Quantification3d

// main.cpp:
// ---------
//
//
// --- IPSDK includes
// ------------------

// used to initialize IPSDK environment
#include <IPSDKCore/Config/LibraryInitializer.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 compute the separated bilateral 3d smoothing
#include <IPSDKIPL/IPSDKIPLFiltering/Processor/SeparatedBilateral3dImg/SeparatedBilateral3dImg.h>

// used to compute the Otsu threshold
#include <IPSDKIPL/IPSDKIPLBinarization/Processor/OtsuThresholdImg/OtsuThresholdImg.h>

// used to compte the 3d binary watershed separation
#include <IPSDKIPL/IPSDKIPLAdvancedMorphology/Processor/WatershedBinarySeparation3dImg/WatershedBinarySeparation3dImg.h>

// used to compute the connected component analysis
#include <IPSDKIPL/IPSDKIPLAdvancedMorphology/Processor/ConnectedComponent3dImg/ConnectedComponent3dImg.h>

// used to compute the 3d label contour extraction
#include <IPSDKIPL/IPSDKIPLShapeSegmentation/Processor/LabelShapeExtraction3d/LabelShapeExtraction3d.h>

// used to compute measures on shapes
#include <IPSDKIPL/IPSDKIPLShapeAnalysis/Processor/ShapeAnalysis3d/ShapeAnalysis3d.h>

// used for saveCsvMeasureFile
#include <IPSDKBaseShapeAnalysis/Measure/Result/MeasureResultUtils.h>

// used for create3dInstance
#include <IPSDKBaseShapeAnalysis/Measure/Info/MeasureInfoSet.h>

// used for createMeasureInfo
#include <IPSDKBaseShapeAnalysis/Measure/Info/MeasureInfoUtils.h>

// used for the getMeasure() method
#include <IPSDKBaseShapeAnalysis/Measure/MeasureSet.h>

// used to specify the maxFeretDiameter measure parameters
#include <IPSDKIPL/IPSDKIPLShapeAnalysis/Measure/Geometry/FormFactor/MaxFeretDiameter/MaxFeretDiameterMsrParams.h>

// used to retrieve the results of the Area3d measure
#include <IPSDKIPL/IPSDKIPLShapeAnalysis/Measure/Geometry/Basic/Area3d/Area3dMsr.h>

// used to display log messages
#include <Sample/Sample_Quantification3d/Logger/Sample_Quantification3dLog.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>

// To deactivate GPU support
#include <IPSDKCore/ComputerInfo/LocalComputerInfoUtils.h>

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

using namespace ipsdk;
using namespace ipsdk::image;
using namespace ipsdk::imaproc;
using namespace ipsdk::sample;

bool
readCmdArguments(int argc, char* argv[],
                 boost::filesystem::path& inImgFilePath,
                 boost::filesystem::path& outputReportPath,
                 ipUInt32& inHalfKnlSize,
                 ipReal64& inSpaceSigma,
                 ipReal32& inDilateFactor);


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_QUANTIFICATION3D_LOG_WARN(
            [eSample_Quantification3dMessage::eIPSDKLibInitWarn]
            % initRes.getMsg());
        break;
    case ipsdk::core::eLibInitStatus::eLIS_Failed:
        // IPSDK library initialization; notify the user and exit
        SAMPLE_QUANTIFICATION3D_LOG_ERROR(
            [eSample_Quantification3dMessage::eIPSDKLibInitFailed] % initRes.getMsg());
        return -1;
        break;
    default:
        break;
    }

    // Deactivate GPU support
    if (ipsdk::core::isGpuSupportActivated())
        ipsdk::core::deactivateGpuSupport();

    // boost objects, used to store input and output files pathes
    boost::filesystem::path inputImgPath, outputReportPath;
    ipUInt32 inHalfKnlSize;
    ipReal32 inDilateFactor;
    ipReal64 inSpaceSigma;

    // read program options from command line, and, if appropriate,
    // initialize input and output images files paths
    if(!readCmdArguments(argc, argv, inputImgPath, outputReportPath, inHalfKnlSize, inSpaceSigma, inDilateFactor)) {
        // clear IPSDK environment features; should be called before exiting
        // program
        ipsdk::core::LibraryInitializer::getInstance().clear();

        return -1;
    }
    
    // display a log message in "INFO" level, to notify the user of the current step
    SAMPLE_QUANTIFICATION3D_LOG_INFO(
        [eSample_Quantification3dMessage::eLoadingInputImgFromTiffFile]
        % inputImgPath.string());

