#include <itkPSMShapeEntropyFunction.h>

Inheritance diagram for itk::PSMShapeEntropyFunction< VDimension >:

Collaboration diagram for itk::PSMShapeEntropyFunction< VDimension >:

Public Types
typedef PSMShapeEntropyFunction	Self

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef PSMCostFunction< VDimension >	Superclass

typedef Superclass::ParticleSystemType	ParticleSystemType

typedef PSMShapeMatrixAttribute< double, VDimension >	ShapeMatrixType

typedef ShapeMatrixType::DataType	DataType

typedef Superclass::VectorType	VectorType

typedef ParticleSystemType::PointType	PointType

typedef vnl_vector< DataType >	vnl_vector_type

typedef vnl_matrix< DataType >	vnl_matrix_type

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

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef LightObject	Superclass

typedef PSMParticleSystem< VDimension >	ParticleSystemType

typedef vnl_vector_fixed< double, VDimension >	VectorType

Public Member Functions
	itkTypeMacro (PSMShapeEntropyFunction, PSMCostFunction)

	itkNewMacro (Self)

	itkStaticConstMacro (Dimension, unsigned int, VDimension)

virtual VectorType	Evaluate (unsigned int, unsigned int, const ParticleSystemType *, double &, double &) const

virtual VectorType	Evaluate (unsigned int a, unsigned int b, const ParticleSystemType *c, double &d) const

virtual double	Energy (unsigned int a, unsigned int b, const ParticleSystemType *c) const

void	SetShapeMatrix (ShapeMatrixType *s)

ShapeMatrixType *	GetShapeMatrix ()

const ShapeMatrixType *	GetShapeMatrix () const

virtual void	BeforeIteration ()

virtual void	AfterIteration ()

void	SetMinimumVariance (double d)

double	GetMinimumVariance () const

void	SetMinimumVarianceDecay (double initial_value, double final_value, double time_period)

bool	GetMinimumVarianceDecayConstant () const

bool	GetHoldMinimumVariance () const

void	SetHoldMinimumVariance (bool b)

void	SetRecomputeCovarianceInterval (int i)

int	GetRecomputeCovarianceInterval () const

const std::vector< double > &	GetShapePCAVariances () const

Public Member Functions inherited from itk::PSMCostFunction< VDimension >
	itkTypeMacro (PSMCostFunction, LightObject)

	itkStaticConstMacro (Dimension, unsigned int, VDimension)

virtual void	ResetBuffers ()

virtual void	BeforeEvaluate (unsigned int, unsigned int, const ParticleSystemType *)

virtual void	SetParticleSystem (ParticleSystemType *p)

virtual ParticleSystemType *	GetParticleSystem () const

virtual void	SetDomainNumber (unsigned int i)

virtual int	GetDomainNumber () const

Protected Member Functions
void	operator= (const PSMShapeEntropyFunction &)

	PSMShapeEntropyFunction (const PSMShapeEntropyFunction &)

virtual void	ComputeCovarianceMatrix ()

Protected Member Functions inherited from itk::PSMCostFunction< VDimension >
void	operator= (const PSMCostFunction &)

	PSMCostFunction (const PSMCostFunction &)

Protected Attributes
ShapeMatrixType::Pointer	m_ShapeMatrix

std::vector< double >	m_ShapePCAVariances

vnl_matrix_type	m_PointsUpdate

double	m_MinimumVariance

double	m_MinimumEigenValue

double	m_CurrentEnergy

bool	m_HoldMinimumVariance

double	m_MinimumVarianceDecayConstant

int	m_RecomputeCovarianceInterval

int	m_Counter

Protected Attributes inherited from itk::PSMCostFunction< VDimension >
ParticleSystemType *	m_ParticleSystem

unsigned int	m_DomainNumber

Detailed Description

template<unsigned int VDimension>
class itk::PSMShapeEntropyFunction< VDimension >

This function estimates the entropy of a distribution of particle-system-based shapes (itkPSMParticleSystem) in shape space. It also computes the gradient of the entropy function. This class is used to optimize the correspondence of particle positions across shapes samples through minimization of the entropy of their distribution in shape space.

