|
|
CrystalLattice latt_i(50,60,70,90,96,90);
|
|
|
|
auto uc_i = latt_i.GetUnitCell();
|
|
|
|
BraggPredictionSettings prediction_settings{
|
|
.high_res_A = 1.5,
|
|
.ewald_dist_cutoff = 0.001
|
|
};
|
|
BraggPrediction prediction;
|
|
auto count = prediction.Calc(exp_i, latt_i, prediction_settings);
|
|
|
|
std::vector<SpotToSave> spots;
|
|
|
|
for (int i = 0; i < count; ++i) {
|
|
auto refl = prediction.GetReflections().at(i);
|
|
spots.push_back(SpotToSave{refl.predicted_x, refl.predicted_y});
|
|
}
|
|
|
|
XtalOptimizerData xtal_opt;
|
|
xtal_opt.latt = CrystalLattice(49.5, 60.5, 69.8, 90, 95.5, 90);
|
|
xtal_opt.geom.BeamX_pxl(1007).BeamY_pxl(990).DetectorDistance_mm(200)
|
|
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
|
|
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
|
|
auto start = std::chrono::high_resolution_clock::now();
|
|
REQUIRE(XtalOptimizer(xtal_opt, spots));
|
|
auto end = std::chrono::high_resolution_clock::now();
|
|
std::cout << "XtalOptimizer took " << std::chrono::duration_cast<std::chrono::microseconds>(end - start).count()
|
|
<< " microseconds" << std::endl;
|
|
|
|
auto uc_o = xtal_opt.latt.GetUnitCell();
|
|
|
|
std::cout << "Beam center: " << xtal_opt.geom.GetBeamX_pxl() << " " << xtal_opt.geom.GetBeamY_pxl() << std::endl;
|
|
std::cout << "Unit cell: " << uc_o.a << " " << uc_o.b << " " << uc_o.c << " " << uc_o.alpha << " " << uc_o.beta << " " << uc_o.gamma << std::endl;
|
|
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2);
|
|
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2);
|
|
|
|
CHECK(fabsf(uc_i.a - uc_o.a) < 0.1);
|
|
CHECK(fabsf(uc_i.b - uc_o.b) < 0.1);
|
|
CHECK(fabsf(uc_i.c - uc_o.c) < 0.2);
|
|
CHECK(fabs(uc_o.alpha - 90) < 0.05);
|
|
CHECK(fabs(uc_o.beta - uc_i.beta) < 0.05);
|
|
CHECK(fabs(uc_o.gamma - 90) < 0.05);
|
|
}
|
|
|
|
TEST_CASE("LatticeToRodrigues") {
|
|
double rod[3];
|
|
double lengths[3];
|
|
|
|
CrystalLattice latt_i(40,50,80,90,90,90);
|
|
|
|
LatticeToRodriguesAndLengths_GS(latt_i, rod, lengths);
|
|
CHECK(lengths[0] == Catch::Approx(40.0));
|
|
CHECK(lengths[1] == Catch::Approx(50.0));
|
|
CHECK(lengths[2] == Catch::Approx(80.0));
|
|
CHECK(fabs(rod[0]) < 0.001);
|
|
CHECK(fabs(rod[1]) < 0.001);
|
|
CHECK(fabs(rod[2]) < 0.001);
|
|
|
|
auto latt_o = AngleAxisAndLengthsToLattice(rod, lengths, false);
|
|
|
|
CHECK(latt_o.Vec0().Length() == Catch::Approx(40.0));
|
|
