#include <itkPSMImplicitSurfaceDomain.h>

Inheritance diagram for itk::PSMImplicitSurfaceDomain< T, VDimension >:

Collaboration diagram for itk::PSMImplicitSurfaceDomain< T, VDimension >:

Public Types
typedef PSMImplicitSurfaceDomain	Self

typedef PSMImageDomainWithCurvature< T, VDimension >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef WeakPointer< const Self >	ConstWeakPointer

typedef Superclass::ImageType	ImageType

typedef Superclass::PointType	PointType

typedef T	PixelType

Public Types inherited from itk::PSMImageDomainWithCurvature< T, VDimension >
typedef PSMImageDomainWithCurvature	Self

typedef PSMImageDomainWithHessians< T, VDimension >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef WeakPointer< const Self >	ConstWeakPointer

typedef Superclass::PointType	PointType

typedef Superclass::ImageType	ImageType

typedef Superclass::ScalarInterpolatorType	ScalarInterpolatorType

typedef Superclass::VnlMatrixType	VnlMatrixType

Public Types inherited from itk::PSMImageDomainWithHessians< T, VDimension >
typedef PSMImageDomainWithHessians	Self

typedef PSMImageDomainWithGradients< T, VDimension >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef WeakPointer< const Self >	ConstWeakPointer

typedef Superclass::PointType	PointType

typedef Superclass::ImageType	ImageType

typedef Superclass::ScalarInterpolatorType	ScalarInterpolatorType

typedef vnl_matrix_fixed< T, VDimension, VDimension >	VnlMatrixType

Public Types inherited from itk::PSMImageDomainWithGradients< T, VDimension >
typedef PSMImageDomainWithGradients	Self

typedef PSMImageDomain< T, VDimension >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef WeakPointer< const Self >	ConstWeakPointer

typedef Superclass::PointType	PointType

typedef Superclass::ImageType	ImageType

typedef Superclass::ScalarInterpolatorType	ScalarInterpolatorType

typedef GradientImageFilter< ImageType >	GradientImageFilterType

typedef GradientImageFilterType::OutputImageType	GradientImageType

typedef VectorLinearInterpolateImageFunction< GradientImageType, typename PointType::CoordRepType >	GradientInterpolatorType

typedef FixedArray< T, VDimension >	VectorType

typedef vnl_vector_fixed< T, VDimension >	VnlVectorType

Public Types inherited from itk::PSMImageDomain< T, VDimension >
typedef PSMImageDomain	Self

typedef PSMRegionDomain< VDimension >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef WeakPointer< const Self >	ConstWeakPointer

typedef Image< T, VDimension >	ImageType

typedef Superclass::PointType	PointType

typedef LinearInterpolateImageFunction< ImageType, typename PointType::CoordRepType >	ScalarInterpolatorType

Public Types inherited from itk::PSMRegionDomain< VDimension >
typedef PSMRegionDomain	Self

typedef PSMDomain< VDimension >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef WeakPointer< const Self >	ConstWeakPointer

typedef Point< double, VDimension >	PointType

Public Types inherited from itk::PSMDomain< VDimension >
typedef PSMDomain	Self

typedef DataObject	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef WeakPointer< const Self >	ConstWeakPointer

typedef Point< double, VDimension >	PointType

Public Member Functions
	itkNewMacro (Self)

	itkTypeMacro (PSMImplicitSurfaceDomain, ParticleClipByRegionDomain)

	itkStaticConstMacro (Dimension, unsigned int, VDimension)

	itkSetMacro (Tolerance, T)

	itkGetMacro (Tolerance, T)

virtual bool	ApplyConstraints (PointType &p) const

virtual bool	ApplyVectorConstraints (vnl_vector_fixed< double, VDimension > &gradE, const PointType &pos, double maxtimestep) const

virtual double	Distance (const PointType &, const PointType &) const

void	SetCuttingPlane (const vnl_vector< double > &a, const vnl_vector< double > &b, const vnl_vector< double > &c)

void	RemoveCuttingPlane ()

bool	IsCuttingPlaneDefined () const

const vnl_vector_fixed< double, VDimension > &	GetCuttingPlanePoint () const

const vnl_vector_fixed< double, VDimension > &	GetCuttingPlaneNormal () const

void	AddSphere (const vnl_vector_fixed< double, VDimension > &v, double r)

double	GetSphereRadius (unsigned int i) const

vnl_vector_fixed< double, VDimension >	GetSphereCenter (unsigned int i) const

unsigned int	GetNumberOfSpheres () const

Public Member Functions inherited from itk::PSMImageDomainWithCurvature< T, VDimension >
	itkNewMacro (Self)

	itkTypeMacro (PSMImageDomainWithCurvature, PSMImageDomainWithHessians)

	itkStaticConstMacro (Dimension, unsigned int, VDimension)

void	SetImage (ImageType *I)

double	GetCurvature (const PointType &pos) const

ImageType::Pointer *	GetCurvatureImage ()

