A facade class that manages interactions with a particle system. More...

#include <itkPSMParticleSystem.h>

Inheritance diagram for itk::PSMParticleSystem< VDimension >:

Collaboration diagram for itk::PSMParticleSystem< VDimension >:

Public Types
typedef PSMParticleSystem	Self

typedef DataObject	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef WeakPointer< const Self >	ConstWeakPointer

typedef PSMDomain< VDimension >	DomainType

typedef Point< double, VDimension >	PointType

typedef PSMNeighborhood< VDimension >	NeighborhoodType

typedef PSMContainer< PointType >	PointContainerType

typedef NeighborhoodType::PointVectorType	PointVectorType

typedef vnl_matrix_fixed< double, VDimension+1, VDimension+1 >	TransformType

typedef vnl_vector_fixed< double, VDimension >	VectorType

Public Member Functions
	itkNewMacro (Self)

	itkTypeMacro (PSMParticleSystem, DataObject)

	itkStaticConstMacro (Dimension, unsigned int, VDimension)

void	RegisterAttribute (PSMAttribute< VDimension > *)

void	SynchronizePositions ()

unsigned long int	GetNumberOfParticles (unsigned int d=0) const

const PointType &	AddPosition (const PointType &, unsigned int d=0, int threadId=0)

const PointType &	SetPosition (const PointType &, unsigned long int k, unsigned int d=0, int threadId=0)

void	RemovePosition (unsigned long int k, unsigned int d=0, int threadId=0)

PointType &	GetPosition (unsigned long int k, unsigned int d=0)

const PointType &	GetPosition (unsigned long int k, unsigned int d=0) const

PointType	GetTransformedPosition (unsigned long int k, unsigned int d=0) const

void	SplitAllParticles (double epsilon, int threadId=0)

void	SplitAllParticlesInDomain (const vnl_vector_fixed< double, VDimension > &, double epsilon, unsigned int d=0, int threadId=0)

void	SplitParticle (double epsilon, unsigned int idx, unsigned int d=0, int threadId=0)

void	SetNeighborhood (unsigned int, NeighborhoodType *, int threadId=0)

void	SetNeighborhood (NeighborhoodType *n, int threadId=0)

NeighborhoodType::ConstPointer	GetNeighborhood (unsigned int k) const

PointVectorType	FindNeighborhoodPoints (const PointType &p, double r, unsigned int d=0) const

PointVectorType	FindNeighborhoodPoints (const PointType &p, std::vector< double > &w, double r, unsigned int d=0) const

PointVectorType	FindNeighborhoodPoints (unsigned int idx, double r, unsigned int d=0) const

PointVectorType	FindNeighborhoodPoints (unsigned int idx, std::vector< double > &w, double r, unsigned int d=0) const

void	AddDomain (DomainType *, int threadId=0)

std::vector< typename DomainType::Pointer >::const_iterator	GetDomainsBegin () const

std::vector< typename DomainType::Pointer >::const_iterator	GetDomainsEnd () const

DomainType *	GetDomain (unsigned int i)

DomainType *	GetDomain ()

const DomainType *	GetDomain (unsigned int i) const

const DomainType *	GetDomain () const

unsigned int	GetNumberOfDomains () const

void	SetTransform (unsigned int i, const TransformType &, int threadId=0)

void	SetTransform (const TransformType &p, int threadId=0)

void	SetPrefixTransform (unsigned int i, const TransformType &, int threadId=0)

void	SetPrefixTransform (const TransformType &p, int threadId=0)

std::vector< TransformType >::const_iterator	GetTransformsBegin () const

std::vector< TransformType >::const_iterator	GetTransformsEnd () const

const TransformType &	GetTransform (unsigned int i) const

const TransformType &	GetTransform () const

TransformType	GetTransform (unsigned int i)

TransformType	GetTransform ()

const TransformType &	GetPrefixTransform (unsigned int i) const

const TransformType &	GetPrefixTransform () const

TransformType	GetPrefixTransform (unsigned int i)