CHECK(latt_o.Vec1().Length() == Catch::Approx(50.0));
|
|
CHECK(latt_o.Vec2().Length() == Catch::Approx(80.0));
|
|
}
|
|
|
|
TEST_CASE("LatticeToRodrigues_irregular") {
|
|
double rod[3];
|
|
double lengths[3];
|
|
|
|
CrystalLattice latt_i(Coord(40,0,0),
|
|
Coord(0, 50 / sqrt(2), -50 / sqrt(2)),
|
|
Coord(0, 80 / sqrt(2), 80 / sqrt(2)));
|
|
|
|
LatticeToRodriguesAndLengths_GS(latt_i, rod, lengths);
|
|
CHECK(lengths[0] == Catch::Approx(40.0));
|
|
CHECK(lengths[1] == Catch::Approx(50.0));
|
|
CHECK(lengths[2] == Catch::Approx(80.0));
|
|
|
|
|
|
auto latt_o = AngleAxisAndLengthsToLattice(rod, lengths, false);
|
|
|
|
CHECK(latt_o.Vec0().Length() == Catch::Approx(40.0));
|
|
CHECK(latt_o.Vec1().Length() == Catch::Approx(50.0));
|
|
CHECK(latt_o.Vec2().Length() == Catch::Approx(80.0));
|
|
}
|
|
|
|
TEST_CASE("LatticeToRodrigues_Hex") {
|
|
double rod[3];
|
|
double lengths[3];
|
|
|
|
Coord a = Coord(40,0,0);
|
|
Coord b = Coord(40 / 2, 40 * sqrt(3)/ 2.0, 0);
|
|
Coord c = Coord(0, 0, 70);
|
|
|
|
RotMatrix R(1.0, Coord(0,1,1));
|
|
CrystalLattice latt_i(R*a,R*b,R*c);
|
|
|
|
LatticeToRodriguesAndLengths_Hex(latt_i, rod, lengths);
|
|
CHECK(lengths[0] == Catch::Approx(40.0));
|
|
CHECK(lengths[1] == Catch::Approx(40.0));
|
|
CHECK(lengths[2] == Catch::Approx(70.0));
|
|
|
|
auto latt_o = AngleAxisAndLengthsToLattice(rod, lengths, true);
|
|
auto uc_o = latt_o.GetUnitCell();
|
|
CHECK(uc_o.a == Catch::Approx(40.0));
|
|
CHECK(uc_o.b == Catch::Approx(40.0));
|
|
CHECK(uc_o.c == Catch::Approx(70.0));
|
|
CHECK(uc_o.alpha == Catch::Approx(90.0));
|
|
CHECK(uc_o.beta == Catch::Approx(90.0));
|
|
CHECK(uc_o.gamma == Catch::Approx(120.0));
|
|
}
|
|
|
|
TEST_CASE("XtalOptimizer_rotation") {
|
|
// Geometry
|
|
DiffractionExperiment exp_i;
|
|
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
|
|
.BeamX_pxl(1000)
|
|
.BeamY_pxl(1000)
|
|
.PoniRot1_rad(0.01)
|
|
.PoniRot2_rad(0.02)
|
|
.DetectorDistance_mm(200);
|
|
|
|
// Base lattice (non-pathological)
|
|
CrystalLattice latt_base(40, 50, 80, 90, 95, 90);
|
|
auto uc_ref = latt_base.GetUnitCell();
|
|
|
|
// Rotation axis: around X with 3 deg per image
|
|
GoniometerAxis axis("omega", 0.0f, 3.0f, Coord(1,0,0), std::nullopt);
|
|
|
|
BraggPredictionSettings prediction_settings{
|
|
.high_res_A = 1.5,
|
|
.ewald_dist_cutoff = 0.002
|
|
};
|
|
|
|
std::vector<SpotToSave> spots;
|
|
BraggPrediction prediction;
|
|
|
|
// Predict reflections for images at 0-30 deg.
