Jungfraujoch/writer/FileWriter.cpp

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

#include "FileWriter.h"
#include <nlohmann/json.hpp>
#include "MakeDirectory.h"
#include "../common/CheckPath.h"
#include "../common/Logger.h"
#include "../common/JFJochException.h"
#include "../preview/JFJochTIFF.h"
#include "JFJochDecompress.h"

FileWriter::FileWriter(const StartMessage &request)
        : start_message(request) {
    if (start_message.file_format)
        format = start_message.file_format.value();

    CheckPath(start_message.file_prefix);
    MakeDirectory(start_message.file_prefix);
    if (start_message.write_master_file && start_message.write_master_file.value()) {
        switch (format) {
            case FileWriterFormat::NXmxLegacy:
            case FileWriterFormat::NXmxVDS:
                CreateHDF5MasterFile(request);
                break;
            case FileWriterFormat::CBF:
                cbf_writer = std::make_unique<CBFWriter>(start_message);
                break;
            default:
                // Do nothing
                break;
        }
    }
}

void FileWriter::Write(const DataMessage &msg) {
    switch (format) {
        case FileWriterFormat::DataOnly:
        case FileWriterFormat::NXmxLegacy:
        case FileWriterFormat::NXmxVDS:
            WriteHDF5(msg);
            break;
        case FileWriterFormat::CBF:
            cbf_writer->WriteImage(msg);
            break;
        case FileWriterFormat::TIFF:
            WriteTIFF(msg);
            break;
        case FileWriterFormat::NoFile:
            // Do nothing
            break;
    }
}

void FileWriter::WriteTIFF(const DataMessage &msg) {
    const std::string file_name = fmt::format("{:s}{:06d}.tiff", start_message.file_prefix, msg.number);
    WriteTIFFToFile(file_name,msg.image);
}


void FileWriter::WriteHDF5(const DataMessage& msg) {
    std::lock_guard<std::mutex> lock(hdf5_mutex);
    if (msg.image.GetCompressedSize() == 0)
        return;

    if (msg.number < 0)
        throw JFJochException(JFJochExceptionCategory::ArrayOutOfBounds, "No support for negative images");

    uint64_t file_number = 0;
    size_t image_number = msg.number;
    if (start_message.images_per_file > 0) {
        file_number = msg.number / start_message.images_per_file;
        image_number = msg.number % start_message.images_per_file;
    }

    if (closed_files.contains(file_number))
        return;

    if (files.size() <= file_number)
        files.resize(file_number + 1);

    if (!files[file_number])
        files[file_number] = std::make_unique<HDF5DataFile>(start_message, file_number);

    files[file_number]->Write(msg, image_number);

    if (files[file_number]->GetNumImages() == start_message.images_per_file) {
        CloseFile(file_number);
    } else {
        CloseOldFiles(static_cast<uint64_t>(msg.number));
    }
}

void FileWriter::CloseFile(uint64_t file_number) {
    if (file_number >= files.size())
        return;
    if (!files[file_number])
        return;
    if (closed_files.contains(file_number))
        return;

    AddStats(files[file_number]->Close());
    files[file_number].reset();
    closed_files.insert(file_number);
}

void FileWriter::CloseOldFiles(uint64_t current_image_number) {
    if (start_message.images_per_file == 0)
        return;

    for (uint64_t f = 0; f < files.size(); ++f) {
        if (!files[f] || closed_files.contains(f))
            continue;

        const uint64_t file_end_image = (f + 1) * start_message.images_per_file - 1;
        if (current_image_number > file_end_image + close_file_lag_images) {
            CloseFile(f);
        }
    }
}

std::vector<HDF5DataFileStatistics> FileWriter::Finalize() {

    if (master_file) {
        std::lock_guard<std::mutex> lock(hdf5_mutex);
        master_file.reset();
    }

    for (uint64_t f = 0; f < files.size(); ++f) {
        if (files[f] && !closed_files.contains(f))
            CloseFile(f);
    }
    return stats;
}

void FileWriter::AddStats(const std::optional<HDF5DataFileStatistics>& s) {
    if (!s)
        return;

    stats.push_back(*s);
    if (finalized_file_socket) {
        nlohmann::json j;
        j["filename"] = s->filename;
        j["nimages"] = s->total_images;
        j["file_number"] = s->file_number;

        j["detector_distance_m"] = start_message.detector_distance;
        j["beam_x_pxl"] = start_message.beam_center_x;
        j["beam_y_pxl"] = start_message.beam_center_y;
        j["pixel_size_m"] = start_message.pixel_size_x;
        j["detector_width_pxl"] = start_message.image_size_x;
        j["detector_height_pxl"] = start_message.image_size_y;
        j["incident_energy_eV"] = start_message.incident_energy;
        j["saturation"] = start_message.saturation_value;
        j["sample_name"] = start_message.sample_name;
        j["run_number"] = start_message.run_number;
        j["run_name"] = start_message.run_name;

        if (!start_message.experiment_group.empty())
            j["experiment_group"] = start_message.experiment_group;

        if (start_message.unit_cell) {
            j["unit_cell"]["a"] = start_message.unit_cell->a;
            j["unit_cell"]["b"] = start_message.unit_cell->b;
            j["unit_cell"]["c"] = start_message.unit_cell->c;
            j["unit_cell"]["alpha"] = start_message.unit_cell->alpha;
            j["unit_cell"]["beta"] = start_message.unit_cell->beta;
            j["unit_cell"]["gamma"] = start_message.unit_cell->gamma;
        }
        if (start_message.space_group_number)
            j["space_group_number"] = start_message.space_group_number.value();
        if (start_message.error_value)
            j["underload"] = start_message.error_value.value();

        j["user_data"] = start_message.user_data;
        finalized_file_socket->Send(j.dump());
    }
}

void FileWriter::SetupFinalizedFileSocket(const std::string &addr) {
    finalized_file_socket = std::make_unique<ZMQSocket>(ZMQSocketType::Pub);
    finalized_file_socket->Bind(addr);
}

std::optional<std::string> FileWriter::GetZMQAddr() {
    if (finalized_file_socket) {
        return finalized_file_socket->GetEndpointName();
    } else
        return {};
}

void FileWriter::CreateHDF5MasterFile(const StartMessage &msg) {
    std::lock_guard<std::mutex> lock(hdf5_mutex);
    master_file = std::make_unique<NXmx>(msg);
}

void FileWriter::WriteHDF5(const CompressedImage &msg) {
    if (master_file) {
        std::lock_guard<std::mutex> lock(hdf5_mutex);
        try {
            master_file->WriteCalibration(msg);
        } catch (const JFJochException &e) {
            spdlog::error("Calibration {} not written {}", msg.GetChannel(), e.what());
        }
    }
}

void FileWriter::WriteHDF5(const EndMessage &msg) {
    if (master_file) {
        std::lock_guard<std::mutex> lock(hdf5_mutex);
        master_file->Finalize(msg);
    }
}