Jungfraujoch/writer/HDF5DataFilePluginMX.h

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

#pragma once

#include "HDF5DataFilePlugin.h"
#include "../common/AutoIncrVector.h"

class HDF5DataFilePluginMX : public HDF5DataFilePlugin {
    const size_t max_spots;
    const size_t max_extra_lattices;
    const bool indexing;
    // spots
    std::vector<float> spot_x;
    std::vector<float> spot_y;
    std::vector<float> spot_int;
    std::vector<int8_t> spot_indexed;
    std::vector<int8_t> spot_ice_ring;
    std::vector<int8_t> spot_lattice;
    std::vector<int32_t> spot_h;
    std::vector<int32_t> spot_k;
    std::vector<int32_t> spot_l;
    std::vector<float> spot_dist_ewald;
    std::vector<int16_t> spot_panel;
    bool spot_panel_present = false; // written only for a detector with a panel table

    AutoIncrVector<float> beam_corr_x{NAN};
    AutoIncrVector<float> beam_corr_y{NAN};

    AutoIncrVector<uint32_t> npeaks;
    AutoIncrVector<uint32_t> strong_pixel_count;

    AutoIncrVector<uint32_t> spot_count_total;
    AutoIncrVector<uint32_t> spot_count_ice;
    AutoIncrVector<float> spot_count_ice_control{NAN};
    AutoIncrVector<uint32_t> spot_count_indexed;
    AutoIncrVector<uint32_t> spot_count_low_res;

    // indexing
    AutoIncrVector<uint8_t> indexed;
    AutoIncrVector<uint32_t> indexing_lattice_count;
    std::vector<float> indexed_lattice;
    std::vector<float> extra_lattices; // [nimages, max_extra_lattices, 9], NaN-filled

    // crystal
    AutoIncrVector<float> profile_radius{NAN};
    AutoIncrVector<float> mosaicity_deg{NAN};
    AutoIncrVector<float> b_factor{NAN};

    // bkg_estimate
    AutoIncrVector<float> bkg_estimate{NAN};
    AutoIncrVector<float> ice_ring_score{NAN};
    // NaN = the frame had no value (CANNOT SAY), which is not a zero - see SpindleTrigger.
    AutoIncrVector<float> spindle_blind_fraction{NAN};

    // resolution_estimation
    AutoIncrVector<float> resolution_estimate{NAN};

    AutoIncrVector<uint32_t> niggli_class;
    AutoIncrVector<std::string> bravais_lattice;

    AutoIncrVector<int64_t> integrated_reflections;

    // scaling
    bool image_scale_present = false;
    AutoIncrVector<float> image_scale_factor{NAN};
    AutoIncrVector<float> image_scale_cc{NAN};
    AutoIncrVector<float> image_scale_mosaicity{NAN};
public:
    explicit HDF5DataFilePluginMX(const StartMessage& msg);
    void OpenFile(HDF5File &data_file, const DataMessage& msg, size_t images_per_file) override;
    void Write(const DataMessage& msg, uint64_t image_number) override;
    void WriteFinal(HDF5File &data_file) override;
};