int testImageToItkAndBack(mitk::Image* imgMem) { int result; int *p = (int*)imgMem->GetData(); if(p==NULL) { std::cout<<"[FAILED]"<<std::endl; return EXIT_FAILURE; } std::cout<<"[PASSED]"<<std::endl; std::cout << "Testing for dimension " << dim << ": " << std::flush; std::cout << "Testing mitk::ImageToItk: " << std::flush; typedef itk::Image<int,dim> ImageType; typename mitk::ImageToItk<ImageType>::Pointer toItkFilter = mitk::ImageToItk<ImageType>::New(); toItkFilter->SetInput(imgMem); toItkFilter->Update(); typename ImageType::Pointer itkImage = toItkFilter->GetOutput(); result = testBackCasting<ImageType>(imgMem, itkImage, false); if(result != EXIT_SUCCESS) return result; std::cout << "Testing mitk::ImageToItk (with subsequent DisconnectPipeline, see below): " << std::flush; result = testBackCasting<ImageType>(imgMem, itkImage, true); if(result != EXIT_SUCCESS) return result; return EXIT_SUCCESS; }
itk::Object::Pointer QmitkVersorRigid3DTransformView::GetTransform2(itk::Image<TPixelType, VImageDimension>* itkImage1) { if (VImageDimension == 3) { typedef typename itk::Image< TPixelType, 3 > FixedImage3DType; typedef typename itk::Image< TPixelType, 3 > MovingImage3DType; // the fixedImage is the input parameter (fix for Bug #14626) typename FixedImage3DType::Pointer fixedImage = itkImage1; // the movingImage type is known, use the ImageToItk filter (fix for Bug #14626) typename mitk::ImageToItk<MovingImage3DType>::Pointer movingImageToItk = mitk::ImageToItk<MovingImage3DType>::New(); movingImageToItk->SetInput(m_MovingImage); movingImageToItk->Update(); typename MovingImage3DType::Pointer movingImage = movingImageToItk->GetOutput(); typename itk::VersorRigid3DTransform< double >::Pointer transformPointer = itk::VersorRigid3DTransform< double >::New(); transformPointer->SetIdentity(); typedef typename itk::VersorRigid3DTransform< double > VersorRigid3DTransformType; if (m_Controls.m_CenterForInitializerVersorRigid3D->isChecked()) { typedef typename itk::CenteredTransformInitializer<VersorRigid3DTransformType, FixedImage3DType, MovingImage3DType> TransformInitializerType; typename TransformInitializerType::Pointer transformInitializer = TransformInitializerType::New(); transformInitializer->SetFixedImage( fixedImage ); transformInitializer->SetMovingImage( movingImage ); transformInitializer->SetTransform( transformPointer ); if (m_Controls.m_MomentsVersorRigid3D->isChecked()) { transformInitializer->MomentsOn(); } else { transformInitializer->GeometryOn(); } transformInitializer->InitializeTransform(); } typedef VersorRigid3DTransformType::VersorType VersorType; typedef VersorType::VectorType VectorType; VersorType rotation; VectorType axis; axis[0] = 0.0; axis[1] = 0.0; axis[2] = 1.0; const double angle = 0; rotation.Set( axis, angle ); transformPointer->SetRotation( rotation ); m_CenterX = transformPointer->GetCenter()[0]; m_CenterY = transformPointer->GetCenter()[1]; m_CenterZ = transformPointer->GetCenter()[2]; m_TransformObject = transformPointer.GetPointer(); return transformPointer.GetPointer(); } return NULL; }
itk::Object::Pointer QmitkCenteredRigid2DTransformView::GetTransform2( itk::Image<TPixelType, VImageDimension> *itkImage1) { if (VImageDimension == 2) { typedef typename itk::Image<TPixelType, 2> FixedImage2DType; typedef typename itk::Image<TPixelType, 2> MovingImage2DType; // the fixedImage is the input parameter (fix for Bug #14626) typename FixedImage2DType::Pointer fixedImage2D = itkImage1; // the movingImage type is known, use the ImageToItk filter (fix for Bug #14626) typename mitk::ImageToItk<MovingImage2DType>::Pointer movingImageToItk = mitk::ImageToItk<MovingImage2DType>::New(); movingImageToItk->SetInput(m_MovingImage); movingImageToItk->Update(); typename MovingImage2DType::Pointer movingImage2D = movingImageToItk->GetOutput(); typename itk::CenteredRigid2DTransform<double>::Pointer transformPointer = itk::CenteredRigid2DTransform<double>::New(); transformPointer->SetIdentity(); if (m_Controls.m_CenterForInitializerCenteredRigid2D->isChecked()) { typedef