void mitk::ExtractImageFilter::ItkImageProcessing( itk::Image<TPixel,VImageDimension>* itkImage )
{
// use the itk::ExtractImageFilter to get a 2D image
typedef itk::Image< TPixel, VImageDimension > ImageType3D;
typedef itk::Image< TPixel, VImageDimension-1 > ImageType2D;
typename ImageType3D::RegionType inSliceRegion = itkImage->GetLargestPossibleRegion();
inSliceRegion.SetSize( m_SliceDimension, 0 );
typedef itk::ExtractImageFilter<ImageType3D, ImageType2D> ExtractImageFilterType;
typename ExtractImageFilterType::Pointer sliceExtractor = ExtractImageFilterType::New();
sliceExtractor->SetInput( itkImage );
inSliceRegion.SetIndex( m_SliceDimension, m_SliceIndex );
sliceExtractor->SetExtractionRegion( inSliceRegion );
// calculate the output
sliceExtractor->UpdateLargestPossibleRegion();
typename ImageType2D::Pointer slice = sliceExtractor->GetOutput();
// re-import to MITK
Image::Pointer resultImage = ImageToImageFilter::GetOutput();
GrabItkImageMemory(slice, resultImage, NULL, false);
}
typename itk::Image<TPixel, VImageDimension>::Pointer MaskUtilities<TPixel, VImageDimension>::ExtractMaskImageRegion()
{
if (m_Mask==nullptr || m_Image==nullptr)
{
MITK_ERROR << "Set an image and a mask first";
}
bool maskSanity = CheckMaskSanity();
if (!maskSanity)
{
MITK_ERROR << "Mask and image are not compatible";
}
typedef itk::Image< TPixel, VImageDimension > ImageType;
typedef itk::Image< unsigned short, VImageDimension > MaskType;
typedef itk::ExtractImageFilter< ImageType, ImageType > ExtractImageFilterType;
typename ImageType::SizeType imageSize = m_Image->GetBufferedRegion().GetSize();
typename ImageType::SizeType maskSize = m_Mask->GetBufferedRegion().GetSize();
typename itk::Image<TPixel, VImageDimension>::Pointer extractedImg = itk::Image<TPixel, VImageDimension>::New();
bool maskSmallerImage = false;
for ( unsigned int i = 0; i < ImageType::ImageDimension; ++i )
{
if ( maskSize[i] < imageSize[i] )
{
maskSmallerImage = true;
}
}
if ( maskSmallerImage )
{
typename ExtractImageFilterType::Pointer extractImageFilter = ExtractImageFilterType::New();
typename MaskType::PointType maskOrigin = m_Mask->GetOrigin();
typename ImageType::PointType imageOrigin = m_Image->GetOrigin();
typename MaskType::SpacingType maskSpacing = m_Mask->GetSpacing();
typename ImageType::RegionType extractionRegion;
typename ImageType::IndexType extractionRegionIndex;
for (unsigned int i=0; i < maskOrigin.GetPointDimension(); i++)
{
extractionRegionIndex[i] = (maskOrigin[i] - imageOrigin[i]) / maskSpacing[i];
}
extractionRegion.SetIndex(extractionRegionIndex);
extractionRegion.SetSize(m_Mask->GetLargestPossibleRegion().GetSize());
extractImageFilter->SetInput( m_Image );
extractImageFilter->SetExtractionRegion( extractionRegion );
extractImageFilter->SetCoordinateTolerance( 0.001 );
extractImageFilter->SetDirectionTolerance( 0.001 );
extractImageFilter->Update();
extractedImg = extractImageFilter->GetOutput();
extractedImg->SetOrigin(m_Mask->GetOrigin());
extractedImg->SetLargestPossibleRegion(m_Mask->GetLargestPossibleRegion());
extractedImg->SetBufferedRegion(m_Mask->GetBufferedRegion());
}
else
{
extractedImg = m_Image;
}
return extractedImg;
}
