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

#include <random>
#include <catch2/catch_all.hpp>
#include <cmath>
#include <filesystem>
#include <mutex>
#include <set>

#include "../common/DiffractionExperiment.h"
#include "../common/ScanResultGenerator.h"
#include "../writer/FileWriter.h"
#include "../reader/JFJochHDF5Reader.h"
#include "../reader/JFJochMultiReader.h"
#include "../rugnux/Rugnux.h"
#include "../rugnux/RugnuxCommandLine.h"
#include "../rugnux/RugnuxOutputFiles.h"
#include "../rugnux/RugnuxDefaults.h"
#include "../image_analysis/bragg_integration/SpotWidth.h"
#include "../image_analysis/geom_refinement/Calibrants.h"

namespace {
    // Write a small VDS dataset of `n` flat images and return nothing (prefix_master.h5 +
    // prefix_data_000001.h5 land in the test working directory).
    void WriteTestDataset(const std::string &prefix, int n, bool rotation = false) {
        RegisterHDF5Filter();

        DiffractionExperiment x(DetJF(1));
        if (rotation)
            x.Goniometer(GoniometerAxis("omega", 0.0f, 1.0f, Coord(1, 0, 0), std::nullopt));
        x.FilePrefix(prefix).ImagesPerTrigger(n).OverwriteExistingFiles(true);
        x.BitDepthImage(16).ImagesPerFile(n).SetFileWriterFormat(FileWriterFormat::NXmxVDS).PixelSigned(true);
        x.Compression(CompressionAlgorithm::NO_COMPRESSION);
        x.BeamX_pxl(512).BeamY_pxl(256).DetectorDistance_mm(150).IncidentEnergy_keV(WVL_1A_IN_KEV)
                .FrameTime(std::chrono::microseconds(500), std::chrono::microseconds(10));

        std::vector<int16_t> image(x.GetPixelsNum(), 5);
        StartMessage start_message;
        x.FillMessage(start_message);
        FileWriter file_set(start_message);
        ScanResultGenerator generator(x);
        for (int i = 0; i < n; i++) {
            DataMessage message{};
            message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
            message.number = i;
            REQUIRE_NOTHROW(file_set.WriteHDF5(message));
            generator.Add(message);
        }
        EndMessage end_message;
        end_message.max_image_number = n;
        generator.FillEndMessage(end_message);
        file_set.WriteHDF5(end_message);
        file_set.Finalize();
    }
}

TEST_CASE("Rugnux_AzInt", "[HDF5][Full]") {
    WriteTestDataset("process_azint_in", 8);

    JFJochHDF5Reader reader;
    REQUIRE_NOTHROW(reader.ReadFile("process_azint_in_master.h5"));
    auto dataset = reader.GetDataset();
    REQUIRE(dataset);

    ProcessConfig config;
    config.mode = ProcessMode::AzimuthalIntegration;
    config.nthreads = 2;
    // The per-image analysis goes to the caller's sink, which writes it.
    ProcessFileSink sink("process_azint_out");
    config.image_sink = &sink;

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

    CHECK_FALSE(result.cancelled);
    CHECK(result.images_processed == 8);

    {
        // The _process.h5 links back to the source images and carries an azimuthal profile per image.
        JFJochHDF5Reader out;
        REQUIRE_NOTHROW(out.ReadFile("process_azint_out_process.h5"));
        CHECK(out.GetNumberOfImages() == 8);
        std::shared_ptr<JFJochReaderImage> img;
        REQUIRE_NOTHROW(img = out.LoadImage(0));
        REQUIRE(img);
        CHECK_FALSE(img->ImageData().az_int_profile.empty());
    }

    reader.Close();
    remove("process_azint_in_master.h5");
    remove("process_azint_in_data_000001.h5");
    remove("process_azint_out_process.h5");
    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}

TEST_CASE("Rugnux_ProcessFileWithoutImages", "[HDF5][Full]") {
    // A reader with no single HDF5 file to link to (here several inputs read as one) gets a _process.h5
    // with the per-image analysis and no /entry/data/data, which reads back with its images' metadata
    // and no pixels.
    WriteTestDataset("process_noimg_in", 4);

    std::vector<std::unique_ptr<JFJochReader>> inputs;
    auto input = std::make_unique<JFJochHDF5Reader>();
    REQUIRE_NOTHROW(input->ReadFile("process_noimg_in_master.h5"));
    inputs.push_back(std::move(input));
    JFJochMultiReader reader(std::move(inputs));
    auto dataset = reader.GetDataset();
    REQUIRE(dataset);

    ProcessConfig config;
    config.mode = ProcessMode::AzimuthalIntegration;
    config.nthreads = 2;
    ProcessFileSink sink("process_noimg_out");
    config.image_sink = &sink;

    Rugnux process(reader, dataset->experiment, *dataset->pixel_mask, config);
    ProcessResult result;
    REQUIRE_NOTHROW(result = process.Run());
    CHECK(result.images_processed == 4);

    {
        HDF5ReadOnlyFile file("process_noimg_out_process.h5");
        CHECK_FALSE(file.Exists("/entry/data/data"));
    }
    {
        JFJochHDF5Reader out;
        REQUIRE_NOTHROW(out.ReadFile("process_noimg_out_process.h5"));
        CHECK(out.GetNumberOfImages() == 4);
        CHECK(out.LoadImage(0) == nullptr);
        CHECK_NOTHROW(out.ReadReflections(0, 3));
    }

    reader.Close();
    remove("process_noimg_in_master.h5");
    remove("process_noimg_in_data_000001.h5");
    remove("process_noimg_out_process.h5");
    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}

TEST_CASE("Rugnux_NoOutput", "[HDF5][Full]") {
    WriteTestDataset("process_noout_in", 6);

    JFJochHDF5Reader reader;
    REQUIRE_NOTHROW(reader.ReadFile("process_noout_in_master.h5"));
    auto dataset = reader.GetDataset();

    // No image sink => nothing is streamed anywhere.
    ProcessConfig config;
    config.mode = ProcessMode::AzimuthalIntegration;
    config.nthreads = 3;

    Rugnux process(reader, dataset->experiment, *dataset->pixel_mask, config);
    auto result = process.Run();

    CHECK_FALSE(result.cancelled);
    CHECK(result.images_processed == 6);

    reader.Close();
    remove("process_noout_in_master.h5");
    remove("process_noout_in_data_000001.h5");
    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}

TEST_CASE("Rugnux_Cancel", "[HDF5][Full]") {
    WriteTestDataset("process_cancel_in", 8);

    JFJochHDF5Reader reader;
    REQUIRE_NOTHROW(reader.ReadFile("process_cancel_in_master.h5"));
    auto dataset = reader.GetDataset();

