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(); }