TransformType	GetPrefixTransform ()

std::vector< TransformType >::const_iterator	GetInverseTransformsBegin () const

std::vector< TransformType >::const_iterator	GetInverseTransformsEnd () const

const TransformType &	GetInverseTransform (unsigned int i) const

const TransformType &	GetInverseTransform () const

const TransformType &	GetInversePrefixTransform (unsigned int i) const

const TransformType &	GetInversePrefixTransform () const

const std::vector< typename PointContainerType::Pointer > &	GetPositions () const

const PointContainerType::Pointer &	GetPositions (unsigned int d) const

void	AddPositionList (const std::vector< PointType > &, unsigned int d, int threadId=0)

PointType	TransformPoint (const PointType &, const TransformType &) const

VectorType	TransformVector (const VectorType &, const TransformType &) const

TransformType	InvertTransform (const TransformType &T) const

void	FlagDomain (unsigned int i)

void	UnflagDomain (unsigned int i)

bool	GetDomainFlag (unsigned int i) const

const std::vector< bool > &	GetDomainFlags () const

void	SetDomainFlags ()

void	ResetDomainFlags ()

void	SetFixedParticleFlag (unsigned int i)

void	ResetFixedParticleFlag (unsigned int i)

bool	GetFixedParticleFlag (unsigned int i) const

void	ResetFixedParticleFlags ()

template<>
PSMParticleSystem< 3 >::PointType	TransformPoint (const PointType &p, const TransformType &T) const

template<>
PSMParticleSystem< 2 >::PointType	TransformPoint (const PointType &p, const TransformType &T) const

template<>
PSMParticleSystem< 3 >::VectorType	TransformVector (const VectorType &p, const TransformType &T) const

template<>
PSMParticleSystem< 2 >::VectorType	TransformVector (const VectorType &p, const TransformType &T) const

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

void	SetNumberOfDomains (unsigned int)

std::vector< typename DomainType::Pointer >::iterator	GetDomainsBegin ()

std::vector< typename DomainType::Pointer >::iterator	GetDomainsEnd ()

std::vector< TransformType >::iterator	GetTransformsBegin ()

std::vector< TransformType >::iterator	GetTransformsEnd ()

std::vector< TransformType >::iterator	GetInverseTransformsBegin ()

std::vector< TransformType >::iterator	GetInverseTransformsEnd ()

TransformType &	GetInverseTransform (unsigned int i)

TransformType &	GetInverseTransform ()

TransformType &	GetInversePrefixTransform (unsigned int i)

TransformType &	GetInversePrefixTransform ()

Detailed Description

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

A facade class that manages interactions with a particle system.

A particle system consists of a set of particle locations and domains in which those locations are defined. For example, a particle system may simply be a set of points in 3D Euclidean space that are constrained to a specified bounding box. A more complex example is a set of 3D points constrained to a given surface. The itkPSMParticleSystem class is also designed to manage multiple sets of points across multiple domains. For example, one may create a system of dozens of point sets that are each defined in different spaces. The itkPSMParticleSystem class can also maintain a set of transformations associated with each domain that map that particular domain into another coordinate frame, for example, a common coordinate frame.

All operations on the particle system must happen through the interface of the PSMParticleSystem class.

Author: Josh Cates

Definition at line 68 of file itkPSMParticleSystem.h.

Member Typedef Documentation

template<unsigned int VDimension>

typedef PSMDomain<VDimension> itk::PSMParticleSystem< VDimension >::DomainType

Define the base domain type.

Definition at line 88 of file itkPSMParticleSystem.h.

template<unsigned int VDimension>

typedef PSMNeighborhood<VDimension> itk::PSMParticleSystem< VDimension >::NeighborhoodType

Class used to compute neighborhoods of points. One is associated with each domain.

Definition at line 95 of file itkPSMParticleSystem.h.

template<unsigned int VDimension>

typedef PSMContainer<PointType> itk::PSMParticleSystem< VDimension >::PointContainerType

Point container type. One is associated with each domain.

