Jungfraujoch/tools/jfjoch_process.cpp

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#include <algorithm>
#include <atomic>
#include <csignal>
#include <getopt.h>
#include <iostream>
#include <sstream>
#include <string>
#include <vector>

#include "../reader/JFJochHDF5Reader.h"
#include "../common/Logger.h"
#include "../common/DiffractionExperiment.h"
#include "../common/PixelMask.h"
#include "../common/print_license.h"
#include "../image_analysis/LoadFCalcFromMtz.h"
#include "../process/JFJochProcess.h"

void print_usage() {
    std::cout << "Usage jfjoch_process {<options>} <input.h5>" << std::endl;
    std::cout << "Options:" << std::endl;
    std::cout << "   -o, --output-prefix <txt>        Output file prefix (default: output)" << std::endl;
    std::cout << "   -N, --threads <num>              Number of threads (default: 1)" << std::endl;
    std::cout << "   -s, --start-image <num>          Start image number (default: 0)" << std::endl;
    std::cout << "   -e, --end-image <num>            End image number (default: all)" << std::endl;
    std::cout << "   -t, --stride <num>               Image stride (default: 1)" << std::endl;
    std::cout << "   -v, --verbose                    Verbose output" << std::endl;
    std::cout << std::endl;

    std::cout << "  Spot finding" << std::endl;
    std::cout << "   --spot-sigma <num>               Noise sigma level for spot finding (default: 3.0)" << std::endl;
    std::cout << "   --spot-threshold <num>           Photon count threshold for spot finding (default: 10)" << std::endl;
    std::cout << "   --spot-high-resolution <num>     High resolution limit for spot finding (default: 1.5)" << std::endl;
    std::cout << "   --max-spots <num>                Max spot count (default: 250)" << std::endl;
    std::cout << std::endl;

    std::cout << "  Indexing" << std::endl;
    std::cout << "   -R, --two-pass-rotation[=num]    Two-pass offline rotation indexing (optional: number of images, default: 100)" << std::endl;
    std::cout << "   --single-pass-rotation[=num]     Use online-like single-pass rotation indexing (optional: min angular range deg)" << std::endl;
    std::cout << "   --redo-rotation-spots            Redo spot finding for two-pass rotation indexing" << std::endl;
    std::cout << "   --force-rotation-lattice <vec>   Force rotation indexer with external lattice (in Angstrom) : \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, skips first pass)" << std::endl;
    std::cout << "   -X, --indexing-algorithm <txt>   Indexing algorithm (FFBIDX|FFT|FFTW|Auto|None)" << std::endl;
    std::cout << "   -S, --space-group <num>          Space group number - used for both indexing and scaling" << std::endl;
    std::cout << "   -C, --unit-cell <cell>           Fix reference unit cell: \"a,b,c,alpha,beta,gamma\"" << std::endl;
    std::cout << "   -r, --refine <txt>               Geometry refinement algorithm (none|orientation|beam_and_lattice|pixelrefine)" << std::endl;
    std::cout << std::endl;

    std::cout << "  Scaling and merging" << std::endl;
    std::cout << "   -M, --scale-merge               Scale and merge (refine mosaicity) and write scaled.hkl + image.dat" << std::endl;
    std::cout << "   --scale-fulls                   After -P rot3d combine, refit a per-frame scale on the fulls (XDS order, Unity model); implies -M" << std::endl;
    std::cout << "   -P, --partiality <txt>          Partiality model fixed|rot|rot3d|unity (default: fixed). rot3d = rot + 3D combine of per-frame partials" << std::endl;
    std::cout << "   -A, --anomalous                 Anomalous mode (don't merge Friedel pairs)" << std::endl;
    std::cout << "   -B, --refine-bfactor            Refine per image B-factor" << std::endl;
    std::cout << "   -w, --wedge[=num]               Refine image wedge during scaling with starting wedge value" << std::endl;
    std::cout << "   --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" << std::endl;
    std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
    std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median (default: off; e.g. 6, XDS/DIALS-style)" << std::endl;
    std::cout << "   --reject-delta-cchalf <num>     Per-crystal CC1/2-delta rejection: drop images with deltaCChalf below mean - N*stddev (default: off; e.g. 2.5)" << std::endl;
    std::cout << "   --min-image-cc <num>            Per-image CC limit in percent (default: no limit)" << std::endl;
    std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
    std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
    std::cout << "   -z, --reference-mtz <file>      Reference MTZ file" << std::endl;
    std::cout << "   --reference-column <label>      Reference MTZ column to use (default: auto - F-model, else IMEAN/I/...)" << std::endl;
    std::cout << std::endl;