    ProcessConfig config;
    config.mode = ProcessMode::AzimuthalIntegration;
    config.nthreads = 2;

    Rugnux process(reader, dataset->experiment, *dataset->pixel_mask, config);
    process.Cancel();   // cancel before running: the worker loop stops immediately
    auto result = process.Run();

    CHECK(result.cancelled);
    CHECK(result.images_processed == 0);

    reader.Close();
    remove("process_cancel_in_master.h5");
    remove("process_cancel_in_data_000001.h5");
    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}

// A rotation run that finds no lattice still reports every image - its spots, resolution and background,
// and that it did not index - as the canonical pass, and hands the same back with the failure.
TEST_CASE("Rugnux_NoLatticeReportsEveryImage", "[HDF5][Full]") {
    WriteTestDataset("process_nolattice_in", 8, true);

    JFJochHDF5Reader reader;
    REQUIRE_NOTHROW(reader.ReadFile("process_nolattice_in_master.h5"));
    auto dataset = reader.GetDataset();
    DiffractionExperiment x = dataset->experiment;
    auto indexing = x.GetIndexingSettings();
    indexing.RotationIndexing(true);
    indexing.Algorithm(IndexingAlgorithmEnum::Auto);
    x.ImportIndexingSettings(indexing);
    REQUIRE(x.IsRotationIndexing());

    struct Observer : RugnuxObserver {
        std::atomic<bool> canonical{false};
        std::mutex m;
        std::set<int64_t> images;
        bool complete = true;
        void OnImagePass(bool c) override { canonical = c; }
        void OnImageProcessed(const DataMessage &msg) override {
            if (!canonical)
                return;
            std::lock_guard lock(m);
            images.insert(msg.number);
            complete &= msg.spot_count.has_value() && msg.bkg_estimate.has_value()
                        && msg.indexing_result == false;
        }
    } observer;

    ProcessConfig config;
    config.nthreads = 2;
    config.rotation_indexing = true;
    config.rotation_postrefine_geometry = true;
    config.spot_finding = RugnuxDefaultSpotFinding(true);

    Rugnux process(reader, x, *dataset->pixel_mask, config);
    std::shared_ptr<ProcessResult> per_image;
    try {
        process.Run(&observer);
    } catch (const NoLatticeFound &e) {
        per_image = e.per_image;
    }
    REQUIRE(per_image);
    CHECK(per_image->images_processed == 8);
    CHECK(per_image->end_message.max_image_number == 8);
    REQUIRE(per_image->outputs);
    CHECK(per_image->outputs->process_start.has_value());
    CHECK(per_image->end_message.spot_count.size() == 8);
    CHECK(per_image->end_message.v_bkg_estimate.size() == 8);
    CHECK(observer.images.size() == 8);
    CHECK(observer.complete);

    reader.Close();
    remove("process_nolattice_in_master.h5");
    remove("process_nolattice_in_data_000001.h5");
    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}

// A calibration re-integrates its images binned about the geometry it fitted, and fits again. That
// second profile must be the sum over every image: here each of six frames carries a different sixth
// of the LaB6 rings, so a profile missing a frame is missing rings. The header's beam centre is 5 px
// out, far enough that the first pass's smeared profile loses to the re-binned one - so the geometry
// that comes out is the one fitted on the re-binned sum, and it must not depend on the thread count.
TEST_CASE("Rugnux_CalibrationRebinsEveryImage", "[HDF5][DetGeomCalib]") {
    RegisterHDF5Filter();
    constexpr int n = 6;
    constexpr float true_beam_x = 1090.0f, true_beam_y = 1100.0f;
    const std::vector<float> rings_q = CalibrantRings("lab6");

    DiffractionExperiment x(DetJF4M());
    x.FilePrefix("process_calib_in").ImagesPerTrigger(n).OverwriteExistingFiles(true);
    x.BitDepthImage(16).ImagesPerFile(n).SetFileWriterFormat(FileWriterFormat::NXmxVDS).PixelSigned(true);
    x.Compression(CompressionAlgorithm::NO_COMPRESSION);
    x.BeamX_pxl(true_beam_x).BeamY_pxl(true_beam_y).DetectorDistance_mm(100).IncidentEnergy_keV(WVL_1A_IN_KEV)
            .FrameTime(std::chrono::microseconds(500), std::chrono::microseconds(10));
    const DiffractionGeometry geom_true = x.GetDiffractionGeometry();
    x.BeamX_pxl(true_beam_x + 5.0f);   // what the header says

    // Radii of the rings the beam reaches, in pixels about the true centre.
    std::vector<float> ring_radius;
    for (const float q : rings_q) {
        const float d = static_cast<float>(2.0 * PI) / q;
        if (d > geom_true.GetWavelength_A() / 2.0f)
            ring_radius.push_back(geom_true.ResToPxl(d));
    }

    {
        StartMessage start_message;
        x.FillMessage(start_message);
        FileWriter file_set(start_message);
        ScanResultGenerator generator(x);
        std::vector<int16_t> image(x.GetPixelsNum());
        for (int i = 0; i < n; i++) {
            for (int64_t p = 0; p < x.GetPixelsNum(); p++) {
                const float px = static_cast<float>(p % x.GetXPixelsNum());
                const float py = static_cast<float>(p / x.GetXPixelsNum());
                const float r = std::hypot(px - true_beam_x, py - true_beam_y);
                float v = 5.0f;
                for (size_t k = i; k < ring_radius.size(); k += n) {
                    const float dr = r - ring_radius[k];
                    v += 400.0f * std::exp(-0.5f * dr * dr / (1.5f * 1.5f));
                }
                image[p] = static_cast<int16_t>(std::lround(v));
            }
            DataMessage message{};
            message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
            message.number = i;
            REQUIRE_NOTHROW(file_set.WriteHDF5(message));
            generator.Add(message);
        }
        EndMessage end_message;
        end_message.max_image_number = n;
        generator.FillEndMessage(end_message);
        file_set.WriteHDF5(end_message);
        file_set.Finalize();
    }

    JFJochHDF5Reader reader;
    REQUIRE_NOTHROW(reader.ReadFile("process_calib_in_master.h5"));
    auto dataset = reader.GetDataset();
    REQUIRE(dataset);
    DiffractionExperiment experiment(dataset->experiment);
    auto azint = experiment.GetAzimuthalIntegrationSettings();
    azint.AzimuthalBinCount(32);
    experiment.ImportAzimuthalIntegrationSettings(azint);

    std::vector<CalibrationResult> results;
    for (const int nthreads : {1, 4}) {
        ProcessConfig config;
        config.mode = ProcessMode::Calibration;
        config.calibrant_ring_q = rings_q;
        config.nthreads = nthreads;
        config.beam_center_check = false;
        config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
        config.spot_finding.indexing = false;

