main.cpp

#include "czi_parser.h"
#include "file_system.h"

int main(int argc, char **argv)
{
    std::string cziFile;
    // #if DEBUG
    //     printf("***DEBUG MODE***\n");
    //     if (argc == 1)
    //     {
    //         argv[1] = (char *)"/home/mor0146/gitlab/data_project/czi-format/data/MultiResolution-Mosaic.czi";
    //         argv[2] = (char *)"--dump-image-data";
    //         argv[3] = (char *)"imgdump/";
    //     }
    //     argc = 4;
    //     cziFile = argv[1];
    // #else

    // #endif
    cziFile = (argc > 1) ? argv[1] : "/home/mor0146/gitlab/data_project/czi-format/data/CZT-Stack-Anno.czi"; //"/home/mor0146/gitlab/data_project/czi-format/data/m2/exampleSingleChannel.czi";

    always_assert(is_file(cziFile));

    std::string method = argc > 2 ? argv[2] : "";
    std::string dumpName = argc > 3 ? argv[3] : "";

    bool report = method == "--report";
    bool reportAll = method == "--report-verbose";
    bool dumpRawImageData = method == "--dump-raw-image-data";
    bool dumpImageData = method == "--dump-image-data";

    auto name = get_filename_without_extension(cziFile);
    auto x = get_files_in_parent_directory(cziFile, true);
    auto y = get_files_with_same_prefix(x, name);

    CziParser parser;
    auto parseResult = parser.parse_czi_file(cziFile);

    if (reportAll)
        parseResult.report_verbose();
    else if (report)
        parseResult.report();
    else if (dumpRawImageData)
        parseResult.dump_image_data(dumpName);
    else if (dumpImageData)
    {
        auto imgMat = parseResult.get_image(0);
        imgMat.save_as_ppm("matrix");
        //TODO: Re-Enable it.
        //parseResult.extract_images(dumpName);
    }

    printf("Finished.\n");

    return 0;
}