    std::cout << "  Pixel refinement (experimental, select via -r pixelrefine, needs --reference-mtz)" << std::endl;
    std::cout << "   --bandwidth <num>               Relative X-ray bandwidth FWHM (e.g. 0.01 for 1% DMM); default from file or 0" << std::endl;
    std::cout << "   --integration-radius <r>        Signal-box radius r1, or r1,r2,r3 (px). One value => r2=r1+2, r3=r1+4" << std::endl;
    std::cout << "   --integrator <txt>              Spot integrator boxsum|gaussian|empirical (default: boxsum; experimental profile-fit)" << std::endl;
    std::cout << "   --profile-multiplier <num>      PixelRefine: scale the measured tangential profile width R1 (default: 6; XDS-style generous aperture)" << std::endl;
    }

enum {
    OPT_SPOT_SIGMA = 1000,
    OPT_SPOT_THRESHOLD,
    OPT_SPOT_RESOLUTION,
    OPT_MAX_SPOTS,
    OPT_MIN_PARTIALITY,
    OPT_MIN_IMAGE_CC,
    OPT_SCALING_ITERATIONS,
    OPT_SCALING_HIGH_RESOLUTION,
    OPT_SCALING_OUTPUT,
    OPT_SINGLE_PASS_ROTATION,
    OPT_REDO_ROTATION_SPOTS,
    OPT_FORCE_ROTATION_LATTICE,
    OPT_BANDWIDTH,
    OPT_INTEGRATION_RADIUS,
    OPT_REJECT_OUTLIERS,
    OPT_PROFILE_MULTIPLIER,
    OPT_REJECT_DELTA_CCHALF,
    OPT_REFERENCE_COLUMN,
    OPT_DUMP_OBSERVATIONS,
    OPT_INTEGRATOR,
    OPT_SCALE_FULLS
};

static option long_options[] = {
    {"verbose", no_argument, nullptr, 'v'},
    {"output-prefix", required_argument, nullptr, 'o'},
    {"threads", required_argument, nullptr, 'N'},
    {"start-image", required_argument, nullptr, 's'},
    {"end-image", required_argument, nullptr, 'e'},
    {"stride", required_argument, nullptr, 't'},
    {"indexing-algorithm", required_argument, nullptr, 'X'},
    {"unit-cell", required_argument, nullptr, 'C'},
    {"reference-mtz", required_argument, nullptr, 'z'},
    {"reference-column", required_argument, nullptr, OPT_REFERENCE_COLUMN},
    {"dump-observations", required_argument, nullptr, OPT_DUMP_OBSERVATIONS},
    {"space-group", required_argument, nullptr, 'S'},
    {"partiality", required_argument, nullptr, 'P'},
    {"anomalous", no_argument, nullptr, 'A'},
    {"refine-bfactor", no_argument, nullptr, 'B'},
    {"wedge", optional_argument, nullptr, 'w'},
    {"scale-merge", no_argument, nullptr, 'M'},
    {"scale-fulls", no_argument, nullptr, OPT_SCALE_FULLS},
    {"refine", required_argument, nullptr, 'r'},

    {"two-pass-rotation", optional_argument, nullptr, 'R'},
    {"single-pass-rotation", optional_argument, nullptr, OPT_SINGLE_PASS_ROTATION},
    {"redo-rotation-spots", no_argument, nullptr, OPT_REDO_ROTATION_SPOTS},
    {"force-rotation-lattice", required_argument, nullptr, OPT_FORCE_ROTATION_LATTICE},


    {"spot-sigma", required_argument, nullptr, OPT_SPOT_SIGMA},
    {"spot-threshold", required_argument, nullptr, OPT_SPOT_THRESHOLD},
    {"spot-high-resolution", required_argument, nullptr, OPT_SPOT_RESOLUTION},
    {"max-spots", required_argument, nullptr, OPT_MAX_SPOTS},
    {"min-partiality", required_argument, nullptr, OPT_MIN_PARTIALITY},
    {"min-image-cc", required_argument, nullptr, OPT_MIN_IMAGE_CC},
    {"scaling-iterations", required_argument, nullptr, OPT_SCALING_ITERATIONS},
    {"scaling-high-resolution", required_argument, nullptr, OPT_SCALING_HIGH_RESOLUTION},
    {"scaling-output", required_argument, nullptr, OPT_SCALING_OUTPUT},
    {"bandwidth", required_argument, nullptr, OPT_BANDWIDTH},
    {"integration-radius", required_argument, nullptr, OPT_INTEGRATION_RADIUS},
    {"integrator", required_argument, nullptr, OPT_INTEGRATOR},
    {"reject-outliers", required_argument, nullptr, OPT_REJECT_OUTLIERS},
    {"reject-delta-cchalf", required_argument, nullptr, OPT_REJECT_DELTA_CCHALF},
    {"profile-multiplier", required_argument, nullptr, OPT_PROFILE_MULTIPLIER},
    {nullptr, 0, nullptr, 0}
};

