Jungfraujoch/tests/JFJochProcessLargeTest.cpp

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

// End-to-end JFJochProcess runs over real JUNGFRAU datasets that are kept in git-LFS under
// tests/data. They are tagged [large] and SKIP() when the data is not present (e.g. LFS not
// pulled), so the default test run stays fast and CI without the data still passes.

#include <catch2/catch_all.hpp>
#include <catch2/reporters/catch_reporter_event_listener.hpp>
#include <catch2/reporters/catch_reporter_registrars.hpp>

#include <iostream>
#include <thread>

#include "TestData.h"
#include "../common/DiffractionExperiment.h"
#include "../common/IndexingSettings.h"
#include "../reader/JFJochHDF5Reader.h"
#include "../process/JFJochProcess.h"

namespace {
    // Start-up hook: report once whether the large datasets are available, so it is obvious why
    // the [large] tests skip when they do.
    class LargeDataListener : public Catch::EventListenerBase {
    public:
        using Catch::EventListenerBase::EventListenerBase;
        void testRunStarting(Catch::TestRunInfo const &) override {
            const bool rot = jfjoch_test::LargeDataFile("lyso_rotation_master.h5").has_value();
            const bool ser = jfjoch_test::LargeDataFile("lyso_serial_master.h5").has_value();
            std::cout << "[jfjoch_test] large datasets in " << jfjoch_test::LargeDataDir()
                      << ": rotation=" << (rot ? "yes" : "no")
                      << " serial=" << (ser ? "yes" : "no")
                      << " ([large] tests skip when absent)" << std::endl;
        }
    };

    int default_threads() {
        const unsigned hc = std::thread::hardware_concurrency();
        return hc == 0 ? 4 : static_cast<int>(hc);
    }
}

CATCH_REGISTER_LISTENER(LargeDataListener)

TEST_CASE("JFJochProcess_LysoRotation", "[large]") {
    const auto master = jfjoch_test::LargeDataFile("lyso_rotation_master.h5");
    if (!master)
        SKIP("lyso_rotation_master.h5 not available (git-lfs data not pulled)");

    RegisterHDF5Filter();
    JFJochHDF5Reader reader;
    REQUIRE_NOTHROW(reader.ReadFile(*master));
    auto dataset = reader.GetDataset();
    REQUIRE(dataset);

    DiffractionExperiment experiment(dataset->experiment);
    IndexingSettings indexing;
    indexing.Algorithm(IndexingAlgorithmEnum::Auto);
    indexing.RotationIndexing(true);
    indexing.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
    experiment.ImportIndexingSettings(indexing);

    ProcessConfig config;
    config.mode = ProcessMode::FullAnalysis;
    config.nthreads = default_threads();
    config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
    config.spot_finding.indexing = true;
    config.rotation_indexing = true;
    config.two_pass_rotation = true;
    config.reuse_rotation_spots = false;   // redo spot finding (raw dataset may carry no spots)

    JFJochProcess process(reader, experiment, dataset->pixel_mask, config);
    ProcessResult result;
    REQUIRE_NOTHROW(result = process.Run());

    CHECK_FALSE(result.cancelled);
    CHECK(result.images_processed == reader.GetNumberOfImages());
    REQUIRE(result.indexing_rate.has_value());
    CHECK(result.indexing_rate.value() > 0.1f);          // a real rotation series indexes well
    CHECK(result.consensus_cell.has_value());

    reader.Close();
    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}

TEST_CASE("JFJochProcess_LysoSerial", "[large]") {
    const auto master = jfjoch_test::LargeDataFile("lyso_serial_master.h5");
    if (!master)
        SKIP("lyso_serial_master.h5 not available (git-lfs data not pulled)");

    RegisterHDF5Filter();
    JFJochHDF5Reader reader;
    REQUIRE_NOTHROW(reader.ReadFile(*master));
    auto dataset = reader.GetDataset();
    REQUIRE(dataset);

    DiffractionExperiment experiment(dataset->experiment);
    IndexingSettings indexing;
    indexing.Algorithm(IndexingAlgorithmEnum::Auto);
    indexing.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
    experiment.ImportIndexingSettings(indexing);

    ProcessConfig config;
    config.mode = ProcessMode::FullAnalysis;
    config.nthreads = default_threads();
    config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
    config.spot_finding.indexing = true;

    JFJochProcess process(reader, experiment, dataset->pixel_mask, config);
    ProcessResult result;
    REQUIRE_NOTHROW(result = process.Run());

    CHECK_FALSE(result.cancelled);
    CHECK(result.images_processed == reader.GetNumberOfImages());
    REQUIRE(result.indexing_rate.has_value());
    CHECK(result.indexing_rate.value() > 0.0f);          // serial stills: at least some hits index

    reader.Close();
    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}