static mitk::Image::Pointer GenerateMaskImage(unsigned int dimX,
unsigned int dimY,
unsigned int dimZ,
float spacingX = 1,
float spacingY = 1,
float spacingZ = 1)
{
typedef itk::Image< TPixelType, 3 > ImageType;
typename ImageType::RegionType imageRegion;
imageRegion.SetSize(0, dimX);
imageRegion.SetSize(1, dimY);
imageRegion.SetSize(2, dimZ);
typename ImageType::SpacingType spacing;
spacing[0] = spacingX;
spacing[1] = spacingY;
spacing[2] = spacingZ;
mitk::Point3D origin; origin.Fill(0.0);
itk::Matrix<double, 3, 3> directionMatrix; directionMatrix.SetIdentity();
typename ImageType::Pointer image = ImageType::New();
image->SetSpacing( spacing );
image->SetOrigin( origin );
image->SetDirection( directionMatrix );
image->SetLargestPossibleRegion( imageRegion );
image->SetBufferedRegion( imageRegion );
image->SetRequestedRegion( imageRegion );
image->Allocate();
image->FillBuffer(1);
mitk::Image::Pointer mitkImage = mitk::Image::New();
mitkImage->InitializeByItk( image.GetPointer() );
mitkImage->SetVolume( image->GetBufferPointer() );
return mitkImage;
}
static mitk::Image::Pointer GenerateGradientWithDimXImage(unsigned int dimX,
unsigned int dimY,
unsigned int dimZ,
float spacingX = 1,
float spacingY = 1,
float spacingZ = 1)
{
typedef itk::Image< TPixelType, 3 > ImageType;
typename ImageType::RegionType imageRegion;
imageRegion.SetSize(0, dimX);
imageRegion.SetSize(1, dimY);
imageRegion.SetSize(2, dimZ);
typename ImageType::SpacingType spacing;
spacing[0] = spacingX;
spacing[1] = spacingY;
spacing[2] = spacingZ;
mitk::Point3D origin; origin.Fill(0.0);
itk::Matrix<double, 3, 3> directionMatrix; directionMatrix.SetIdentity();
typename ImageType::Pointer image = ImageType::New();
image->SetSpacing( spacing );
image->SetOrigin( origin );
image->SetDirection( directionMatrix );
image->SetLargestPossibleRegion( imageRegion );
image->SetBufferedRegion( imageRegion );
image->SetRequestedRegion( imageRegion );
image->Allocate();
image->FillBuffer(0.0);
typedef itk::ImageRegionIterator<ImageType> IteratorOutputType;
IteratorOutputType it(image, imageRegion);
it.GoToBegin();
TPixelType val = 0;
while(!it.IsAtEnd())
{
it.Set(val % dimX);
val++;
++it;
}
mitk::Image::Pointer mitkImage = mitk::Image::New();
mitkImage->InitializeByItk( image.GetPointer() );
mitkImage->SetVolume( image->GetBufferPointer() );
return mitkImage;
}
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);
}
