Class DisplacementFieldJacobianDeterminantFilter

java.lang.Object
org.itk.simple.ProcessObject
org.itk.simple.ImageFilter
org.itk.simple.DisplacementFieldJacobianDeterminantFilter

public class DisplacementFieldJacobianDeterminantFilter extends ImageFilter
Computes a scalar image from a vector image (e.g., deformation field) input, where each output scalar at each pixel is the Jacobian determinant of the vector field at that location. This calculation is correct in the case where the vector image is a "displacement" from the current location. The computation for the jacobian determinant is: det[ dT/dx ] = det[ I + du/dx ]. Overview This filter is based on itkVectorGradientMagnitudeImageFilter and supports the m_DerivativeWeights weights for partial derivatives. Note that the determinant of a zero vector field is also zero, whereas the Jacobian determinant of the corresponding identity warp transformation is 1.0. In order to compute the effective deformation Jacobian determinant 1.0 must be added to the diagonal elements of Jacobian prior to taking the derivative. i.e. det([ (1.0+dx/dx) dx/dy dx/dz ; dy/dx (1.0+dy/dy) dy/dz; dz/dx dz/dy (1.0+dz/dz) ]) Template Parameters (Input and Output) This filter has one required template parameter which defines the input image type. The pixel type of the input image is assumed to be a vector (e.g., itk::Vector , itk::RGBPixel , itk::FixedArray ). The scalar type of the vector components must be castable to floating point. Instantiating with an image of RGBPixel<unsigned short>, for example, is allowed, but the filter will convert it to an image of Vector<float,3> for processing. The second template parameter, TRealType, can be optionally specified to define the scalar numerical type used in calculations. This is the component type of the output image, which will be of itk::Vector<TRealType, N>, where N is the number of channels in the multiple component input image. The default type of TRealType is float. For extra precision, you may safely change this parameter to double. The third template parameter is the output image type. The third parameter will be automatically constructed from the first and second parameters, so it is not necessary (or advisable) to set this parameter explicitly. Given an M-channel input image with dimensionality N, and a numerical type specified as TRealType, the output image will be of type itk::Image<TRealType, N>. Filter Parameters The method UseImageSpacingOn will cause derivatives in the image to be scaled (inversely) with the pixel size of the input image, effectively taking derivatives in world coordinates (versus isotropic image space). UseImageSpacingOff turns this functionality off. Default is UseImageSpacingOn. The parameter UseImageSpacing can be set directly with the method SetUseImageSpacing(bool) . Weights can be applied to the derivatives directly using the SetDerivativeWeights method. Note that if UseImageSpacing is set to TRUE (ON), then these weights will be overridden by weights derived from the image spacing when the filter is updated. The argument to this method is a C array of TRealValue type. Constraints We use vnl_det for determinant computation, which only supports square matrices. So the vector dimension of the input image values must be equal to the image dimensions, which is trivially true for a deformation field that maps an n-dimensional space onto itself. Currently, dimensions up to and including 4 are supported. This limitation comes from the presence of vnl_det() functions for matrices of dimension up to 4x4. The template parameter TRealType must be floating point (float or double) or a user-defined "real" numerical type with arithmetic operations defined sufficient to compute derivatives. See: Image Neighborhood NeighborhoodOperator NeighborhoodIterator This class was adapted by Hans J. Johnson, The University of Iowa from code provided by Tom Vercauteren, INRIA & Mauna Kea Technologies Torsten Rohlfing, Neuroscience Program, SRI International. See: itk::simple::DisplacementFieldJacobianDeterminantFilter for the procedural interface itk::DisplacementFieldJacobianDeterminantFilter for the Doxygen on the original ITK class. C++ includes: sitkDisplacementFieldJacobianDeterminantFilter.h
  • Constructor Details

    • DisplacementFieldJacobianDeterminantFilter

      protected DisplacementFieldJacobianDeterminantFilter(long cPtr, boolean cMemoryOwn)
    • DisplacementFieldJacobianDeterminantFilter

      public DisplacementFieldJacobianDeterminantFilter()
      itk::simple::DisplacementFieldJacobianDeterminantFilter::DisplacementFieldJacobianDeterminantFilter() Default Constructor that takes no arguments and initializes default parameters
  • Method Details

    • getCPtr

      protected static long getCPtr(DisplacementFieldJacobianDeterminantFilter obj)
    • swigRelease

      protected static long swigRelease(DisplacementFieldJacobianDeterminantFilter obj)
    • finalize

      protected void finalize()
      Overrides:
      finalize in class ImageFilter
    • delete

      public void delete()
      virtual itk::simple::DisplacementFieldJacobianDeterminantFilter::~DisplacementFieldJacobianDeterminantFilter() Destructor
      Overrides:
      delete in class ImageFilter
    • setUseImageSpacing

      public void setUseImageSpacing(boolean UseImageSpacing)
      Self& itk::simple::DisplacementFieldJacobianDeterminantFilter::SetUseImageSpacing(bool UseImageSpacing) Set/Get whether or not the filter will use the spacing of the input image (1/spacing) in the calculation of the Jacobian determinant. Use On to compute the Jacobian determinant in the space in which the data was acquired; use Off to reset the derivative weights, ignore the image spacing, and to compute the Jacobian determinant in the image space. Default is On.
    • useImageSpacingOn

      public void useImageSpacingOn()
      Self& itk::simple::DisplacementFieldJacobianDeterminantFilter::UseImageSpacingOn() Set the value of UseImageSpacing to true or false respectfully.
    • useImageSpacingOff

      public void useImageSpacingOff()
      Self& itk::simple::DisplacementFieldJacobianDeterminantFilter::UseImageSpacingOff()
    • getUseImageSpacing

      public boolean getUseImageSpacing()
      bool itk::simple::DisplacementFieldJacobianDeterminantFilter::GetUseImageSpacing() const Set/Get whether or not the filter will use the spacing of the input image (1/spacing) in the calculation of the Jacobian determinant. Use On to compute the Jacobian determinant in the space in which the data was acquired; use Off to reset the derivative weights, ignore the image spacing, and to compute the Jacobian determinant in the image space. Default is On.
    • setDerivativeWeights

      public void setDerivativeWeights(VectorDouble DerivativeWeights)
      Self& itk::simple::DisplacementFieldJacobianDeterminantFilter::SetDerivativeWeights(std::vector< double > DerivativeWeights) Directly Set/Get the array of weights used in the gradient calculations. Note that calling UseImageSpacingOn will clobber these values.
    • getDerivativeWeights

      public VectorDouble getDerivativeWeights()
      std::vector<double> itk::simple::DisplacementFieldJacobianDeterminantFilter::GetDerivativeWeights() const Directly Set/Get the array of weights used in the gradient calculations. Note that calling UseImageSpacingOn will clobber these values.
    • getName

      public String getName()
      std::string itk::simple::DisplacementFieldJacobianDeterminantFilter::GetName() const Name of this class
      Overrides:
      getName in class ProcessObject
    • toString

      public String toString()
      std::string itk::simple::DisplacementFieldJacobianDeterminantFilter::ToString() const Print ourselves out
      Overrides:
      toString in class ProcessObject
    • execute

      public Image execute(Image image1)
      Image itk::simple::DisplacementFieldJacobianDeterminantFilter::Execute(const Image &image1) Execute the filter on the input image