        Rugnux process(reader, experiment, *dataset->pixel_mask, config);
        ProcessResult result;
        REQUIRE_NOTHROW(result = process.Run());
        REQUIRE(result.calibration.has_value());
        results.push_back(*result.calibration);
    }

    for (const auto &cal : results) {
        CHECK(cal.converged);
        CHECK(cal.geometry.GetBeamX_pxl() == Catch::Approx(true_beam_x).margin(0.5));
        CHECK(cal.geometry.GetBeamY_pxl() == Catch::Approx(true_beam_y).margin(0.5));
    }
    CHECK(results[0].ring_points == results[1].ring_points);
    CHECK(results[0].rms_radial_pxl == results[1].rms_radial_pxl);
    CHECK(results[0].geometry.GetBeamX_pxl() == results[1].geometry.GetBeamX_pxl());
    CHECK(results[0].geometry.GetBeamY_pxl() == results[1].geometry.GetBeamY_pxl());
    CHECK(results[0].geometry.GetDetectorDistance_mm() == results[1].geometry.GetDetectorDistance_mm());

    reader.Close();
    remove("process_calib_in_master.h5");
    remove("process_calib_in_data_000001.h5");
    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}

TEST_CASE("RugnuxCommandLine_Full", "[process]") {
    DiffractionExperiment x(DetJF(1));
    IndexingSettings idx;
    idx.Algorithm(IndexingAlgorithmEnum::FFT);
    idx.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
    x.ImportIndexingSettings(idx);
    x.SpaceGroupNumber(96);

    ProcessConfig config;
    config.mode = ProcessMode::FullAnalysis;
    config.nthreads = 8;
    config.end_image = 500;
    config.rotation_indexing = true;
    config.two_pass_rotation = true;
    config.rotation_indexing_image_count = 30;
    config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();

    const std::string cmd = RugnuxCommandLine(config, x, "/data/test_master.h5", "run1", false);
    CHECK(cmd.rfind("rugnux", 0) == 0);
    CHECK(cmd.find("-N 8") != std::string::npos);
    CHECK(cmd.find("-e 500") != std::string::npos);
    CHECK(cmd.find("-o run1") != std::string::npos);
    CHECK(cmd.find("-X cufft") != std::string::npos);
    CHECK(cmd.find("-S 96") != std::string::npos);
    // -R takes an optional argument, so its value must be attached (-R30); a separate "-R 30" token
    // would not re-parse (getopt would leave 30 as a positional and drop the count).
    CHECK(cmd.find("-R30") != std::string::npos);
    CHECK(cmd.find("-R 30") == std::string::npos);
    CHECK(cmd.find("/data/test_master.h5") != std::string::npos);
    CHECK(cmd.find("--model") == std::string::npos);

    // --mr is --model with the search forced, and is given back as itself.
    auto model = std::make_shared<RugnuxModel>();
    model->name = "model.cif";
    config.model = model;
    CHECK(RugnuxCommandLine(config, x, "in.h5", "", false).find("--model model.cif") != std::string::npos);
    // A placed model is refined by default: only --no-refine is given back.
    CHECK(RugnuxCommandLine(config, x, "in.h5", "", false).find("--no-refine") != std::string::npos);
    config.refine = true;
    CHECK(RugnuxCommandLine(config, x, "in.h5", "", false).find("--no-refine") == std::string::npos);
    // The solvent build is off by default: only --refine-solvent is given back.
    CHECK(RugnuxCommandLine(config, x, "in.h5", "", false).find("--refine-solvent") == std::string::npos);
    config.refine_solvent = true;
    CHECK(RugnuxCommandLine(config, x, "in.h5", "", false).find("--refine-solvent") != std::string::npos);
    config.refine_solvent = false;
    config.force_mr = true;
    const std::string mr_cmd = RugnuxCommandLine(config, x, "in.h5", "", false);
    CHECK(mr_cmd.find("--mr model.cif") != std::string::npos);
    CHECK(mr_cmd.find("--model") == std::string::npos);
}

TEST_CASE("RugnuxDefaults_BareRun", "[process]") {
    // What both front ends (the rugnux CLI and the viewer's "Analyze dataset") start a run from.
    const SpotFindingSettings rot = RugnuxDefaultSpotFinding(true);
    const SpotFindingSettings stills = RugnuxDefaultSpotFinding(false);
    CHECK(rot.adaptive_threshold);
    CHECK(stills.adaptive_threshold);
    CHECK(rot.min_pix_per_spot == 2);
    CHECK(!stills.min_pix_per_spot.has_value());
    CHECK(!rot.high_resolution_limit.has_value());
    CHECK(rot.indexing);

    DiffractionExperiment x(DetJF(1));
    ApplyRugnuxExperimentDefaults(x);
    CHECK(x.GetPolarizationFactor() == 0.99f);
    CHECK(!x.GetBraggIntegrationSettings().GetBackgroundRadialCorrection().has_value());   // auto

    DiffractionExperiment rot_x = x, stills_x = x;
    ApplyRugnuxIntegrationRadii(rot_x, true);
    ApplyRugnuxIntegrationRadii(stills_x, false);
    CHECK(rot_x.GetBraggIntegrationSettings().GetR1() == BraggIntegrationSettings().GetR1());
    CHECK(stills_x.GetBraggIntegrationSettings().GetR1() == 6.0f);
    CHECK(stills_x.GetBraggIntegrationSettings().GetR3() == 14.0f);

    CHECK(RugnuxDetectIceRings(std::nullopt, true));
    CHECK(!RugnuxDetectIceRings(std::nullopt, false));
    CHECK(!RugnuxDetectIceRings(false, true));

    // A stationary axis is stills, the same test everywhere the workflow is decided.
    DiffractionExperiment still_axis = x, turning_axis = x;
    still_axis.Goniometer(GoniometerAxis("omega", 0.0f, 0.0f, Coord(1, 0, 0), std::nullopt));
    turning_axis.Goniometer(GoniometerAxis("omega", 0.0f, 0.1f, Coord(1, 0, 0), std::nullopt));
    CHECK(!RugnuxRotationData(x));
    CHECK(!RugnuxRotationData(still_axis));
    CHECK(RugnuxRotationData(turning_axis));
}

