void Cell::ComputeMaskedImage()
{
typedef itk::MaskNegatedImageFilter< ImageType, MaskImageType, ImageType > MaskFilterType;
MaskFilterType::Pointer maskFilter = MaskFilterType::New();
maskFilter->SetMaskImage(this->mask);
maskFilter->SetInput(this->image);
try
{
//ftk::TimeStampOverflowSafeUpdate( maskFilter.GetPointer() );
maskFilter->Update();
}
catch (itk::ExceptionObject &err)
{
std::cerr << "maskFilter Exception: " << err << std::endl;
}
this->masked_image = maskFilter->GetOutput();
this->masked_image->DisconnectPipeline(); //Disconnect pipeline so we don't propagate...
//Make the file name of the masked cell image
std::stringstream masked_cell_filename_stream;
masked_cell_filename_stream << cell_x << "_" << cell_y << "_" << cell_z << "_masked.TIF"; //X_Y_Z_masked.TIF
//Write the masked cell image
//WriteImage(masked_cell_filename_stream.str(), this->masked_image);
}
int main(int argc, char *argv[])
{
if(argc != 3)
{
std::cerr << "Required arguments: image mask" << std::endl;
return EXIT_FAILURE;
}
std::string imageFilename = argv[1];
std::string maskFilename = argv[2];
std::cout << "Reading image: " << imageFilename << std::endl;
std::cout << "Reading mask: " << maskFilename << std::endl;
typedef itk::ImageFileReader<FloatVectorImageType> ImageReaderType;
ImageReaderType::Pointer imageReader = ImageReaderType::New();
imageReader->SetFileName(imageFilename.c_str());
imageReader->Update();
std::cout << "Read image " << imageReader->GetOutput()->GetLargestPossibleRegion() << std::endl;
typedef itk::ImageFileReader<Mask> MaskReaderType;
MaskReaderType::Pointer maskReader = MaskReaderType::New();
maskReader->SetFileName(maskFilename.c_str());
maskReader->Update();
std::cout << "Read mask " << maskReader->GetOutput()->GetLargestPossibleRegion() << std::endl;
// Prepare image
RGBImageType::Pointer rgbImage = RGBImageType::New();
// Helpers::VectorImageToRGBImage(imageReader->GetOutput(), rgbImage);
// TODO: Update this call to new API
//maskReader->GetOutput()->ApplyToImage(rgbImage.GetPointer(), Qt::black);
OutputHelpers::WriteImage<RGBImageType>(rgbImage, "Test/TestIsophotes.rgb.mha");
typedef itk::RGBToLuminanceImageFilter< RGBImageType, FloatScalarImageType > LuminanceFilterType;
LuminanceFilterType::Pointer luminanceFilter = LuminanceFilterType::New();
luminanceFilter->SetInput(rgbImage);
luminanceFilter->Update();
OutputHelpers::WriteImage<FloatScalarImageType>(luminanceFilter->GetOutput(), "Test/Luminance.mha");
// PatchBasedInpainting inpainting;
// inpainting.SetDebugImages(true);
// inpainting.SetMask(maskReader->GetOutput());
// inpainting.SetImage(imageReader->GetOutput());
//Helpers::Write2DVectorImage(inpainting.GetIsophoteImage(), "Test/TestIsophotes.isophotes.mha");
//inpainting.FindBoundary();
// After blurVariance == 4, you cannot tell the difference in the output.