void trim_in_place(std::string &t) {
    size_t b = 0;
    while (b < t.size() && std::isspace(static_cast<unsigned char>(t[b]))) b++;
    size_t e = t.size();
    while (e > b && std::isspace(static_cast<unsigned char>(t[e - 1]))) e--;
    t = t.substr(b, e - b);
};

bool parse_float_strict(const std::string &t, float &out) {
    try {
        size_t idx = 0;
        out = std::stof(t, &idx);
        return idx == t.size();
    } catch (...) {
        return false;
    }
};

std::optional<UnitCell> parse_unit_cell_arg(const char *arg) {
    if (!arg)
        return std::nullopt;

    std::string s(arg);


    trim_in_place(s);

    if (s.size() >= 2 && ((s.front() == '"' && s.back() == '"') || (s.front() == '\'' && s.back() == '\''))) {
        s = s.substr(1, s.size() - 2);
        trim_in_place(s);
    }

    std::vector<std::string> parts;
    parts.reserve(6);
    size_t start = 0;
    while (true) {
        size_t pos = s.find(',', start);
        if (pos == std::string::npos) {
            parts.push_back(s.substr(start));
            break;
        }
        parts.push_back(s.substr(start, pos - start));
        start = pos + 1;
    }

    if (parts.size() != 6)
        return std::nullopt;



    UnitCell uc{};
    if (!parse_float_strict(parts[0], uc.a)) return std::nullopt;
    if (!parse_float_strict(parts[1], uc.b)) return std::nullopt;
    if (!parse_float_strict(parts[2], uc.c)) return std::nullopt;
    if (!parse_float_strict(parts[3], uc.alpha)) return std::nullopt;
    if (!parse_float_strict(parts[4], uc.beta)) return std::nullopt;
    if (!parse_float_strict(parts[5], uc.gamma)) return std::nullopt;

    return uc;
}

std::optional<CrystalLattice> parse_lattice_arg(const char *arg) {
    if (!arg)
        return std::nullopt;

    std::string s(arg);
    trim_in_place(s);

    if (s.size() >= 2 && ((s.front() == '"' && s.back() == '"') || (s.front() == '\'' && s.back() == '\''))) {
        s = s.substr(1, s.size() - 2);
        trim_in_place(s);
    }

    std::vector<std::string> parts;
    parts.reserve(9);
    size_t start = 0;
    while (true) {
        size_t pos = s.find(',', start);
        if (pos == std::string::npos) {
            parts.push_back(s.substr(start));
            break;
        }
        parts.push_back(s.substr(start, pos - start));
        start = pos + 1;
    }

    if (parts.size() != 9)
        return std::nullopt;

    std::vector<float> vals(9);
    for (int i = 0; i < 9; i++) {
        if (!parse_float_strict(parts[i], vals[i]))
            return std::nullopt;
    }

    return CrystalLattice(vals);
}

namespace {
    std::atomic<JFJochProcess *> g_active_process{nullptr};
    void handle_sigint(int) {
        if (auto *p = g_active_process.load())
            p->Cancel();
    }
}

int main(int argc, char **argv) {
    for (int i = 0; i < argc; i++) {
        std::cout << argv[i] << " ";
    }
    std::cout << std::endl << std::endl;


    RegisterHDF5Filter();

    print_license("jfjoch_process");

    Logger logger("jfjoch_process");

    std::string input_file;
    std::string output_prefix = "output";
    int nthreads = 1;
    int start_image = 0;
    int end_image = -1; // -1 indicates process until end
    int image_stride = 1;

    bool verbose = false;
    bool rotation_indexing = false;
    bool two_pass_rotation = true;
    bool reuse_rotation_spots = true;
    int rotation_indexing_image_count = 100;
    std::optional<float> rotation_indexing_range;
    bool run_scaling = false;
    bool scale_fulls = false;
    bool anomalous_mode = false;
    std::optional<int64_t> space_group_number;
    std::optional<UnitCell> fixed_reference_unit_cell;
    std::optional<int64_t> max_spot_count_override;
    float sigma_spot_finding = 3.0;
    int64_t photon_count_threshold_spot_finding = 10;
    bool refine_bfactor = false;
    bool refine_wedge = false;
    std::optional<double> wedge_for_scaling;
    std::string ref_mtz;
    std::string ref_column;
    std::string dump_observations;   // diagnostic: dump unmerged -P rot3d fulls to this path
    double min_partiality = 0.02;
    double min_image_cc = 0.0;
    int64_t scaling_iter = 3;
    std::optional<CrystalLattice> forced_rotation_lattice;

    std::optional<float> bandwidth_fwhm; // relative FWHM of dlambda/lambda

    IndexingAlgorithmEnum indexing_algorithm = IndexingAlgorithmEnum::Auto;
    GeomRefinementAlgorithmEnum refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;