    // declare the variable that will contain the input image, loaded from TIFF file
    ipsdk::image::ImagePtr pInGreyImg;
    try {
        // read input image from specified path
        pInGreyImg = ipsdk::image::file::loadTiffImageFile(inputImgPath, ipsdk::image::file::eTiffDirectoryMode::eTDM_Volume);
    } catch(const image::file::IPSDKImageFileException& e) {

        // loadTiffImageFile function threw an exception; display error log
        // message
        SAMPLE_QUANTIFICATION3D_LOG_ERROR(
            [eSample_Quantification3dMessage::eErrorLoadingInputImgFromTiffFile]
            % inputImgPath.string() % 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;
    }
    
    // display a log message in "INFO" level, to notify the user of the current step
    SAMPLE_QUANTIFICATION3D_LOG_INFO(
        [eSample_Quantification3dMessage::eComputingFilter]);

    // filtering of input image to smooth defaults
    ipsdk::image::ImagePtr pGreyFilteredImg = ipsdk::imaproc::filter::separatedBilateral3dImg(pInGreyImg, 3, 8);

    // Define the path to save the output images
    const path binImgPath =
            getIPSDKDefaultDirectory(eDefaultExternalDirectory::eDED_Tmp) / "Sample";

    // display a log message in "INFO" level, to notify the user of the current step
    SAMPLE_QUANTIFICATION3D_LOG_INFO(
        [eSample_Quantification3dMessage::eComputingBinarization]);

    // auto threshold on filtered image
    ipsdk::imaproc::bin::OtsuResult otsuResult = ipsdk::imaproc::bin::otsuThresholdImg(pGreyFilteredImg);
    ipsdk::image::file::saveTiffImageFile(binImgPath/"binImg.tif", otsuResult._pOutImg);

    // display a log message in "INFO" level, to notify the user of the current step
    SAMPLE_QUANTIFICATION3D_LOG_INFO(
        [eSample_Quantification3dMessage::eComputingBinSep]);

    // automatic separation of binary shapes
    ipsdk::image::ImagePtr pBinSepImg =
        ipsdk::imaproc::advmorpho::watershedBinarySeparation3dImg(otsuResult._pOutImg, inDilateFactor,
                                                                  ipsdk::imaproc::attr::eWatershedSeparationMode::eWSM_Split);
    ipsdk::image::file::saveTiffImageFile(binImgPath/"binSepImg.tif", pBinSepImg);
    
    // display a log message in "INFO" level, to notify the user of the current step
    SAMPLE_QUANTIFICATION3D_LOG_INFO(
        [eSample_Quantification3dMessage::eComputingConnComp]);

    // connected components analysis of separated binary image
    ipsdk::image::ImagePtr pLabelImg = ipsdk::imaproc::advmorpho::connectedComponent3dImg(pBinSepImg);
    ipsdk::image::file::saveTiffImageFile(binImgPath/"labelImg.tif", pLabelImg);
    
    // display a log message in "INFO" level, to notify the user of the current step
    SAMPLE_QUANTIFICATION3D_LOG_INFO(
        [eSample_Quantification3dMessage::eDefiningMeasures]);

    // definition of measure set on shapes
    ipsdk::shape::analysis::MeasureInfoSetPtr pMeasureInfoSet3d = ipsdk::shape::analysis::MeasureInfoSet::create3dInstance();
    createMeasureInfo(pMeasureInfoSet3d, "Area3dMsr");
    createMeasureInfo(pMeasureInfoSet3d, "EquivalentRayMsr");
    createMeasureInfo(pMeasureInfoSet3d, "MaxFeretDiameterMsr", ipsdk::imaproc::shape::analysis::createMaxFeretDiameterMsrParams(180));
    createMeasureInfo(pMeasureInfoSet3d, "MeanMsr");
    
    // display a log message in "INFO" level, to notify the user of the current step
    SAMPLE_QUANTIFICATION3D_LOG_INFO(
        [eSample_Quantification3dMessage::eComputingMeasures]);

    // extract contours from connected component (label) image
    ipsdk::shape::segmentation::Shape3dCollPtr pShape3dColl = ipsdk::imaproc::shape::segmentation::labelShapeExtraction3d(pLabelImg);

    // shape analysis computation
    ipsdk::shape::analysis::MeasureSetPtr pMeasureSet = ipsdk::imaproc::shape::analysis::shapeAnalysis3d(pInGreyImg,  pShape3dColl,  pMeasureInfoSet3d);
    
