template <class ImagePixelType, class MaskPixelType> int update()
{
typedef itk::Image<ImagePixelType, 3> ImageType;
typedef itk::Image<MaskPixelType, 3> MaskType;
if ( !input ||!input->data() || !mask ||!mask->data())
return EXIT_FAILURE;
typedef itk::MaskImageFilter< ImageType, MaskType> MaskFilterType;
typename MaskFilterType::Pointer maskFilter = MaskFilterType::New();
typename ImageType::Pointer imgInput = dynamic_cast<ImageType *> ( ( itk::Object* ) ( input->data() )) ;
typename MaskType::Pointer maskInput = dynamic_cast<MaskType *> ( ( itk::Object* ) ( mask->data() )) ;
try
{
maskInput->SetOrigin(imgInput->GetOrigin());
maskInput->SetSpacing(imgInput->GetSpacing());
maskFilter->SetInput(imgInput);
maskFilter->SetMaskingValue(maskBackgroundValue);
maskFilter->SetMaskImage(maskInput);
//Outside values set to the lowest reachable value
typedef itk::MinimumMaximumImageCalculator <ImageType> ImageCalculatorFilterType;
typename ImageCalculatorFilterType::Pointer imageCalculatorFilter
= ImageCalculatorFilterType::New ();
imageCalculatorFilter->SetImage(imgInput);
imageCalculatorFilter->ComputeMinimum();
maskFilter->SetOutsideValue(std::min(double(imageCalculatorFilter->GetMinimum()), 0.0));
maskFilter->Update();
output->setData(maskFilter->GetOutput());
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught in medMaskApplication!" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
medUtilities::setDerivedMetaData(output, input, "masked");
return EXIT_SUCCESS;
}
void CreateNewMask(const itk::Image< TPixel, VImageDimension > *image, MaskParameter param, mitk::Image::Pointer &output)
{
int transform[3][2];
transform[0][0] = 1; transform[0][1] = 2;
transform[1][0] = 0; transform[1][1] = 2;
transform[2][0] = 0; transform[2][1] = 1;
typedef itk::Image<unsigned short, VImageDimension> MaskType;
typedef itk::Image<unsigned short, 2> Mask2DType;
typename Mask2DType::Pointer mask = Mask2DType::New();
mitk::CastToItkImage(param.mask, mask);
typename MaskType::Pointer mask3D = MaskType::New();
mask3D->SetRegions(image->GetLargestPossibleRegion());
mask3D->SetSpacing(image->GetSpacing());
mask3D->SetOrigin(image->GetOrigin());
mask3D->Allocate();
itk::ImageRegionIteratorWithIndex<MaskType> iter(mask3D, mask3D->GetLargestPossibleRegion());
while (!iter.IsAtEnd())
{
auto index = iter.GetIndex();
iter.Set(0);
if (index[param.axis] == param.slice)
{
Mask2DType::IndexType index2D;
index2D[0] = index[transform[param.axis][0]];
index2D[1] = index[transform[param.axis][1]];
auto pixel = mask->GetPixel(index2D);
iter.Set(pixel);
}
++iter;
}
mitk::CastToMitkImage(mask3D, output);
}