// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#include <fstream>

#include "../reader/JFJochHDF5Reader.h"
#include "../common/print_license.h"
#include "../common/Logger.h"


void print_usage(Logger &logger) {
    logger.Info("Usage ./jfjoch_extract_hkl {<options>} <path to master file>");
    logger.Info("Options:");
    logger.Info("   -I<num>    Number of images");
    logger.Info("   -o<file>   Output filename");
    logger.Info("   -x<num>    Max dist from Ewald sphere");
}

int main(int argc, char **argv) {

    int64_t image_number = 0;
    float max_dist_ewald_sphere = 1.0;

    std::string output_filename = "out.hkl";

    print_license("jfjoch_extract_hkl");

    Logger logger("jfjoch_extract_hkl");
    logger.Verbose(true);
    int opt;
    while ((opt = getopt(argc, argv, "I:x:o:")) != -1) {
        switch (opt) {
            case 'I':
                image_number = atol(optarg);
                break;
            case 'x':
                max_dist_ewald_sphere = atof(optarg);
                break;
            case 'o':
                output_filename = optarg;
                break;
            default: /* '?' */
                print_usage(logger);
                exit(EXIT_FAILURE);
        }
    }

    if (optind != argc - 1) {
        print_usage(logger);
        exit(EXIT_FAILURE);
    }

    JFJochHDF5Reader reader;
    reader.ReadFile(argv[optind]);

    auto dataset = reader.LoadImage(image_number);

    if (dataset) {
        auto geom = dataset->Dataset().experiment.GetDiffractionGeometry();

        std::fstream f(output_filename, std::ios::out);
        if (dataset->ImageData().indexing_lattice) {
            auto latt = dataset->ImageData().indexing_lattice.value();

            Coord astar = latt.Astar();
            Coord bstar = latt.Bstar();
            Coord cstar = latt.Cstar();
            auto uc = latt.GetUnitCell();
            logger.Info("Cell {} {} {} {} {} {}",uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
            logger.Info("A {} {} {}", astar.x, astar.y, astar.z);
            logger.Info("B {} {} {}", bstar.x, bstar.y, bstar.z);
            logger.Info("C {} {} {}", cstar.x, cstar.y, cstar.z);

            logger.Info("{} reflections identified", dataset->ImageData().reflections.size());
            for (const auto &r: dataset->ImageData().reflections) {
                auto recip = astar * r.h + bstar * r.k + cstar * r.l;
                auto dist = geom.DistFromEwaldSphere(recip);
                if (dist < max_dist_ewald_sphere)
                    f << r.l << " " << r.k << " " << r.h << " " << r.I << " " << r.sigma << " " << dist << std::endl;
            }
        }
    }
}