    // display a log message in "INFO" level, to notify the user of the current step
    SAMPLE_QUANTIFICATION3D_LOG_INFO(
        [eSample_Quantification3dMessage::eSavingReport] % outputReportPath);

    // save report in csv format
    ipsdk::shape::analysis::saveCsvMeasureFile(outputReportPath, *pMeasureSet);

    // retrieve area measure results
    const ipsdk::shape::analysis::MeasureConstPtr& pArea3dOutMsr = pMeasureSet->getMeasure("Area3dMsr");
    const ipsdk::shape::analysis::ValueMeasureResult<ipReal64>& outAreaMsrResults = 
        static_cast<const ipsdk::shape::analysis::ValueMeasureResult<ipReal64>&>(pArea3dOutMsr->getMeasureResult());

    // extract associated results collection
    const std::vector<ipReal64> areaValues = outAreaMsrResults.getColl();

    // access to the first label area
    const ipReal64 firstLabelArea = areaValues[1];
    
    // display a log message in "INFO" level, to notify the user of the current step
    SAMPLE_QUANTIFICATION3D_LOG_INFO(
        [eSample_Quantification3dMessage::eDisplayFirstLabelArea] % firstLabelArea);


    return 0;
}

bool
readCmdArguments(int argc, char* argv[],
                 boost::filesystem::path& inputImgPath,
                 boost::filesystem::path& outputReportPath,
                 ipUInt32& inHalfKnlSize,
                 ipReal64& inSpaceSigma,
                 ipReal32& inDilateFactor)
{
    // list of allowed program options
    boost::program_options::options_description desc("Allowed options");
    desc.add_options()
        ("help", "produce help message")
        ("inputImg3dFilePath", value<path>(),
            "3d input image file path (optional; only TIFF format is accepted)")
        ("outputReportPath", value<path>(), 
            "output file path (optional; CSV resulting file path)")
        ("inHalfKnlSize", value<ipUInt32>(), 
            "half kernel size (optional; default value = 3)")
        ("inSpaceSigma", value<ipReal64>(), 
            "spatial Gaussien standard deviation (optional; default value = 8)")
        ("inDilateFactor", value<ipReal32>(), 
            "dilation factor (optional; CSV resulting file 5)")
        ;

    // 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_QUANTIFICATION3D_LOG_ERROR(
                    [eSample_Quantification3dMessage::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 image file path with a default file path
    inputImgPath = getIPSDKDirectory(eInternalDirectory::eID_Images) / "blobs3d_483x348x31_UInt8.tif";

    // if the user specified his own input image file path as argument...
    if(vm.count("inputImg3dFilePath"))
        // ... replace the default one by his own
        inputImgPath = vm["inputImg3dFilePath"].as<path>();
    
    // if the user specified his own output csv file path as argument...
    if(vm.count("outputReportPath"))
        // ... replace the default one by his own
        outputReportPath = vm["outputReportPath"].as<path>();
    else {
        // ... otherwise, output csv file 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_QUANTIFICATION3D_LOG_ERROR(
                    [eSample_Quantification3dMessage::eErrorSavingResultToCSVFile]
                    % outputDir % e.what());
            }
        }

        // initialize output image file path with a default file path
        outputReportPath = outputDir / "quantification3d.csv";
    }

    // if the user specified his own half kernel size as argument...
    inHalfKnlSize = 3;
    if(vm.count("inHalfKnlSize"))
        // ... replace the default one by his own
        inHalfKnlSize = vm["inHalfKnlSize"].as<ipUInt32>();

    // if the user specified his own spatial sigma as argument...
    inSpaceSigma = 8;
    if(vm.count("inSpaceSigma"))
        // ... replace the default one by his own
        inSpaceSigma = vm["inSpaceSigma"].as<ipReal64>();

    // if the user specified his own dilation factor as argument...
    inDilateFactor = 5;
    if(vm.count("inDilateFactor"))
        // ... replace the default one by his own
        inDilateFactor = vm["inDilateFactor"].as<ipReal32>();

    // check that input image file path exists. If not...
    if(!boost::filesystem::exists(inputImgPath)) {
        // ... notify the user, and abort
        SAMPLE_QUANTIFICATION3D_LOG_ERROR(
            [eSample_Quantification3dMessage::eErrorInputImgTiffFileNotFound]
            % inputImgPath);
        return false;
    }

    return true;
}