main.cpp

#include "czi_parser.h"
#include "file_system.h"
#include "compression/rle.h"
#include "utilities/args.hxx"
int main(int argc, char **argv)
{
    args::ArgumentParser argParser("CZI file tools", "Optional arguments are in [ ] necessary in < >.");
    args::Group cziFileGroup(argParser, "CZI file input - necessary.", args::Group::Validators::All);
    args::Group mainMethodGroup(argParser, "Main method - what to do with parsed file", args::Group::Validators::AtMostOne);
    args::Group parserOptionsGroup(argParser, "CZI parser options", args::Group::Validators::DontCare);
    args::Group optionsGroup(argParser, "Program options", args::Group::Validators::DontCare);

    args::ValueFlag<std::string> cziFile(cziFileGroup, "czi file", "CZI file to load.", {'i', "input"});

    args::HelpFlag helpMethod(mainMethodGroup, "help", "Print help", {'h', "help"});
    args::Flag reportMethod(mainMethodGroup, "report", "Basic information about CZI file. [verbose]", {"report"});

    args::Flag dontParseMetadataOption(parserOptionsGroup, "no metadata", "Dont read metadata byte", {"no-metadata"});

    args::Flag verboseOption(optionsGroup, "verbose", "Extend output of method", {'v', "verbose"});

    try
    {
        argParser.ParseCLI(argc, argv);
    }
    catch (args::Help)
    {
        std::cout << argParser;
        return 0;
    }
    catch (args::ValidationError e)
    {
        std::cout << e.what() << std::endl;
        std::cout << argParser;
        return 1;
    }
    catch (args::ParseError pe)
    {
        std::cout << pe.what() << std::endl;
        std::cout << argParser;
        return 1;
    }
    /*
    std::string 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";
    if (cziFile == "-v" || cziFile == "--version")
    {
#if DEBUG
        printf("Running `Debug` version\n.");
#else
        printf("Running `Release` version\n.");
#endif
        return 0;
    }

    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-images";
    bool nextImageDiff = method == "--diff-next";
    bool testRle = method == "--rle-report";

    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)
    {
        parseResult.extract_images(dumpName);
    }
    else if (nextImageDiff)
    {
        always_assert(dumpName != "");
        parseResult.differences_between_next(dumpName);
    }
    else if (testRle)
    {
        parseResult.test_rle_encode();
    }

    printf("Finished.\n");
*/
    return 0;
}