Definition at line 98 of file itkPSMParticleSystem.h.

template<unsigned int VDimension>

typedef Point<double, VDimension> itk::PSMParticleSystem< VDimension >::PointType

Point type used to store particle locations.

Definition at line 91 of file itkPSMParticleSystem.h.

template<unsigned int VDimension>

typedef PSMParticleSystem itk::PSMParticleSystem< VDimension >::Self

Standard class typedefs

Definition at line 72 of file itkPSMParticleSystem.h.

template<unsigned int VDimension>

typedef vnl_matrix_fixed<double, VDimension +1, VDimension +1> itk::PSMParticleSystem< VDimension >::TransformType

Defines a transform class type. One is associated with each domain. Transforms are affine for simplicity.

Definition at line 104 of file itkPSMParticleSystem.h.

Member Function Documentation

template<unsigned int VDimension>

void itk::PSMParticleSystem< VDimension >::AddDomain	(	DomainType *	input,
		int	threadId = `0`
	)

Add a domain to the particle system. This method also allocates space for a list of positions that are contained within the domain, and a default neighborhood calculator. The final, optional argument indicates the calling thread id.

Definition at line 55 of file itkPSMParticleSystem.hxx.

 {
   this->Modified();
   
   for (unsigned int idx = 0; idx < m_Domains.size(); ++idx)
     {
     if (!m_Domains[idx])
       {
       m_Domains[idx] = input;
       m_Positions[idx]  =  PointContainerType::New();
       m_IndexCounters[idx] = 0;
       return;
       }
     }
 
   this->SetNumberOfDomains(static_cast<int>(m_Domains.size() + 1));
   m_Domains[ static_cast<int>( m_Domains.size() ) - 1] = input;
   m_Positions[static_cast<int>( m_Domains.size() ) - 1] = PointContainerType::New();
   m_IndexCounters[static_cast<int>( m_Domains.size() -1)] = 0;
   m_Neighborhoods[static_cast<int>( m_Domains.size() -1)] = NeighborhoodType::New();
   m_Transforms[static_cast<int>( m_Domains.size() -1)].set_identity();
   m_InverseTransforms[static_cast<int>( m_Domains.size() -1)].set_identity();
   m_PrefixTransforms[static_cast<int>( m_Domains.size() -1)].set_identity();
   m_InversePrefixTransforms[static_cast<int>( m_Domains.size() -1)].set_identity();
   m_DomainFlags[static_cast<int>( m_Domains.size() -1)] = false;
   
   // Notify any observers.
   ParticleDomainAddEvent e;
   e.SetDomainIndex(m_Domains.size() - 1);
   e.SetPositionIndex(0);
   e.SetThreadID(threadId);
   this->InvokeEvent(e);
 }

template<unsigned int VDimension>

const PSMParticleSystem< VDimension >::PointType & itk::PSMParticleSystem< VDimension >::AddPosition	(	const PointType &	p,
		unsigned int	d = `0`,
		int	threadId = `0`
	)

Add/Set/Remove a single particle position. The actual position added or set will be returned. If, for example, the domain imposes any constraints on this location (e.g. out-of-bounds, projection onto a surface), then the method returns the location after constraints are applied. Both the Add and Set methods require a domain index. If unspecified, the domain index is zero. The Set method requires a specific particle index. If the given index does not exist, an exception is thrown. Set is intended to be used for moving particles. The SetTransformedPosition sets the position using a Point transformed by the m_Transform associated with the given domain.

Definition at line 145 of file itkPSMParticleSystem.hxx.

