Class TransformGeometryImageFilter

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

public class TransformGeometryImageFilter extends ImageFilter
Modify an image's geometric meta-data, changing its "physical" extent. The TransformGeometryImageFilter "physically" changes the image in space using the given transformation. The resulting image is an image with the same voxel values as the input, but with different physical space representation as affected by the transform. The specific transformation type can be any type derived from the MatrixOffsetTransformBase and the TranslationTransform . The modification of the geometric meta-data is an alternative to resampling the moving image onto the fixed image grid, after registration. The advantages of using this approach over resampling are two-fold, it does not introduce artifacts into the result because the original intensity information is not modified, and it is computationally more efficient. When the filter is used with a rigid or translation transformation the resulting image can be saved in any desired format. When the filter is used with an affine transformation the resulting image should be saved in a format that supports a non ortho-normal direction cosine matrix (e.g. nrrd). Let us call the transform operation from the fixed image to moving image TfmF2M . Given a set of points from the fixed image in physical space (i.e. physicalFixedImagePoints ), the aim is to convert those points into the moving image physical space as physicalMovingImagePoints = TfmF2M( physicalFixedImagePoints ) , and then be able to get the image values as movingContinuousIndexPoints = movingImage->TransformPhysicalPointToContinuousIndex( physicalMovingImagePoints ) . We desire to change the moving image direction cosine $\\mathbf{D}$ and origin $\\mathbf{o}$ such that we can compute the moving image points as movingContinuousIndexPoints = newMovingImage->TransformPhysicalPointToContinuousIndex( physicalFixedImagePoints ) Let us introduce the notation that will be used to formalize the transformation: Image-related parameters: $\\mathbf{D}$ : direction cosine matrix $\\mathbf{o}$ : origin vector $\\mathbf{S}$ : spacing $\\mathbf{ci}$ : continuous index $\\mathbf{D}^{'}$ : new direction cosine matrix $\\mathbf{o}^{'}$ : new origin vector Image content in corresponding space: $\\mathbf{f}_{p}$ : fixed image points in physical space $\\mathbf{m}_{p}$ : moving image points in physical space Rigid transform-related parameters: $\\mathbf{R}$ : rotation matrix $\\mathbf{c}$ : center of rotation vector $\\mathbf{t}$ : translation vector The TransformPhysicalPointToContinuousIndex method performs then: \\begin{eqnarray*} \\mathbf{ci} &= \\mathbf{S}^{-1}\\mathbf{D}^{-1}( \\mathbf{m}_{p} - \\mathbf{o} ) \\ \\mathbf{m}_{p} &= \\mathbf{R}(\\mathbf{f}_{p} - \\mathbf{c}) + \\mathbf{c} + \\mathbf{t} \\end{eqnarray*} After substitution: \\begin{eqnarray*} \\mathbf{m}_{c} &= \\underbrace{\\mathbf{R}^{-1}\\mathbf{D}}_\\text{new cosine}\\mathbf{S} * \\mathbf{i} + \\underbrace{\\mathbf{R}^{-1} * \\mathbf{o} - \\mathbf{R}^{-1} \\mathbf{c} - \\mathbf{R}^{-1}*t}_\\text{new origin} + \\mathbf{c} \\ \\ \\mathbf{D}^{'} &= \\mathbf{R}^{-1}\\mathbf{D} \\ \\mathbf{o}^{'} &= \\mathbf{R}^{-1} * ( \\mathbf{o} - \\mathbf{c} - \\mathbf{t} ) + \\mathbf{c} \\end{eqnarray*} See: itk::simple::TransformGeometry for the procedural interface itk::TransformGeometryImageFilter for the Doxygen on the original ITK class. C++ includes: sitkTransformGeometryImageFilter.h
  • Constructor Details

    • TransformGeometryImageFilter

      protected TransformGeometryImageFilter(long cPtr, boolean cMemoryOwn)
    • TransformGeometryImageFilter

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

    • getCPtr

      protected static long getCPtr(TransformGeometryImageFilter obj)
    • swigRelease

      protected static long swigRelease(TransformGeometryImageFilter obj)
    • finalize

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

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

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

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

      public Image execute(Image image, Transform transform)
      Image itk::simple::TransformGeometryImageFilter::Execute(Image &&image, const Transform &transform) Execute the filter on the input image