TEST_CASE("RugnuxCommandLine_AutomaticChoices", "[process]") {
    // A run left to rugnux's automatic choices must give back a command line that leaves them automatic:
    // -N, --max-spots and --integration-radius each switch one of them off.
    DiffractionExperiment x(DetJF(1));
    ProcessConfig config;
    config.mode = ProcessMode::FullAnalysis;
    config.nthreads = 8;
    config.nthreads_auto = true;
    config.measure_spot_budget = true;
    config.adaptive_integration_radius = true;
    config.rotation_indexing = true;

    const std::string cmd = RugnuxCommandLine(config, x, "in.h5", "", false);
    CHECK(cmd.find("-N ") == std::string::npos);
    CHECK(cmd.find("--max-spots") == std::string::npos);
    CHECK(cmd.find("--integration-radius") == std::string::npos);

    config.nthreads_auto = false;
    config.measure_spot_budget = false;
    config.adaptive_integration_radius = false;
    const std::string pinned = RugnuxCommandLine(config, x, "in.h5", "", false);
    CHECK(pinned.find("-N 8") != std::string::npos);
    CHECK(pinned.find("--max-spots") != std::string::npos);
    CHECK(pinned.find("--integration-radius") != std::string::npos);
}

TEST_CASE("RugnuxCommandLine_AzInt", "[process]") {
    DiffractionExperiment x(DetJF(1));
    AzimuthalIntegrationSettings a;
    a.AzimuthalBinCount(4);
    x.ImportAzimuthalIntegrationSettings(a);

    ProcessConfig config;
    config.mode = ProcessMode::AzimuthalIntegration;
    config.nthreads = 2;

    const std::string cmd = RugnuxCommandLine(config, x, "in.h5", "az", false);
    CHECK(cmd.rfind("rugnux", 0) == 0);
    CHECK(cmd.find("--mode azint") != std::string::npos);
    CHECK(cmd.find("--azim-phi-bins 4") != std::string::npos);
    CHECK(cmd.find("--azim-min-q") != std::string::npos);
    CHECK(cmd.find("in.h5") != std::string::npos);
}

namespace {
    // A field of identical round Gaussian spots on three rings, so that the width estimator sees
    // several resolution bands with the same true width and its 1/d fit has to come back flat.
    void PaintGaussianSpots(ImagePreprocessorBuffer &image, int w, double sigma, double total_counts,
                            std::vector<DiffractionSpot> &spots) {
        constexpr int BKG = 3;
        for (size_t i = 0; i < image.size(); i++) image[i] = BKG;
        const double amp = total_counts / (2.0 * M_PI * sigma * sigma);
        for (int radius : {150, 350, 550})
            for (int k = 0; k < 20; k++) {
                const double phi = 2.0 * M_PI * k / 20.0 + 0.1 * radius;
                const int cx = static_cast<int>(std::lround(600 + radius * std::cos(phi)));
                const int cy = static_cast<int>(std::lround(600 + radius * std::sin(phi)));
                for (int dy = -14; dy <= 14; dy++)
                    for (int dx = -14; dx <= 14; dx++)
                        image[static_cast<size_t>(cy + dy) * w + (cx + dx)] +=
                                static_cast<int32_t>(std::lround(
                                        amp * std::exp(-(dx * dx + dy * dy) / (2.0 * sigma * sigma))));
                spots.emplace_back(static_cast<uint32_t>(cx), static_cast<uint32_t>(cy),
                                   static_cast<int64_t>(total_counts));
            }
    }
}

// The width the adaptive integration radius is set from. A round Gaussian of width sigma holds 80 %
// of its flux inside sqrt(2 ln 5) * sigma = 1.794 * sigma, and that is what the estimator has to
// return - over an aperture that owes nothing to the integrator's r1, which is the whole point of
// measuring it here rather than reading the integrator's own second moment.
TEST_CASE("SpotWidth_Gaussian", "[process]") {
    constexpr int W = 1200, H = 1200;
    DiffractionGeometry geometry;
    geometry.BeamX_pxl(600).BeamY_pxl(600).DetectorDistance_mm(200).PixelSize_mm(0.075)
            .Wavelength_A(1.0);

    for (double sigma : {1.0, 2.2}) {
        ImagePreprocessorBuffer image(static_cast<size_t>(W) * H);
        std::vector<DiffractionSpot> spots;
        PaintGaussianSpots(image, W, sigma, 20000.0, spots);

        std::vector<spot_width::FluxCurve> curves;
        MeasureSpotFluxCurves(image, W, H, geometry, DetectorModules(), spots, curves);
        REQUIRE(curves.size() >= 45);

        const auto r80 = spot_width::R80AtReference(curves);
        REQUIRE(r80.has_value());
        CHECK(*r80 == Catch::Approx(1.794 * sigma).margin(0.3));
    }

    // The rule the measurement drives: the shipped radius below the line, the capped one above it.
    CHECK(spot_width::R1ForWidth(1.0f) == 4.0f);
    CHECK(spot_width::R1ForWidth(1.794f) == 4.0f);
    CHECK(spot_width::R1ForWidth(2.4f) == 5.0f);
    CHECK(spot_width::R1ForWidth(3.947f) == 6.0f);
    CHECK(spot_width::R1ForWidth(9.0f) == 6.0f);
}

