// Copyright (2019-2024) Paul Scherrer Institute

#include "HDF5DataFilePluginMX.h"

HDF5DataFilePluginMX::HDF5DataFilePluginMX(size_t in_max_spots) : max_spots(in_max_spots) {}

void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg) {
    if (max_spots == 0)
        return;

    HDF5Group(data_file, "/entry/MX").NXClass("NXcollection");

    HDF5DataSpace data_space_spots({1, max_spots}, {H5S_UNLIMITED, max_spots});
    HDF5Dcpl dcpl_spots;
    dcpl_spots.SetChunking({1, max_spots});
    data_set_spot_x = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakXPosRaw", HDF5DataType(0.0f),
                                                    data_space_spots, dcpl_spots);
    data_set_spot_y = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakYPosRaw", HDF5DataType(0.0f),
                                                    data_space_spots, dcpl_spots);
    data_set_spot_int = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakTotalIntensity", HDF5DataType(0.0f),
                                                      data_space_spots, dcpl_spots);
    data_set_spot_indexed = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakIndexed", HDF5DataType(1, false),
                                                          data_space_spots, dcpl_spots);
}

void HDF5DataFilePluginMX::Write(const DataMessage &msg) {
    if (max_spots == 0)
        return;

    size_t image_number = msg.number;

    if (image_number >= max_image_number) {
        max_image_number = image_number;
        data_set_spot_x->SetExtent({max_image_number+1, max_spots});
        data_set_spot_y->SetExtent({max_image_number+1, max_spots});
        data_set_spot_int->SetExtent({max_image_number+1, max_spots});
        data_set_spot_indexed->SetExtent({max_image_number+1, max_spots});

        npeaks.resize(max_image_number + 1);
        strong_pixel_count.resize(max_image_number + 1);
        indexed.resize(max_image_number + 1);
        indexed_lattice.resize((max_image_number + 1) * 9);
    }

    std::vector<float> spot_x(max_spots), spot_y(max_spots), spot_intensity(max_spots);
    std::vector<uint8_t> spot_indexed(max_spots);

    uint32_t spot_cnt = std::min(msg.spots.size(), max_spots);

    for (int i = 0; i < spot_cnt; i++) {
        spot_x[i] = msg.spots[i].x;
        spot_y[i] =  msg.spots[i].y;
        spot_intensity[i] = msg.spots[i].intensity;
        spot_indexed[i] = msg.spots[i].indexed;
    }
    data_set_spot_x->WriteVec(spot_x, {image_number, 0}, {1, max_spots});
    data_set_spot_y->WriteVec(spot_y, {image_number, 0}, {1, max_spots});
    data_set_spot_int->WriteVec(spot_intensity, {image_number, 0}, {1, max_spots});
    data_set_spot_indexed->WriteVec(spot_indexed, {image_number, 0}, {1, max_spots});

    npeaks[image_number] = spot_cnt;
    strong_pixel_count[image_number] = msg.strong_pixel_count;
    indexed[image_number] = msg.indexing_result;
    if (msg.indexing_lattice.size() == 9) {
        for (int i = 0; i < 9; i++)
            indexed_lattice[image_number * 9 + i] = msg.indexing_lattice[i];
    }
}

void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
    if (!npeaks.empty())
        data_file.SaveVector("/entry/MX/nPeaks", npeaks);
    if (!strong_pixel_count.empty())
        data_file.SaveVector("/entry/MX/strongPixels", strong_pixel_count);
    if (!indexed.empty())
        data_file.SaveVector("/entry/MX/imageIndexed", indexed);
    if (!indexed_lattice.empty())
        data_file.SaveVector("/entry/MX/latticeIndexed", indexed_lattice, {(hsize_t) (max_image_number + 1), 9});
}