Public Member Functions inherited from itk::PSMImageDomainWithHessians< T, VDimension >
	itkNewMacro (Self)

	itkTypeMacro (PSMImageDomainWithHessians, PSMImageDomainWithGradients)

	itkStaticConstMacro (Dimension, unsigned int, VDimension)

void	SetImage (ImageType *I)

VnlMatrixType	SampleHessianVnl (const PointType &p) const

	itkSetMacro (Sigma, double)

	itkGetMacro (Sigma, double)

ScalarInterpolatorType::Pointer *	GetInterpolators ()

ImageType::Pointer *	GetPartialDerivatives ()

Public Member Functions inherited from itk::PSMImageDomainWithGradients< T, VDimension >
	itkNewMacro (Self)

	itkTypeMacro (PSMImageDomainWithGradients, PSMImageDomain)

	itkStaticConstMacro (Dimension, unsigned int, VDimension)

void	SetImage (ImageType *I)

	itkGetObjectMacro (GradientImage, GradientImageType)

VectorType	SampleGradient (const PointType &p) const

VnlVectorType	SampleGradientVnl (const PointType &p) const

VnlVectorType	SampleNormalVnl (const PointType &p, T epsilon=1.0e-5) const

	itkGetObjectMacro (GradientInterpolator, GradientInterpolatorType)

Public Member Functions inherited from itk::PSMImageDomain< T, VDimension >
	itkNewMacro (Self)

	itkTypeMacro (PSMImageDomain, PSMRegionDomain)

	itkStaticConstMacro (Dimension, unsigned int, VDimension)

void	SetImage (ImageType *I)

	itkGetObjectMacro (Image, ImageType)

	itkGetConstObjectMacro (Image, ImageType)

T	Sample (const PointType &p) const

bool	IsInsideBuffer (const PointType &p) const

	itkGetObjectMacro (ScalarInterpolator, ScalarInterpolatorType)

Public Member Functions inherited from itk::PSMRegionDomain< VDimension >
	itkNewMacro (Self)

	itkTypeMacro (PSMRegionDomain, PSMDomain)

	itkStaticConstMacro (Dimension, unsigned int, VDimension)

	itkSetMacro (LowerBound, PointType)

	itkSetMacro (UpperBound, PointType)

virtual const PointType &	GetUpperBound () const

virtual const PointType &	GetLowerBound () const

void	SetRegion (const PointType &l, const PointType &u)

Public Member Functions inherited from itk::PSMDomain< VDimension >
	itkNewMacro (Self)

	itkTypeMacro (PSMDomain, DataObject)

	itkStaticConstMacro (Dimension, unsigned int, VDimension)

void	DisableConstraints ()

void	EnableConstraints ()

bool	GetConstraintsEnabled () const

void	SetConstraintsEnabled (bool g)

Protected Member Functions
void	PrintSelf (std::ostream &os, Indent indent) const

Protected Member Functions inherited from itk::PSMImageDomainWithCurvature< T, VDimension >
void	PrintSelf (std::ostream &os, Indent indent) const

double	MeanCurvature (const PointType &pos)

double	vnl_trace (const VnlMatrixType &m) const

Protected Member Functions inherited from itk::PSMImageDomainWithHessians< T, VDimension >
void	PrintSelf (std::ostream &os, Indent indent) const

void	DeletePartialDerivativeImages ()

Protected Member Functions inherited from itk::PSMImageDomainWithGradients< T, VDimension >
void	PrintSelf (std::ostream &os, Indent indent) const

Protected Member Functions inherited from itk::PSMImageDomain< T, VDimension >
void	PrintSelf (std::ostream &os, Indent indent) const

Protected Member Functions inherited from itk::PSMRegionDomain< VDimension >
void	PrintSelf (std::ostream &os, Indent indent) const

Protected Member Functions inherited from itk::PSMDomain< VDimension >
void	PrintSelf (std::ostream &os, Indent indent) const

Additional Inherited Members
Protected Attributes inherited from itk::PSMDomain< VDimension >
bool	m_ConstraintsEnabled

Detailed Description

template<class T, unsigned int VDimension>
class itk::PSMImplicitSurfaceDomain< T, VDimension >

A 3D cartesian domain that constrains points so that they always lie an implicit surface. The implicit surface is defined as the zero isosurface of the given image. Constraints are applied using a Newton-Raphson iteration, and this class assumes it has a distance transform as an image.