// The rotation two-pass quality guard. The refined pass is sent back to the header geometry only for
// a decisive loss of signal - reflections at I/sigma >= 2 net of the noise tail at <= -2 - over no
// more of reciprocal space.
TEST_CASE("DoubledCellDecision", "[process]") {
    // Shells of the supercell probe's trend: d range, excess over the null, z, the strongest null z and
    // the lattice's <I/sigma>.
    const auto trend = [](std::vector<std::array<double, 3>> excess_z_lattice) {
        ProcessResult::SupercellClass sc;
        float d = 20.0f;
        for (const auto &[excess, z, lattice] : excess_z_lattice) {
            ProcessResult::SupercellClass::Shell sh;
            sh.d_low_A = d;
            sh.d_high_A = d *= 0.7f;
            sh.excess = excess;
            sh.z = z;
            sh.sibling_z = 3.0;
            sh.lattice_i_over_sigma = lattice;
            sh.resolved = 0.9;
            sc.trend.push_back(sh);
        }
        return sc;
    };
    // A pseudo-translation that breaks down: weak at low resolution, a third of the lattice where the
    // lattice is still measured.
    const auto breaks_down = trend({{0.02, 17, 18}, {0.10, 38, 7}, {0.26, 36, 6}, {0.35, 45, 2.4}, {0.46, 33, 0.8}});
    CHECK(DoubledCellWorthMerging(breaks_down));
    CHECK(!DoubledCellRises(breaks_down).empty());
    // A class that stays a tenth of the lattice at every resolution: merged as well, but it does not rise.
    const auto flat = trend({{0.09, 10, 70}, {0.11, 23, 28}, {0.10, 24, 33}, {0.11, 24, 18}, {0.10, 23, 8}});
    CHECK(DoubledCellWorthMerging(flat));
    CHECK(DoubledCellRises(flat).empty());
    // A class no stronger than the null: nothing.
    const auto null_class = trend({{0.01, 4, 20}, {0.02, 5, 10}, {0.03, 2, 5}, {0.05, 1, 2}});
    CHECK(!DoubledCellWorthMerging(null_class));
    // A class that rises significantly but stays a few percent of the lattice: the half cell holds.
    const auto small = trend({{0.009, 40, 500}, {0.014, 60, 300}, {0.016, 90, 170}, {0.03, 60, 50}, {0.06, 40, 2}});
    CHECK(DoubledCellRises(small).empty());
    // The weak-sweep arm speaks only where the probe measures the lattice in no shell.
    CHECK(!DoubledCellWorthMergingWeak(breaks_down));
    CHECK(!DoubledCellWorthMergingWeak(flat));
    // Lattice unmeasured on the probe's frames: the class clears the null (z > 2 x 3) in two shells.
    const auto weak = trend({{0.12, 2.4, 0.3}, {0.37, 2.8, 0.0}, {0.62, 6.8, 0.0}, {0.56, 7.0, 0.0}});
    CHECK(!DoubledCellWorthMerging(weak));
    CHECK(DoubledCellWorthMergingWeak(weak));
    // ... and in one shell only: not enough.
    const auto weak_one = trend({{0.12, 2.4, 0.3}, {0.37, 2.8, 0.0}, {0.62, 6.8, 0.0}, {0.56, 4.0, 0.0}});
    CHECK(!DoubledCellWorthMergingWeak(weak_one));
}

TEST_CASE("MergedDoubledClassTrend", "[process]") {
    // A doubled cell whose l-odd class is a fifth of the l-even intensity at low resolution and all of it
    // at high: the trend reads the ratio per probe shell, and rises.
    const UnitCell doubled{50, 60, 140, 90, 90, 90}, half{50, 60, 70, 90, 90, 90};
    const auto parity = DoubledClassParity(doubled, half, 'P');
    REQUIRE(parity.has_value());
    CHECK((*parity == std::array<int, 3>{0, 0, 1}));
    std::mt19937 rng(7);
    std::exponential_distribution<double> wilson(1.0);
    std::vector<MergedReflection> merged;
    for (int h = 0; h <= 20; h++)
        for (int k = 0; k <= 24; k++)
            for (int l = 0; l <= 56; l++) {
                const double s2 = h * h / 2500.0 + k * k / 3600.0 + l * l / 19600.0;
                if (s2 <= 0.0 || s2 > 1.0 / (2.5 * 2.5))
                    continue;
                MergedReflection r;
                r.h = h; r.k = k; r.l = l;
                r.d = static_cast<float>(1.0 / std::sqrt(s2));
                const double t = std::clamp((1.0 / 8.0 - 1.0 / r.d) / (1.0 / 8.0 - 1.0 / 2.5), 0.0, 1.0);
                const double share = (l % 2) ? 0.2 + 0.8 * t : 1.0;
                r.I = static_cast<float>(100.0 * share * wilson(rng));
                r.sigma = 5.0f;
                merged.push_back(r);
            }
    ProcessResult::SupercellClass sc;
    sc.trend = MergedDoubledClassTrend(merged, *parity);
    REQUIRE(sc.trend.size() >= 4);
    CHECK(sc.trend.front().excess < 0.4);
    CHECK(sc.trend.back().excess > 0.7);
    CHECK(!DoubledCellRises(sc).empty());
}

TEST_CASE("FitDoubledClassTranslation", "[process]") {
    // A doubled orthorhombic cell whose two halves are one copy translated by c/2 + (0.03, 0, 0): the
    // reflections with l odd carry |F|^2 sin^2(pi h.eps), the others cos^2. With nothing else on the
    // added class the fit finds the translation and leaves nothing over; with a flat 0.3 added to
    // the class, most of the class is left unexplained.
    const UnitCell doubled{50, 60, 140, 90, 90, 90}, half{50, 60, 70, 90, 90, 90};
    std::mt19937 rng(1);
    std::exponential_distribution<double> wilson(1.0);
    std::vector<MergedReflection> clean, contaminated;
    for (int h = -25; h <= 25; h++)
        for (int k = 0; k <= 30; k++)
            for (int l = 0; l <= 70; l++) {
                if (h == 0 && k == 0 && l == 0)
                    continue;
                MergedReflection r;
                r.h = h; r.k = k; r.l = l;
                r.d = 1.0f / std::sqrt(static_cast<float>(h * h / 2500.0 + k * k / 3600.0 + l * l / 19600.0));
                if (r.d < 2.0f)
                    continue;
                const double base = wilson(rng), x = std::pow(std::sin(PI * 0.03 * h), 2);
                r.I = static_cast<float>(base * ((l & 1) ? x : 1.0 - x));
                clean.push_back(r);
                if (l & 1)
                    r.I += 0.3f;
                contaminated.push_back(r);
            }
    const DoubledClassTranslation a = FitDoubledClassTranslation(clean, doubled, half);
    REQUIRE(a.tested);
    CHECK(a.parity == std::array<int, 3>{0, 0, 1});
    const DoubledClassTranslation b = FitDoubledClassTranslation(contaminated, doubled, half);
    REQUIRE(b.tested);
    const auto weakest = [](const DoubledClassTranslation &t) {
        double w = INFINITY;
        for (const auto &sh : t.shells)
            w = std::min(w, sh.modulated_share);
        return w;
    };
    CHECK(weakest(a) > 0.8);
    CHECK(weakest(b) < 0.5);

    // A small sample - a few hundred added reflections, below the probe arm's floor of 1000: refused at that
    // floor, fitted without it, and then the share over all shells, two standard errors down, decides. Over
    // all shells a flat 0.3 is too little to tell from noise on this many reflections; a class that is
    // mostly flat (1.0 added) is told.
    std::vector<MergedReflection> small_clean, small_contaminated;
    for (size_t i = 0; i < clean.size(); i += 30) {
        small_clean.push_back(clean[i]);
        small_contaminated.push_back(clean[i]);
        if (clean[i].l & 1)
            small_contaminated.back().I += 1.0f;
    }
    CHECK(!FitDoubledClassTranslation(small_clean, doubled, half).tested);
    const DoubledClassTranslation c = FitDoubledClassTranslation(small_clean, doubled, half, 'P', 0);
    const DoubledClassTranslation e = FitDoubledClassTranslation(small_contaminated, doubled, half, 'P', 0);
    REQUIRE(c.tested);
    REQUIRE(e.tested);
    CHECK(c.share_se > 0.0);
    CHECK(c.share - 2.0 * c.share_se >= 0.5);
    CHECK(e.share - 2.0 * e.share_se < 0.5);
}