    IntensityFormat intensity_format = IntensityFormat::MTZ;
    PartialityModel partiality_model = PartialityModel::Fixed;
    bool combine_3d = false;   // -P rot3d: weight-sum per-frame partials into fulls before merging

    float d_min_spot_finding = 1.5;
    std::optional<float> d_min_scale_merge;
    std::optional<std::string> integration_radius_arg; // "r1" or "r1,r2,r3"
    std::optional<IntegratorMode> integrator_mode;     // --integrator boxsum|gaussian|empirical
    std::optional<double> outlier_reject_nsigma;       // merge per-observation outlier rejection
    std::optional<double> delta_cchalf_nsigma;         // per-crystal CC1/2-delta rejection
    std::optional<float> profile_multiplier;           // PixelRefine Term-2 profile-width multiplier

    if (argc == 1) {
        print_usage();
        exit(EXIT_FAILURE);
    }

    int opt;
    int option_index = 0;
    const char *short_opts = "vo:N:s:e:t:R::X:C:z:FABw::S:MP:r:";

  while ((opt = getopt_long(argc, argv, short_opts, long_options, &option_index)) != -1) {
    switch (opt) {
        case 'o':
            output_prefix = optarg;
            break;
        case 'v':
            verbose = true;
            break;
        case 'N':
            nthreads = atoi(optarg);
            break;
        case 's':
            start_image = atoi(optarg);
            break;
        case 'e':
            end_image = atoi(optarg);
            break;
        case 't':
            image_stride = atoi(optarg);
            break;
        case 'R':
            if (rotation_indexing) {
                logger.Error("Rotation indexing already enabled");
                exit(EXIT_FAILURE);
            }
            rotation_indexing = true;
            two_pass_rotation = true;
            if (optarg)
                rotation_indexing_image_count = atoi(optarg);

            break;
        case OPT_SINGLE_PASS_ROTATION:
            if (rotation_indexing) {
                logger.Error("Rotation indexing already enabled");
                exit(EXIT_FAILURE);
            }
            rotation_indexing = true;
            two_pass_rotation = false;

            if (optarg)
                rotation_indexing_range = atof(optarg);
            break;
        case OPT_REDO_ROTATION_SPOTS:
            reuse_rotation_spots = false;
            break;
        case OPT_FORCE_ROTATION_LATTICE: {
            if (rotation_indexing) {
                logger.Error("Rotation indexing already enabled");
                exit(EXIT_FAILURE);
            }
            rotation_indexing = true;

            auto latt = parse_lattice_arg(optarg);
            if (!latt.has_value()) {
                logger.Error(
                    "Invalid rotation lattice. Expected: \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, comma-separated). Got: {}",
                    optarg ? optarg : "<null>");
                print_usage();
                exit(EXIT_FAILURE);
            }
            forced_rotation_lattice = latt;
            auto uc = latt->GetUnitCell();
            logger.Info(
                "Forced rotation lattice set: a={:.3f} b={:.3f} c={:.3f} alpha={:.3f} beta={:.3f} gamma={:.3f}",
                uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
            break;
        }
        case 'X': {
            std::string alg = optarg ? optarg : "";
            std::transform(alg.begin(), alg.end(), alg.begin(),
                           [](unsigned char c) { return static_cast<char>(std::tolower(c)); });