Author: Josh Cates

Definition at line 44 of file itkPSMShapeEntropyFunction.h.

Member Typedef Documentation

template<unsigned int VDimension>

typedef Superclass::ParticleSystemType itk::PSMShapeEntropyFunction< VDimension >::ParticleSystemType

Type of particle system.

Definition at line 55 of file itkPSMShapeEntropyFunction.h.

template<unsigned int VDimension>

typedef PSMShapeEntropyFunction itk::PSMShapeEntropyFunction< VDimension >::Self

Standard class typedefs.

Definition at line 48 of file itkPSMShapeEntropyFunction.h.

template<unsigned int VDimension>

typedef Superclass::VectorType itk::PSMShapeEntropyFunction< VDimension >::VectorType

Vector & Point types.

Definition at line 62 of file itkPSMShapeEntropyFunction.h.

Member Function Documentation

template<unsigned int VDimension>

virtual void itk::PSMShapeEntropyFunction< VDimension >::AfterIteration ( )

inlinevirtual

Called after each iteration of the solver.

Reimplemented from itk::PSMCostFunction< VDimension >.

Definition at line 119 of file itkPSMShapeEntropyFunction.h.

   {
     m_ShapeMatrix->AfterIteration();
     // Update the annealing parameter.
     if (m_HoldMinimumVariance != true)
       {
       m_Counter ++;
       if (m_Counter >=  m_RecomputeCovarianceInterval)
         {
         m_Counter = 0;
         m_MinimumVariance *= m_MinimumVarianceDecayConstant;
         }
       }
   }

template<unsigned int VDimension>

virtual void itk::PSMShapeEntropyFunction< VDimension >::BeforeIteration ( )

inlinevirtual

Called before each iteration of a solver.

Reimplemented from itk::PSMCostFunction< VDimension >.

Definition at line 108 of file itkPSMShapeEntropyFunction.h.

   {
     m_ShapeMatrix->BeforeIteration();
     
     if (m_Counter == 0)
       {
       this->ComputeCovarianceMatrix();
       }
   }

template<unsigned int VDimension>

PSMShapeEntropyFunction< VDimension >::VectorType itk::PSMShapeEntropyFunction< VDimension >::Evaluate	(	unsigned int	idx,
		unsigned int	d,
		const ParticleSystemType *	system,
		double &	maxdt,
		double &	energy
	)		const

virtual

The first argument is a pointer to the particle system. The second argument is the index of the domain within that particle system. The third argument is the index of the particle location within the given domain.

Implements itk::PSMCostFunction< VDimension >.

Definition at line 125 of file itkPSMShapeEntropyFunction.hxx.

 {
   // NOTE: This code requires that indices be contiguous, i.e. it
   // won't work if you start deleting particles.
   energy = m_CurrentEnergy;
   maxdt  = m_MinimumEigenValue;
   const unsigned int DomainsPerShape = m_ShapeMatrix->GetDomainsPerShape();
   const unsigned int PointsPerDomain = system->GetNumberOfParticles(d);
    
   VectorType gradE;
   unsigned int k = ((d % DomainsPerShape) * PointsPerDomain * VDimension)
       + (idx * VDimension);
   for (unsigned int i = 0; i< VDimension; i++)
     { 
     gradE[i] = m_PointsUpdate(k + i, d / DomainsPerShape); 
     }
 
 
   return system->TransformVector(gradE,
                    system->GetInversePrefixTransform(d) * 
                                  system->GetInverseTransform(d));
 }

template<unsigned int VDimension>

virtual VectorType itk::PSMShapeEntropyFunction< VDimension >::Evaluate	(	unsigned int	int,
		unsigned int	int,
		const ParticleSystemType *	,
		double &	maxtimestep
	)		const

inlinevirtual

Evaluate returns the vector-valued result of the function. The first argument is a pointer to the particle system. The second argument is the index of the domain within that particle system. The third argument is the index of the particle location within the given domain.

Implements itk::PSMCostFunction< VDimension >.

Definition at line 79 of file itkPSMShapeEntropyFunction.h.