TEST_CASE("RefinedPassIsWorse", "[process]") {
    const auto pass = [](const UnitCell &cell, char centering, int64_t strong, int64_t negative,
                         int64_t reflections) {
        ProcessResult r;
        r.has_merge_statistics = true;
        r.consensus_cell = cell;
        r.consensus_centering = centering;
        r.search_merge_strong_reflections = strong;
        r.search_merge_negative_reflections = negative;
        r.search_merge_reflections = reflections;
        return r;
    };
    const UnitCell cell{50.0f, 60.0f, 70.0f, 90.0f, 90.0f, 90.0f};

    // Same lattice: a loss of more than 10 % of the signal is decisive, a smaller one is not.
    const ProcessResult header = pass(cell, 'P', 50000, 1000, 200000);
    CHECK(!RefinedPassIsWorse(header, pass(cell, 'P', 40000, 1000, 200000)).empty());
    CHECK(RefinedPassIsWorse(header, pass(cell, 'P', 46000, 1000, 200000)).empty());
    // ... unless the refined pass reaches into more of reciprocal space: a dilution, not a loss.
    CHECK(RefinedPassIsWorse(header, pass(cell, 'P', 40000, 1000, 420000)).empty());

    // The header pass on a 7x supercell: seven times the reflections, six in seven of them empty,
    // and their noise tail alone reaches the strong count. Raw, 120k against 80k would read as a
    // decisive loss for the refined pass on the crystal's own lattice; net of the noise it is none.
    const UnitCell supercell{350.0f, 60.0f, 70.0f, 90.0f, 90.0f, 90.0f};
    const ProcessResult on_supercell = pass(supercell, 'P', 120000, 40000, 1400000);
    CHECK(RefinedPassIsWorse(on_supercell, pass(cell, 'P', 80000, 1500, 200000)).empty());

    // The rescue the guard is there for is kept: a refined pass that drops to a sub-cell of the
    // header's lattice loses the reflections the sub-cell cannot index. Half the volume, half the
    // reflections - the same coverage - and half the signal.
    const UnitCell subcell{25.0f, 60.0f, 70.0f, 90.0f, 90.0f, 90.0f};
    CHECK(!RefinedPassIsWorse(header, pass(subcell, 'P', 25500, 500, 100000)).empty());

    // A centred setting of the same lattice counts only the reflections its centring allows, so the
    // counts compare as they are; the primitive volume puts the coverage on the same footing.
    const UnitCell doubled{100.0f, 60.0f, 70.0f, 90.0f, 90.0f, 90.0f};
    CHECK(RefinedPassIsWorse(header, pass(doubled, 'C', 49000, 1000, 200000)).empty());
    CHECK(!RefinedPassIsWorse(header, pass(doubled, 'C', 40000, 1000, 200000)).empty());

    // The axial arm: half of the low-order axial rows lost in the same setting, with no more signal.
    ProcessResult lost_rows = pass(cell, 'P', 50000, 1000, 200000);
    ProcessResult with_rows = header;
    with_rows.search_merge_axial_reflections = 16;
    lost_rows.search_merge_axial_reflections = 8;
    CHECK(!RefinedPassIsWorse(with_rows, lost_rows).empty());

    // A refined pass that left a twin overlap of index 3 out of integration merged two thirds of the
    // nodes: two thirds of the signal is no loss, and its axial rows are not the header pass's rows.
    ProcessResult twin = pass(cell, 'P', 34000, 700, 132000);
    twin.twin_overlap_index = 3;
    twin.search_merge_axial_reflections = 10;
    CHECK(RefinedPassIsWorse(with_rows, twin).empty());
    twin.search_merge_strong_reflections = 28000;
    CHECK(!RefinedPassIsWorse(with_rows, twin).empty());
}

// The beam-centre arbitration between a first pass at the file's centre and one at the measured
// centre. Two arms on the same lattice are two geometries of one hypothesis: they are judged on the
// signal each measured, not on a CC1/2 that reads the same on both.
TEST_CASE("MeasuredCentreWins", "[process]") {
    const auto arm = [](const UnitCell &cell, gemmi::CrystalSystem system, double cc_half, int64_t strong) {
        ProcessResult r;
        r.has_merge_statistics = true;
        r.consensus_cell = cell;
        r.consensus_centering = 'P';
        r.rotation_lattice_type = LatticeMessage{'P', 0, system};
        r.search_merge_cc_half = cc_half;
        r.search_merge_strong_reflections = strong;
        r.search_merge_reflections = 40000;
        return r;
    };
    const UnitCell triclinic{40.0f, 41.0f, 100.0f, 86.0f, 84.0f, 72.0f};
    // The same lattice in the setting with a and b exchanged, as a noisy a ~ b can come out.
    const UnitCell swapped{41.02f, 39.98f, 100.1f, 84.0f, 86.0f, 72.0f};
    const auto tri = gemmi::CrystalSystem::Triclinic;

    const ProcessResult file = arm(triclinic, tri, 0.87, 9000);
    REQUIRE(ArmsHoldSameLattice(file, arm(swapped, tri, 0.87, 9000)));

    // Same lattice, same CC1/2: the arm that measured more signal wins, whichever centre it is...
    CHECK(!MeasuredCentreWins(file, arm(swapped, tri, 0.87, 9500)).empty());
    CHECK(MeasuredCentreWins(file, arm(swapped, tri, 0.87, 8500)).empty());
    // ...but not by less than twice the Poisson noise of the two counts (sqrt(18100) = 135)...
    CHECK(MeasuredCentreWins(file, arm(swapped, tri, 0.87, 9100)).empty());
    // ...a tie keeps the file's centre, and a higher CC1/2 alone does not move it.
    CHECK(MeasuredCentreWins(file, arm(swapped, tri, 0.99, 9000)).empty());

    // Different lattices: the metric question, decided on the search merges.
    const UnitCell monoclinic{57.0f, 42.0f, 100.0f, 90.0f, 95.0f, 90.0f};
    const auto mono = gemmi::CrystalSystem::Monoclinic;
    REQUIRE(!ArmsHoldSameLattice(file, arm(monoclinic, mono, 0.87, 9000)));
    CHECK(!MeasuredCentreWins(file, arm(monoclinic, mono, 0.95, 9000)).empty());
    CHECK(MeasuredCentreWins(file, arm(monoclinic, mono, 0.88, 20000)).empty());
}

