leonarski_fandClaude Opus 4.8
abbee2d4dc
Datasets may be confidential; sample names and measured unit cells committed to the repo can leak outside the group working on them. Scrub existing occurrences and add a "No sample identities in the repository" section to CLAUDE.md (forbidden: sample/dataset names, internal codes, measured cells tied to a sample; fine: space group / lattice / twinning descriptors). - Comments: replace internal dataset codes and protein names with the crystallographic situation they illustrate (centred vs pseudo-symmetric, holohedral, cubic, F-cubic/hexagonal, ...). - Docs: same, in the analysis/writer/stream references and example configs. - Tests: rename sample-named identifiers, TEST_CASE names, file prefixes and asserted labels to neutral crystallographic names (e.g. tetragonal_uc); behaviour unchanged. Reduce the CrystFEL reference PDB to a bare CRYST1 cell file (cell.pdb) and rename the reference data file. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
83 lines
3.2 KiB
C++
83 lines
3.2 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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// End-to-end Rugnux runs over real JUNGFRAU datasets that are kept in git-LFS under
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// tests/data. They are tagged [large] and SKIP() when the data is not present (e.g. LFS not
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// pulled), so the default test run stays fast and CI without the data still passes.
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#include <catch2/catch_all.hpp>
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#include <catch2/reporters/catch_reporter_event_listener.hpp>
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#include <catch2/reporters/catch_reporter_registrars.hpp>
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#include <iostream>
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#include <thread>
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#include "TestData.h"
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#include "../common/DiffractionExperiment.h"
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#include "../common/IndexingSettings.h"
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#include "../reader/JFJochHDF5Reader.h"
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#include "../rugnux/Rugnux.h"
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namespace {
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// Start-up hook: report once whether the large datasets are available, so it is obvious why
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// the [large] tests skip when they do.
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class LargeDataListener : public Catch::EventListenerBase {
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public:
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using Catch::EventListenerBase::EventListenerBase;
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void testRunStarting(Catch::TestRunInfo const &) override {
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const bool rot = jfjoch_test::LargeDataFile("rotation_master.h5").has_value();
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std::cout << "[jfjoch_test] large dataset in " << jfjoch_test::LargeDataDir()
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<< ": rotation=" << (rot ? "yes" : "no")
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<< " ([large] tests skip when absent)" << std::endl;
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}
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};
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int default_threads() {
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const unsigned hc = std::thread::hardware_concurrency();
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return hc == 0 ? 4 : static_cast<int>(hc);
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}
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}
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CATCH_REGISTER_LISTENER(LargeDataListener)
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TEST_CASE("Rugnux_Rotation", "[large]") {
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const auto master = jfjoch_test::LargeDataFile("rotation_master.h5");
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if (!master)
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SKIP("rotation_master.h5 not available (git-lfs data not pulled)");
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RegisterHDF5Filter();
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JFJochHDF5Reader reader;
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REQUIRE_NOTHROW(reader.ReadFile(*master));
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auto dataset = reader.GetDataset();
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REQUIRE(dataset);
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DiffractionExperiment experiment(dataset->experiment);
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IndexingSettings indexing;
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indexing.Algorithm(IndexingAlgorithmEnum::Auto);
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indexing.RotationIndexing(true);
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indexing.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
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experiment.ImportIndexingSettings(indexing);
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ProcessConfig config;
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config.mode = ProcessMode::FullAnalysis;
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config.nthreads = default_threads();
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config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
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config.spot_finding.indexing = true;
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config.rotation_indexing = true;
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config.two_pass_rotation = true;
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config.reuse_rotation_spots = false; // redo spot finding (raw dataset may carry no spots)
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Rugnux process(reader, experiment, *dataset->pixel_mask, config);
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ProcessResult result;
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REQUIRE_NOTHROW(result = process.Run());
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CHECK_FALSE(result.cancelled);
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CHECK(result.images_processed == reader.GetNumberOfImages());
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REQUIRE(result.indexing_rate.has_value());
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CHECK(result.indexing_rate.value() > 0.1f); // a real rotation series indexes well
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CHECK(result.consensus_cell.has_value());
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reader.Close();
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REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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}
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