            if (alg == "ffbidx")
                indexing_algorithm = IndexingAlgorithmEnum::FFBIDX;
            else if (alg == "fft")
                indexing_algorithm = IndexingAlgorithmEnum::FFT;
            else if (alg == "fftw")
                indexing_algorithm = IndexingAlgorithmEnum::FFTW;
            else if (alg == "auto")
                indexing_algorithm = IndexingAlgorithmEnum::Auto;
            else if (alg == "none")
                indexing_algorithm = IndexingAlgorithmEnum::None;
            else {
                logger.Error("Invalid indexing algorithm: {}", alg);
                print_usage();
                exit(EXIT_FAILURE);
            }
            break;
        }
        case 'r': {
            std::string alg = optarg ? optarg : "";
            std::transform(alg.begin(), alg.end(), alg.begin(),
                           [](unsigned char c) { return static_cast<char>(std::tolower(c)); });
            if (alg == "none")
                refinement_algorithm = GeomRefinementAlgorithmEnum::None;
            else if (alg == "beam_and_lattice")
                refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;
            else if (alg == "orientation")
                refinement_algorithm = GeomRefinementAlgorithmEnum::OrientationOnly;
            else if (alg == "pixelrefine")
                refinement_algorithm = GeomRefinementAlgorithmEnum::PixelRefine;
            else {
                logger.Error("Invalid geom refinement algorithm: {}", alg);
                print_usage();
                exit(EXIT_FAILURE);
            }
            break;
        }
        case 'C': {
            auto uc = parse_unit_cell_arg(optarg);
            if (!uc.has_value()) {
                logger.Error(
                    "Invalid unit cell. Expected: \"a,b,c,alpha,beta,gamma\" (6 floats, comma-separated, no spaces). Got: {}",
                    optarg ? optarg : "<null>");
                print_usage();
                exit(EXIT_FAILURE);
            }
            fixed_reference_unit_cell = uc;
            logger.Info(
                "Fixed reference unit cell set: a={:.3f} b={:.3f} c={:.3f} alpha={:.3f} beta={:.3f} gamma={:.3f}",
                uc->a, uc->b, uc->c, uc->alpha, uc->beta, uc->gamma);
            break;
        }
        case 'z':
            ref_mtz = optarg;
            break;
        case OPT_REFERENCE_COLUMN:
            ref_column = optarg;
            break;
        case OPT_DUMP_OBSERVATIONS:
            dump_observations = optarg;
            break;
        case 'F':
            indexing_algorithm = IndexingAlgorithmEnum::FFT;
            break;
        case 'A':
            anomalous_mode = true;
            break;
        case 'B':
            refine_bfactor = true;
            break;
        case 'w':
            refine_wedge = true;
            if (optarg)
                wedge_for_scaling = std::stod(optarg);
            break;
        case 'S':
            space_group_number = atoi(optarg);
            break;
        case 'P':
            if (strcmp(optarg, "unity") == 0)
                partiality_model = PartialityModel::Unity;
            else if (strcmp(optarg, "fixed") == 0)
                partiality_model = PartialityModel::Fixed;
            else if (strcmp(optarg, "rot") == 0)
                partiality_model = PartialityModel::Rotation;
            else if (strcmp(optarg, "rot3d") == 0) {
                partiality_model = PartialityModel::Rotation;
                combine_3d = true;
            }
            else {
                logger.Error("Invalid partiality mode: {}", optarg);
                print_usage();
                exit(EXIT_FAILURE);
            }
            break;
        case OPT_SPOT_SIGMA:
            sigma_spot_finding = atof(optarg);
            logger.Info("Noise threshold level for spot finding set to {:.2f} sigma", sigma_spot_finding);
            break;
        case OPT_SPOT_THRESHOLD:
            photon_count_threshold_spot_finding = atoi(optarg);
            logger.Info("Photon-count threshold level for spot finding set to {:d}",
                        photon_count_threshold_spot_finding);
            break;
        case OPT_SPOT_RESOLUTION:
            d_min_spot_finding = atof(optarg);
            logger.Info("High resolution limit for spot finding set to {:.2f} A", d_min_spot_finding);
            break;
        case OPT_MAX_SPOTS:
            max_spot_count_override = atoll(optarg);
            logger.Info("Max spot count overridden to {}", max_spot_count_override.value());
            break;
        case 'M':
            run_scaling = true;
            break;
        case OPT_SCALE_FULLS:
            run_scaling = true;
            scale_fulls = true;
            break;
        case OPT_MIN_PARTIALITY:
            min_partiality = std::stod(optarg);
            break;
        case OPT_INTEGRATION_RADIUS:
            integration_radius_arg = optarg;
            break;
        case OPT_INTEGRATOR:
            if (strcmp(optarg, "boxsum") == 0) integrator_mode = IntegratorMode::BoxSum;
            else if (strcmp(optarg, "gaussian") == 0) integrator_mode = IntegratorMode::ProfileGaussian;
            else if (strcmp(optarg, "empirical") == 0) integrator_mode = IntegratorMode::ProfileEmpirical;
            else { logger.Error("--integrator expects boxsum|gaussian|empirical"); return 1; }
            break;
        case OPT_REJECT_OUTLIERS:
            outlier_reject_nsigma = std::stod(optarg);
            break;
        case OPT_REJECT_DELTA_CCHALF:
            delta_cchalf_nsigma = std::stod(optarg);
            break;
        case OPT_PROFILE_MULTIPLIER:
            profile_multiplier = std::stof(optarg);
            break;
        case OPT_MIN_IMAGE_CC:
            min_image_cc = std::stod(optarg);
            break;
        case OPT_SCALING_HIGH_RESOLUTION:
            d_min_scale_merge = atof(optarg);
            break;
        case OPT_SCALING_OUTPUT:
            if (strcmp(optarg, "mtz") == 0) {
                intensity_format = IntensityFormat::MTZ;
            } else if (strcmp(optarg, "cif") == 0) {
                intensity_format = IntensityFormat::mmCIF;
            } else if (strcmp(optarg, "txt") == 0) {
                intensity_format = IntensityFormat::Text;
            } else {
                logger.Error("Invalid intensity format: {}", optarg);
                exit(EXIT_FAILURE);
            }
            break;
        case OPT_SCALING_ITERATIONS:
            scaling_iter = atoi(optarg);
            if (scaling_iter <= 0) {
                logger.Error("Invalid scaling iteration count: {}", scaling_iter);
                exit(EXIT_FAILURE);
            }
            break;
        case OPT_BANDWIDTH:
            bandwidth_fwhm = atof(optarg);
            if (!(bandwidth_fwhm.value() >= 0.0f)) {
                logger.Error("Invalid bandwidth: {}", optarg);
                exit(EXIT_FAILURE);
            }
            break;

