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

#include "JFJochHDF5Reader.h"
#include "../include/spdlog/fmt/fmt.h"

std::vector<hsize_t> GetDimension(HDF5Object& object, const std::string& path) {
    const auto dim = object.GetDimension(path);
    if (dim.size() != 3)
        throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong dimension of /entry/data/data");
    return dim;
}

template <class T>
void JFJochHDF5Reader::ReadVector(std::vector<T> &v,
                                  HDF5Object &file,
                                  const std::string &dataset_name,
                                  size_t image0,
                                  size_t nimages) {
    try {
        auto tmp = file.ReadOptVector<T>(dataset_name);
        if (tmp.size() == nimages) {
            v.resize(image0 + nimages);
            for (int i = 0; i < nimages; i++)
                v[image0 + i] = tmp[i];
        }
    } catch (JFJochException &e) {}
}

std::string removeSuffix(const std::string& s, const std::string& suffix)
{
    if (s.rfind(suffix) == s.size() - suffix.size()) {
        return s.substr(0, s.size() - suffix.size());
    }
    return s;
}

std::string dataset_name(const std::string& path) {
    std::string file = path;
    int pos = file.rfind('/');
    if (pos != std::string::npos)
        file = file.substr(pos+1);
    file = removeSuffix(file, "_master.h5");
// If previous suffix was not found, try removing this one
    file = removeSuffix(file, ".h5");
    return file;
}

void JFJochHDF5Reader::ReadFile(const std::string& filename) {
    std::unique_lock ul(master_file_mutex);
    try {
        auto dataset = std::make_shared<JFJochReaderDataset>();
        master_file = std::make_unique<HDF5ReadOnlyFile>(filename);

        std::filesystem::path fsPath(filename);
        dataset->experiment.FilePrefix(dataset_name(filename));

        // JFJochReader is always using int32_t
        dataset->experiment.BitDepthImage(32);
        dataset->experiment.PixelSigned(true);

        size_t image_size_x = 0;
        size_t image_size_y = 0;
        if (master_file->Exists("/entry/data/data")) {
            legacy_format = false;
            auto dim = GetDimension(*master_file, "/entry/data/data");
            number_of_images = dim[0];
            image_size_y = dim[1];
            image_size_x = dim[2];

            images_per_file = number_of_images;

            dataset->efficiency = master_file->ReadVector<float>(
                    "/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image");

            dataset->spot_count = master_file->ReadOptVector<uint32_t>("/entry/MX/nPeaks");
            dataset->indexing_result = master_file->ReadOptVector<uint8_t>("/entry/MX/imageIndexed");
            dataset->bkg_estimate = master_file->ReadOptVector<float>("/entry/MX/bkgEstimate");
            dataset->resolution_estimate = master_file->ReadOptVector<float>("/entry/MX/resolutionEstimate");
        } else if (master_file->Exists("/entry/data/data_000001")) {
            legacy_format = true;
            legacy_format_files.clear();

            image_size_x = master_file->GetInt("/entry/instrument/detector/detectorSpecific/x_pixels_in_detector");
            image_size_y = master_file->GetInt("/entry/instrument/detector/detectorSpecific/y_pixels_in_detector");

            //size_t expected_images = master_file->GetInt("/entry/instrument/detector/detectorSpecific/nimages");

            images_per_file = 0;
            number_of_images = 0;
            uint32_t nfiles = 0;

            std::filesystem::path file_path(filename);
            std::filesystem::path directory = file_path.parent_path();

            while (true) {
                std::string dname = fmt::format("/entry/data/data_{:06d}", nfiles + 1);
                if (!master_file->Exists(dname))
                    break;

                size_t fimages = 0;

                try {
                    auto fname = master_file->GetLinkedFileName(dname);

                    if (!directory.empty())
                        fname = fmt::format("{}/{}", directory.string(),fname);

                    HDF5ReadOnlyFile data_file(fname);

                    fimages = GetDimension(data_file, "/entry/data/data")[0];

                    legacy_format_files.push_back(fname);

                    ReadVector(dataset->efficiency,
                               data_file, "/entry/detector/data_collection_efficiency_image",
                               number_of_images, fimages);

                    ReadVector(dataset->spot_count,
                               data_file, "/entry/MX/nPeaks",
                               number_of_images, fimages);

                    ReadVector(dataset->indexing_result,
                               data_file, "/entry/MX/imageIndexed",
                               number_of_images, fimages);