 {
   m_Positions[d]->operator[](m_IndexCounters[d]) = p;
 
   // Apply constraints to the given position.  Note that the following
   // operation potentially modifes that position.
   m_Domains[d]->ApplyConstraints( m_Positions[d]->operator[](m_IndexCounters[d]));
   
   m_Neighborhoods[d]->AddPosition( m_Positions[d]->operator[](m_IndexCounters[d]),
                                    m_IndexCounters[d], threadId);
   
   // Increase the FixedParticleFlag list size if necessary.
   if (m_IndexCounters[0] >= m_FixedParticleFlags.size())
     {
       m_FixedParticleFlags.push_back(false);
     }
   
   // Notify any observers.
   ParticlePositionAddEvent e;
   e.SetThreadID(threadId);
   e.SetDomainIndex(d);
   e.SetPositionIndex(m_IndexCounters[d]);
   this->InvokeEvent(e);
   m_IndexCounters[d]++;
  
   return m_Positions[d]->operator[](m_IndexCounters[d]-1);
 }

template<unsigned int VDimension>

void itk::PSMParticleSystem< VDimension >::AddPositionList	(	const std::vector< PointType > &	p,
		unsigned int	d,
		int	threadId = `0`
	)

Adds a list of points to the specified domain. The arguments are the std::vector of points and the domain number.

Definition at line 221 of file itkPSMParticleSystem.hxx.

 {
   // Traverse the list and add each point to the domain.
   for (typename std::vector<PointType>::const_iterator it= p.begin();
        it != p.end(); it++)
     {
       this->AddPosition(*it, d, threadId);    
     }
 }

template<unsigned int VDimension>

PointVectorType itk::PSMParticleSystem< VDimension >::FindNeighborhoodPoints	(	const PointType &	p,
		double	r,
		unsigned int	d = `0`
	)		const

inline

Return the neighborhood of points with radius r around point p in domain k. This is just a convenience method to avoid exposing the underlying Neighborhood objects. FindTransformedNeighborhoodPoints returns the list with all points transformed by the transform associated with the given domain.

Definition at line 200 of file itkPSMParticleSystem.h.

   {  
     return m_Neighborhoods[d]->FindNeighborhoodPoints(p, r); 
   }

template<unsigned int VDimension>

void itk::PSMParticleSystem< VDimension >::FlagDomain ( unsigned int i )

inline

Flag/Unflag a domain. Flagging a domain has different meanings according to the application using this particle system.

Definition at line 397 of file itkPSMParticleSystem.h.

398 { m_DomainFlags[i] = true; }

template<unsigned int VDimension>

DomainType* itk::PSMParticleSystem< VDimension >::GetDomain ( unsigned int i )

inline

Return the i'th domain object.

Definition at line 254 of file itkPSMParticleSystem.h.

255 { return m_Domains[i].GetPointer(); }

template<unsigned int VDimension>

DomainType* itk::PSMParticleSystem< VDimension >::GetDomain ( )

inline

API for the single domain case.

Definition at line 258 of file itkPSMParticleSystem.h.

259 {return m_Domains[0].GetPointer(); }

template<unsigned int VDimension>

const DomainType* itk::PSMParticleSystem< VDimension >::GetDomain ( unsigned int i ) const

inline

Return the i'th domain object.

Definition at line 262 of file itkPSMParticleSystem.h.

263 { return m_Domains[i].GetPointer(); }

template<unsigned int VDimension>

const DomainType* itk::PSMParticleSystem< VDimension >::GetDomain ( ) const

inline

API for the single domain case.

Definition at line 266 of file itkPSMParticleSystem.h.

267 {return m_Domains[0].GetPointer(); }

template<unsigned int VDimension>

std::vector< typename DomainType::Pointer >::const_iterator itk::PSMParticleSystem< VDimension >::GetDomainsBegin ( ) const

inline

Return an iterator that points to the first element of the list of the domains.

Definition at line 245 of file itkPSMParticleSystem.h.

246 { return m_Domains.begin(); }

template<unsigned int VDimension>

std::vector< typename DomainType::Pointer >::iterator itk::PSMParticleSystem< VDimension >::GetDomainsBegin ( )

inlineprotected

Return an iterator that points to the first element of the list of the domains.

Definition at line 444 of file itkPSMParticleSystem.h.