        default:
            print_usage();
            exit(EXIT_FAILURE);
    }
}

    if (optind != argc - 1) {
        logger.Error("Input file not specified");
        print_usage();
        exit(EXIT_FAILURE);
    }

    input_file = argv[optind];
    logger.Verbose(verbose);

    // Validate space group number early
    const gemmi::SpaceGroup *space_group = nullptr;
    if (space_group_number.has_value()) {
        space_group = gemmi::find_spacegroup_by_number(space_group_number.value());
        if (!space_group) {
            logger.Error("Unknown space group number {}", space_group_number.value());
            exit(EXIT_FAILURE);
        }
        logger.Info("Using space group {} (number {})", space_group->hm, space_group_number.value());
    }

    // 1. Read Input File
    JFJochHDF5Reader reader;
    try {
        reader.ReadFile(input_file);
    } catch (const std::exception &e) {
        logger.Error("Error reading input file: {}", e.what());
        exit(EXIT_FAILURE);
    }

    const auto dataset = reader.GetDataset();
    if (!dataset) {
        logger.Error("No experiment dataset found in the input file");
        exit(EXIT_FAILURE);
    }

    if (rotation_indexing_image_count <= 0) {
        logger.Error("Invalid number of rotation indexing images: {}", rotation_indexing_image_count);
        exit(EXIT_FAILURE);
    }

    logger.Info("Loaded dataset from {}", input_file);

    std::vector<MergedReflection> reference_data;
    if (!ref_mtz.empty()) {
        try {
            const auto reference = LoadReferenceMtz(
                ref_mtz, ref_column.empty() ? std::nullopt : std::optional<std::string>(ref_column));
            reference_data = reference.reflections;

            logger.Info("Loaded {} reference reflections from {} (column {}{}{})",
                        reference_data.size(), ref_mtz, reference.used_column,
                        reference.squared ? ", squared to intensity" : "",
                        reference.default_column ? ", auto-selected" : ", user-specified");
            if (reference.d_max > 0.0)
                logger.Info("Reference resolution range {:.2f} - {:.2f} A", reference.d_max, reference.d_min);
            if (reference.cell.has_value())
                logger.Info("Reference unit cell: a={:.3f} b={:.3f} c={:.3f} alpha={:.2f} beta={:.2f} gamma={:.2f}",
                            reference.cell->a, reference.cell->b, reference.cell->c,
                            reference.cell->alpha, reference.cell->beta, reference.cell->gamma);
            if (!reference.space_group_name.empty())
                logger.Info("Reference space group: {} (number {})",
                            reference.space_group_name, reference.space_group_number.value_or(0));

            const auto warning = ReferenceConsistencyWarning(
                reference, fixed_reference_unit_cell,
                space_group_number.has_value() ? std::optional<int>(static_cast<int>(*space_group_number))
                                               : std::nullopt);
            if (!warning.empty())
                logger.Warning("{}", warning);
        } catch (const std::exception &e) {
            logger.Error("Error reading reference MTZ {}: {}", ref_mtz, e.what());
            exit(EXIT_FAILURE);
        }
    }

    uint64_t total_images_in_file = reader.GetNumberOfImages();
    if (end_image < 0 || end_image > total_images_in_file)
        end_image = total_images_in_file;

    if (image_stride < 0) {
        logger.Error("Image stride cannot be negative");
        exit(EXIT_FAILURE);
    }

    if (image_stride == 0) {
        logger.Error("Image stride cannot be zero");
        exit(EXIT_FAILURE);
    }

    int images_to_process = (end_image - start_image) / image_stride;

    if (images_to_process <= 0) {
        logger.Warning("No images to process (Start: {}, End: {} Stride: {}, Total: {})", start_image, end_image,
            image_stride, total_images_in_file);
        return 0;
    }

    logger.Info("Starting analysis of {} images (range {}-{}) using {} threads",
                images_to_process, start_image, end_image, nthreads);

