ShapeFiltering2dImg

// main.cpp:
// ---------
//
//

// --- IPSDK includes
// ------------------

// used to initialize IPSDK environment
#include <IPSDKCore/Config/LibraryInitializer.h>

// used to process shape 2d filtering
#include <IPSDKIPL/IPSDKIPLShapeAnalysis/Processor/ShapeFiltering2dImg/ShapeFiltering2dImg.h>

// used to manage exceptions possibly thrown by algorithms functions
#include <IPSDKBaseProcessing/Logger/IPSDKBaseProcessingException.h>

// used to catch exceptions potentially thrown  by functions loadTiffImageFile and saveTiffImageFile
#include <IPSDKImageFile/Logger/IPSDKImageFileException.h>

// used to read/write an image from/to a TIFF file:
#include <IPSDKImageFile/Tiff/TiffImageFileUtils.h>

// used to retrieve usual folders (IPSDK temporary folder, root development folder, etc.)
#include <IPSDKUtil/Tools/LibraryPath.h>

// used to display log messages
#include <Sample/Sample_ShapeFiltering2dImg/Logger/Sample_ShapeFiltering2dImgLog.h>

// --- third-party boost includes
// ------------------------------

// boost/filesystem/*: contains functions and classes providing facilities to
// manipulate files and directories, and associated paths
#include <boost/filesystem/path.hpp>
#include <boost/filesystem/convenience.hpp>

// boost/program_options/*: contains functions and classes used to manage and
// interpret arguments of command line
#include <boost/program_options/cmdline.hpp>
#include <boost/program_options/options_description.hpp>
#include <boost/program_options/parsers.hpp>
#include <boost/program_options/variables_map.hpp>

// --- third-party log4cplus include
// ---------------------------------

// used to add console as output support of logs
#include <log4cplus/consoleappender.h>

// --- STL include
// ---------------

// for std::cout
#include <iostream>

using namespace boost::filesystem;
using namespace boost::program_options;

using namespace ipsdk;
using namespace ipsdk::image;
using namespace ipsdk::image::file;
using namespace ipsdk::imaproc;
using namespace ipsdk::imaproc::shape::analysis;
using namespace ipsdk::sample;

bool
readCmdArguments(int argc, char* argv[],
                 boost::filesystem::path& inputGreyImgPath,
                 boost::filesystem::path& inputBinLabImgPath,
                 std::string& inputFilterFormula,
                 boost::filesystem::path& outputImgPath);


int
main(int argc, char* argv[])
{
    // add console appender for application logs
    log4cplus::SharedAppenderPtr pConsole(new log4cplus::ConsoleAppender);
    log4cplus::Logger::getRoot().addAppender(pConsole);
    log4cplus::Logger::getRoot().setLogLevel(log4cplus::INFO_LOG_LEVEL);

    // initialize IPSDK environment (first call to be done before calling any
    // function or using any entity of IPSDK environment)
    const ipsdk::core::LibInitResult initRes =
        ipsdk::core::LibraryInitializer::getInstance().init();

    switch(initRes.getResult().value()) {
    case ipsdk::core::eLibInitStatus::eLIS_Warn:
        // IPSDK library is initialized but there were warnings;
        // notify the user by displaying a message
        SAMPLE_SHAPEFILTERING2DIMG_LOG_WARN(
            [eSample_ShapeFiltering2dImgMessage::eIPSDKLibInitWarn]
            % initRes.getMsg());
        break;
    case ipsdk::core::eLibInitStatus::eLIS_Failed:
        // IPSDK library initialization; notify the user and exit
        SAMPLE_SHAPEFILTERING2DIMG_LOG_ERROR(
            [eSample_ShapeFiltering2dImgMessage::eIPSDKLibInitFailed] % initRes.getMsg());
        return -1;
        break;
    default:
        break;
    }

    // read program options from command line, and, if appropriate,
    // initialize input and output images files and used filtering formula
    boost::filesystem::path inputGreyImgPath, inputBinLabImgPath, outputImgPath;
    std::string inputFilterFormula;
    if(!readCmdArguments(argc, argv, inputGreyImgPath, inputBinLabImgPath, inputFilterFormula, outputImgPath))
        return -1;

    // display a log message in "INFO" level, to notify the user of the current
    // step
    SAMPLE_SHAPEFILTERING2DIMG_LOG_INFO(
        [eSample_ShapeFiltering2dImgMessage::eLoadingInputGreyImgFromTiffFile]
        % inputGreyImgPath.string());

    // opening grey level input image
    ImagePtr pInGreyImg = loadTiffImageFile(inputGreyImgPath);

    // display a log message in "INFO" level, to notify the user of the current
    // step
    SAMPLE_SHAPEFILTERING2DIMG_LOG_INFO(
        [eSample_ShapeFiltering2dImgMessage::eLoadingInputBinLabImgFromTiffFile]
        % inputBinLabImgPath.string());

    // opening binary/label input image
    ImagePtr pInBinLabImg = loadTiffImageFile(inputBinLabImgPath);

