Jungfraujoch/tests/WriteReflectionsTest.cpp

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

#include <catch2/catch_all.hpp>

#include <filesystem>
#include <string>

#include <gemmi/mtz.hpp>

#include "../common/DiffractionExperiment.h"
#include "../image_analysis/WriteReflections.h"
#include "SyntheticMergedReflections.h"

namespace {
    // The wavelength CCP4's mtzlib substitutes when the data columns belong to dataset 0, which it
    // takes for the reserved HKL_base: Cu K-alpha, and the wrong edge for anything reading f'/f''
    // out of the file.
    constexpr double CU_KALPHA_A = 1.54187;

    constexpr UnitCell TETRAGONAL_CELL{47.0f, 47.0f, 63.0f, 90.0f, 90.0f, 90.0f};

    DiffractionExperiment TestExperiment() {
        DiffractionExperiment x;
        x.IncidentEnergy_keV(12.7f);         // ~0.976 A, nowhere near the Cu K-alpha default
        x.SpaceGroupNumber(96);              // P 43 21 2
        x.SetUnitCell(TETRAGONAL_CELL);
        return x;
    }
}

TEST_CASE("Merged MTZ: the data dataset is id 1 and carries the wavelength", "[write_reflections]") {
    jfjoch_test::SyntheticMergeParams params;
    params.true_space_group = "P 43 21 2";
    params.twin_supergroup = "P 43 21 2";
    params.d_min_A = 5.0;
    const auto reflections = jfjoch_test::GenerateSyntheticMerged(params);
    REQUIRE(!reflections.empty());

    const auto experiment = TestExperiment();
    const auto path = (std::filesystem::temp_directory_path() / "rugnux_merged_wavelength.mtz").string();
    WriteMtzReflections(reflections, TETRAGONAL_CELL, experiment, path);
    const gemmi::Mtz mtz = gemmi::read_mtz_file(path);
    std::filesystem::remove(path);

    // HKL_base at id 0, the data at id 1. A data dataset written at id 0 occupies the id MTZ
    // reserves for the base, and mtzlib then reports CU_KALPHA_A instead of the real wavelength.
    REQUIRE(mtz.datasets.size() == 2);
    CHECK(mtz.datasets[0].id == 0);
    CHECK(mtz.datasets[0].dataset_name == "HKL_base");
    CHECK(mtz.datasets[1].id == 1);
    CHECK(mtz.datasets[1].wavelength == Catch::Approx(experiment.GetWavelength_A()).epsilon(1e-5));
    CHECK(mtz.datasets[1].wavelength != Catch::Approx(CU_KALPHA_A).epsilon(1e-3));

    // The wavelength is read off the dataset the data columns belong to, so they have to be on the
    // data dataset and not on the base.
    for (const char *label : {"IMEAN", "SIGIMEAN", "F", "SIGF", "FreeR_flag"}) {
        const gemmi::Mtz::Column *col = mtz.column_with_label(label);
        REQUIRE(col != nullptr);
        CHECK(col->dataset_id == 1);
    }

    // Cell and space group travel in the same header.
    CHECK(mtz.spacegroup != nullptr);
    CHECK(mtz.spacegroup->number == 96);
    CHECK(mtz.cell.a == Catch::Approx(TETRAGONAL_CELL.a).epsilon(1e-5));
    CHECK(mtz.cell.c == Catch::Approx(TETRAGONAL_CELL.c).epsilon(1e-5));
    CHECK(mtz.cell.gamma == Catch::Approx(90.0).epsilon(1e-5));
    CHECK(mtz.datasets[1].cell.a == Catch::Approx(TETRAGONAL_CELL.a).epsilon(1e-5));

    CHECK(mtz.nreflections == static_cast<int>(reflections.size()));
}