Filip Leonarski
07fe4dd3bb
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This is an UNSTABLE release. This version significantly rewrites code to predict reflection position and integrate them, especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123. * jfjoch_broker: Improve refection position prediction and Bragg integration code. * jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation. * jfjoch_writer: Fix saving mosaicity properly in HDF5 file. * jfjoch_viewer: Introduce high-dynamic range mode for images * jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%) * jfjoch_viewer: Zoom-in numbers have better readability Reviewed-on: #31 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
91 lines
3.2 KiB
C++
91 lines
3.2 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include <catch2/catch_all.hpp>
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#include <iostream>
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#include "../image_analysis/RotationIndexer.h"
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#include "../image_analysis/bragg_prediction/BraggPrediction.h"
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TEST_CASE("RotationIndexer") {
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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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.ImagesPerTrigger(50);
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IndexingSettings settings;
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#ifdef JFJOCH_USE_CUDA
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settings.Algorithm(IndexingAlgorithmEnum::FFT);
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#elif JFJOCH_USE_FFTW
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settings.Algorithm(IndexingAlgorithmEnum::FFTW);
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#else
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return;
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#endif
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settings.RotationIndexing(true).RotationIndexingAngularStride_deg(1.0).RotationIndexingMinAngularRange_deg(30.0);
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exp_i.ImportIndexingSettings(settings);
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// Base lattice (non-pathological)
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CrystalLattice latt_base(40, 50, 80, 90, 90, 90);
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latt_base = latt_base.Multiply(RotMatrix(2.0, Coord(sqrt(3)/3,sqrt(3)/3,sqrt(3)/3)));
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// Rotation axis: around X with 1 deg per image
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GoniometerAxis axis("omega", 0.0f, 1.0f, Coord(1,0,0), std::nullopt);
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exp_i.Goniometer(axis);
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BraggPredictionSettings prediction_settings{
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.high_res_A = 1.3,
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.ewald_dist_cutoff = 0.002
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};
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IndexerThreadPool indexer_thread_pool(exp_i.GetIndexingSettings());
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RotationIndexer indexer(exp_i, indexer_thread_pool);
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BraggPrediction prediction;
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int cnt = 0;
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// Predict reflections for images at 0-30 deg.
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for (int img = 0; img < 50; ++img) {
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std::vector<SpotToSave> spots;
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// For a rotated image, per-image lattice is obtained as Multiply(rot.transpose())
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const float angle_deg = axis.GetAngle_deg(img) + axis.GetWedge_deg() / 2.0f;
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const RotMatrix rot = axis.GetTransformationAngle(angle_deg);
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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 = img; // provide image index for rotation-aware refinement
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s.intensity = 1.0f; // minimal positive value
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s.ice_ring = false;
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s.indexed = true;
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spots.push_back(s);
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}
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if (indexer.ProcessImage(img, spots).has_value())
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cnt++;
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}
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CHECK(cnt == 20);
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auto ret = indexer.GetLattice();
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REQUIRE(ret.has_value());
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auto uc = ret->lattice.GetUnitCell();
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auto uc_ref = latt_base.GetUnitCell();
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REQUIRE(std::fabs(uc.a - uc_ref.a) < 0.02 );
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REQUIRE(std::fabs(uc.b - uc_ref.b) < 0.02 );
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REQUIRE(std::fabs(uc.c - uc_ref.c) < 0.02 );
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REQUIRE(std::fabs(uc.alpha - uc_ref.alpha) < 0.1);
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REQUIRE(std::fabs(uc.beta - uc_ref.beta) < 0.1);
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REQUIRE(std::fabs(uc.gamma - uc_ref.gamma) < 0.1);
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CHECK(ret->search_result.centering == 'P');
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CHECK(ret->search_result.system == gemmi::CrystalSystem::Orthorhombic);
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}
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