int main(int argc, const char *argv[])
{
	// Validate input parameters
	if (argc < 15) {
		std::cerr << "Missing parameters! Usage:" << std::endl;
		std::cerr << argv[0];
		std::cerr << " <Read/WriteDir> <InputImg> <OutputImg> ";
		std::cerr << "[seedX] [seedY] [seedZ] [initDist] ";
		std::cerr << "[sigma] [sigmoid K1] [sigmoid K2] ";
		std::cerr << "[propagation] [curvature] [advection] [iterations]";
		std::cerr << std::endl;
		return EXIT_FAILURE;
	}
	
	const unsigned int Dimension = 3;
	typedef float InputPixelType;
	typedef unsigned char OutputPixelType;
    typedef itk::Image< InputPixelType, Dimension > InputImageType;
	typedef itk::Image< OutputPixelType, Dimension > OutputImageType;

    ////////////////////////////////////////////////
    // 1) Read the input image

	typedef itk::ImageFileReader< InputImageType >  ReaderType;
	ReaderType::Pointer reader = ReaderType::New();
	std::string readpath( argv[1] );
	readpath.append( argv[2] );
	reader->SetFileName( readpath );
	reader->Update();
	
    ////////////////////////////////////////////////
    // 2) Curvature anisotropic diffusion
	
	typedef itk::CurvatureAnisotropicDiffusionImageFilter< 
		InputImageType, InputImageType > SmoothingFilterType;
	SmoothingFilterType::Pointer smoothing = SmoothingFilterType::New();
	smoothing->SetTimeStep(0.04);
	smoothing->SetNumberOfIterations(5);
	smoothing->SetConductanceParameter(9.0);
	smoothing->SetInput( reader->GetOutput() );
	
    ////////////////////////////////////////////////
    // 3) Gradient magnitude recursive Gaussian
	
	const double sigma = atof(argv[8]);
	typedef itk::GradientMagnitudeRecursiveGaussianImageFilter< 
		InputImageType, InputImageType > GradientFilterType;
	GradientFilterType::Pointer gradientMagnitude = GradientFilterType::New();
	gradientMagnitude->SetSigma( sigma );
	gradientMagnitude->SetInput( smoothing->GetOutput() );
	
    ////////////////////////////////////////////////
    // 4) Sigmoid mapping
	
	const double K1 = atof(argv[9]);
	const double K2 = atof(argv[10]);
	typedef itk::SigmoidImageFilter< InputImageType, InputImageType > 
		SigmoidFilterType;
	SigmoidFilterType::Pointer sigmoid = SigmoidFilterType::New();
	sigmoid->SetOutputMinimum(0.0);
	sigmoid->SetOutputMaximum(1.0);
	sigmoid->SetAlpha( (K2 - K1)/6 );
	sigmoid->SetBeta( (K1 + K2)/2 );
	sigmoid->SetInput( gradientMagnitude->GetOutput() );
	
    ////////////////////////////////////////////////
    // 5) Segmentation with geodesic active contour
	
	typedef itk::FastMarchingImageFilter< InputImageType, InputImageType > 
		FastMarchingFilterType;
	FastMarchingFilterType::Pointer fastMarching = FastMarchingFilterType::New();
	
	typedef itk::GeodesicActiveContourLevelSetImageFilter< 
		InputImageType, InputImageType > GeodesicActiveContourFilterType;
	GeodesicActiveContourFilterType::Pointer geodesicActiveContour = 
		GeodesicActiveContourFilterType::New();
	
	const double propagation = atof( argv[11] );
	const double curvature = atof( argv[12] );
	const double advection = atof( argv[13] );
	const double iterations = atoi( argv[14] );
	geodesicActiveContour->SetPropagationScaling( propagation );
	geodesicActiveContour->SetCurvatureScaling( curvature );
	geodesicActiveContour->SetAdvectionScaling( advection );
	geodesicActiveContour->SetMaximumRMSError(0.01);
	geodesicActiveContour->SetNumberOfIterations( iterations );
	
	geodesicActiveContour->SetInput( fastMarching->GetOutput() );
	geodesicActiveContour->SetFeatureImage( sigmoid->GetOutput() );
	
