template <class ImagePixelType, class MaskPixelType> int update()
{
typedef itk::Image<ImagePixelType, 3> ImageType;
typedef itk::Image<MaskPixelType, 3> MaskType;
if ( !input ||!input->data() || !mask ||!mask->data())
return EXIT_FAILURE;
typedef itk::MaskImageFilter< ImageType, MaskType> MaskFilterType;
typename MaskFilterType::Pointer maskFilter = MaskFilterType::New();
typename ImageType::Pointer imgInput = dynamic_cast<ImageType *> ( ( itk::Object* ) ( input->data() )) ;
typename MaskType::Pointer maskInput = dynamic_cast<MaskType *> ( ( itk::Object* ) ( mask->data() )) ;
try
{
maskInput->SetOrigin(imgInput->GetOrigin());
maskInput->SetSpacing(imgInput->GetSpacing());
maskFilter->SetInput(imgInput);
maskFilter->SetMaskingValue(maskBackgroundValue);
maskFilter->SetMaskImage(maskInput);
//Outside values set to the lowest reachable value
typedef itk::MinimumMaximumImageCalculator <ImageType> ImageCalculatorFilterType;
typename ImageCalculatorFilterType::Pointer imageCalculatorFilter
= ImageCalculatorFilterType::New ();
imageCalculatorFilter->SetImage(imgInput);
imageCalculatorFilter->ComputeMinimum();
maskFilter->SetOutsideValue(std::min(double(imageCalculatorFilter->GetMinimum()), 0.0));
maskFilter->Update();
output->setData(maskFilter->GetOutput());
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught in medMaskApplication!" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
medUtilities::setDerivedMetaData(output, input, "masked");
return EXIT_SUCCESS;
}
void BoundaryNormals::ComputeBoundaryNormals(TNormalsImage* const boundaryNormalsImage, const float maskBlurVariance)
{
// Blur the mask, compute the gradient, then keep the normals only at the original mask boundary
// Compute the boundary of the mask
typedef itk::Image<unsigned char, 2> BoundaryImageType;
BoundaryImageType::Pointer boundaryImage = BoundaryImageType::New();
this->MaskImage->CreateBoundaryImage(boundaryImage, Mask::VALID, 255);
if(this->IsDebugOn())
{
ITKHelpers::WriteImage(boundaryImage.GetPointer(),
"ComputeBoundaryNormals.BoundaryImage.mha");
}
// Blur the mask so that the normals are not quantized so much. Also, pixels with only diagonal
// valid neighbors have undefined gradients without this blurring.
typedef itk::DiscreteGaussianImageFilter<Mask, ITKHelpers::FloatScalarImageType> BlurFilterType;
BlurFilterType::Pointer gaussianFilter = BlurFilterType::New();
gaussianFilter->SetInput(this->MaskImage);
gaussianFilter->SetVariance(maskBlurVariance);
gaussianFilter->Update();
if(this->IsDebugOn())
{
ITKHelpers::WriteImage(gaussianFilter->GetOutput(),
"ComputeBoundaryNormals.BlurredMask.mha");
}
// Compute the gradient of the blurred mask
typedef itk::GradientImageFilter<ITKHelpers::FloatScalarImageType, float, float> GradientFilterType;
GradientFilterType::Pointer gradientFilter = GradientFilterType::New();
gradientFilter->SetInput(gaussianFilter->GetOutput());
gradientFilter->Update();
if(this->IsDebugOn())
{
ITKHelpers::WriteImage(gradientFilter->GetOutput(),
"ComputeBoundaryNormals.BlurredMaskGradient.mha");
}
// Only keep the normals at the boundary
typedef itk::MaskImageFilter<TNormalsImage, ITKHelpers::UnsignedCharScalarImageType, TNormalsImage> MaskFilterType;
typename MaskFilterType::Pointer maskFilter = MaskFilterType::New();
maskFilter->SetInput(gradientFilter->GetOutput());
maskFilter->SetMaskImage(boundaryImage);
maskFilter->Update();
if(this->IsDebugOn())
{
ITKHelpers::WriteImage(maskFilter->GetOutput(),
"ComputeBoundaryNormals.BoundaryNormalsUnnormalized.mha");
}
// Allocate the image to return
// ITKHelpers::DeepCopy(maskFilter->GetOutput(), boundaryNormalsImage);
ITKHelpers::InitializeImage(boundaryNormalsImage, this->MaskImage->GetLargestPossibleRegion());
// Normalize the vectors because we just care about their direction
std::vector<itk::Index<2> > boundaryPixels = ITKHelpers::GetNonZeroPixels(boundaryImage.GetPointer());
for(std::vector<itk::Index<2> >::const_iterator boundaryPixelIterator = boundaryPixels.begin();
boundaryPixelIterator != boundaryPixels.end(); ++boundaryPixelIterator)
{
typename TNormalsImage::PixelType p = maskFilter->GetOutput()->GetPixel(*boundaryPixelIterator);
p.Normalize();
boundaryNormalsImage->SetPixel(*boundaryPixelIterator, p);
}
}
