typename ImageType::Pointer swcFile2itkImage(const SwcFileContent swcFileContent, typename ImageType::Pointer &inputImage){
// Allocate empty image
// itk::Index<3> start; start.Fill(0);
// itk::Size<3> size; size.Fill(100);
// typename ImageType::RegionType region(inputImage->GetOrigin(), inputImage->GetLargestPossibleRegion().GetSize());
// std::cout << "HereA!\n" << std::flush;
// typename ImageType::RegionType region(inputImage->GetLargestPossibleRegion());
std::cout << "I am HereB!\n" << std::flush;
typedef itk::ImageDuplicator< ImageType > DuplicatorType;
typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
duplicator->SetInputImage(inputImage);
duplicator->Update();
std::cout << "I am HereC!\n" << std::flush;
typename ImageType::Pointer groundTruthImage = duplicator->GetOutput();
// groundTruthImage->SetRegions(region);
// std::cout << "And I am HereC!\n" << std::flush;
// groundTruthImage->Allocate();
// std::cout << "And I am HereD!\n" << std::flush;
// groundTruthImage->FillBuffer(0);
std::cout << "I am HereD!\n" << std::flush;
return groundTruthImage;
}
void VectorOfMitkImagesToMitkVectorImage(const itk::Image<TPixel, VImageDimension>* /*source*/, mitk::Image::Pointer &output, mitk::LabelSetImage::ConstPointer input)
{
typedef itk::ComposeImageFilter< itk::Image<TPixel, VImageDimension> > ComposeFilterType;
unsigned int numberOfLayers = input->GetNumberOfLayers();
// 2015/07/01 At the time of writing MITK has problems with mitk::Images encapsulating itk::VectorImage
// if the vector length is less than 2, which might very well happen for segmentations.
if ( numberOfLayers > 1 )
{ // if we have only one image we do not need to create a vector
typename ComposeFilterType::Pointer vectorImageComposer = ComposeFilterType::New();
unsigned int activeLayer = input->GetActiveLayer();
for (unsigned int layer(0); layer < numberOfLayers; layer++)
{
typename itk::Image<TPixel, VImageDimension>::Pointer itkCurrentLayer;
// for the active layer use the current state not the saved one in the vector
if (layer == activeLayer)
{
mitk::CastToItkImage(dynamic_cast<const mitk::Image*>(input.GetPointer()), itkCurrentLayer);
}
else
{
mitk::CastToItkImage(input->GetLayerImage(layer), itkCurrentLayer);
}
vectorImageComposer->SetInput(layer, itkCurrentLayer);
}
try
{
vectorImageComposer->Update();
}
catch (const itk::ExceptionObject& e)
{
MITK_ERROR << "Caught exception while updating compose filter: " << e.what();
}
output = mitk::GrabItkImageMemory(vectorImageComposer->GetOutput());
}
else
{
// we want the clone to be a mitk::Image, not a mitk::LabelSetImage
typename itk::Image<TPixel, VImageDimension>::Pointer itkCurrentLayer;
mitk::CastToItkImage(dynamic_cast<const mitk::Image*>(input.GetPointer()), itkCurrentLayer);
typedef itk::ImageDuplicator< itk::Image<TPixel, VImageDimension> > DuplicatorType;
typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
duplicator->SetInputImage(itkCurrentLayer);
duplicator->Update();
output = mitk::GrabItkImageMemory(duplicator->GetOutput());
}
}
static void
CreateNoNaNMask(itk::Image<TPixel, VImageDimension>* itkValue, mitk::Image::Pointer mask, mitk::Image::Pointer& newMask)
{
typedef itk::Image< TPixel, VImageDimension> LFloatImageType;
typedef itk::Image< unsigned short, VImageDimension> LMaskImageType;
typename LMaskImageType::Pointer itkMask = LMaskImageType::New();
mitk::CastToItkImage(mask, itkMask);
typedef itk::ImageDuplicator< LMaskImageType > DuplicatorType;
typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
duplicator->SetInputImage(itkMask);
duplicator->Update();
auto tmpMask = duplicator->GetOutput();
itk::ImageRegionIterator<LMaskImageType> mask1Iter(itkMask, itkMask->GetLargestPossibleRegion());
itk::ImageRegionIterator<LMaskImageType> mask2Iter(tmpMask, tmpMask->GetLargestPossibleRegion());
itk::ImageRegionIterator<LFloatImageType> imageIter(itkValue, itkValue->GetLargestPossibleRegion());
while (!mask1Iter.IsAtEnd())
{
mask2Iter.Set(0);
if (mask1Iter.Value() > 0)
{
// Is not NaN
if (imageIter.Value() == imageIter.Value())
{
mask2Iter.Set(1);
}
}
++mask1Iter;
++mask2Iter;
++imageIter;
}
newMask->InitializeByItk(tmpMask);
mitk::GrabItkImageMemory(tmpMask, newMask);
}