   {
     double e;
     return this->Evaluate(a,b,c,d,e);
   }

template<unsigned int VDimension>

bool itk::PSMShapeEntropyFunction< VDimension >::GetHoldMinimumVariance ( ) const

inline

This method gets/sets the HoldMinimumVariance parameter, which turns on (true) or off (false) the gradual decrease in the m_MinumumVariance regularization parameter with successive invocations of the

Definition at line 172 of file itkPSMShapeEntropyFunction.h.

173 { return m_HoldMinimumVariance; }

template<unsigned int VDimension>

bool itk::PSMShapeEntropyFunction< VDimension >::GetMinimumVarianceDecayConstant ( ) const

inline

Returns the decay constant value computed from SetMinimumVarianceDecay.

Definition at line 163 of file itkPSMShapeEntropyFunction.h.

   {
     return m_MinimumVarianceDecayConstant;
   }

template<unsigned int VDimension>

const std::vector<double>& itk::PSMShapeEntropyFunction< VDimension >::GetShapePCAVariances ( ) const

inline

Returns a vector of the variances associated with the PCA decomposition of the shape space. There will be only number_of_samples - 1 total valid PCA modes.

Definition at line 192 of file itkPSMShapeEntropyFunction.h.

   {
     return m_ShapePCAVariances;
   }

template<unsigned int VDimension>

itk::PSMShapeEntropyFunction< VDimension >::itkNewMacro ( Self )

Method for creation through the object factory.

template<unsigned int VDimension>

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

Dimensionality of the domain of the particle system.

template<unsigned int VDimension>

void itk::PSMShapeEntropyFunction< VDimension >::SetMinimumVariance ( double d )

inline

MinimumVariance is a regularization parameter that is added to the diagonal elements of the covariance matrix of the particle positions on shape. Higher MinimumVariance produces larger gradients, thus allowing shapes to move larger distances in shape space during optimization of positions with this function. Higher MinimumVariance values minimize the effects of smaller modes of variation in the covariance matrix. Conversely, smaller MinimumVariance values increase the significance of the smaller modes of variation on the gradient calculation. This class allows for an "annealing" type optimization using the SetMinumumVarianceDecay function.

Definition at line 145 of file itkPSMShapeEntropyFunction.h.

146 { m_MinimumVariance = d;}

template<unsigned int VDimension>

void itk::PSMShapeEntropyFunction< VDimension >::SetMinimumVarianceDecay	(	double	initial_value,
		double	final_value,
		double	time_period
	)

inline

Sets up an "annealing" type of optimization strategy when this method is used within a PSMOptimizer class. This method specifies and initial value, a final value, and a time period (number of iterations) over which MinimumValue regularization parameter will decay.

Definition at line 155 of file itkPSMShapeEntropyFunction.h.

   {
     m_MinimumVarianceDecayConstant =  exp(log(final_value / initial_value) / time_period);
     m_MinimumVariance = initial_value;
     m_HoldMinimumVariance = false;
   } 

template<unsigned int VDimension>

void itk::PSMShapeEntropyFunction< VDimension >::SetRecomputeCovarianceInterval ( int i )

inline

Set/Get the number of times this function can be called before the covariance matrix is recomputed. In general, it may not be necessary to recompute the covariance matrix every time that particle positions are updated. However, the default value of 1 is the most accurate. For small numbers of samples and reasonably small numbers of particles (e.g. < 2000 per shape), a default value of 1 should not incur much of a time penalty.

Definition at line 184 of file itkPSMShapeEntropyFunction.h.

185 { m_RecomputeCovarianceInterval = i; }

template<unsigned int VDimension>

void itk::PSMShapeEntropyFunction< VDimension >::SetShapeMatrix ( ShapeMatrixType * s )

inline

Write the first n modes to +- 3 std dev and the mean of the model described by the covariance matrix. The string argument is a prefix to the file names. Access the shape matrix.

Definition at line 100 of file itkPSMShapeEntropyFunction.h.

101 { m_ShapeMatrix = s; }

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

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

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<unsigned int VDimension> class itk::PSMShapeEntropyFunction< VDimension >

Member Typedef Documentation

Member Function Documentation

template<unsigned int VDimension>
class itk::PSMShapeEntropyFunction< VDimension >