Class LevelSetMotionRegistrationFilter

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

public class LevelSetMotionRegistrationFilter extends ImageFilter
Deformably register two images using level set motion. LevelSetMotionFilter implements a deformable registration algorithm that aligns a fixed and a moving image under level set motion. The equations of motion are similar to those of the DemonsRegistrationFilter . The main differences are: (1) Gradients of the moving image are calculated on a smoothed image while intensity difference are measured on the original images (2) Magnitude of the motion vector is a function of the differences in intensity between the fixed and moving pixel. An adaptive timestep is calculated based on the maximum motion vector over the entire field to ensure stability. The timestep also implicitly converts the motion vector measured in units of intensity to a vector measured in physical units. Demons, on the other hand, defines its motion vectors as function of both the intensity differences and gradient magnitude at each respective pixel. Consider two separate pixels with the same intensity differences between the corresponding fixed and moving pixel pairs. In demons, the motion vector of the pixel over a low gradient region will be larger than the motion vector of the pixel over a large gradient region. This leads to an unstable vector field. In the levelset approach, the motion vectors will be proportional to the gradients, scaled by the maximum gradient over the entire field. The pixel with at the lower gradient position will more less than the pixel at the higher gradient position. (3) Gradients are calculated using minmod finite difference instead of using central differences. A deformation field is represented as a image whose pixel type is some vector type with at least N elements, where N is the dimension of the fixed image. The vector type must support element access via operator []. It is assumed that the vector elements behave like floating point scalars. This class is templated over the fixed image type, moving image type and the deformation field type. The input fixed and moving images are set via methods SetFixedImage and SetMovingImage respectively. An initial deformation field maybe set via SetInitialDisplacementField or SetInput. If no initial field is set, a zero field is used as the initial condition. The algorithm has one parameters: the number of iteration to be performed. The output deformation field can be obtained via methods GetOutput or GetDisplacementField. This class make use of the finite difference solver hierarchy. Update for each iteration is computed in LevelSetMotionFunction. WARNING: This filter assumes that the fixed image type, moving image type and deformation field type all have the same number of dimensions. Ref: B.C. Vemuri, J. Ye, Y. Chen, C.M. Leonard. " Image registration via level-set motion: applications to atlas-based segmentation". Medical Image Analysis. Vol. 7. pp. 1-20. 2003. See: LevelSetMotionRegistrationFunction DemonsRegistrationFilter itk::LevelSetMotionRegistrationFilter for the Doxygen on the original ITK class. C++ includes: sitkLevelSetMotionRegistrationFilter.h
  • Constructor Details

    • LevelSetMotionRegistrationFilter

      protected LevelSetMotionRegistrationFilter(long cPtr, boolean cMemoryOwn)
    • LevelSetMotionRegistrationFilter

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

    • getCPtr

      protected static long getCPtr(LevelSetMotionRegistrationFilter obj)
    • swigRelease

      protected static long swigRelease(LevelSetMotionRegistrationFilter obj)
    • finalize

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

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

      public void setGradientSmoothingStandardDeviations(double GradientSmoothingStandardDeviations)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetGradientSmoothingStandardDeviations(double GradientSmoothingStandardDeviations) Set/Get the standard deviation used for smoothing the moving image prior to calculating gradients. The standard deviation is measured in physical units (for instance mm). Note that this smoothing value is not to be confused with the PDEDeformableRegistrationFilter::SetStandardDeviations() method. The method in PDEDeformableRegistrationFilter is for setting the smoothing parameters for regularizing the deformation field between iterations. Those smoothing parameters are set in pixel units not physical units. Deformation field smoothing is not done by default in LevelSetMotionRegistration. This smoothing parameter is to condition the gradient calculation and parameter is specified in physical units.
    • getGradientSmoothingStandardDeviations

      public double getGradientSmoothingStandardDeviations()
      double itk::simple::LevelSetMotionRegistrationFilter::GetGradientSmoothingStandardDeviations() const
    • setNumberOfIterations

      public void setNumberOfIterations(long NumberOfIterations)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetNumberOfIterations(uint32_t NumberOfIterations)
    • getNumberOfIterations

      public long getNumberOfIterations()
      uint32_t itk::simple::LevelSetMotionRegistrationFilter::GetNumberOfIterations() const
    • setMaximumRMSError

      public void setMaximumRMSError(double MaximumRMSError)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetMaximumRMSError(double MaximumRMSError)
    • getMaximumRMSError

