leonarski_f
67dca388bd
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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
676 lines
27 KiB
C++
676 lines
27 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});
|
|
}
|
|
|
|
XtalOptimizerData xtal_opt{};
|
|
xtal_opt.latt = CrystalLattice(39.5,39.8,70.1, 90,90, 119.5);
|
|
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::Hexagonal;
|
|
xtal_opt.max_time = 60.0;
|
|
auto start = std::chrono::high_resolution_clock::now();
|
|
bool ret = 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;
|
|
REQUIRE(ret);
|
|
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()) < 0.1);
|
|
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.
|
|
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(203.0)
|
|
.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 = 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);
|
|
|
|
// 700 micron is a lot, but for now it is important to see that refinement improves in the right direction
|
|
CHECK(fabsf(xtal_opt.geom.GetDetectorDistance_mm() - exp_i.GetDetectorDistance_mm()) < 0.7f);
|
|
|
|
// 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_distance_mm = false;
|
|
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);
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// Lattice checks
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CHECK(fabsf(uc_ref.a - uc_out.a) < 0.2f);
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CHECK(fabsf(uc_ref.b - uc_out.b) < 0.2f);
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CHECK(fabsf(uc_ref.c - uc_out.c) < 0.3f);
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CHECK(fabsf(uc_ref.alpha - uc_out.alpha) < 0.2f);
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CHECK(fabsf(uc_ref.beta - uc_out.beta) < 0.2f);
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CHECK(fabsf(uc_ref.gamma - uc_out.gamma) < 0.2f);
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CHECK(fabsf(xtal_opt.axis->GetAxis().x - 1.0) < 0.01f);
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CHECK(fabsf(xtal_opt.axis->GetAxis().y) < 0.01f);
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CHECK(fabsf(xtal_opt.axis->GetAxis().z) < 0.01f);
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}
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// --- helpers for lattice sanity tests ---
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#include <Eigen/Dense>
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