Filip Leonarski
06949caf1a
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This is an UNSTABLE release and not recommended for production use (please use rc.11 instead). * jfjoch_broker: Experimental rotation (3D) indexing * jfjoch_broker: Minor fix to error in optimizer potentially returning NaN values Reviewed-on: #18 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
82 lines
3.2 KiB
C++
82 lines
3.2 KiB
C++
// SPDX-FileCopyrightText: 2024 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 "../reader/JFJochHDF5Reader.h"
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#include "../image_analysis/indexing/IndexerFactory.h"
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#include "../common/Logger.h"
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#include "../image_analysis/IndexAndRefine.h"
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#include "../image_analysis/bragg_integration/BraggPredictionFactory.h"
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#include "../writer/FileWriter.h"
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#include "../image_analysis/indexing/AnalyzeIndexing.h"
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int main(int argc, char** argv) {
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Logger logger("jfjoch_indexing_test");
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if (argc != 2) {
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Usage: ./jfjoch_indexing_test <file>");
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}
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JFJochHDF5Reader reader;
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reader.ReadFile(argv[1]);
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if (!reader.GetDataset())
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Error opening file");
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IndexingSettings indexing_settings;
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indexing_settings.Algorithm(IndexingAlgorithmEnum::FFT);
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indexing_settings.RotationIndexing(true);
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indexing_settings.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
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DiffractionExperiment experiment(reader.GetDataset()->experiment);
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experiment.ImportIndexingSettings(indexing_settings);
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experiment.SetUnitCell({});
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experiment.FilePrefix("output");
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StartMessage msg;
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experiment.FillMessage(msg);
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// FileWriter fw(msg);
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IndexerThreadPool indexer(experiment.GetIndexingSettings());
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SpotFindingSettings settings{};
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settings.quick_integration = false;
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settings.indexing = true;
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auto geom = experiment.GetDiffractionGeometry();
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IndexAndRefine rot_index(experiment, &indexer);
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auto prediction = CreateBraggPrediction();
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int cnt = 0;
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for (int i = 0; i < reader.GetNumberOfImages(); i++) {
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auto img = reader.LoadImage(i);
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if (!img)
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continue;
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DataMessage msg = img->ImageData();
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rot_index.ProcessImage(msg, settings, msg.image, *prediction);
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if (msg.indexing_result && msg.indexing_result.value())
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cnt++;
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if (i % 200 == 0)
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logger.Info("Image {} {}", i, cnt);
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}
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auto latt_1 = rot_index.Finalize(false);
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if (latt_1) {
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auto uc = latt_1->lattice.GetUnitCell();
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logger.Info("Unit cell {} {} {} {} {} {}", uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
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logger.Info("Latt1 {} {} {}", latt_1->lattice.Vec0().x, latt_1->lattice.Vec0().y, latt_1->lattice.Vec0().z);
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logger.Info("Latt1 {} {} {}", latt_1->lattice.Vec1().x, latt_1->lattice.Vec1().y, latt_1->lattice.Vec1().z);
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logger.Info("Latt1 {} {} {}", latt_1->lattice.Vec2().x, latt_1->lattice.Vec2().y, latt_1->lattice.Vec2().z);
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}
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auto latt_2 = rot_index.Finalize(true);
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if (latt_2) {
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auto uc = latt_2->lattice.GetUnitCell();
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logger.Info("Unit cell {} {} {} {} {} {}", uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
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logger.Info("Latt1 {} {} {}", latt_2->lattice.Vec0().x, latt_2->lattice.Vec0().y, latt_2->lattice.Vec0().z);
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logger.Info("Latt1 {} {} {}", latt_2->lattice.Vec1().x, latt_2->lattice.Vec1().y, latt_2->lattice.Vec1().z);
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logger.Info("Latt1 {} {} {}", latt_2->lattice.Vec2().x, latt_2->lattice.Vec2().y, latt_2->lattice.Vec2().z);
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}
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} |