      public double getMaximumRMSError()
      double itk::simple::LevelSetMotionRegistrationFilter::GetMaximumRMSError() const
    • setStandardDeviations

      public void setStandardDeviations(VectorDouble StandardDeviations)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetStandardDeviations(std::vector< double > StandardDeviations) Set/Get the Gaussian smoothing standard deviations for the displacement field. The values are set with respect to pixel coordinates.
    • setStandardDeviations

      public void setStandardDeviations(double value)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetStandardDeviations(std::vector< double > StandardDeviations) Set/Get the Gaussian smoothing standard deviations for the displacement field. The values are set with respect to pixel coordinates.
    • getStandardDeviations

      public VectorDouble getStandardDeviations()
      std::vector<double> itk::simple::LevelSetMotionRegistrationFilter::GetStandardDeviations() const Set/Get the Gaussian smoothing standard deviations for the displacement field. The values are set with respect to pixel coordinates.
    • setSmoothDisplacementField

      public void setSmoothDisplacementField(boolean SmoothDisplacementField)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetSmoothDisplacementField(bool SmoothDisplacementField) Set/Get whether the displacement field is smoothed (regularized). Smoothing the displacement yields a solution elastic in nature. If SmoothDisplacementField is on, then the displacement field is smoothed with a Gaussian whose standard deviations are specified with SetStandardDeviations()
    • smoothDisplacementFieldOn

      public void smoothDisplacementFieldOn()
      Self& itk::simple::LevelSetMotionRegistrationFilter::SmoothDisplacementFieldOn() Set the value of SmoothDisplacementField to true or false respectfully.
    • smoothDisplacementFieldOff

      public void smoothDisplacementFieldOff()
      Self& itk::simple::LevelSetMotionRegistrationFilter::SmoothDisplacementFieldOff()
    • getSmoothDisplacementField

      public boolean getSmoothDisplacementField()
      bool itk::simple::LevelSetMotionRegistrationFilter::GetSmoothDisplacementField() const Set/Get whether the displacement field is smoothed (regularized). Smoothing the displacement yields a solution elastic in nature. If SmoothDisplacementField is on, then the displacement field is smoothed with a Gaussian whose standard deviations are specified with SetStandardDeviations()
    • setUpdateFieldStandardDeviations

      public void setUpdateFieldStandardDeviations(VectorDouble UpdateFieldStandardDeviations)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetUpdateFieldStandardDeviations(std::vector< double > UpdateFieldStandardDeviations) Set the Gaussian smoothing standard deviations for the update field. The values are set with respect to pixel coordinates.
    • setUpdateFieldStandardDeviations

      public void setUpdateFieldStandardDeviations(double value)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetUpdateFieldStandardDeviations(std::vector< double > UpdateFieldStandardDeviations) Set the Gaussian smoothing standard deviations for the update field. The values are set with respect to pixel coordinates.
    • getUpdateFieldStandardDeviations

      public VectorDouble getUpdateFieldStandardDeviations()
      std::vector<double> itk::simple::LevelSetMotionRegistrationFilter::GetUpdateFieldStandardDeviations() const Set the Gaussian smoothing standard deviations for the update field. The values are set with respect to pixel coordinates.
    • setSmoothUpdateField

      public void setSmoothUpdateField(boolean SmoothUpdateField)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetSmoothUpdateField(bool SmoothUpdateField) Set/Get whether the update field is smoothed (regularized). Smoothing the update field yields a solution viscous in nature. If SmoothUpdateField is on, then the update field is smoothed with a Gaussian whose standard deviations are specified with SetUpdateFieldStandardDeviations()
    • smoothUpdateFieldOn

      public void smoothUpdateFieldOn()
      Self& itk::simple::LevelSetMotionRegistrationFilter::SmoothUpdateFieldOn() Set the value of SmoothUpdateField to true or false respectfully.
    • smoothUpdateFieldOff

      public void smoothUpdateFieldOff()
      Self& itk::simple::LevelSetMotionRegistrationFilter::SmoothUpdateFieldOff()
    • getSmoothUpdateField

      public boolean getSmoothUpdateField()
      bool itk::simple::LevelSetMotionRegistrationFilter::GetSmoothUpdateField() const Set/Get whether the update field is smoothed (regularized). Smoothing the update field yields a solution viscous in nature. If SmoothUpdateField is on, then the update field is smoothed with a Gaussian whose standard deviations are specified with SetUpdateFieldStandardDeviations()
    • setMaximumKernelWidth