    ////////////////////////////////////////////////
    // 6) Binary thresholding
	
	typedef itk::BinaryThresholdImageFilter< InputImageType, OutputImageType > 
		ThresholdingFilterType;
	ThresholdingFilterType::Pointer thresholder = ThresholdingFilterType::New();
	thresholder->SetLowerThreshold(-1000.0);
	thresholder->SetUpperThreshold(0.0);
	thresholder->SetOutsideValue(0);
	thresholder->SetInsideValue(255);
	thresholder->SetInput( geodesicActiveContour->GetOutput() );
	
    ////////////////////////////////////////////////
    // 7) Finish setting up fast marching
	
	typedef FastMarchingFilterType::NodeContainer NodeContainer;
	typedef FastMarchingFilterType::NodeType NodeType;
	
	NodeContainer::Pointer seeds = NodeContainer::New();
	InputImageType::IndexType seedPosition;
	seedPosition[0] = atoi( argv[4] );
	seedPosition[1] = atoi( argv[5] );
	seedPosition[2] = atoi( argv[6] );
	const double initialDistance = atof( argv[7] );
	const double seedValue = -initialDistance;
	NodeType node;
	node.SetValue( seedValue );
	node.SetIndex( seedPosition );
	seeds->Initialize();
	seeds->InsertElement(0, node);
	
	fastMarching->SetTrialPoints( seeds );
	fastMarching->SetSpeedConstant(1.0);
	fastMarching->SetOutputSize( reader->GetOutput()->GetBufferedRegion().GetSize() );
	fastMarching->SetOutputRegion( reader->GetOutput()->GetBufferedRegion() );
	fastMarching->SetOutputSpacing( reader->GetOutput()->GetSpacing() );
	fastMarching->SetOutputOrigin( reader->GetOutput()->GetOrigin() );
	
	////////////////////////////////////////////////
    // 7) Write output image
	
	typedef itk::ImageFileWriter< OutputImageType > WriterType;
	WriterType::Pointer writer = WriterType::New();
	std::string writepath( argv[1] );
	writepath.append( argv[3] );
	writer->SetFileName( writepath );
	writer->SetInput( thresholder->GetOutput() );
	
	try {
		writer->Update();
	}
	catch( itk::ExceptionObject &excep ) {
		std::cerr << "Exception caught!" << std::endl;
		std::cerr << excep << std::endl;
		return EXIT_FAILURE;
	}
	
	// The following writer is used to save the output of the sigmoid mapping
	typedef itk::ImageFileWriter< InputImageType > InternalWriterType;
	InternalWriterType::Pointer speedWriter = InternalWriterType::New();
	speedWriter->SetInput( sigmoid->GetOutput() );
	std::string sigmoidpath( argv[1] );
	speedWriter->SetFileName( sigmoidpath.append("SigmoidForGeodesic.mha"));
	speedWriter->Update();
	
	return 0;
}
Exemple #2
0
void segment::Execute(int first,int last,double sig_min, double sig_max, double propagation, double curvature, double advection, double rms, int iterations, double alpha, double beta, double distance){
    ifstream myfile ("/home/gustavo/temp/endocardium.txt");
    for(int i =first; i<last;i++){
        typedef   float           InternalPixelType;
        const     unsigned int    Dimension = 2;

        typedef itk::Image< InternalPixelType, Dimension >  InternalImageType;

        typedef unsigned char                            OutputPixelType;
        typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
        typedef itk::BinaryThresholdImageFilter<
                InternalImageType,
                OutputImageType    >       ThresholdingFilterType;
        ThresholdingFilterType::Pointer thresholder = ThresholdingFilterType::New();
        thresholder->SetLowerThreshold( -1000.0 );
        thresholder->SetUpperThreshold(     0.0 );
        thresholder->SetOutsideValue(  0  );
        thresholder->SetInsideValue(  255 );

        typedef  itk::ImageFileReader< InternalImageType > ReaderType;
        typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
        ReaderType::Pointer reader = ReaderType::New();
        WriterType::Pointer writer = WriterType::New();
        //WriterType::Pointer writer_out = WriterType::New();
        stringstream ss;

        string name = "/home/gustavo/temp/cine_";
        string type = ".tif";

        ss<<name<<(i+1)<<type;

        string filename = ss.str();
        ss.str("");

        reader->SetFileName(filename);
        reader->Update();