typename itk::CenteredRigid2DTransform<double> CenteredRigid2DTransformType; typedef typename itk::CenteredTransformInitializer<CenteredRigid2DTransformType, FixedImage2DType, MovingImage2DType> TransformInitializerType; typename TransformInitializerType::Pointer transformInitializer = TransformInitializerType::New(); transformInitializer->SetFixedImage(fixedImage2D); transformInitializer->SetMovingImage(movingImage2D); transformInitializer->SetTransform(transformPointer); if (m_Controls.m_MomentsCenteredRigid2D->isChecked()) { transformInitializer->MomentsOn(); } else { transformInitializer->GeometryOn(); } transformInitializer->InitializeTransform(); } transformPointer->SetAngle(m_Controls.m_AngleCenteredRigid2D->text().toFloat()); m_CenterX = transformPointer->GetCenter()[0]; m_CenterY = transformPointer->GetCenter()[1]; m_TransformObject = transformPointer.GetPointer(); return transformPointer.GetPointer(); } return nullptr; }
itk::Object::Pointer QmitkAffineTransformView::GetTransform2(itk::Image<TPixelType, VImageDimension>* itkImage1) { typedef typename itk::Image< TPixelType, VImageDimension > FixedImageType; typedef typename itk::Image< TPixelType, VImageDimension > MovingImageType; // the fixedImage is the input parameter (fix for Bug #14626) typename FixedImageType::Pointer fixedImage = itkImage1; // the movingImage type is known, use the ImageToItk filter (fix for Bug #14626) typename mitk::ImageToItk<MovingImageType>::Pointer movingImageToItk = mitk::ImageToItk<MovingImageType>::New(); movingImageToItk->SetInput(m_MovingImage); movingImageToItk->Update(); typename MovingImageType::Pointer movingImage = movingImageToItk->GetOutput(); typename itk::AffineTransform< double, VImageDimension>::Pointer transformPointer = itk::AffineTransform< double, VImageDimension>::New(); transformPointer->SetIdentity(); if (m_Controls.m_CenterForInitializerAffine->isChecked()) { typedef typename itk::AffineTransform< double, VImageDimension > AffineTransformType; typedef typename itk::CenteredTransformInitializer<AffineTransformType, FixedImageType, MovingImageType> TransformInitializerType; typename TransformInitializerType::Pointer transformInitializer = TransformInitializerType::New(); transformInitializer->SetFixedImage( fixedImage ); transformInitializer->SetMovingImage( movingImage ); transformInitializer->SetTransform( transformPointer ); if (m_Controls.m_MomentsAffine->isChecked()) { transformInitializer->MomentsOn(); } else { transformInitializer->GeometryOn(); } transformInitializer->InitializeTransform(); } m_CenterX = transformPointer->GetCenter()[0]; m_CenterY = transformPointer->GetCenter()[1]; m_CenterZ = transformPointer->GetCenter()[2]; m_TransformObject = transformPointer.GetPointer(); return transformPointer.GetPointer(); }
void mitk::MaskImageFilter::InternalComputeMask(itk::Image<TPixel, VImageDimension>* inputItkImage) { typedef itk::Image<TPixel, VImageDimension> ItkInputImageType; typedef itk::Image<unsigned char, VImageDimension> ItkMaskImageType; typedef itk::Image<TPixel, VImageDimension> ItkOutputImageType; typedef itk::ImageRegionConstIterator< ItkInputImageType > ItkInputImageIteratorType; typedef itk::ImageRegionConstIterator< ItkMaskImageType > ItkMaskImageIteratorType; typedef itk::ImageRegionIteratorWithIndex< ItkOutputImageType > ItkOutputImageIteratorType; typename mitk::ImageToItk<ItkMaskImageType>::Pointer maskimagetoitk = mitk::ImageToItk<ItkMaskImageType>::New(); maskimagetoitk->SetInput(m_MaskTimeSelector->GetOutput()); maskimagetoitk->Update(); typename ItkMaskImageType::Pointer maskItkImage = maskimagetoitk->GetOutput(); typename mitk::ImageToItk<ItkOutputImageType>::Pointer outputimagetoitk = mitk::ImageToItk<ItkOutputImageType>::New(); outputimagetoitk->SetInput(m_OutputTimeSelector->GetOutput()); outputimagetoitk->Update(); typename ItkOutputImageType::Pointer outputItkImage = outputimagetoitk->GetOutput(); // create the iterators typename ItkInputImageType::RegionType inputRegionOfInterest = inputItkImage->GetLargestPossibleRegion(); ItkInputImageIteratorType