ShapeAnalysis3d

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

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

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

// used to process shape 3d analysis
#include <IPSDKIPL/IPSDKIPLShapeAnalysis/Measure/Geometry/Basic/HolesBasicPolicyMsrParams.h>
#include <IPSDKIPL/IPSDKIPLShapeAnalysis/Measure/Geometry/FormFactor/MaxFeretDiameter/MaxFeretDiameterMsrParams.h>
#include <IPSDKIPL/IPSDKIPLShapeAnalysis/Measure/Geometry/FormFactor/MinFeretDiameter/MinFeretDiameterMsrParams.h>
#include <IPSDKIPL/IPSDKIPLShapeSegmentation/Processor/LabelShapeExtraction3d/LabelShapeExtraction3d.h>
#include <IPSDKIPL/IPSDKIPLAdvancedMorphology/Processor/ConnectedComponent3dImg/ConnectedComponent3dImg.h>
#include <IPSDKIPL/IPSDKIPLShapeAnalysis/Processor/ShapeAnalysis3d/ShapeAnalysis3d.h>
#include <IPSDKBaseShapeAnalysis/Measure/BaseMeasure.h>
#include <IPSDKBaseShapeAnalysis/Measure/Result/ValueMeasureResult.h>
#include <IPSDKBaseShapeAnalysis/Measure/Result/MeasureResultUtils.h>
#include <IPSDKBaseShapeAnalysis/Measure/Info/MeasureInfoSet.h>
#include <IPSDKBaseShapeAnalysis/Measure/Info/MeasureInfoUtils.h>
#include <IPSDKBaseShapeAnalysis/Measure/MeasureSet.h>
#include <IPSDKBaseShapeSegmentation/Entity/3d/Shape3dColl.h>

// used to manage exceptions possibly thrown by algoritms 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_ShapeAnalysis3d/Logger/Sample_ShapeAnalysis3dLog.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::geom;
using namespace ipsdk::shape::analysis;
using namespace ipsdk::shape::segmentation;
using namespace ipsdk::image;
using namespace ipsdk::image::file;
using namespace ipsdk::imaproc;
using namespace ipsdk::imaproc::advmorpho;
using namespace ipsdk::imaproc::shape::analysis;
using namespace ipsdk::imaproc::shape::segmentation;
using namespace ipsdk::sample;

bool
readCmdArguments(int argc, char* argv[],
                 boost::filesystem::path& inputGreyImgPath,
                 boost::filesystem::path& inputBinImgPath,
                 boost::filesystem::path& outputCsvResultPath);


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_SHAPEANALYSIS3D_LOG_WARN(
            [eSample_ShapeAnalysis3dMessage::eIPSDKLibInitWarn]
            % initRes.getMsg());
        break;
    case ipsdk::core::eLibInitStatus::eLIS_Failed:
        // IPSDK library initialization; notify the user and exit
        SAMPLE_SHAPEANALYSIS3D_LOG_ERROR(
            [eSample_ShapeAnalysis3dMessage::eIPSDKLibInitFailed] % initRes.getMsg());
        return -1;
        break;
    default:
        break;
    }

    // read program options from command line, and, if appropriate,
    // initialize input images files and output csv results paths
    boost::filesystem::path inputGreyImgPath, inputBinImgPath, outputCsvResultPath;
    if(!readCmdArguments(argc, argv, inputGreyImgPath, inputBinImgPath, outputCsvResultPath))
        return -1;

    // display a log message in "INFO" level, to notify the user of the current
    // step
    SAMPLE_SHAPEANALYSIS3D_LOG_INFO(
        [eSample_ShapeAnalysis3dMessage::eLoadingInputGreyImgFromTiffFile]
        % inputGreyImgPath.string());

    // opening grey level input image
    ImagePtr pInGreyImg3d = loadTiffImageFile(inputGreyImgPath, eTiffDirectoryMode::eTDM_Volume);

    // display a log message in "INFO" level, to notify the user of the current
    // step
    SAMPLE_SHAPEANALYSIS3D_LOG_INFO(
        [eSample_ShapeAnalysis3dMessage::eLoadingInputBinImgFromTiffFile]
        % inputBinImgPath.string());