for(unsigned int blurVariance = 0; blurVariance < 5; ++blurVariance)
{
std::string fileNumber = Helpers::ZeroPad(blurVariance, 2);
FloatScalarImageType::Pointer blurredLuminance = FloatScalarImageType::New();
// Blur with a Gaussian kernel
MaskOperations::MaskedBlur(luminanceFilter->GetOutput(), maskReader->GetOutput(),
blurVariance, blurredLuminance.GetPointer());
std::stringstream ssBlurredLuminance;
ssBlurredLuminance << "Test/BlurredLuminance_" << fileNumber << ".mha";
OutputHelpers::WriteImage(blurredLuminance.GetPointer(), ssBlurredLuminance.str());
//Helpers::WriteImage<FloatScalarImageType>(blurredLuminance, "Test/TestIsophotes.blurred.mha");
FloatVector2ImageType::Pointer gradient = FloatVector2ImageType::New();
Derivatives::MaskedGradient(blurredLuminance.GetPointer(), maskReader->GetOutput(), gradient.GetPointer());
// Boundary gradient
typedef itk::MaskImageFilter< FloatVector2ImageType, UnsignedCharScalarImageType, FloatVector2ImageType > MaskFilterType;
MaskFilterType::Pointer maskFilter = MaskFilterType::New();
maskFilter->SetInput(gradient);
//maskFilter->SetMaskImage(inpainting.GetBoundaryImage());
maskFilter->Update();
vtkSmartPointer<vtkPolyData> boundaryGradient = vtkSmartPointer<vtkPolyData>::New();
// TODO: Convert this call to new API
//Helpers::ConvertNonZeroPixelsToVectors(maskFilter->GetOutput(), boundaryGradient);
std::stringstream ssPolyData;
ssPolyData << "Test/BoundaryGradient_" << fileNumber << ".vtp";
OutputHelpers::WritePolyData(boundaryGradient, ssPolyData.str());
}
return EXIT_SUCCESS;
}
void CriminisiInpainting::ComputeBoundaryNormals()
{
try
{
// Blur the mask, compute the gradient, then keep the normals only at the original mask boundary
if(this->DebugImages)
{
Helpers::WriteImage<UnsignedCharScalarImageType>(this->BoundaryImage, "Debug/ComputeBoundaryNormals.BoundaryImage.mha");
Helpers::WriteImage<Mask>(this->CurrentMask, "Debug/ComputeBoundaryNormals.CurrentMask.mha");
}
// Blur the mask
typedef itk::DiscreteGaussianImageFilter< Mask, FloatScalarImageType > BlurFilterType;
BlurFilterType::Pointer gaussianFilter = BlurFilterType::New();
gaussianFilter->SetInput(this->CurrentMask);
gaussianFilter->SetVariance(2);
gaussianFilter->Update();
if(this->DebugImages)
{
Helpers::WriteImage<FloatScalarImageType>(gaussianFilter->GetOutput(), "Debug/ComputeBoundaryNormals.BlurredMask.mha");
}
// Compute the gradient of the blurred mask
typedef itk::GradientImageFilter< FloatScalarImageType, float, float> GradientFilterType;
GradientFilterType::Pointer gradientFilter = GradientFilterType::New();
gradientFilter->SetInput(gaussianFilter->GetOutput());
gradientFilter->Update();
if(this->DebugImages)
{
Helpers::WriteImage<FloatVector2ImageType>(gradientFilter->GetOutput(), "Debug/ComputeBoundaryNormals.BlurredMaskGradient.mha");
}
// Only keep the normals at the boundary
typedef itk::MaskImageFilter< FloatVector2ImageType, UnsignedCharScalarImageType, FloatVector2ImageType > MaskFilterType;
MaskFilterType::Pointer maskFilter = MaskFilterType::New();
//maskFilter->SetInput1(gradientFilter->GetOutput());
//maskFilter->SetInput2(this->BoundaryImage);
maskFilter->SetInput(gradientFilter->GetOutput());
maskFilter->SetMaskImage(this->BoundaryImage);
maskFilter->Update();
if(this->DebugImages)
{
Helpers::WriteImage<FloatVector2ImageType>(maskFilter->GetOutput(), "Debug/ComputeBoundaryNormals.BoundaryNormalsUnnormalized.mha");
}
//this->BoundaryNormals = maskFilter->GetOutput();
//this->BoundaryNormals->Graft(maskFilter->GetOutput());
Helpers::DeepCopy<FloatVector2ImageType>(maskFilter->GetOutput(), this->BoundaryNormals);
// Normalize the vectors because we just care about their direction (the Data term computation calls for the normalized boundary normal)
itk::ImageRegionIterator<FloatVector2ImageType> boundaryNormalsIterator(this->BoundaryNormals, this->BoundaryNormals->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<UnsignedCharScalarImageType> boundaryIterator(this->BoundaryImage, this->BoundaryImage->GetLargestPossibleRegion());
while(!boundaryNormalsIterator.IsAtEnd())
{
if(boundaryIterator.Get()) // The pixel is on the boundary
{
FloatVector2ImageType::PixelType p = boundaryNormalsIterator.Get();
p.Normalize();
boundaryNormalsIterator.Set(p);
}
++boundaryNormalsIterator;
++boundaryIterator;
}
if(this->DebugImages)
{
Helpers::WriteImage<FloatVector2ImageType>(this->BoundaryNormals, "Debug/ComputeBoundaryNormals.BoundaryNormals.mha");
}
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught in ComputeBoundaryNormals!" << std::endl;
std::cerr << err << std::endl;
exit(-1);
}
}
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");
}
