void WorkbenchUtils::resampleImageItk(itk::Image <PixelType, ImageDimension> *itkImage, Interpolator interpolType,
unsigned int *newDimensions, Image::Pointer outImage) {
typedef itk::Image <PixelType, ImageDimension> ImageType;
// get original image informations
const typename ImageType::RegionType &inputRegion = itkImage->GetLargestPossibleRegion();
const typename ImageType::SizeType &inputDimensions = inputRegion.GetSize();
const typename ImageType::SpacingType &inputSpacing = itkImage->GetSpacing();
// calculate spacing
double outputSpacing[ImageDimension];
itk::Size <ImageDimension> outputSize;
for (unsigned int i = 0; i < ImageDimension; ++i) {
outputSpacing[i] = inputSpacing[i] * (double) inputDimensions[i] / newDimensions[i];
outputSize[i] = newDimensions[i];
}
// transform
typedef itk::IdentityTransform<double, ImageDimension> TransformType;
typename TransformType::Pointer transform = TransformType::New();
transform->SetIdentity();
// interpolator typedefs
typedef double CoordinateType;
typedef itk::LinearInterpolateImageFunction <ImageType, CoordinateType> LinearInterpolatorType;
typedef itk::NearestNeighborInterpolateImageFunction <ImageType, CoordinateType> NearestNeighborInterpolatorType;
typedef itk::GaussianInterpolateImageFunction <ImageType, CoordinateType> GaussianInterpolatorType;
typedef itk::BSplineInterpolateImageFunction <ImageType, CoordinateType> BSplineInterpolatorType;
// set up the filter
typedef itk::ResampleImageFilter <ImageType, ImageType> ResampleFilterType;
typename ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
resampleFilter->SetTransform(transform);
resampleFilter->SetOutputOrigin(itkImage->GetOrigin());
resampleFilter->SetOutputSpacing(outputSpacing);
resampleFilter->SetSize(outputSize);
switch (interpolType) {
case Interpolator::LINEAR: // the default;
resampleFilter->SetInterpolator(LinearInterpolatorType::New());
break;
case Interpolator::NEAREST_NEIGHBOR:
resampleFilter->SetInterpolator(NearestNeighborInterpolatorType::New());
break;
case Interpolator::GAUSSIAN:
resampleFilter->SetInterpolator(GaussianInterpolatorType::New());
break;
case Interpolator::BSPLINE:
resampleFilter->SetInterpolator(BSplineInterpolatorType::New());
break;
}
resampleFilter->SetInput(itkImage);
resampleFilter->UpdateLargestPossibleRegion();
// get the results and cast them back to mitk. return via out parameter.
outImage->InitializeByItk(resampleFilter->GetOutput());
CastToMitkImage(resampleFilter->GetOutput(), outImage);
}
void WorkbenchUtils::addPaddingItk(itk::Image <PixelType, ImageDimension> *itkImage, Axis axis, bool append,
int numberOfSlices, float pixelValue, Image::Pointer outImage) {
// pixel type is templated. The input field for the value is set to float, so the user might enter some invalid values for the image type at hand.
// since all primitive built-in types have well defined casting behaviour between each other, we'll just do a typecast. we will clip the entered
// value at PixelTypes min/max to prevent an overflow. The possible loss of precision is ignored.
float lower = itk::NumericTraits<PixelType>::min();
float upper = itk::NumericTraits<PixelType>::max();
float clippedPixelValue = std::max(lower, std::min(pixelValue, upper));
PixelType paddingPixelValue = (PixelType) clippedPixelValue;
typedef itk::Image <PixelType, ImageDimension> ImageType;
// gather all data
typename ImageType::SizeType lowerBound;
typename ImageType::SizeType upperBound;
lowerBound.Fill(0);
upperBound.Fill(0);
unsigned int itkAxis = convertToItkAxis(axis);
if (append) {
upperBound[itkAxis] = numberOfSlices;
} else {
lowerBound[itkAxis] = numberOfSlices;
}
// setup the filter
typedef itk::ConstantPadImageFilter <ImageType, ImageType> PadFilterType;
typename PadFilterType::Pointer padFilter = PadFilterType::New();
padFilter->SetInput(itkImage);
padFilter->SetConstant(paddingPixelValue);
padFilter->SetPadLowerBound(lowerBound);
padFilter->SetPadUpperBound(upperBound);
padFilter->UpdateLargestPossibleRegion();
// Update the origin, since padding creates negative index that is lost when returned to MITK
typename ImageType::Pointer paddedImage = padFilter->GetOutput();
typename ImageType::RegionType paddedImageRegion = paddedImage->GetLargestPossibleRegion();
typename ImageType::PointType origin;
paddedImage->TransformIndexToPhysicalPoint(paddedImageRegion.GetIndex(), origin);
paddedImage->SetOrigin(origin);
// get the results and cast them back to mitk. return via out parameter.
outImage->InitializeByItk(paddedImage.GetPointer());
CastToMitkImage(paddedImage, outImage);
}