TEST_CASE("MeasuredCentreClearlyLoses", "[process]") {
    // Same lattice: the measured centre loses only where it is behind on the signal by more than the
    // Poisson noise of the two counts AND its inner shell does not agree better by the margin.
    const SearchMergeSignal file{.strong = 9000, .reflections = 40000, .cc_half = 0.9,
                                 .inner_cc_half = 0.98, .inner_reflections = 2000};
    SearchMergeSignal m = file;
    m.strong = 8500;   // 500 behind, noise sqrt(17500) = 132
    CHECK(MeasuredCentreClearlyLoses(file, m, true, 2.0));
    m.strong = 8800;   // 200 behind: within two sigmas
    CHECK_FALSE(MeasuredCentreClearlyLoses(file, m, true, 2.0));
    // A file centre whose few inner reflections disagree: the measured centre's inner shell might
    // still carry it, so behind on the signal is not yet a loss.
    SearchMergeSignal inconsistent = file;
    inconsistent.inner_cc_half = 0.6;
    inconsistent.inner_reflections = 20;
    m.strong = 8500;
    m.inner_cc_half = 0.64;
    m.inner_reflections = 20;
    CHECK_FALSE(MeasuredCentreClearlyLoses(inconsistent, m, true, 2.0));

    // Different lattices: the count alone - the subset's CC1/2 is not read.
    SearchMergeSignal d = file;
    d.strong = 3000;
    d.cc_half = 0.99;
    CHECK(MeasuredCentreClearlyLoses(file, d, false, 2.0));
    d.strong = 8900;   // 100 behind: within two sigmas
    d.cc_half = 0.50;
    CHECK_FALSE(MeasuredCentreClearlyLoses(file, d, false, 2.0));
    // A merge with no strong reflection in it measured none of the crystal. (An arm without a merge
    // is never asked: RunAllPasses judges it on all the frames.)
    CHECK(MeasuredCentreClearlyLoses(file, SearchMergeSignal{}, false, 2.0));
}

TEST_CASE("ResolvableAxisLength", "[LongAxis]") {
    // 500 mm, 1 A, 100 um pixels, 2 px spots: rows of a 2500 A axis are still a spot apart.
    CHECK(ResolvableAxisLength_A(500.0f, 1.0f, 0.1f, 2.0f) == Catch::Approx(2500.0));
    // A short distance and large pixels resolve only a protein-sized axis: the hypothesis is not asked.
    CHECK(ResolvableAxisLength_A(180.0f, 1.0f, 0.172f, 3.0f) < 500.0f);
    // Twice the distance, twice the axis; twice the spot width, half of it.
    CHECK(ResolvableAxisLength_A(400.0f, 1.0f, 0.075f, 2.0f)
          == Catch::Approx(2.0 * ResolvableAxisLength_A(200.0f, 1.0f, 0.075f, 2.0f)));
    CHECK(ResolvableAxisLength_A(200.0f, 1.0f, 0.075f, 4.0f)
          == Catch::Approx(0.5 * ResolvableAxisLength_A(200.0f, 1.0f, 0.075f, 2.0f)));
}

TEST_CASE("IsSuperLattice", "[LongAxis]") {
    const CrystalLattice cell(60.0f, 70.0f, 200.0f, 90.0f, 95.0f, 90.0f);
    const Coord a = cell.Vec0(), b = cell.Vec1(), c = cell.Vec2();
    // An exact index-4 supercell in another basis: every node of it is a node of the cell.
    const CrystalLattice super(a * 2.0f, b + a, c * 2.0f);
    CHECK(IsSuperLattice(super, cell));
    // The relation runs one way: the cell is a SUB-lattice of its supercell, not a superlattice.
    CHECK_FALSE(IsSuperLattice(cell, super));
    // The same lattice in another basis is not a superlattice of itself.
    CHECK_FALSE(IsSuperLattice(CrystalLattice(a, b + a, c - b), cell));
    // A cell 1.37x longer along c - the volume of a wrong long axis against the true one - is not
    // related to it at all, in either direction.
    const CrystalLattice longer(a, b, c * 1.37f);
    CHECK_FALSE(IsSuperLattice(longer, cell));
    CHECK_FALSE(IsSuperLattice(cell, longer));
    // A 4.06x volume that is not exact (a triclinic cell near a 4x multiple) is not a superlattice.
    CHECK_FALSE(IsSuperLattice(CrystalLattice(a * 2.0f, b + a * 0.5f, c * 2.03f), cell));
}

TEST_CASE("LongAxisChoice_PooledSpotsNotFrames", "[LongAxis]") {
    // Shares of 10000 pooled spots; `reflections` is what the beats-chance test reads.
    const auto ev = [](int64_t on, int64_t chance) {
        return ValidationSpotEvidence{.spots = 10000, .on_lattice = on, .by_chance = chance,
                                      .reflections = on, .reflections_by_chance = chance};
    };
    // The standing lattice takes 20% of the spots. A long-axis cell taking 60% is adopted.
    const ValidationSpotEvidence standing = ev(2000, 60);
    CHECK(LongAxisChoice(standing, {{ev(6000, 60), false}}) == std::optional<size_t>(0));
    // Of two candidates the one with more spots beyond chance wins - not the first, not the longer.
    CHECK(LongAxisChoice(standing, {{ev(3900, 50), false}, {ev(7800, 50), false}}) == std::optional<size_t>(1));
    // One with a large share by chance is credited only the excess.
    CHECK(LongAxisChoice(standing, {{ev(6000, 4500), false}, {ev(5000, 50), false}}) == std::optional<size_t>(1));
    // Within the noise of the standing share, the standing lattice is kept.
    CHECK_FALSE(LongAxisChoice(standing, {{ev(2050, 60), false}}).has_value());
    // A superlattice of the standing cell is not adopted on the pooled count, which is biased toward it.
    CHECK_FALSE(LongAxisChoice(standing, {{ev(6000, 60), true}}).has_value());
    CHECK(LongAxisChoice(standing, {{ev(9000, 60), true}, {ev(5000, 60), false}}) == std::optional<size_t>(1));
    // A standing pass with no lattice is zero evidence; a candidate must still beat chance.
    CHECK(LongAxisChoice({}, {{ev(3000, 60), false}}) == std::optional<size_t>(0));
    CHECK_FALSE(LongAxisChoice({}, {{ev(50, 60), false}}).has_value());
    CHECK_FALSE(LongAxisChoice(standing, {}).has_value());
}