|
|
for (int img = 0; img < 10; ++img) {
|
|
// For a rotated image, per-image lattice is obtained as Multiply(rot.transpose())
|
|
const float angle_deg = axis.GetAngle_deg(img) + axis.GetWedge_deg() / 2.0f;
|
|
const RotMatrix rot = axis.GetTransformationAngle(angle_deg);
|
|
const CrystalLattice latt_img = latt_base.Multiply(rot.transpose());
|
|
|
|
const auto n = prediction.Calc(exp_i, latt_img, prediction_settings);
|
|
for (int i = 0; i < n; ++i) {
|
|
const auto& r = prediction.GetReflections().at(i);
|
|
SpotToSave s{};
|
|
s.x = r.predicted_x;
|
|
s.y = r.predicted_y;
|
|
s.image = img; // provide image index for rotation-aware refinement
|
|
s.phi = angle_deg;
|
|
s.intensity = 1.0f; // minimal positive value
|
|
s.ice_ring = false;
|
|
s.indexed = true;
|
|
spots.push_back(s);
|
|
}
|
|
}
|
|
|
|
// Seed slightly perturbed geometry and lattice; provide rotation axis for refinement
|
|
XtalOptimizerData xtal_opt;
|
|
xtal_opt.latt = CrystalLattice(39.7f, 50.6f, 79.6f, 90.0f, 94.5f, 90.5f);
|
|
xtal_opt.geom.BeamX_pxl(1003).BeamY_pxl(997).DetectorDistance_mm(200.0)
|
|
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
|
|
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
|
|
xtal_opt.axis = axis;
|
|
xtal_opt.min_spots = 200;
|
|
xtal_opt.refine_beam_center = true;
|
|
xtal_opt.refine_distance_mm = false;
|
|
xtal_opt.refine_detector_angles = false;
|
|
|
|
auto t0 = std::chrono::high_resolution_clock::now();
|
|
REQUIRE(XtalOptimizer(xtal_opt, spots));
|
|
auto t1 = std::chrono::high_resolution_clock::now();
|
|
std::cout << "XtalOptimizer (rotation 4 images) took "
|
|
<< std::chrono::duration_cast<std::chrono::microseconds>(t1 - t0).count()
|
|
<< " microseconds" << std::endl;
|
|
|
|
const auto uc_out = xtal_opt.latt.GetUnitCell();
|
|
|
|
// Geometry checks
|
|
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2f);
|
|
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2f);
|
|
|
|
// Lattice checks
|
|
CHECK(fabsf(uc_ref.a - uc_out.a) < 0.2f);
|
|
CHECK(fabsf(uc_ref.b - uc_out.b) < 0.2f);
|
|
CHECK(fabsf(uc_ref.c - uc_out.c) < 0.3f);
|
|
CHECK(fabsf(uc_ref.alpha - uc_out.alpha) < 0.2f);
|
|
CHECK(fabsf(uc_ref.beta - uc_out.beta) < 0.2f);
|
|
CHECK(fabsf(uc_ref.gamma - uc_out.gamma) < 0.2f);
|
|
}
|
|
|
|
TEST_CASE("XtalOptimizer_refine_rotation_axis") {
|
|
// Geometry
|
|
DiffractionExperiment exp_i;
|
|
exp_i.IncidentEnergy_keV(WVL_1A_IN_KEV)
|
|
.BeamX_pxl(1000)
|
|
.BeamY_pxl(1000)
|
|
.PoniRot1_rad(0.01)
|
|
.PoniRot2_rad(0.02)
|
|
.DetectorDistance_mm(200);
|
|
|
|
// Base lattice (non-pathological)
|
|
CrystalLattice latt_base(40, 50, 80, 90, 95, 90);
|
|
auto uc_ref = latt_base.GetUnitCell();
|
|
|
|
// Rotation axis: around X with 3 deg per image
|
|
GoniometerAxis axis("omega", 0.0f, 3.0f, Coord(1,0,0), std::nullopt);
|
|
|
|
BraggPredictionSettings prediction_settings{
|
|
.high_res_A = 1.5,
|
|
.ewald_dist_cutoff = 0.002
|
|
};
|
|
|
|
std::vector<SpotToSave> spots;
|
|
BraggPrediction prediction;
|
|
|
|
// Predict reflections for images at 0-30 deg.