                    ReadVector(dataset->bkg_estimate,
                               data_file, "/entry/MX/bkgEstimate",
                               number_of_images, fimages);
                } catch (JFJochException &e) {}

                if (nfiles == 0)
                    images_per_file = fimages;
                number_of_images += fimages;
                nfiles++;
            }
        } else {
            image_size_x = master_file->GetInt("/entry/instrument/detector/detectorSpecific/x_pixels_in_detector");
            image_size_y = master_file->GetInt("/entry/instrument/detector/detectorSpecific/y_pixels_in_detector");
            number_of_images = 0;
        }

        dataset->experiment.BeamX_pxl(master_file->GetFloat("/entry/instrument/detector/beam_center_x"));
        dataset->experiment.BeamY_pxl(master_file->GetFloat("/entry/instrument/detector/beam_center_y"));

        float det_distance = master_file->GetFloat("/entry/instrument/detector/distance");
        if (det_distance < 0.001)
            det_distance = 0.1; // Set to 100 mm, if det distance is less than 1 mm
        dataset->experiment.DetectorDistance_mm(det_distance * 1000.0);

        dataset->experiment.IncidentEnergy_keV(WVL_1A_IN_KEV / master_file->GetFloat("/entry/instrument/beam/incident_wavelength"));

        dataset->error_value = master_file->GetOptInt("/entry/instrument/detector/error_value");

        dataset->jfjoch_release = master_file->GetString("/entry/instrument/detector/jfjoch_release");

        InstrumentMetadata metadata;
        metadata.InstrumentName(master_file->GetString("/entry/instrument/name"));
        metadata.SourceName(master_file->GetString("/entry/source/name"));
        dataset->experiment.ImportInstrumentMetadata(metadata);

        auto tmp = master_file->ReadOptVector<float>("/entry/sample/unit_cell");
        if (tmp.size() == 6)
            dataset->experiment.SetUnitCell(UnitCell{
                    .a = tmp[0],
                    .b = tmp[1],
                    .c = tmp[2],
                    .alpha = tmp[3],
                    .beta = tmp[4],
                    .gamma = tmp[5]});
        dataset->experiment.SpaceGroupNumber(master_file->GetOptInt("/entry/sample/space_group").value_or(0));
        dataset->experiment.SampleName(master_file->GetString("/entry/sample/name"));


        if (master_file->Exists("/entry/roi"))
            dataset->roi = master_file->FindLeafs("/entry/roi");
        for (const auto &s: dataset->roi) {
            dataset->roi_max.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/max"));
            dataset->roi_sum.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/sum"));
            dataset->roi_sum_sq.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/sum_sq"));
            dataset->roi_npixel.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/npixel"));
        }
        if (master_file->Exists("/entry/instrument/attenuator"))
            dataset->experiment.AttenuatorTransmission(master_file->GetOptFloat("/entry/instrument/attenuator/attenuator_transmission"));
        dataset->experiment.TotalFlux(master_file->GetOptFloat("/entry/instrument/beam/total_flux"));

        if (master_file->Exists("/entry/image/max_value"))
            dataset->max_value = master_file->ReadVector<int64_t>("/entry/image/max_value");

        if (master_file->Exists("/entry/azint") && master_file->Exists("/entry/azint/bin_to_q")) {
            HDF5DataSet bin_to_q_dataset(*master_file, "/entry/azint/bin_to_q");
            bin_to_q_dataset.ReadVector(dataset->az_int_bin_to_q);
        }

        auto detector_name = master_file->GetString("/entry/instrument/detector/description");

        DetectorSetup detector = DetDECTRIS(image_size_x, image_size_y, detector_name, {});
        detector.PixelSize_um(master_file->GetFloat("/entry/instrument/detector/x_pixel_size") * 1e6);
        detector.SaturationLimit(master_file->GetInt("/entry/instrument/detector/saturation_value"));
        detector.MinFrameTime(std::chrono::microseconds(0));
        detector.MinCountTime(std::chrono::microseconds(0));
        detector.ReadOutTime(std::chrono::microseconds (0));
        dataset->experiment.Detector(detector);

        dataset->experiment.FrameTime(
                std::chrono::microseconds(std::lround(master_file->GetFloat("/entry/instrument/detector/frame_time") * 1e6)),
                std::chrono::microseconds(std::lround(master_file->GetFloat("/entry/instrument/detector/count_time") * 1e6)));

        if (image_size_x * image_size_y > 0) {
            auto mask_tmp = master_file->ReadOptVector<uint32_t>(
                    "/entry/instrument/detector/pixel_mask",
                    {0, 0},
                    {image_size_y, image_size_x}
            );
            if (mask_tmp.empty())
                mask_tmp = std::vector<uint32_t>(image_size_x * image_size_y);
            dataset->pixel_mask = PixelMask(mask_tmp);
        }
        dataset->experiment.ImagesPerTrigger(number_of_images);
        SetStartMessage(dataset);
    } catch (const std::exception& e) {
        master_file = {};
        number_of_images = 0;
        SetStartMessage({});
        throw;
    }
}

uint64_t JFJochHDF5Reader::GetNumberOfImages() const {
    std::unique_lock ul(master_file_mutex);
    return number_of_images;
}

CompressedImage JFJochHDF5Reader::LoadImageDataset(std::vector<uint8_t> &tmp, HDF5Object &file, hsize_t number) {
    std::vector<hsize_t> start = {static_cast<hsize_t>(number), 0, 0};