      public void setMaximumKernelWidth(long MaximumKernelWidth)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetMaximumKernelWidth(unsigned int MaximumKernelWidth) Set/Get the desired limits of the Gaussian kernel width.
    • getMaximumKernelWidth

      public long getMaximumKernelWidth()
      unsigned int itk::simple::LevelSetMotionRegistrationFilter::GetMaximumKernelWidth() const Set/Get the desired limits of the Gaussian kernel width.
    • setMaximumError

      public void setMaximumError(double MaximumError)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetMaximumError(double MaximumError) Set/Get the desired maximum error of the Guassian kernel approximate.
    • getMaximumError

      public double getMaximumError()
      double itk::simple::LevelSetMotionRegistrationFilter::GetMaximumError() const Set/Get the desired maximum error of the Guassian kernel approximate.
    • setAlpha

      public void setAlpha(double Alpha)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetAlpha(double Alpha) Set/Get the parameter alpha. Alpha is added to the calculated gradient magnitude prior to normalizing the gradient to protect against numerical instability as the gradient magnitude approaches zero. This should be set as a small fraction of the intensity dynamic range, for instance 0.04%. Default is the absolute (not percentage) value of 0.1.
    • getAlpha

      public double getAlpha()
      double itk::simple::LevelSetMotionRegistrationFilter::GetAlpha() const
    • setIntensityDifferenceThreshold

      public void setIntensityDifferenceThreshold(double IntensityDifferenceThreshold)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetIntensityDifferenceThreshold(double IntensityDifferenceThreshold) Set/Get the threshold below which the absolute difference of intensity yields a match. When the intensities match between a moving and fixed image pixel, the update vector (for that iteration) will be the zero vector. Default is 0.001.
    • getIntensityDifferenceThreshold

      public double getIntensityDifferenceThreshold()
      double itk::simple::LevelSetMotionRegistrationFilter::GetIntensityDifferenceThreshold() const
    • setGradientMagnitudeThreshold

      public void setGradientMagnitudeThreshold(double GradientMagnitudeThreshold)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetGradientMagnitudeThreshold(double GradientMagnitudeThreshold) Set/Get the threshold below which the gradient magnitude is considered the zero vector. Default is 1e-9.
    • getGradientMagnitudeThreshold

      public double getGradientMagnitudeThreshold()
      double itk::simple::LevelSetMotionRegistrationFilter::GetGradientMagnitudeThreshold() const
    • setUseImageSpacing

      public void setUseImageSpacing(boolean UseImageSpacing)
      Self& itk::simple::LevelSetMotionRegistrationFilter::SetUseImageSpacing(bool UseImageSpacing)
    • useImageSpacingOn

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

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

      public boolean getUseImageSpacing()
      bool itk::simple::LevelSetMotionRegistrationFilter::GetUseImageSpacing() const
    • getElapsedIterations

      public long getElapsedIterations()
      uint32_t itk::simple::LevelSetMotionRegistrationFilter::GetElapsedIterations() const Number of iterations run. This is a measurement. Its value is updated in the Execute methods, so the value will only be valid after an execution.
    • getRMSChange

      public double getRMSChange()
      double itk::simple::LevelSetMotionRegistrationFilter::GetRMSChange() const The Root Mean Square of the levelset upon termination. This is a measurement. Its value is updated in the Execute methods, so the value will only be valid after an execution.
    • getMetric

      public double getMetric()
      double itk::simple::LevelSetMotionRegistrationFilter::GetMetric() const Get the metric value. The metric value is the mean square difference in intensity between the fixed image and transforming moving image computed over the the overlapping region between the two images. This is value is only available for the previous iteration and NOT the current iteration. This is a measurement. Its value is updated in the Execute methods, so the value will only be valid after an execution.
    • getName

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

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

      public Image execute(Image fixedImage, Image movingImage, Image initialDisplacementField)
      Image itk::simple::LevelSetMotionRegistrationFilter::Execute(const Image &fixedImage, const Image &movingImage, const Image &initialDisplacementField) Execute the filter on the input image
    • execute

      public Image execute(Image fixedImage, Image movingImage)
      Image itk::simple::LevelSetMotionRegistrationFilter::Execute(const Image &fixedImage, const Image &movingImage, const Image &initialDisplacementField) Execute the filter on the input image