    // opening binary input image
    ImagePtr pInBinImg3d = loadTiffImageFile(inputBinImgPath, eTiffDirectoryMode::eTDM_Volume);

    // connected components analysis
    ImagePtr pInLabelImg3d = connectedComponent3dImg(pInBinImg3d);

    // extract contours from connected component (label) image
    Shape3dCollPtr pShape3dColl = labelShapeExtraction3d(pInLabelImg3d);
    
    // define a measure info set
    MeasureInfoSetPtr pMeasureInfoSet = MeasureInfoSet::create3dInstance();
    createMeasureInfo(pMeasureInfoSet, "AreaMinusHoles", "Area3dMsr", createHolesBasicPolicyMsrParams(true));
    createMeasureInfo(pMeasureInfoSet, "AreaWithHoles", "Area3dMsr", createHolesBasicPolicyMsrParams(false));
    createMeasureInfo(pMeasureInfoSet, "VolumeMinusHoles", "Volume3dMsr", createHolesBasicPolicyMsrParams(true));
    createMeasureInfo(pMeasureInfoSet, "VolumeWithHoles", "Volume3dMsr", createHolesBasicPolicyMsrParams(false));
    createMeasureInfo(pMeasureInfoSet, "EquivalentRay", "EquivalentRayMsr");
    createMeasureInfo(pMeasureInfoSet, "SumMsr");
    createMeasureInfo(pMeasureInfoSet, "Convexity", "ConvexityMsr", createHolesBasicPolicyMsrParams(true));
    
    // compute measure on extracted data
    MeasureSetPtr pOutMeasureSet = shapeAnalysis3d(pInGreyImg3d, pShape3dColl, pMeasureInfoSet);

    // retrieve area 3d results for 'minus holes' parametrization for example
    const MeasureConstPtr& pAreaMinusHolesOutMsr = pOutMeasureSet->getMeasure("AreaMinusHoles");
    const std::vector<ipReal64>& pAreaMinusHolesRes = extractValueResults<ipReal64>(pAreaMinusHolesOutMsr);

    // display a log message in "INFO" level, to notify the user of the current
    // step
    SAMPLE_SHAPEANALYSIS3D_LOG_INFO(
        [eSample_ShapeAnalysis3dMessage::eSavingOutputCsvResultsFile]
        % outputCsvResultPath.string());

    // save all analysis results to output csv file
    BoolResult bWritten = saveCsvMeasureFile(outputCsvResultPath, *pOutMeasureSet);

    
    if (bWritten == false) {

        SAMPLE_SHAPEANALYSIS3D_LOG_ERROR(
            [eSample_ShapeAnalysis3dMessage::eFailedToSaveCsvResultsFile]
            % outputCsvResultPath.string() % bWritten.getMsg());

        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& inputBinImgPath,
                 boost::filesystem::path& outputCsvResultPath)
{
    // 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)")
        ("inputBinImgPath", value<path>(), 
            "input binary image file path (optional; only TIFF format is accepted)")
        ("outputCsvResultPath", value<path>(),
            "output csv result file 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_SHAPEANALYSIS3D_LOG_ERROR(
                    [eSample_ShapeAnalysis3dMessage::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) / "blobs3d_483x348x31_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 binRelToRootDir =
        path("data") / "Sample" / "images" / "blobs3d_483x348x31_Binary.tif";
    
    // initialize input binary image file path with a default file path
    inputBinImgPath = getProjectRootDirectory() / binRelToRootDir;
    if(!boost::filesystem::exists(inputBinImgPath))
        inputBinImgPath = getIPSDKRootDirectory() / binRelToRootDir;

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

    // initialize output csv results path with a default file path
    outputCsvResultPath = getProjectRootDirectory() / binRelToRootDir;
    if(vm.count("outputCsvResultPath"))
        // ... replace the default one by his own
        outputCsvResultPath = vm["outputCsvResultPath"].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_SHAPEANALYSIS3D_LOG_ERROR(
                    [eSample_ShapeAnalysis3dMessage::eErrorSavingCsvResultsFile]
                    % outputDir % e.what());
            }
        }

        // initialize output csv result path with a default file path
        outputCsvResultPath = outputDir / "shapeAnalysis3d.csv";
    }

    return true;
}