445 { return m_Domains.begin(); }

template<unsigned int VDimension>

std::vector< typename DomainType::Pointer >::const_iterator itk::PSMParticleSystem< VDimension >::GetDomainsEnd ( ) const

inline

Return an iterator that points one position past the last element of the list of the domains.

Definition at line 250 of file itkPSMParticleSystem.h.

251 { return m_Domains.end(); }

template<unsigned int VDimension>

std::vector< typename DomainType::Pointer >::iterator itk::PSMParticleSystem< VDimension >::GetDomainsEnd ( )

inlineprotected

Return an iterator that points one position past the last element of the list of the domains.

Definition at line 449 of file itkPSMParticleSystem.h.

450 { return m_Domains.end(); }

template<unsigned int VDimension>

const TransformType& itk::PSMParticleSystem< VDimension >::GetInversePrefixTransform ( unsigned int i ) const

inline

Return the i'th transform object.

Definition at line 350 of file itkPSMParticleSystem.h.

351 { return m_InversePrefixTransforms[i]; }

template<unsigned int VDimension>

const TransformType& itk::PSMParticleSystem< VDimension >::GetInversePrefixTransform ( ) const

inline

API for the single transform case.

Definition at line 354 of file itkPSMParticleSystem.h.

355 {return m_InversePrefixTransforms[0]; }

template<unsigned int VDimension>

TransformType& itk::PSMParticleSystem< VDimension >::GetInversePrefixTransform ( unsigned int i )

inlineprotected

Return the i'th transform object.

Definition at line 483 of file itkPSMParticleSystem.h.

484 { return m_InversePrefixTransforms[i]; }

template<unsigned int VDimension>

TransformType& itk::PSMParticleSystem< VDimension >::GetInversePrefixTransform ( )

inlineprotected

API for the single transform case.

Definition at line 487 of file itkPSMParticleSystem.h.

488 {return m_InversePrefixTransforms[0]; }

template<unsigned int VDimension>

const TransformType& itk::PSMParticleSystem< VDimension >::GetInverseTransform ( unsigned int i ) const

inline

Return the i'th transform object.

Definition at line 342 of file itkPSMParticleSystem.h.

343 { return m_InverseTransforms[i]; }

template<unsigned int VDimension>

const TransformType& itk::PSMParticleSystem< VDimension >::GetInverseTransform ( ) const

inline

API for the single transform case.

Definition at line 346 of file itkPSMParticleSystem.h.

347 {return m_InverseTransforms[0]; }

template<unsigned int VDimension>

TransformType& itk::PSMParticleSystem< VDimension >::GetInverseTransform ( unsigned int i )

inlineprotected

Return the i'th transform object.

Definition at line 475 of file itkPSMParticleSystem.h.

476 { return m_InverseTransforms[i]; }

template<unsigned int VDimension>

TransformType& itk::PSMParticleSystem< VDimension >::GetInverseTransform ( )

inlineprotected

API for the single transform case.

Definition at line 479 of file itkPSMParticleSystem.h.

480 {return m_InverseTransforms[0]; }

template<unsigned int VDimension>

std::vector< TransformType >::const_iterator itk::PSMParticleSystem< VDimension >::GetInverseTransformsBegin ( ) const

inline

Return an iterator that points to the first element of the list of the inverse transforms.

Definition at line 332 of file itkPSMParticleSystem.h.

333 { return m_InverseTransforms.begin(); }

template<unsigned int VDimension>

std::vector< TransformType >::iterator itk::PSMParticleSystem< VDimension >::GetInverseTransformsBegin ( )

inlineprotected

Return an iterator that points to the first element of the list of the inverse transforms.

Definition at line 465 of file itkPSMParticleSystem.h.

466 { return m_InverseTransforms.begin(); }

template<unsigned int VDimension>

std::vector< TransformType >::const_iterator itk::PSMParticleSystem< VDimension >::GetInverseTransformsEnd ( ) const

inline

Return an iterator that points one position past the last element of the list of the transforms.

Definition at line 338 of file itkPSMParticleSystem.h.