Definition at line 35 of file itkPSMImplicitSurfaceDomain.h.

Member Typedef Documentation

template<class T, unsigned int VDimension>

typedef PSMImplicitSurfaceDomain itk::PSMImplicitSurfaceDomain< T, VDimension >::Self

Standard class typedefs

Definition at line 40 of file itkPSMImplicitSurfaceDomain.h.

Member Function Documentation

template<class T, unsigned int VDimension>

void itk::PSMImplicitSurfaceDomain< T, VDimension >::AddSphere	(	const vnl_vector_fixed< double, VDimension > &	v,
		double	r
	)

inline

Maintain a list of spheres within the domain. These are used as soft constraints by some particle forcing functions.

Definition at line 104 of file itkPSMImplicitSurfaceDomain.h.

   {
     if (r > 0)
     {
       m_SphereCenterList.push_back(v);
       m_SphereRadiusList.push_back(r);
     }
   }

template<class T , unsigned int VDimension>

bool itk::PSMImplicitSurfaceDomain< T, VDimension >::ApplyConstraints ( PointType & p ) const

virtual

Apply any constraints to the given point location. This method constrains points to lie within the given domain and on a given implicit surface. If the point is not already on the surface, it is projected back to the surface using a Newton-Raphson iteration. IMPORTANT: This method returns the true/false value of its superclass, and does not indicate changes only due to projection. This is done for speed: we typically will only want to know if a point tried to move outside of the bounding box domain, since movement off the surface will be very common. Consider subclassing this method to add a check for significant differences in the input and output points.

Reimplemented from itk::PSMRegionDomain< VDimension >.

Definition at line 89 of file itkPSMImplicitSurfaceDomain.hxx.

 {
   // First apply and constraints imposed by superclasses.  This will
   // guarantee the point starts in the correct image domain.
   bool flag = Superclass::ApplyConstraints(p);
 
   if (this->m_ConstraintsEnabled == true)
     {
   
     unsigned int k = 0;
     double mult = 1.0;
     
     const T epsilon = m_Tolerance * 0.001;
     T f = this->Sample(p);
     
     T gradmag = 1.0;
     while ( fabs(f) > (m_Tolerance * mult) || gradmag < epsilon)
       //  while ( fabs(f) > m_Tolerance || gradmag < epsilon)
       {
       vnl_vector_fixed<T, VDimension> grad = this->SampleGradientVnl(p);
       
       gradmag = grad.magnitude();
       vnl_vector_fixed<T, VDimension> vec   =  grad  * ( f / (gradmag + epsilon) );
       for (unsigned int i = 0; i < VDimension; i++)
         {
         p[i] -= vec[i];
         }
       
       f = this->Sample(p);
             
       // Raise the tolerance if we have done too many iterations.
       k++;
       if (k > 10000)
         {
         mult *= 2.0;
         k = 0;
         }
       } // end while
     } // end if m_ConstraintsEnabled == true
 
   return flag; 
 }

template<class T , unsigned int VDimension>

bool itk::PSMImplicitSurfaceDomain< T, VDimension >::ApplyVectorConstraints	(	vnl_vector_fixed< double, VDimension > &	gradE,
		const PointType &	pos,
		double	maxtimestep
	)		const

virtual

Optionally add a repulsion from a planar boundar specified in m_CuttingPlane

Reimplemented from itk::PSMImageDomainWithGradients< T, VDimension >.

Definition at line 50 of file itkPSMImplicitSurfaceDomain.hxx.

