static void ReadPixel(const PixelType&, Image::Pointer image, const itk::Index<3>& index, ScalarType* returnValue)
{
switch (image->GetDimension())
{
case 2:
{
ImagePixelReadAccessor<T, 2> readAccess(image, image->GetSliceData(0));
*returnValue = readAccess.GetPixelByIndex(reinterpret_cast<const itk::Index<2>&>(index));
break;
}
case 3:
{
ImagePixelReadAccessor<T, 3> readAccess(image, image->GetVolumeData(0));
*returnValue = readAccess.GetPixelByIndex(index);
break;
}
default:
*returnValue = 0;
break;
}
}
void mitk::CorrectorAlgorithm::GenerateData()
{
Image::Pointer inputImage = const_cast<Image*>(ImageToImageFilter::GetInput(0));
if (inputImage.IsNull() || inputImage->GetDimension() != 2)
{
itkExceptionMacro("CorrectorAlgorithm needs a 2D image as input.");
}
if (m_Contour.IsNull())
{
itkExceptionMacro("CorrectorAlgorithm needs a Contour object as input.");
}
// copy the input (since m_WorkingImage will be changed later)
m_WorkingImage = Image::New();
m_WorkingImage->Initialize( inputImage );
m_WorkingImage->SetVolume( inputImage.GetPointer()->GetData() );
if (inputImage->GetTimeSlicedGeometry() )
{
AffineGeometryFrame3D::Pointer originalGeometryAGF = inputImage->GetTimeSlicedGeometry()->Clone();
TimeSlicedGeometry::Pointer originalGeometry = dynamic_cast<TimeSlicedGeometry*>( originalGeometryAGF.GetPointer() );
m_WorkingImage->SetGeometry( originalGeometry );
}
else
{
itkExceptionMacro("Original image does not have a 'Time sliced geometry'! Cannot copy.");
}
// Convert to ipMITKSegmentationTYPE (because TobiasHeimannCorrectionAlgorithm relys on that data type)
itk::Image< ipMITKSegmentationTYPE, 2 >::Pointer correctPixelTypeImage;
CastToItkImage( m_WorkingImage, correctPixelTypeImage );
assert (correctPixelTypeImage.IsNotNull() );
// possible bug in CastToItkImage ?
// direction maxtrix is wrong/broken/not working after CastToItkImage, leading to a failed assertion in
// mitk/Core/DataStructures/mitkSlicedGeometry3D.cpp, 479:
// virtual void mitk::SlicedGeometry3D::SetSpacing(const mitk::Vector3D&): Assertion `aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0' failed
// solution here: we overwrite it with an unity matrix
itk::Image< ipMITKSegmentationTYPE, 2 >::DirectionType imageDirection;
imageDirection.SetIdentity();
correctPixelTypeImage->SetDirection(imageDirection);
Image::Pointer temporarySlice = this->GetOutput();
// temporarySlice = ImportItkImage( correctPixelTypeImage );
CastToMitkImage( correctPixelTypeImage, temporarySlice );
TobiasHeimannCorrectionAlgorithm( temporarySlice->GetSliceData()->GetPicDescriptor() );
// temporarySlice is our return value (user can get it by calling GetOutput() )
CalculateDifferenceImage( temporarySlice, inputImage );
if ( m_DifferenceImage.IsNotNull() && inputImage->GetTimeSlicedGeometry() )
{
AffineGeometryFrame3D::Pointer originalGeometryAGF = inputImage->GetTimeSlicedGeometry()->Clone();
TimeSlicedGeometry::Pointer originalGeometry = dynamic_cast<TimeSlicedGeometry*>( originalGeometryAGF.GetPointer() );
m_DifferenceImage->SetGeometry( originalGeometry );
}
else
{
itkExceptionMacro("Original image does not have a 'Time sliced geometry'! Cannot copy.");
}
}