339 { return m_InverseTransforms.end(); }

template<unsigned int VDimension>

std::vector< TransformType >::iterator itk::PSMParticleSystem< VDimension >::GetInverseTransformsEnd ( )

inlineprotected

Return an iterator that points one position past the last element of the list of the transforms.

Definition at line 471 of file itkPSMParticleSystem.h.

472 { return m_InverseTransforms.end(); }

template<unsigned int VDimension>

unsigned int itk::PSMParticleSystem< VDimension >::GetNumberOfDomains ( ) const

inline

Returns the number of domains contained in the particle system.

Definition at line 270 of file itkPSMParticleSystem.h.

271 { return m_Domains.size(); }

template<unsigned int VDimension>

unsigned long int itk::PSMParticleSystem< VDimension >::GetNumberOfParticles ( unsigned int d = 0 ) const

inline

Returns the number of particles in domain k.

Definition at line 136 of file itkPSMParticleSystem.h.

137 { return m_Positions[d]->GetSize(); }

template<unsigned int VDimension>

PointType& itk::PSMParticleSystem< VDimension >::GetPosition	(	unsigned long int	k,
		unsigned int	d = `0`
	)

inline

Return a position with index k from domain d. Note the order in which the 2 integers must be specified! The domain number is specified second and the position index within the domain is specified first. Note that the domain index may be omitted if the particle system only contains a single domain. GetTransformedPosition returns the position premultiplied by the transform matrix for the given domain.

Definition at line 169 of file itkPSMParticleSystem.h.

170 { return m_Positions[d]->operator[](k); }

template<unsigned int VDimension>

const std::vector<typename PointContainerType::Pointer>& itk::PSMParticleSystem< VDimension >::GetPositions ( ) const

inline

Return the array of particle positions.

Definition at line 358 of file itkPSMParticleSystem.h.

359 { return m_Positions; }

template<unsigned int VDimension>

const TransformType& itk::PSMParticleSystem< VDimension >::GetPrefixTransform ( unsigned int i ) const

inline

Return the i'th transform object.

Definition at line 314 of file itkPSMParticleSystem.h.

315 { return m_PrefixTransforms[i]; }

template<unsigned int VDimension>

const TransformType& itk::PSMParticleSystem< VDimension >::GetPrefixTransform ( ) const

inline

API for the single transform case.

Definition at line 318 of file itkPSMParticleSystem.h.

319 {return m_PrefixTransforms[0]; }

template<unsigned int VDimension>

TransformType itk::PSMParticleSystem< VDimension >::GetPrefixTransform ( unsigned int i )

inline

Return the i'th transform object.

Definition at line 322 of file itkPSMParticleSystem.h.

323 { return m_PrefixTransforms[i]; }

template<unsigned int VDimension>

TransformType itk::PSMParticleSystem< VDimension >::GetPrefixTransform ( )

inline

API for the single transform case.

Definition at line 326 of file itkPSMParticleSystem.h.

327 {return m_PrefixTransforms[0]; }

template<unsigned int VDimension>

const TransformType& itk::PSMParticleSystem< VDimension >::GetTransform ( unsigned int i ) const

inline

Return the i'th transform object.

Definition at line 298 of file itkPSMParticleSystem.h.

299 { return m_Transforms[i]; }

template<unsigned int VDimension>

const TransformType& itk::PSMParticleSystem< VDimension >::GetTransform ( ) const

inline

API for the single transform case.

Definition at line 302 of file itkPSMParticleSystem.h.

303 {return m_Transforms[0]; }

template<unsigned int VDimension>

TransformType itk::PSMParticleSystem< VDimension >::GetTransform ( unsigned int i )

inline

Return the i'th transform object.

Definition at line 306 of file itkPSMParticleSystem.h.

307 { return m_Transforms[i]; }

template<unsigned int VDimension>

TransformType itk::PSMParticleSystem< VDimension >::GetTransform ( )

inline

API for the single transform case.

