leonarski_f
680c36c20d
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* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands. * `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion. * Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants. * `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing. * A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed. * `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing. * Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences. * The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to. * The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after. * The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution. * `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have. * Twinning is no longer reported when the L-test contradicts it. * The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's. * `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots. * The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area. Reviewed-on: #76 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
744 lines
30 KiB
C++
744 lines
30 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.max_time = 30.0;
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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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xtal_opt.max_time = 30.0;
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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.max_time = 30.0;
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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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xtal_opt.max_time = 36.0;
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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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xtal_opt.max_time = 30.0;
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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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xtal_opt.max_time = 60.0;
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auto start = std::chrono::high_resolution_clock::now();
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bool ret = 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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REQUIRE(ret);
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auto uc_i = latt_i.GetUnitCell();
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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()) < 0.1);
|
|
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) < 0.01);
|
|
CHECK(fabs(uc_o.gamma - 120) < 0.01);
|
|
}
|
|
|
|
TEST_CASE("XtalOptimizer_hexagonal_unconstrained") {
|
|
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(40,40,70,90,90,120);
|
|
|
|
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;
|
|
xtal_opt.max_time = 30.0;
|
|
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;
|
|
xtal_opt.max_time = 30.0;
|
|
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(50,60,70,90,115,90);
|
|
|
|
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, 113.5, 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;
|
|
xtal_opt.max_time = 30.0;
|
|
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("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
|
|
};
|
|
|
|
size_t nimages = 10;
|
|
|
|
std::vector<std::vector<SpotToSave>> spots(nimages);
|
|
BraggPrediction prediction;
|
|
|
|
// Predict reflections for images at 0-30 deg.
|
|
for (int img = 0; img < nimages; ++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[img].push_back(s);
|
|
}
|
|
}
|
|
|
|
// Seed slightly perturbed geometry and lattice; provide rotation axis for refinement.
|
|
// The beam-centre component PARALLEL to the spindle (here X, the rotation axis) is a gauge-weak
|
|
// direction that XtalOptimizer now deliberately restrains toward the header rather than refining
|
|
// freely (see the BeamComponentPrior in XtalOptimizer.cpp). So only the perpendicular component
|
|
// (Y) is seeded off-truth to exercise beam-centre recovery; X is seeded at its true value.
|
|
// The distance is seeded at its true value too: XtalOptimizer does not refine it - the rotation
|
|
// post-refinement fits it globally instead, where the cell is held fixed and the two are no longer
|
|
// degenerate - so a distance seeded off-truth here would simply be absorbed by the cell.
|
|
XtalOptimizerData xtal_opt{};
|
|
xtal_opt.latt = CrystalLattice(39.7f, 50.6f, 79.6f, 90.0f, 94.5f, 90.5f);
|
|
xtal_opt.geom.BeamX_pxl(1000).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_detector_angles = false;
|
|
xtal_opt.max_time = 30.0;
|
|
|
|
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) < 0.4f);
|
|
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
|
|
};
|
|
|
|
|
|
BraggPrediction prediction;
|
|
|
|
const size_t nimages = 10;
|
|
std::vector<std::vector<SpotToSave>> spots(nimages);
|
|
|
|
// Predict reflections for images at 0-30 deg.
|
|
for (int img = 0; img < nimages; ++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.at(img).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_detector_angles = false;
|
|
xtal_opt.refine_rotation_axis = true;
|
|
xtal_opt.max_time = 30.0;
|
|
|
|
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);
|
|
}
|
|
|
|
// The rotation residual applies `angle_rad * |rot_vec|`, so the goniometer axis block must be
|
|
// constrained to unit length or the solve also fits a rotation SCALE that GoniometerAxis::Axis()
|
|
// then normalises away. Generate spots whose true rotation is k times the angles the optimizer is
|
|
// handed - k = 1 for a healthy goniometer, k = 1.01 for a stage that turned 1 % further than it was
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// commanded - and check the axis DIRECTION and the cell come back either way. (Before the axis block
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// was put on the unit sphere, the free length absorbed part of that 1 %: on this noise-free data it
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// reached only 1.00538 of the 1.01 it would have had to reach to be a measurement.)
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TEST_CASE("XtalOptimizer_rotation_axis_direction_only") {
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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).BeamY_pxl(1000)
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.DetectorDistance_mm(200);
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const CrystalLattice latt_base(40, 50, 80, 90, 95, 90);
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const auto uc_ref = latt_base.GetUnitCell();
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const double k_true = GENERATE(1.000, 1.010);
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// The angles the FILE records. The stage actually turned k_true times as far.
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GoniometerAxis nominal("omega", 0.0f, 3.0f, Coord(1, 0, 0), std::nullopt);
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BraggPredictionSettings prediction_settings{.high_res_A = 1.5, .ewald_dist_cutoff = 0.002};
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BraggPrediction prediction;
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const size_t nimages = 40;
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std::vector<std::vector<SpotToSave>> spots(nimages);
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for (size_t img = 0; img < nimages; ++img) {
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const float nominal_deg = nominal.GetAngle_deg(img) + nominal.GetWedge_deg() / 2.0f;
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const RotMatrix rot = nominal.GetTransformationAngle(static_cast<float>(nominal_deg * k_true));
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const CrystalLattice latt_img = latt_base.Multiply(rot.transpose());
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const auto n = prediction.Calc(exp_i, latt_img, prediction_settings);
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for (int i = 0; i < n; ++i) {
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const auto &r = prediction.GetReflections().at(i);
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SpotToSave s{};
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s.x = r.predicted_x;
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s.y = r.predicted_y;
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s.image = static_cast<int32_t>(img);
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s.intensity = 1.0f;
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s.phi = nominal_deg;
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s.indexed = true;
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spots.at(img).push_back(s);
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}
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}
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XtalOptimizerData xtal_opt{};
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xtal_opt.latt = latt_base;
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xtal_opt.geom.BeamX_pxl(1000).BeamY_pxl(1000).DetectorDistance_mm(200.0);
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xtal_opt.crystal_system = gemmi::CrystalSystem::Monoclinic;
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xtal_opt.axis = GoniometerAxis("omega", 0.0f, 3.0f, Coord(0.999, 0.02, 0.02).Normalize(),
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std::nullopt);
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xtal_opt.min_spots = 200;
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xtal_opt.refine_beam_center = true;
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xtal_opt.refine_detector_angles = true;
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xtal_opt.refine_rotation_axis = true;
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xtal_opt.max_iterations = 200;
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REQUIRE(XtalOptimizer(xtal_opt, spots));
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const Coord axis_out = xtal_opt.axis->GetAxis();
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CHECK(std::fabs(axis_out.Length() - 1.0f) < 1e-5f);
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CHECK(std::fabs(axis_out.x - 1.0f) < 0.01f);
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CHECK(std::fabs(axis_out.y) < 0.01f);
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CHECK(std::fabs(axis_out.z) < 0.01f);
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const auto uc_out = xtal_opt.latt.GetUnitCell();
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CHECK(std::fabs(uc_ref.a - uc_out.a) < 0.2f);
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CHECK(std::fabs(uc_ref.b - uc_out.b) < 0.2f);
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CHECK(std::fabs(uc_ref.c - uc_out.c) < 0.3f);
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}
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|
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// --- helpers for lattice sanity tests ---
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#include <Eigen/Dense>
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