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 = inputImage;
TimeGeometry::Pointer originalGeometry = NULL;
if (inputImage->GetTimeGeometry() )
{
originalGeometry = inputImage->GetTimeGeometry()->Clone();
m_WorkingImage->SetTimeGeometry( originalGeometry );
}
else
{
itkExceptionMacro("Original image does not have a 'Time sliced geometry'! Cannot copy.");
}
Image::Pointer temporarySlice;
// 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);
temporarySlice = this->GetOutput();
// temporarySlice = ImportItkImage( correctPixelTypeImage );
m_FillColor = 1;
m_EraseColor = 0;
ImprovedHeimannCorrectionAlgorithm(correctPixelTypeImage);
CastToMitkImage( correctPixelTypeImage, temporarySlice );
}
temporarySlice->SetTimeGeometry(originalGeometry);
}
void mitk::GeometryClipImageFilter::GenerateData()
{
Image::ConstPointer input = this->GetInput();
Image::Pointer output = this->GetOutput();
if ((output->IsInitialized() == false) || (m_ClippingGeometry.IsNull()))
return;
const PlaneGeometry *clippingGeometryOfCurrentTimeStep = nullptr;
if (m_TimeClippingGeometry.IsNull())
{
clippingGeometryOfCurrentTimeStep = dynamic_cast<const PlaneGeometry *>(m_ClippingGeometry.GetPointer());
}
else
{
clippingGeometryOfCurrentTimeStep =
dynamic_cast<const PlaneGeometry *>(m_TimeClippingGeometry->GetGeometryForTimeStep(0).GetPointer());
}
if (clippingGeometryOfCurrentTimeStep == nullptr)
return;
m_InputTimeSelector->SetInput(input);
m_OutputTimeSelector->SetInput(this->GetOutput());
mitk::Image::RegionType outputRegion = output->GetRequestedRegion();
const mitk::TimeGeometry *outputTimeGeometry = output->GetTimeGeometry();
const mitk::TimeGeometry *inputTimeGeometry = input->GetTimeGeometry();
ScalarType timeInMS;
int timestep = 0;
int tstart = outputRegion.GetIndex(3);
int tmax = tstart + outputRegion.GetSize(3);
int t;
for (t = tstart; t < tmax; ++t)
{
timeInMS = outputTimeGeometry->TimeStepToTimePoint(t);
timestep = inputTimeGeometry->TimePointToTimeStep(timeInMS);
m_InputTimeSelector->SetTimeNr(timestep);
m_InputTimeSelector->UpdateLargestPossibleRegion();
m_OutputTimeSelector->SetTimeNr(t);
m_OutputTimeSelector->UpdateLargestPossibleRegion();
if (m_TimeClippingGeometry.IsNotNull())
{
timestep = m_TimeClippingGeometry->TimePointToTimeStep(timeInMS);
if (m_TimeClippingGeometry->IsValidTimeStep(timestep) == false)
continue;
clippingGeometryOfCurrentTimeStep =
dynamic_cast<const PlaneGeometry *>(m_TimeClippingGeometry->GetGeometryForTimeStep(timestep).GetPointer());
}
AccessByItk_2(
m_InputTimeSelector->GetOutput(), _InternalComputeClippedImage, this, clippingGeometryOfCurrentTimeStep);
}
m_TimeOfHeaderInitialization.Modified();
}