animaPatientToGroupODFComparison.cxx

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#include <iostream>
#include <tclap/CmdLine.h>

#include <animaReadWriteFunctions.h>
#include <animaPatientToGroupODFComparisonImageFilter.h>

#include <animaODFFunctions.h>

//Update progression of the process
void eventCallback (itk::Object* caller, const itk::EventObject& event, void* clientData)
{
    itk::ProcessObject * processObject = (itk::ProcessObject*) caller;
    std::cout<<"\033[K\rProgression: "<<(int)(processObject->GetProgress() * 100)<<"%"<<std::flush;
}

int main(int argc, char **argv)
{
    TCLAP::CmdLine cmd("INRIA / IRISA - VisAGeS/Empenn Team", ' ',ANIMA_VERSION);

    TCLAP::ValueArg<std::string> refODFArg("i","inputodf","ODF Test Image",true,"","ODF test image",cmd);

    TCLAP::ValueArg<std::string> dataODFArg("I","databaseodf","ODF Database Image List",true,"","ODF database image list",cmd);
    
    TCLAP::ValueArg<std::string> maskArg("m","maskname","Computation mask",true,"","computation mask",cmd);
    TCLAP::ValueArg<std::string> resArg("o","outputname","Z-Score output image",true,"","Z-Score output image",cmd);
    TCLAP::ValueArg<std::string> resPValArg("O","outpvalname","P-value output image",true,"","P-Value output image",cmd);

    TCLAP::ValueArg<std::string> statTestArg("t","stat-test","Statistical test to use ([fisher],chi)",false,"fisher","statistical test",cmd);
    TCLAP::ValueArg<double> expVarArg("e","expvar","PCA threshold: threshold on eigenvalues to compute the new basis (default: 0.5)",false,0.5,"PCA threshold",cmd);
    TCLAP::ValueArg<unsigned int> numEigenArg("E","numeigenpca","Number of eigenvalues to keep (default: 6)",false,6,"Number of PCA eigen values",cmd);
    
    TCLAP::ValueArg<unsigned int> nbpArg("p","numberofthreads","Number of threads to run on (default: all cores)",false,itk::MultiThreaderBase::GetGlobalDefaultNumberOfThreads(),"number of threads",cmd);

    TCLAP::ValueArg<unsigned int> nbThetaArg("T","theta","Number of theta values (theta varies between 0 and pi/2",false,0,"number of theta values",cmd);
    TCLAP::ValueArg<unsigned int> nbPhiArg("P","phi","Number of phi values (theta varies between 0 and 2 pi",false,0,"number of phi values",cmd);

    TCLAP::ValueArg<std::string> samplesFileNameArg("d","sampledirectionsfile","Samples directions in a text file",false,"","Samples directions file",cmd);

    try
    {
        cmd.parse(argc,argv);
    }
    catch (TCLAP::ArgException& e)
    {
        std::cerr << "Error: " << e.error() << "for argument " << e.argId() << std::endl;
        return EXIT_FAILURE;
    }

    typedef itk::VectorImage<double,3> ODFImageType;
    typedef anima::PatientToGroupODFComparisonImageFilter<double> MAOZScoreImageFilterType;

    itk::CStyleCommand::Pointer callback = itk::CStyleCommand::New();
    callback->SetCallback(eventCallback);

    MAOZScoreImageFilterType::Pointer mainFilter = MAOZScoreImageFilterType::New();
    mainFilter->SetComputationMask(anima::readImage < itk::Image <unsigned char,3> > (maskArg.getValue()));
    mainFilter->SetNumberOfWorkUnits(nbpArg.getValue());

    mainFilter->SetInput(anima::readImage <ODFImageType> (refODFArg.getValue()));
    mainFilter->SetExplainedRatio(expVarArg.getValue());
    mainFilter->SetNumEigenValuesPCA(numEigenArg.getValue());

    std::vector < std::vector <double> > sampleDirections = anima::InitializeSampleDirections(nbThetaArg.getValue(),nbPhiArg.getValue(),
                                                                                              samplesFileNameArg.getValue());

    mainFilter->SetSampleDirections(sampleDirections);

    if (statTestArg.getValue() == "chi")
        mainFilter->SetStatisticalTestType(MAOZScoreImageFilterType::CHI_SQUARE);
    else
        mainFilter->SetStatisticalTestType(MAOZScoreImageFilterType::FISHER);

    std::ifstream fileIn(dataODFArg.getValue());
    if (!fileIn.is_open())
    {
        std::cerr << "Could not open ODF data file (" << dataODFArg.getValue() << ")" << std::endl;
        return EXIT_FAILURE;
    }
    
    while (!fileIn.eof())
    {
        char tmpStr[2048];
        fileIn.getline(tmpStr,2048);
        
        if (strcmp(tmpStr,"") == 0)
            continue;
        
        std::cout << "Loading ODF image " << tmpStr << "..." << std::endl;
        mainFilter->AddDatabaseInput(anima::readImage <ODFImageType> (tmpStr));
    }
    fileIn.close();
    
    mainFilter->AddObserver(itk::ProgressEvent(), callback);

    try
    {
        mainFilter->Update();
    }
    catch(itk::ExceptionObject &e)
    {
        std::cerr << e << std::endl;
        return EXIT_FAILURE;
    }
    
    anima::writeImage < itk::Image <double, 3> > (resArg.getValue(),mainFilter->GetOutput(0));
    anima::writeImage < itk::Image <double, 3> > (resPValArg.getValue(),mainFilter->GetOutput(1));

    return EXIT_SUCCESS;
}