int main(int argc, char** argv) {
if(argc != 3){
std::cout << "Usage: Test2DImage inputFilename outputFilename";
return 1;
}
typedef signed int InputPixelType;
const unsigned int Dimension = 2;
typedef itk::Image<InputPixelType, Dimension> InputImageType;
typedef itk::RGBPixel<unsigned char> RGBPixelType;
typedef itk::Image<RGBPixelType, 2> RGBImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
typedef itk::ImageFileWriter<RGBImageType> WriterType;
typedef itk::GDCMImageIO ImageIOType;
typedef itk::GradientAnisotropicDiffusionImageFilter<InputImageType,
InputImageType> DiffusionFilterType;
typedef itk::GradientMagnitudeImageFilter<InputImageType, InputImageType>
GradientMagnitudeFilterType;
typedef itk::Functor::ScalarToRGBPixelFunctor<int> ColorMapFunctorType;
typedef itk::UnaryFunctorImageFilter<InputImageType,
RGBImageType, ColorMapFunctorType> ColorMapFilterType;
typedef itk::JPEGImageIO JImageIOType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
ImageIOType::Pointer GDCMImageIO = ImageIOType::New();
JImageIOType::Pointer JPEGImageIO = JImageIOType::New();
ColorMapFilterType::Pointer colormapper = ColorMapFilterType::New();
reader->SetFileName(argv[1]);
reader->SetImageIO(GDCMImageIO);
try {
reader->Update();
}
catch (itk::ExceptionObject & e) {
std::cerr << "exception in file reader " << std::endl;
std::cerr << e << std::endl;
return 1;
}
DiffusionFilterType::Pointer diffusion = DiffusionFilterType::New();
diffusion->SetNumberOfIterations(1);
diffusion->SetConductanceParameter(4);
diffusion->SetTimeStep(0.125);
GradientMagnitudeFilterType::Pointer gradient = GradientMagnitudeFilterType::New();
diffusion->SetInput(reader->GetOutput());
gradient->SetInput(diffusion->GetOutput());
gradient->Update();
MyWatershedSegmenter<InputImageType> watershed(gradient->GetOutput());
watershed.buildLowerCompleteImage();
watershed.buildLabeledImage();
colormapper->SetInput(watershed.returnFinalImage());
writer->SetInput(colormapper->GetOutput());
writer->UseInputMetaDataDictionaryOff();
writer->SetImageIO(JPEGImageIO);
writer->SetFileName(argv[2]);
writer->Update();
}
void CreateErroneousGradient(std::string imageFilename)
{
std::cout << "Reading image: " << imageFilename << std::endl;
ColorImageReaderType::Pointer imageReader = ColorImageReaderType::New();
imageReader->SetFileName(imageFilename.c_str());
imageReader->Update();
// Convert the color input image to a grayscale image
UnsignedCharImageType::Pointer grayscaleImage = UnsignedCharImageType::New();
ColorToGrayscale<ColorImageType>(imageReader->GetOutput(), grayscaleImage);
WriteImage<UnsignedCharImageType>(grayscaleImage, "greyscale.png");
// Blur the image to compute better gradient estimates
typedef itk::DiscreteGaussianImageFilter<
UnsignedCharImageType, FloatImageType > filterType;
// Create and setup a Gaussian filter
filterType::Pointer gaussianFilter = filterType::New();
gaussianFilter->SetInput(grayscaleImage);
gaussianFilter->SetVariance(2);
gaussianFilter->Update();
//WriteImage<FloatImageType>(gaussianFilter->GetOutput(), "gaussianBlur.mhd"); // this cannot be png because they are floats
/*
// Compute the gradient
typedef itk::GradientImageFilter<
FloatImageType, float, float> GradientFilterType;
GradientFilterType::Pointer gradientFilter = GradientFilterType::New();
gradientFilter->SetInput(gaussianFilter->GetOutput());
gradientFilter->Update();
WriteImage<VectorImageType>(gradientFilter->GetOutput(), "gradient.mhd"); // this cannot be png because they are floats
*/
// Compute the gradient magnitude
typedef itk::GradientMagnitudeImageFilter<
FloatImageType, UnsignedCharImageType> GradientMagnitudeFilterType;
GradientMagnitudeFilterType::Pointer gradientMagnitudeFilter = GradientMagnitudeFilterType::New();