    // shape 2d filtering operation
    ImagePtr pOutImg;
    try {

        pOutImg = shapeFiltering2dImg(pInBinLabImg, pInGreyImg, inputFilterFormula);
    } catch(const BaseException& e) {

        SAMPLE_SHAPEFILTERING2DIMG_LOG_ERROR(
            [eSample_ShapeFiltering2dImgMessage::eErrorProcessingFiltering]
            % e.getMsg());

        // clear IPSDK environment features; should be called before exiting
        // program
        ipsdk::core::LibraryInitializer::getInstance().clear();

        // quit the application with an exit code indicating an error
        return -1;
    }

    try {
        // save the resulting image in specified path
        ipsdk::image::file::saveTiffImageFile(outputImgPath, pOutImg);
    } catch(const image::file::IPSDKImageFileException& e) {

        SAMPLE_SHAPEFILTERING2DIMG_LOG_ERROR(
            [eSample_ShapeFiltering2dImgMessage::eErrorSavingImgTiffFile]
            % outputImgPath % e.getMsg());

        // clear IPSDK environment features; should be called before exiting
        // program
        ipsdk::core::LibraryInitializer::getInstance().clear();

        // quit the application with an exit code indicating an error
        return -1;
    }

    // clearing IPSDK environment features; should be called before exiting
    // program
    ipsdk::core::LibraryInitializer::getInstance().clear();
    return 0;
}

bool
readCmdArguments(int argc, char* argv[],
                 boost::filesystem::path& inputGreyImgPath,
                 boost::filesystem::path& inputBinLabImgPath,
                 std::string& inputFilterFormula,
                 boost::filesystem::path& outputImgPath)
{
    // list of allowed program options
    boost::program_options::options_description desc("Allowed options");
    desc.add_options()
        ("help", "produce help message")
        ("inputGreyImgPath", value<path>(),
            "input grey image file path (optional; only TIFF format is accepted)")
        ("inputBinLabImgPath", value<path>(), 
            "input binary/label image file path (optional; only TIFF format is accepted)")
        ("inputFilterFormula", value<std::string>(), 
            "input formula string for filtering operation (optional)")
        ("outputImgPath", value<path>(), 
            "output result image path (optional)")
        ;

    // vm stores options found in command line
    boost::program_options::variables_map vm;

    try {
        boost::program_options::store(parse_command_line(argc, argv, desc), vm);
    } catch(const std::exception& e) {
        SAMPLE_SHAPEFILTERING2DIMG_LOG_ERROR(
                    [eSample_ShapeFiltering2dImgMessage::eErrorReadingCmdLine]
                    % e.what());
        return false;
    }
    
    boost::program_options::notify(vm);

    // if the user typed "<app_name>.exe --help"...
    if (vm.count("help")) {
        // ... the application displays help message
        std::cout << desc << "\n";
        return false;
    }

    // initialize input grey image file path with a default file path
    inputGreyImgPath = getIPSDKDirectory(eInternalDirectory::eID_Images) / "blobs_483x348_UInt8.tif";

    // if the user specified his own input image file path as argument...
    if(vm.count("inputGreyImgPath"))
        // ... replace the default one by his own
        inputGreyImgPath = vm["inputGreyImgPath"].as<path>();

    // initialize input image file path with a default file path
    const boost::filesystem::path binLabRelToRootDir =
        path("data") / "Sample" / "images" / "blobs_483x348_Binary.tif";
    
    // initialize input binary image file path with a default file path
    inputBinLabImgPath = getProjectRootDirectory() / binLabRelToRootDir;
    if(!boost::filesystem::exists(inputBinLabImgPath))
        inputBinLabImgPath = getIPSDKRootDirectory() / binLabRelToRootDir;

    // if the user specified his own input image file path as argument...
    if(vm.count("inputBinLabImgPath"))
        // ... replace the default one by his own
        inputBinLabImgPath = vm["inputBinLabImgPath"].as<path>();

    // initialize input filtering formula
    inputFilterFormula = "Area2dMsr > 800";

    // if the user specified his own formula as argument...
    if(vm.count("inputFilterFormula"))
        // ... replace the default one by his own
        inputFilterFormula = vm["inputFilterFormula"].as<std::string>();

    // if the user specified his own input image file path as argument...
    if(vm.count("outputImgFilePath"))
        // ... replace the default one by his own
        outputImgPath = vm["outputImgFilePath"].as<path>();
    else {
        // ... otherwise, output image will be saved in temporary user directory
        const path outputDir =
            getIPSDKDefaultDirectory(eDefaultExternalDirectory::eDED_Tmp) /
            "Sample";

        // if output directory does not exist, we try to create it
        if(!boost::filesystem::exists(outputDir)) {
            try {
                boost::filesystem::create_directories(outputDir);
            } catch(const std::exception& e) {
                SAMPLE_SHAPEFILTERING2DIMG_LOG_ERROR(
                    [eSample_ShapeFiltering2dImgMessage::eErrorSavingImgTiffFile]
                    % outputDir % e.what());
            }
        }

        // initialize output image file path with a default file path
        outputImgPath = outputDir / "shapeFiltering2dImg.tif";
    }

    return true;
}