// The sub-lattice decision: the standing cell's spots on the nodes the sub-lattice drops, against what
// a wrong spindle angle puts on them.
TEST_CASE("SubLatticeSuffices", "[process]") {
    // A sub-lattice that beats chance by far.
    const ValidationSpotEvidence sub{.spots = 1400, .on_lattice = 340, .by_chance = 5, .reflections = 300,
                                     .reflections_by_chance = 30};
    // The dropped nodes hold what chance puts there, or a few more within its noise: halve.
    CHECK(SubLatticeSuffices(3, 2.5, sub));
    CHECK(SubLatticeSuffices(7, 2.5, sub));   // 4.5 over, 3.29 sqrt(2.5) = 5.2
    // A class of its own (a superstructure, a pseudo-translation, or half of a correct protein cell's
    // reflections): keep the standing cell.
    CHECK_FALSE(SubLatticeSuffices(12, 2.5, sub));
    CHECK_FALSE(SubLatticeSuffices(4000, 70.0, sub));
    // A sub-lattice that does not beat chance is no hypothesis.
    const ValidationSpotEvidence chance{.spots = 1400, .on_lattice = 10, .by_chance = 9, .reflections = 10,
                                        .reflections_by_chance = 45};
    CHECK_FALSE(SubLatticeSuffices(0, 2.5, chance));
}

// Two domains of a monoclinic cell twinned by a twofold about c*. With c cos(beta) = -a/4 the twin
// takes c to c + a/2, so the domains coincide on the reflections with h even and their coincidence
// lattice doubles c; any supercell of that one also indexes both. A synthetic cell.
TEST_CASE("TwinCompositeAt", "[process]") {
    const float beta = std::acos(-1.0f / 6.0f) * 180.0f / static_cast<float>(M_PI);
    const CrystalLattice domain(6.0f, 8.0f, 9.0f, 90.0f, beta, 90.0f);
    const Coord a = domain.Vec0(), b = domain.Vec1(), c = domain.Vec2();
    const Coord u = domain.Cstar() * (1.0f / domain.Cstar().Length());
    const auto twin = [&](const Coord &q) { return u * (2.0f * (q * u)) - q; };
    std::vector<Coord> cloud, single;
    for (int h = -4; h <= 4; h++)
        for (int k = -4; k <= 4; k++)
            for (int l = -4; l <= 4; l++) {
                if (h == 0 && k == 0 && l == 0)
                    continue;
                const Coord q = domain.Astar() * h + domain.Bstar() * k + domain.Cstar() * l;
                if (q.Length() > 1.0f)
                    continue;
                cloud.push_back(q);
                cloud.push_back(twin(q));
                single.push_back(q);
            }
    const auto indices = [](const CrystalLattice &s, const std::vector<Coord> &qs) {
        std::vector<std::array<int, 3>> hkl;
        for (const auto &q : qs)
            hkl.push_back({static_cast<int>(std::lround(s.Vec0() * q)), static_cast<int>(std::lround(s.Vec1() * q)),
                           static_cast<int>(std::lround(s.Vec2() * q))});
        return hkl;
    };
    const auto same_cell = [](const CrystalLattice &x, const CrystalLattice &y) {
        const auto ux = x.GetUnitCell(), uy = y.GetUnitCell();
        return std::abs(ux.a - uy.a) < 0.01f && std::abs(ux.b - uy.b) < 0.01f && std::abs(ux.c - uy.c) < 0.01f
               && std::abs(std::abs(std::cos(ux.beta * M_PI / 180.0)) - std::abs(std::cos(uy.beta * M_PI / 180.0))) < 1e-3;
    };
    const CrystalLattice reduced = domain.NiggliReduce();

    // The coincidence lattice, index 2.
    const CrystalLattice doubled = CrystalLattice(a, b, c * 2.0f).NiggliReduce();
    const auto at2 = TwinCompositeAt(doubled, indices(doubled, cloud), 2, 0.01);
    REQUIRE(at2.has_value());
    CHECK(at2->composite);
    CHECK(at2->neither == 0);
    CHECK(at2->p_both == Catch::Approx(0.25));
    CHECK(same_cell(at2->domain, reduced));
    // The twin law, a twofold up to the lattice's own rotations (about c*, or about a, which the
    // monoclinic twofold about b takes it to): either reverses b, so 0k0 is its own partner's Friedel
    // mate and is kept.
    REQUIRE(at2->rotation.has_value());
    const RotMatrix &r = *at2->rotation;
    CHECK(r.Column(0).x + r.Column(1).y + r.Column(2).z == Catch::Approx(-1.0f).margin(1e-3));
    CHECK(((r * b) + b).Length() < 1e-3f * b.Length());
    // The twin fraction from the intensity of the spots on one domain alone: domain two at half the
    // intensity of domain one is a third of the crystal (which domain comes first is the count's tie).
    std::vector<float> intensity;
    for (size_t i = 0; i < cloud.size(); i++)
        intensity.push_back(i % 2 ? 0.5f : 1.0f);
    const auto weighted = TwinCompositeAt(doubled, indices(doubled, cloud), 2, 0.01, intensity);
    REQUIRE(weighted.has_value());
    CHECK(std::min(weighted->fraction, 1.0 - weighted->fraction) == Catch::Approx(1.0 / 3.0).margin(1e-3));

    // A skewed index-5 supercell of it: the domains are index-10 sub-lattices, among them forms with no
    // coefficient prime to 10.
    const CrystalLattice skewed = CrystalLattice(a * 2.0f + b, b * 2.0f - a, c * 2.0f).NiggliReduce();
    const auto at10 = TwinCompositeAt(skewed, indices(skewed, cloud), 10, 0.01);
    REQUIRE(at10.has_value());
    CHECK(at10->composite);
    CHECK(at10->neither == 0);
    CHECK(same_cell(at10->domain, reduced));

    // The same two domains with the class on neither holding far more than the chance share says it
    // can (a share of 1% of the spots by chance): not two domains.
    auto crowded = indices(doubled, cloud);
    const size_t n_domains = crowded.size();
    // Spots on nodes of every class, as strays fall: a quarter of the nodes are on neither.
    std::mt19937 rng(7);
    std::uniform_int_distribution<int> index(-6, 6);
    for (int i = 0; i < 400; i++)
        crowded.push_back({index(rng), index(rng), index(rng)});
    const auto with_neither = TwinCompositeAt(doubled, crowded, 2, 0.01);
    REQUIRE(with_neither.has_value());
    CHECK(with_neither->neither_expected == Catch::Approx(0.01 * (n_domains + 400) * 0.25));
    CHECK_FALSE(with_neither->composite);

    // One domain alone on the doubled cell: one lattice, not a composite.
    const auto alone = TwinCompositeAt(doubled, indices(doubled, single), 2, 0.01);
    CHECK(!(alone.has_value() && alone->composite));
}