inputIt( inputItkImage, inputRegionOfInterest ); ItkMaskImageIteratorType maskIt ( maskItkImage, inputRegionOfInterest ); ItkOutputImageIteratorType outputIt( outputItkImage, inputRegionOfInterest ); //typename ItkOutputImageType::PixelType outsideValue = itk::NumericTraits<typename ItkOutputImageType::PixelType>::min(); if ( !m_OverrideOutsideValue ) m_OutsideValue = itk::NumericTraits<typename ItkOutputImageType::PixelType>::min(); m_MinValue = (float)(itk::NumericTraits<typename ItkOutputImageType::PixelType>::max()); m_MaxValue = (float)(itk::NumericTraits<typename ItkOutputImageType::PixelType>::min()); for ( inputIt.GoToBegin(), maskIt.GoToBegin(), outputIt.GoToBegin(); !inputIt.IsAtEnd() && !maskIt.IsAtEnd(); ++inputIt, ++maskIt, ++outputIt) { if ( maskIt.Get() > itk::NumericTraits<typename ItkMaskImageType::PixelType>::Zero ) { outputIt.Set(inputIt.Get()); m_MinValue = vnl_math_min((float)inputIt.Get(), (float)m_MinValue); m_MaxValue = vnl_math_max((float)inputIt.Get(), (float)m_MaxValue); } else { outputIt.Set(m_OutsideValue); } } }
void mitk::_InternalComputeClippedImage(itk::Image<TPixel, VImageDimension>* inputItkImage, mitk::GeometryClipImageFilter* geometryClipper, const mitk::Geometry2D* clippingGeometry2D) { typedef itk::Image<TPixel, VImageDimension> ItkInputImageType; typedef itk::Image<TPixel, VImageDimension> ItkOutputImageType; typedef itk::ImageRegionConstIteratorWithIndex< ItkInputImageType > ItkInputImageIteratorType; typedef itk::ImageRegionIteratorWithIndex< ItkOutputImageType > ItkOutputImageIteratorType; typename mitk::ImageToItk<ItkOutputImageType>::Pointer outputimagetoitk = mitk::ImageToItk<ItkOutputImageType>::New(); outputimagetoitk->SetInput(geometryClipper->m_OutputTimeSelector->GetOutput()); outputimagetoitk->Update(); typename ItkOutputImageType::Pointer outputItkImage = outputimagetoitk->GetOutput(); // create the iterators typename ItkInputImageType::RegionType inputRegionOfInterest = inputItkImage->GetLargestPossibleRegion(); ItkInputImageIteratorType inputIt( inputItkImage, inputRegionOfInterest ); ItkOutputImageIteratorType outputIt( outputItkImage, inputRegionOfInterest ); typename ItkOutputImageType::PixelType outsideValue; if(geometryClipper->m_AutoOutsideValue) outsideValue = itk::NumericTraits<typename ItkOutputImageType::PixelType>::min(); else outsideValue = (typename ItkOutputImageType::PixelType) geometryClipper->m_OutsideValue; mitk::Geometry3D* inputGeometry = geometryClipper->m_InputTimeSelector->GetOutput()->GetGeometry(); typedef itk::Index<VImageDimension> IndexType; Point3D indexPt; indexPt.Fill(0); int i, dim=IndexType::GetIndexDimension(); Point3D pointInMM; bool above = geometryClipper->m_ClipPartAboveGeometry; bool labelBothSides = geometryClipper->GetLabelBothSides(); if (geometryClipper->GetAutoOrientLabels()) { Point3D leftMostPoint; leftMostPoint.Fill( std::numeric_limits<float>::min() / 2.0 ); if(clippingGeometry2D->IsAbove(pointInMM) != above) { // invert meaning of above --> left is always the "above" side above = !above; MITK_INFO << leftMostPoint << " is BELOW geometry. Inverting meaning of above" << std::endl; } else MITK_INFO << leftMostPoint << " is above geometry" << std::endl; } typename ItkOutputImageType::PixelType aboveLabel = (typename ItkOutputImageType::PixelType)geometryClipper->GetAboveGeometryLabel(); typename ItkOutputImageType::PixelType belowLabel = (typename ItkOutputImageType::PixelType)geometryClipper->GetBelowGeometryLabel(); for ( inputIt.GoToBegin(), outputIt.GoToBegin(); !inputIt.IsAtEnd(); ++inputIt, ++outputIt) { if((typename ItkOutputImageType::PixelType)inputIt.Get() == outsideValue) { outputIt.Set(outsideValue); } else { for(i=0;i<dim;++i) indexPt[i]=(mitk::ScalarType)inputIt.GetIndex()[i]; inputGeometry->IndexToWorld(indexPt, pointInMM); if(clippingGeometry2D->IsAbove(pointInMM) == above) { if ( labelBothSides ) outputIt.Set( aboveLabel ); else outputIt.Set( outsideValue ); } else { if ( labelBothSides) outputIt.Set( belowLabel ); else outputIt.Set( inputIt.Get() ); } } } }