void Mask::CreateBoundaryImageInRegion(const itk::ImageRegion<2>& region, BoundaryImageType* const boundaryImage,
const HoleMaskPixelTypeEnum& whichSideOfBoundary) const
{
// Create a binary image of the mask
unsigned char holeColor = 255;
unsigned char validColor = 0;
UnsignedCharImageType::Pointer fullBinaryImage = UnsignedCharImageType::New();
CreateBinaryImageInRegion(region, fullBinaryImage, holeColor, validColor);
// Extract the relevant region from the binary image
UnsignedCharImageType::Pointer binaryImage = UnsignedCharImageType::New();
binaryImage->SetRegions(region);
binaryImage->Allocate();
CopyRegion(fullBinaryImage.GetPointer(), binaryImage.GetPointer(), region, region);
// Extract the relevant region from the mask
Mask::Pointer extractedRegionMask = Mask::New();
extractedRegionMask->SetRegions(region);
extractedRegionMask->Allocate();
CopyRegion(this, extractedRegionMask.GetPointer(), region, region);
// Since the hole is white (we have specified this at the beginning of this function),
// we want the foreground value of the contour filter to be black.
// This means that the boundary will be detected in the black pixel region,
// which is on the outside edge of the hole like we want. However,
// The BinaryContourImageFilter will change all non-boundary pixels to the background color,
// so the resulting output will be inverted - the boundary pixels will be black and the
// non-boundary pixels will be white.
// Find the boundary
typedef itk::BinaryContourImageFilter<UnsignedCharImageType, UnsignedCharImageType> binaryContourImageFilterType;
binaryContourImageFilterType::Pointer binaryContourFilter = binaryContourImageFilterType::New();
binaryContourFilter->SetInput(binaryImage);
binaryContourFilter->SetFullyConnected(true);
if(whichSideOfBoundary == HoleMaskPixelTypeEnum::VALID)
{
// we want the boundary pixels to be in the valid region.
binaryContourFilter->SetForegroundValue(validColor);
binaryContourFilter->SetBackgroundValue(holeColor);
}
else if(whichSideOfBoundary == HoleMaskPixelTypeEnum::HOLE)
{
// we want the boundary pixels to be in the hole region.
binaryContourFilter->SetForegroundValue(holeColor);
binaryContourFilter->SetBackgroundValue(validColor);
}
else
{
throw std::runtime_error("An invalid side of the boundary was requested.");
}
binaryContourFilter->Update();
DeepCopy(binaryContourFilter->GetOutput(), boundaryImage);
}
bool TestSamePatch(ColorImageType::Pointer image, UnsignedCharImageType::Pointer mask)
{
itk::Index<2> queryPixel;
queryPixel[0] = 10;
queryPixel[1] = 10;
itk::Index<2> fixedPixel;
fixedPixel[0] = 10;
fixedPixel[1] = 10;
unsigned int patchRadius = 5;
float difference = PatchDifference(image.GetPointer(), mask.GetPointer(), queryPixel, fixedPixel, patchRadius);
std::cerr << "Difference: " << difference << std::endl;
if(difference != 0)
{
std::cerr << "Error: the difference between the same pixel should be zero!" << std::endl;
return false;
}
return true;
}
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");
}