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;
}
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();
}