        InternalImageType::Pointer val = reader->GetOutput();

        typedef itk::RescaleIntensityImageFilter<
                InternalImageType,
                OutputImageType >   CastFilterType;

        typedef   itk::GradientMagnitudeRecursiveGaussianImageFilter<
                InternalImageType,
                InternalImageType >  GradientFilterType;
        typedef   itk::SigmoidImageFilter<
                InternalImageType,
                InternalImageType >  SigmoidFilterType;
        GradientFilterType::Pointer  gradientMagnitude = GradientFilterType::New();
        SigmoidFilterType::Pointer sigmoid = SigmoidFilterType::New();

        sigmoid->SetOutputMinimum(sig_min);
        sigmoid->SetOutputMaximum(sig_max);

        typedef  itk::FastMarchingImageFilter<
                InternalImageType,
                InternalImageType >    FastMarchingFilterType;

        FastMarchingFilterType::Pointer  fastMarching = FastMarchingFilterType::New();
        //const InternalImageType * inputImage = reader->GetOutput();
        const InternalImageType * inputImage = val;
        fastMarching->SetOutputRegion( inputImage->GetBufferedRegion() );
        fastMarching->SetOutputSpacing( inputImage->GetSpacing() );
        fastMarching->SetOutputOrigin( inputImage->GetOrigin() );
        fastMarching->SetOutputDirection( inputImage->GetDirection() );

        typedef  itk::GeodesicActiveContourLevelSetImageFilter< InternalImageType,
                InternalImageType >    GeodesicActiveContourFilterType;
        GeodesicActiveContourFilterType::Pointer geodesicActiveContour =
                GeodesicActiveContourFilterType::New();

        const double propagationScaling = propagation;
        //  Software Guide : BeginCodeSnippet
        geodesicActiveContour->SetPropagationScaling( propagationScaling );
        geodesicActiveContour->SetCurvatureScaling(curvature);
        geodesicActiveContour->SetAdvectionScaling(advection);

        geodesicActiveContour->SetMaximumRMSError(rms);
        geodesicActiveContour->SetNumberOfIterations(iterations);

        gradientMagnitude->SetInput(val);
        sigmoid->SetInput( gradientMagnitude->GetOutput() );
        geodesicActiveContour->SetInput(  fastMarching->GetOutput() );
        geodesicActiveContour->SetFeatureImage( sigmoid->GetOutput() );
        thresholder->SetInput( geodesicActiveContour->GetOutput() );
        //ImageOut = thresholder->GetOutput();
        //writer->SetInput( thresholder->GetOutput() );

        const double sigma = 0.5;
        gradientMagnitude->SetSigma(  sigma  );

        sigmoid->SetAlpha( alpha );
        sigmoid->SetBeta(  beta  );

        string line;
        int x;
        int y;

        if (myfile.is_open())
        {
            getline (myfile,line);
            string cmd = line;
            string arg;
            string::size_type pos = cmd.find(' ');
            if(cmd.npos != pos) {
                arg = cmd.substr(pos + 1);
                cmd = cmd.substr(0, pos);
            }
            x = atoi(cmd.c_str());
            y = atoi(arg.c_str());
        }

        typedef FastMarchingFilterType::NodeContainer  NodeContainer;
        typedef FastMarchingFilterType::NodeType       NodeType;
        NodeContainer::Pointer seeds = NodeContainer::New();
        InternalImageType::IndexType  seedPosition;
        seedPosition.SetElement(0,x);
        seedPosition.SetElement(1,y);
        //seedPosition.SetElement(2,(int)z);
        cout<<"X, Y = "<<x<<" "<<y<<endl;
        NodeType node;
        const double seedValue = - distance;
        node.SetValue( seedValue );
        node.SetIndex( seedPosition );

        seeds->Initialize();
        seeds->InsertElement( 0, node );

        fastMarching->SetTrialPoints(  seeds  );

        fastMarching->SetSpeedConstant( 4.0 );