gradientMagnitudeFilter->SetInput(gaussianFilter->GetOutput());
gradientMagnitudeFilter->Update();
WriteImage<UnsignedCharImageType>(gradientMagnitudeFilter->GetOutput(), "gradient.png");
}
void MaskNewGradientWithOriginalMask(std::string imageFilename, std::string maskFilename)
{
// Read image and convert it to grayscale
ColorImageReaderType::Pointer imageReader = ColorImageReaderType::New();
imageReader->SetFileName(imageFilename);
imageReader->Update();
UnsignedCharImageType::Pointer image = UnsignedCharImageType::New();
ColorToGrayscale<ColorImageType>(imageReader->GetOutput(), image);
// Read mask image
UnsignedCharImageReaderType::Pointer maskReader = UnsignedCharImageReaderType::New();
maskReader->SetFileName(maskFilename.c_str());
maskReader->Update();
// Blur the image to compute better gradient estimates
typedef itk::DiscreteGaussianImageFilter<
UnsignedCharImageType, FloatImageType > filterType;
// Create and setup a Gaussian filter
filterType::Pointer gaussianFilter = filterType::New();
gaussianFilter->SetInput(image);
gaussianFilter->SetVariance(2);
gaussianFilter->Update();
//WriteImage<FloatImageType>(gaussianFilter->GetOutput(), "gaussianBlur.mhd"); // this cannot be png because they are floats
/*
// Compute the gradient
typedef itk::GradientImageFilter<
FloatImageType, float, float> GradientFilterType;
GradientFilterType::Pointer gradientFilter = GradientFilterType::New();
gradientFilter->SetInput(gaussianFilter->GetOutput());
gradientFilter->Update();
WriteImage<VectorImageType>(gradientFilter->GetOutput(), "gradient.mhd"); // this cannot be png because they are floats
*/
// Compute the gradient magnitude
typedef itk::GradientMagnitudeImageFilter<
FloatImageType, UnsignedCharImageType> GradientMagnitudeFilterType;
GradientMagnitudeFilterType::Pointer gradientMagnitudeFilter = GradientMagnitudeFilterType::New();
gradientMagnitudeFilter->SetInput(gaussianFilter->GetOutput());
gradientMagnitudeFilter->Update();
WriteImage<UnsignedCharImageType>(gradientMagnitudeFilter->GetOutput(), "gradient.png");
// Expand the mask - this is necessary to prevent the isophotes from being undefined in the target region
typedef itk::FlatStructuringElement<2> StructuringElementType;
StructuringElementType::RadiusType radius;
radius.Fill(5);
StructuringElementType structuringElement = StructuringElementType::Box(radius);
typedef itk::BinaryDilateImageFilter<UnsignedCharImageType, UnsignedCharImageType, StructuringElementType>
BinaryDilateImageFilterType;
BinaryDilateImageFilterType::Pointer expandMaskFilter
= BinaryDilateImageFilterType::New();
expandMaskFilter->SetInput(maskReader->GetOutput());
expandMaskFilter->SetKernel(structuringElement);
expandMaskFilter->Update();
UnsignedCharImageType::Pointer expandedMask = UnsignedCharImageType::New();
expandedMask->Graft(expandMaskFilter->GetOutput());
WriteScaledImage<UnsignedCharImageType>(expandedMask, "ExpandedMasked.png");
// Invert the mask
typedef itk::InvertIntensityImageFilter <UnsignedCharImageType>
InvertIntensityImageFilterType;
InvertIntensityImageFilterType::Pointer invertMaskFilter
= InvertIntensityImageFilterType::New();
invertMaskFilter->SetInput(expandedMask);
invertMaskFilter->Update();
//WriteScaledImage<UnsignedCharImageType>(invertMaskFilter->GetOutput(), "invertedExpandedMask.mhd");
// Keep only values outside the masked region
typedef itk::MaskImageFilter< UnsignedCharImageType, UnsignedCharImageType, UnsignedCharImageType > MaskFilterType;
MaskFilterType::Pointer maskFilter = MaskFilterType::New();
maskFilter->SetInput(gradientMagnitudeFilter->GetOutput());
maskFilter->SetMaskImage(invertMaskFilter->GetOutput());
maskFilter->Update();
WriteScaledImage<UnsignedCharImageType>(maskFilter->GetOutput(), "MaskedGradientMagnitude.png");
}
