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);
}
}
}
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::_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() );
}
}
}
}