    // 2. Setup Experiment & Components
    DiffractionExperiment experiment(dataset->experiment);
    experiment.BitDepthImage(32).Compression(CompressionAlgorithm::BSHUF_LZ4);
    experiment.FilePrefix(output_prefix);
    experiment.Mode(DetectorMode::Standard); // Ensure full image analysis
    experiment.PixelSigned(true);
    experiment.OverwriteExistingFiles(true);
    experiment.PolarizationFactor(0.99);
    experiment.SetFileWriterFormat(FileWriterFormat::NXmxLegacy);
    experiment.SpaceGroupNumber(space_group_number);
    experiment.ImagesPerTrigger(images_to_process);
    experiment.NumTriggers(1);

    if (fixed_reference_unit_cell.has_value())
        experiment.SetUnitCell(*fixed_reference_unit_cell);

    if (max_spot_count_override.has_value()) {
        experiment.MaxSpotCount(max_spot_count_override.value());
        logger.Info("Max spot count overridden to {}", max_spot_count_override.value());
    }

    // X-ray bandwidth: CLI overrides the value carried in the dataset; otherwise
    // keep whatever the dataset provided (0 / none -> monochromatic).
    if (bandwidth_fwhm)
        experiment.BandwidthFWHM(bandwidth_fwhm);
    if (experiment.GetBandwidthFWHM())
        logger.Info("X-ray bandwidth FWHM set to {:.4f}", experiment.GetBandwidthFWHM().value());

    // PixelRefine integration needs reference intensities (the I_true hypothesis).
    if (refinement_algorithm == GeomRefinementAlgorithmEnum::PixelRefine && reference_data.empty()) {
        logger.Warning("-r pixelrefine needs --reference-mtz; falling back to beam_and_lattice");
        refinement_algorithm = GeomRefinementAlgorithmEnum::BeamCenter;
    }

    // Configure Indexing
    IndexingSettings indexing_settings;
    indexing_settings.Algorithm(indexing_algorithm);
    indexing_settings.RotationIndexing(rotation_indexing);
    if (rotation_indexing_range.has_value())
        indexing_settings.RotationIndexingMinAngularRange_deg(rotation_indexing_range.value());
    indexing_settings.GeomRefinementAlgorithm(refinement_algorithm);
    experiment.ImportIndexingSettings(indexing_settings);

    ScalingSettings scaling_settings;
    scaling_settings.SetPartialityModel(partiality_model);
    scaling_settings.Combine3D(combine_3d);
    scaling_settings.ScaleFulls(scale_fulls);
    if (d_min_scale_merge)
        scaling_settings.HighResolutionLimit_A(d_min_scale_merge.value());
    scaling_settings.MergeFriedel(!anomalous_mode);
    scaling_settings.RefineB(refine_bfactor);
    scaling_settings.RefineRotationWedge(refine_wedge);
    if (wedge_for_scaling.has_value())
        scaling_settings.RotationWedgeForScaling(wedge_for_scaling);
    scaling_settings.MinPartiality(min_partiality);
    scaling_settings.MinCCForImage(min_image_cc);
    if (outlier_reject_nsigma)
        scaling_settings.OutlierRejectNsigma(*outlier_reject_nsigma);
    scaling_settings.FileFormat(intensity_format);

    experiment.ImportScalingSettings(scaling_settings);

    // Integration radii: r1 (signal box), r2/r3 (background annulus). PixelRefine reads
    // r1 as its shoebox radius; the classical integrator uses all three.
    if (integration_radius_arg) {
        std::vector<float> rr;
        std::stringstream ss(*integration_radius_arg);
        std::string tok;
        while (std::getline(ss, tok, ',')) {
            trim_in_place(tok);
            if (!tok.empty()) rr.push_back(std::stof(tok));
        }
        float r1, r2, r3;
        if (rr.size() == 1) { r1 = rr[0]; r2 = r1 + 2.0f; r3 = r1 + 4.0f; }
        else if (rr.size() == 3) { r1 = rr[0]; r2 = rr[1]; r3 = rr[2]; }
        else { logger.Error("--integration-radius expects r1 or r1,r2,r3"); return 1; }
        BraggIntegrationSettings bis = experiment.GetBraggIntegrationSettings();
        bis.R1(r1).R2(r2).R3(r3);
        experiment.ImportBraggIntegrationSettings(bis);
        logger.Info("Integration radii set to r1={:.1f} r2={:.1f} r3={:.1f}", r1, r2, r3);
    }