        CastFilterType::Pointer caster2 = CastFilterType::New();
        CastFilterType::Pointer caster3 = CastFilterType::New();
        CastFilterType::Pointer caster4 = CastFilterType::New();
        WriterType::Pointer writer2 = WriterType::New();
        WriterType::Pointer writer3 = WriterType::New();
        WriterType::Pointer writer4 = WriterType::New();

        caster2->SetInput( gradientMagnitude->GetOutput() );
        writer2->SetInput( caster2->GetOutput() );
        writer2->SetFileName("/home/gustavo/temp/GeodesicActiveContourImageFilterOutput2.tif");
        caster2->SetOutputMinimum(   0 );
        caster2->SetOutputMaximum( 255 );
        writer2->Update();
        caster3->SetInput( sigmoid->GetOutput() );
        writer3->SetInput( caster3->GetOutput() );
        writer3->SetFileName("/home/gustavo/temp/GeodesicActiveContourImageFilterOutput3.tif");
        caster3->SetOutputMinimum(   0 );
        caster3->SetOutputMaximum( 255 );
        writer3->Update();
        caster4->SetInput( fastMarching->GetOutput() );
        writer4->SetInput( caster4->GetOutput() );
        writer4->SetFileName("/home/gustavo/temp/GeodesicActiveContourImageFilterOutput4.tif");
        caster4->SetOutputMinimum(   0 );
        caster4->SetOutputMaximum( 255 );

        fastMarching->SetOutputSize(
                    reader->GetOutput()->GetBufferedRegion().GetSize() );
        reader->Update();

        stringstream ss2;

        string name2 = "/home/gustavo/temp/segmented_";
        string type2 = ".tif";

        if(i<9)
            ss2<<name2<<"00"<<(i+1)<<type2;
        if(i>=9 && i<99)
            ss2<<name2<<"0"<<(i+1)<<type2;
        if(i>=99)
            ss2<<name2<<(i+1)<<type2;
        string filename2 = ss2.str();
        ss2.str("");

        typedef itk::GradientMagnitudeImageFilter<OutputImageType, OutputImageType >  GradientType;
        GradientType::Pointer gradient = GradientType::New();
        gradient->SetInput(thresholder->GetOutput());
        gradient->Update();

        try
        {
            writer->SetFileName(filename2);
            writer->SetInput( gradient->GetOutput() );
            writer->Update();
        }
        catch( itk::ExceptionObject & excep )
        {
            std::cerr << "Exception caught !" << std::endl;
            std::cerr << excep << std::endl;
        }

        std::cout << std::endl;
        std::cout << "Max. no. iterations: " << geodesicActiveContour->GetNumberOfIterations() << std::endl;
        std::cout << "Max. RMS error: " << geodesicActiveContour->GetMaximumRMSError() << std::endl;
        std::cout << std::endl;
        std::cout << "No. elpased iterations: " << geodesicActiveContour->GetElapsedIterations() << std::endl;
        std::cout << "RMS change: " << geodesicActiveContour->GetRMSChange() << std::endl;
        writer4->Update();

        typedef itk::ImageFileWriter< InternalImageType > InternalWriterType;
        InternalWriterType::Pointer mapWriter = InternalWriterType::New();
        mapWriter->SetInput( fastMarching->GetOutput() );
        mapWriter->SetFileName("/home/gustavo/temp/GeodesicActiveContourImageFilterOutput4.mha");
        mapWriter->Update();
        InternalWriterType::Pointer speedWriter = InternalWriterType::New();
        speedWriter->SetInput( sigmoid->GetOutput() );
        speedWriter->SetFileName("/home/gustavo/temp/GeodesicActiveContourImageFilterOutput3.mha");
        speedWriter->Update();
        InternalWriterType::Pointer gradientWriter = InternalWriterType::New();
        gradientWriter->SetInput( gradientMagnitude->GetOutput() );
        gradientWriter->SetFileName("/home/gustavo/temp/GeodesicActiveContourImageFilterOutput2.mha");
        gradientWriter->Update();
    }
    myfile.close();

}