|
|
for (int img = 0; img < 10; ++img) {
|
|
// For a rotated image, per-image lattice is obtained as Multiply(rot.transpose())
|
|
const float angle_deg = axis.GetAngle_deg(img) + axis.GetWedge_deg() / 2.0f;
|
|
const RotMatrix rot = axis.GetTransformationAngle(angle_deg);
|
|
const CrystalLattice latt_img = latt_base.Multiply(rot.transpose());
|
|
|
|
const auto n = prediction.Calc(exp_i, latt_img, prediction_settings);
|
|
for (int i = 0; i < n; ++i) {
|
|
const auto& r = prediction.GetReflections().at(i);
|
|
SpotToSave s{};
|
|
s.x = r.predicted_x;
|
|
s.y = r.predicted_y;
|
|
s.image = img; // provide image index for rotation-aware refinement
|
|
s.intensity = 1.0f; // minimal positive value
|
|
s.phi = angle_deg;
|
|
s.ice_ring = false;
|
|
s.indexed = true;
|
|
spots.push_back(s);
|
|
}
|
|
}
|
|
|
|
// Seed slightly perturbed geometry and lattice; provide rotation axis for refinement
|
|
XtalOptimizerData xtal_opt;
|
|
xtal_opt.latt = CrystalLattice(39.7f, 50.6f, 79.6f, 90.0f, 94.5f, 90.5f);
|
|
xtal_opt.geom.BeamX_pxl(1003).BeamY_pxl(997).DetectorDistance_mm(200.0)
|
|
.PoniRot1_rad(0.01).PoniRot2_rad(0.02);
|
|
xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
|
|
xtal_opt.axis = GoniometerAxis("omega", 0.0f, 3.0f,
|
|
Coord(0.8, 0.05, 0.05).Normalize(),
|
|
std::nullopt);
|
|
xtal_opt.min_spots = 200;
|
|
xtal_opt.refine_beam_center = true;
|
|
xtal_opt.refine_distance_mm = false;
|
|
xtal_opt.refine_detector_angles = false;
|
|
xtal_opt.refine_rotation_axis = true;
|
|
|
|
auto t0 = std::chrono::high_resolution_clock::now();
|
|
REQUIRE(XtalOptimizer(xtal_opt, spots));
|
|
auto t1 = std::chrono::high_resolution_clock::now();
|
|
std::cout << "XtalOptimizer (rotation 4 images) took "
|
|
<< std::chrono::duration_cast<std::chrono::microseconds>(t1 - t0).count()
|
|
<< " microseconds" << std::endl;
|
|
|
|
const auto uc_out = xtal_opt.latt.GetUnitCell();
|
|
|
|
// Geometry checks
|
|
CHECK(fabsf(xtal_opt.geom.GetBeamX_pxl() - exp_i.GetBeamX_pxl()) < 0.2f);
|
|
CHECK(fabsf(xtal_opt.geom.GetBeamY_pxl() - exp_i.GetBeamY_pxl()) < 0.2f);
|
|
|
|
// Lattice checks
|
|
CHECK(fabsf(uc_ref.a - uc_out.a) < 0.2f);
|
|
CHECK(fabsf(uc_ref.b - uc_out.b) < 0.2f);
|
|
CHECK(fabsf(uc_ref.c - uc_out.c) < 0.3f);
|
|
CHECK(fabsf(uc_ref.alpha - uc_out.alpha) < 0.2f);
|
|
CHECK(fabsf(uc_ref.beta - uc_out.beta) < 0.2f);
|
|
CHECK(fabsf(uc_ref.gamma - uc_out.gamma) < 0.2f);
|
|
CHECK(fabsf(xtal_opt.axis->GetAxis().x - 1.0) < 0.01f);
|
|
CHECK(fabsf(xtal_opt.axis->GetAxis().y) < 0.01f);
|
|
CHECK(fabsf(xtal_opt.axis->GetAxis().z) < 0.01f);
|
|
} |