BinaryImageType::Pointer readBinaryImage(const std::string& filename) {
ImageReaderType::Pointer reader = ImageReaderType::New();
reader->SetFileName(filename.c_str());
reader->Update();
// we make sure that the image really has value 0 and 1
typedef itk::BinaryThresholdImageFilter<BinaryImageType, BinaryImageType> ThresholdFilterType;
ThresholdFilterType::Pointer thresholdFilter = ThresholdFilterType::New();
thresholdFilter->SetInsideValue(1);
thresholdFilter->SetOutsideValue(0);
thresholdFilter->SetLowerThreshold(1);
thresholdFilter->SetUpperThreshold(255);
thresholdFilter->SetInput(reader->GetOutput());
thresholdFilter->Update();
BinaryImageType::Pointer img = thresholdFilter->GetOutput();
img->DisconnectPipeline();
return img;
}
void mitk::SurfaceStampImageFilter::SurfaceStampBinaryOutputProcessing(MeshType *mesh)
{
auto *inputImage = this->GetInput();
mitk::Image::Pointer outputImage = this->GetOutput();
typedef itk::Image<unsigned char, 3> BinaryImageType;
BinaryImageType::Pointer itkInputImage;
mitk::CastToItkImage(inputImage, itkInputImage);
typedef itk::TriangleMeshToBinaryImageFilter<MeshType, BinaryImageType> FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput(mesh);
filter->SetInfoImage(itkInputImage);
filter->SetInsideValue(1);
filter->SetOutsideValue(0);
filter->Update();
BinaryImageType::Pointer resultImage = filter->GetOutput();
resultImage->DisconnectPipeline();
mitk::CastToMitkImage(resultImage, outputImage);
}
void mitk::SurfaceStampImageFilter::SurfaceStampProcessing(itk::Image<TPixel, 3> *input, MeshType *mesh)
{
typedef itk::Image<TPixel, 3> ImageType;
typedef itk::Image<unsigned char, 3> BinaryImageType;
typedef itk::TriangleMeshToBinaryImageFilter<mitk::SurfaceStampImageFilter::MeshType, BinaryImageType> FilterType;
BinaryImageType::Pointer binaryInput = BinaryImageType::New();
binaryInput->SetSpacing(input->GetSpacing());
binaryInput->SetOrigin(input->GetOrigin());
binaryInput->SetDirection(input->GetDirection());
binaryInput->SetRegions(input->GetLargestPossibleRegion());
binaryInput->Allocate();
binaryInput->FillBuffer(0);
FilterType::Pointer filter = FilterType::New();
filter->SetInput(mesh);
filter->SetInfoImage(binaryInput);
filter->SetInsideValue(1);
filter->SetOutsideValue(0);
filter->Update();
BinaryImageType::Pointer resultImage = filter->GetOutput();
resultImage->DisconnectPipeline();
mitk::Image::Pointer outputImage = this->GetOutput();
typename ImageType::Pointer itkOutputImage;
mitk::CastToItkImage(outputImage, itkOutputImage);
typedef itk::ImageRegionConstIterator<BinaryImageType> BinaryIteratorType;
typedef itk::ImageRegionConstIterator<ImageType> InputIteratorType;
typedef itk::ImageRegionIterator<ImageType> OutputIteratorType;
BinaryIteratorType sourceIter(resultImage, resultImage->GetLargestPossibleRegion());
sourceIter.GoToBegin();
InputIteratorType inputIter(input, input->GetLargestPossibleRegion());
inputIter.GoToBegin();
OutputIteratorType outputIter(itkOutputImage, itkOutputImage->GetLargestPossibleRegion());
outputIter.GoToBegin();
typename ImageType::PixelType inputValue;
unsigned char sourceValue;
auto fgValue = static_cast<typename ImageType::PixelType>(m_ForegroundValue);
auto bgValue = static_cast<typename ImageType::PixelType>(m_BackgroundValue);
while (!sourceIter.IsAtEnd())
{
sourceValue = static_cast<unsigned char>(sourceIter.Get());
inputValue = static_cast<typename ImageType::PixelType>(inputIter.Get());
if (sourceValue != 0)
outputIter.Set(fgValue);
else if (m_OverwriteBackground)
outputIter.Set(bgValue);
else
outputIter.Set(inputValue);
++sourceIter;
++inputIter;
++outputIter;
}
}