    if (profile_multiplier) {
        BraggIntegrationSettings bis = experiment.GetBraggIntegrationSettings();
        bis.ProfileMultiplier(*profile_multiplier);
        experiment.ImportBraggIntegrationSettings(bis);
        logger.Info("PixelRefine profile-width multiplier set to {:.1f}", *profile_multiplier);
    }

    if (integrator_mode) {
        BraggIntegrationSettings bis = experiment.GetBraggIntegrationSettings();
        bis.Integrator(*integrator_mode);
        experiment.ImportBraggIntegrationSettings(bis);
        logger.Info("Integrator set to {}", *integrator_mode == IntegratorMode::BoxSum ? "box-sum"
                    : *integrator_mode == IntegratorMode::ProfileGaussian ? "profile (gaussian)"
                    : "profile (empirical)");
    }

    SpotFindingSettings spot_settings;
    spot_settings.enable = true;
    spot_settings.indexing = true;
    spot_settings.high_resolution_limit = d_min_spot_finding;
    spot_settings.signal_to_noise_threshold = sigma_spot_finding;
    spot_settings.photon_count_threshold = photon_count_threshold_spot_finding;
    if (d_min_spot_finding > 0.0f)
        spot_settings.high_resolution_limit = d_min_spot_finding;

    // Run the shared full-analysis workflow (rotation indexing + scaling/merging live in
    // JFJochProcess; the experiment above carries all algorithm settings).
    ProcessConfig config;
    config.mode = ProcessMode::FullAnalysis;
    config.start_image = start_image;
    config.end_image = end_image;
    config.stride = image_stride;
    config.nthreads = nthreads;
    config.output_prefix = output_prefix;
    config.spot_finding = spot_settings;
    config.rotation_indexing = rotation_indexing;
    config.two_pass_rotation = two_pass_rotation;
    config.reuse_rotation_spots = reuse_rotation_spots;
    config.rotation_indexing_image_count = rotation_indexing_image_count;
    config.forced_rotation_lattice = forced_rotation_lattice;
    config.run_scaling = run_scaling;
    config.scaling_iter = scaling_iter;
    config.reference_data = reference_data;
    config.observation_dump_path = dump_observations;

    JFJochProcess process(reader, experiment, dataset->pixel_mask, config);

    g_active_process = &process;
    std::signal(SIGINT, handle_sigint);

    ProcessResult result;
    try {
        result = process.Run();
    } catch (const std::exception &e) {
        logger.Error("Processing failed: {}", e.what());
        exit(EXIT_FAILURE);
    }
    g_active_process = nullptr;

    if (!result.merge_statistics_text.empty())
        std::cout << std::endl << result.merge_statistics_text << std::endl;

    // Report statistics
    std::cout << fmt::format("Processing time: {:.2f} s", result.processing_time_s) << std::endl;
    std::cout << fmt::format("Frame rate:      {:.2f} Hz", result.frame_rate_hz) << std::endl;
    std::cout << fmt::format("Total throughput:{:.2f} MB/s", result.throughput_MBs) << std::endl;
    if (result.indexing_rate.has_value())
        std::cout << fmt::format("Indexing rate:   {:.2f}%", result.indexing_rate.value() * 100.0) << std::endl;
    if (result.consensus_cell.has_value()) {
        const auto &c = result.consensus_cell.value();
        std::cout << fmt::format("Unit cell:       a={:.2f} b={:.2f} c={:.2f} alpha={:.2f} beta={:.2f} gamma={:.2f}",
                                 c.a, c.b, c.c, c.alpha, c.beta, c.gamma) << std::endl;
    }

    const auto &t = result.mean_processing_time;
    std::cout << fmt::format(
        "Per-image time (mean; ms): decompress {:.2f} preprocess {:.2f} azint {:.2f} spot finding {:.2f} "
        "indexing {:.2f} refinement {:.2f} indexing analysis {:.2f} prediction {:.2f} integration {:.2f} "
        "scaling {:.2f} total {:.2f}",
        t.compression * 1e3, t.preprocessing * 1e3, t.azint * 1e3, t.spot_finding * 1e3,
        t.indexing * 1e3, t.refinement * 1e3, t.indexing_analysis * 1e3, t.bragg_prediction * 1e3,
        t.integration * 1e3, t.image_scale * 1e3, t.processing * 1e3) << std::endl;

    if (result.cancelled)
        logger.Warning("Processing was cancelled after {} images", result.images_processed);
}