void Initialisation::savePointAsBinaryImage(ImageType::Pointer initialImage, string filename, OrientationType orientation)
{
if (points_.size() > 0)
{
typedef itk::Image< unsigned char, 3 > BinaryImageType;
BinaryImageType::Pointer binary = BinaryImageType::New();
ImageType::RegionType region;
ImageType::IndexType start;
start[0] = 0; start[1] = 0; start[2] = 0;
ImageType::SizeType size, imSize = initialImage->GetLargestPossibleRegion().GetSize();
size[0] = imSize[0]; size[1] = imSize[1]; size[2] = imSize[2];
region.SetSize(size);
region.SetIndex(start);
binary->CopyInformation(initialImage);
binary->SetRegions(region);
binary->Allocate();
binary->FillBuffer(false);
typedef ImageType::IndexType IndexType;
ContinuousIndex ind;
IndexType ind2;
unsigned int pSize = points_.size();
unsigned int indexMiddle = 0;
for (unsigned int i=0; i<pSize; i++) {
if (points_[i][1] == startSlice_)
indexMiddle = i;
}
ind[0] = points_[indexMiddle][0]; ind[1] = points_[indexMiddle][1]; ind[2] = points_[indexMiddle][2];
PointType pt;
inputImage_->TransformContinuousIndexToPhysicalPoint(ind, pt);
initialImage->TransformPhysicalPointToIndex(pt, ind2);
binary->SetPixel(ind2,true);
OrientImage<BinaryImageType> orientationFilter;
orientationFilter.setInputImage(binary);
orientationFilter.orientation(orientation);
binary = orientationFilter.getOutputImage();
ImageIterator it( binary, binary->GetRequestedRegion() );
it.GoToBegin();
while(!it.IsAtEnd())
{
if (it.Get()==true)
{
ind2 = it.GetIndex();
break;
}
++it;
}
if (verbose_) cout << "Center of spinal cord saved on pixel : " << ind2 << endl;
WriterBinaryType::Pointer writer = WriterBinaryType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
writer->SetImageIO(io);
writer->SetFileName(filename);
writer->SetInput(binary);
try {
writer->Write();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while writing image " << std::endl;
std::cerr << e << std::endl;
}
}
else cout << "Error: Spinal cord center not detected" << endl;
}
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;
}
}