 {
   if (this->m_UseCuttingPlane == true)
     {    
     // See http://mathworld.wolfram.com/Point-PlaneDistance.html, for example
     vnl_vector_fixed<double, VDimension> x;
     vnl_vector_fixed<T, VDimension> grad = this->SampleGradientVnl(pos);
     for (unsigned int i = 0; i < VDimension; i++)
       { x[i] = pos[i]; }
     const double D = dot_product(m_CuttingPlaneNormal, x- m_CuttingPlanePoint);
     
     //    x = m_CuttingPlaneNormal * fabs(1.0 / (D + 1.0e-3));
     // x = m_CuttingPlaneNormal * lambda * exp(-lambda * fabs(D));
     
     // Gradient of simple force 1/D^2 to push away from cutting plane
     vnl_vector_fixed<double, VDimension> df;
     const double k = (-2.0 / (D * D * D));
     df[0] = k * grad[0] * m_CuttingPlaneNormal[0];
     df[1] = k * grad[1] * m_CuttingPlaneNormal[1];
     df[2] = k * grad[2] * m_CuttingPlaneNormal[2];
 
     gradE = gradE + df;
 
     // Make sure force is not huge relative to other forces.
     if (gradE.magnitude() > maxtimestep)
       {
       gradE.normalize();
       gradE = gradE * maxtimestep;
       }    
     }
 
   
   return Superclass::ApplyVectorConstraints(gradE,pos,maxtimestep);
 }

template<class T , unsigned int VDimension>

double itk::PSMImplicitSurfaceDomain< T, VDimension >::Distance	(	const PointType &	a,
		const PointType &	b
	)		const

virtual

Define a distance measure on the surface. Note that this distance measure is NOT the geodesic distance, as one might expect, but is only a Euclidean distance which ignores points whose normals are not sufficiently aligned (method returns a negative number). The assumption here is that points are sufficiently close to one another on the surface that they may be considered to lie in a tangent plane.

Reimplemented from itk::PSMDomain< VDimension >.

Definition at line 134 of file itkPSMImplicitSurfaceDomain.hxx.

 {
   double sum = 0.0;
   for (unsigned int i = 0; i < VDimension; i++)
     {      sum += (b[i]-a[i]) * (b[i]-a[i]);      }
   return sqrt(sum);
 }

template<class T, unsigned int VDimension>

vnl_vector_fixed<double, VDimension> itk::PSMImplicitSurfaceDomain< T, VDimension >::GetSphereCenter ( unsigned int i ) const

inline

Returns the center point of sphere i. If sphere i does not exist, returns 0 vector.

Definition at line 122 of file itkPSMImplicitSurfaceDomain.h.

   {
     if (m_SphereRadiusList.size() > i) return m_SphereCenterList[i];
     else
       {  return vnl_vector_fixed<double, VDimension>(0.0,0.0,0.0);  }
   }

template<class T, unsigned int VDimension>

double itk::PSMImplicitSurfaceDomain< T, VDimension >::GetSphereRadius ( unsigned int i ) const

inline

Returns the radius of sphere i, or 0.0 if sphere i does not exist

Definition at line 114 of file itkPSMImplicitSurfaceDomain.h.

   {
     if (m_SphereRadiusList.size() > i) return m_SphereRadiusList[i];
     else return 0.0;
   }

template<class T, unsigned int VDimension>

itk::PSMImplicitSurfaceDomain< T, VDimension >::itkNewMacro ( Self )

Method for creation through the object factory.

template<class T, unsigned int VDimension>

itk::PSMImplicitSurfaceDomain< T, VDimension >::itkSetMacro	(	Tolerance	,
		T
	)

Set/Get the precision of the projection operation. The resulting projection will be within the specified tolerance.

template<class T, unsigned int VDimension>

itk::PSMImplicitSurfaceDomain< T, VDimension >::itkStaticConstMacro	(	Dimension	,
		unsigned	int,
		VDimension
	)

Dimensionality of the domain of the particle system.

template<class T, unsigned int VDimension>

itk::PSMImplicitSurfaceDomain< T, VDimension >::itkTypeMacro	(	PSMImplicitSurfaceDomain< T, VDimension >	,
		ParticleClipByRegionDomain
	)

Run-time type information (and related methods).

The documentation for this class was generated from the following files:

C:/Users/Brig/Documents/ShapeWorksStudio/src/ParticleShapeworks/include/itkPSMImplicitSurfaceDomain.h
C:/Users/Brig/Documents/ShapeWorksStudio/src/ParticleShapeworks/include/itkPSMImplicitSurfaceDomain.hxx

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

template<class T, unsigned int VDimension> class itk::PSMImplicitSurfaceDomain< T, VDimension >

Member Typedef Documentation

Member Function Documentation

template<class T, unsigned int VDimension>
class itk::PSMImplicitSurfaceDomain< T, VDimension >