    HDF5DataSet dataset(file, "/entry/data/data");
    HDF5DataSpace dataspace(dataset);
    HDF5DataType datatype(dataset);
    HDF5Dcpl dcpl(dataset);

    if (dataspace.GetNumOfDimensions() != 3)
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "/entry/data/data dataset must be 3D");

    auto dim = dataspace.GetDimensions();

    CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION;
    auto chunk_size = dcpl.GetChunking();

    if ((chunk_size.size() == 3) && (chunk_size[0] == 1) && (chunk_size[1] == dim[1]) && (chunk_size[2] == dim[2])) {
        dataset.ReadDirectChunk(tmp, start);
        algorithm = dcpl.GetCompression();
    } else {
        dataset.ReadVectorToU8(tmp, start, {1, dim[1], dim[2]});
        algorithm = CompressionAlgorithm::NO_COMPRESSION;
    }

    if (datatype.IsFloat())
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,"Float datasets not supported at this time");

    return {tmp, dim[1], dim[2],
            CalcImageMode(datatype.GetElemSize(), datatype.IsFloat(), datatype.IsSigned()),
            algorithm};
}

std::shared_ptr<JFJochReaderImage> JFJochHDF5Reader::LoadImageInternal(int64_t image_number) {
    std::unique_lock ul(master_file_mutex);

    if (!master_file)
        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
                              "Cannot load image if file not loaded");

    if (image_number >= number_of_images)
        throw JFJochException(JFJochExceptionCategory::HDF5, "Image out of bounds");

    std::unique_ptr<HDF5ReadOnlyFile> tmp_data_file;
    uint32_t image_id;
    HDF5Object *source_file;

    if (legacy_format) {
        uint32_t file_id = image_number / images_per_file;
        image_id = image_number % images_per_file;
        tmp_data_file = std::make_unique<HDF5ReadOnlyFile>(legacy_format_files.at(file_id));
        source_file = tmp_data_file.get();
    } else {
        image_id = image_number;
        source_file = master_file.get();
    }

    DataMessage message;
    message.image = LoadImageDataset(buffer, *source_file, image_id);
    message.number = image_number;
    auto dataset = GetStartMessage();

    if (dataset->indexing_result.size() > image_number && dataset->indexing_result[image_number] != 0
        && source_file->Exists("/entry/MX") && source_file->Exists("/entry/MX/latticeIndexed")) {

        std::vector<float> tmp = source_file->ReadVector<float>(
                "/entry/MX/latticeIndexed",
                {(hsize_t) image_id, 0},
                {1, 9}
        );
        message.indexing_lattice = CrystalLattice(tmp);
    }

    if ((dataset->spot_count.size() > image_number)
        && (dataset->spot_count[image_number] > 0)) {
        auto spot_count = dataset->spot_count[image_number];
        auto spot_x = source_file->ReadVector<float>(
                "/entry/MX/peakXPosRaw",
                {(hsize_t) image_id, 0},
                {1, spot_count}
        );
        auto spot_y = source_file->ReadVector<float>(
                "/entry/MX/peakYPosRaw",
                {(hsize_t) image_id, 0},
                {1, spot_count}
        );
        auto spot_intensity = source_file->ReadVector<float>(
                "/entry/MX/peakTotalIntensity",
                {(hsize_t) image_id, 0},
                {1, spot_count}
        );
        auto spot_indexed = source_file->ReadVector<uint8_t>(
                "/entry/MX/peakIndexed",
                {(hsize_t) image_id, 0},
                {1, spot_count}
        );
        for (int i = 0; i < spot_count; i++) {
            message.spots.emplace_back(SpotToSave{
                    .x = spot_x.at(i),
                    .y = spot_y.at(i),
                    .intensity = spot_intensity.at(i),
                    .indexed = (spot_indexed.at(i) != 0)
            });
        }
    }

    if (!dataset->az_int_bin_to_q.empty()) {
        message.az_int_profile = source_file->ReadOptVector<float>(
                "/entry/azint/image",
                {(hsize_t) image_id, 0},
                {1, dataset->az_int_bin_to_q.size()}
        );
    }

    if (dataset->resolution_estimate.size() > image_number)
        message.resolution_estimate = dataset->resolution_estimate[image_number];
    if (dataset->indexing_result.size() > image_number)
        message.indexing_result = dataset->indexing_result[image_number];
    if (dataset->bkg_estimate.size() > image_number)
        message.bkg_estimate = dataset->bkg_estimate[image_number];
    if (dataset->efficiency.size() > image_number)
        message.image_collection_efficiency = dataset->efficiency[image_number];

    return std::make_shared<JFJochReaderImage>(message, dataset);
}

void JFJochHDF5Reader::Close() {
    std::unique_lock ul(master_file_mutex);
    master_file = {};
    number_of_images = 0;
    legacy_format_files.clear();
    SetStartMessage({});
}