Definition at line 310 of file itkPSMParticleSystem.h.

311 {return m_Transforms[0]; }

template<unsigned int VDimension>

std::vector< TransformType >::const_iterator itk::PSMParticleSystem< VDimension >::GetTransformsBegin ( ) const

inline

Return an iterator that points to the first element of the list of the transforms.

Definition at line 290 of file itkPSMParticleSystem.h.

290 { return m_Transforms.begin(); }

template<unsigned int VDimension>

std::vector< TransformType >::iterator itk::PSMParticleSystem< VDimension >::GetTransformsBegin ( )

inlineprotected

Return an iterator that points to the first element of the list of the transforms.

Definition at line 454 of file itkPSMParticleSystem.h.

455 { return m_Transforms.begin(); }

template<unsigned int VDimension>

std::vector< TransformType >::const_iterator itk::PSMParticleSystem< VDimension >::GetTransformsEnd ( ) const

inline

Return an iterator that points one position past the last element of the list of the transforms.

Definition at line 295 of file itkPSMParticleSystem.h.

295 { return m_Transforms.end(); }

template<unsigned int VDimension>

std::vector< TransformType >::iterator itk::PSMParticleSystem< VDimension >::GetTransformsEnd ( )

inlineprotected

Return an iterator that points one position past the last element of the list of the transforms.

Definition at line 459 of file itkPSMParticleSystem.h.

460 { return m_Transforms.end(); }

template<unsigned int VDimension>

TransformType itk::PSMParticleSystem< VDimension >::InvertTransform ( const TransformType & T ) const

inline

Returns the inverse of a transformation matrix.

Definition at line 377 of file itkPSMParticleSystem.h.

   {
     double det = vnl_det(T);
     // Check if the inverse can be calculated. If not, set the inverse
     // to identity.
     if (det == 0)
     {
       TransformType identity;
       identity.set_identity();
       return identity;
     }
     else
     {
       // Note, vnl_inverse is optimized for small matrices 1x1 - 4x4
       return vnl_inverse(T);
     }
   }

template<unsigned int VDimension>

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

Method for creation through the object factory.

template<unsigned int VDimension>

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

Dimensionality of the domain of the particle system.

template<unsigned int VDimension>

itk::PSMParticleSystem< VDimension >::itkTypeMacro	(	PSMParticleSystem< VDimension >	,
		DataObject
	)

Run-time type information (and related methods).

template<unsigned int VDimension>

void itk::PSMParticleSystem< VDimension >::RegisterAttribute ( PSMAttribute< VDimension > * attr )

Register an attribute object with this particle system. This action adds the attribute object as an observer for the particle system so that it will receive published updates. For example, a gradient attribute object may need to know when particle positions have changed so that it can update its internal state appropriately (e.g. precompute a gradient that corresponds to the new particle position). Internally, this method manages registering the appropriate itk::Command and itk::Object as an observer of this itk::Object (AddObserver). Relevant state information is passed to objects in particle events.

Definition at line 310 of file itkPSMParticleSystem.hxx.

 {
   // Register any methods defined by the attribute as observers of this
   // PSMParticleSystem with appropriate events.
   if (attr->m_DefinedCallbacks.Event == true)
     {
     typename MemberCommand< PSMAttribute<VDimension> >::Pointer tmpcmd
       = MemberCommand< PSMAttribute<VDimension> >::New();
     tmpcmd->SetCallbackFunction(attr, &PSMAttribute<VDimension>::EventCallback);
     this->AddObserver(ParticleEvent(), tmpcmd);
     }
   if (attr->m_DefinedCallbacks.EventWithIndex == true)
     {
     typename MemberCommand< PSMAttribute<VDimension> >::Pointer tmpcmd
       = MemberCommand< PSMAttribute<VDimension> >::New();
     tmpcmd->SetCallbackFunction(attr, &PSMAttribute<VDimension>::EventWithIndexCallback);
     this->AddObserver(ParticleEventWithIndex(), tmpcmd);
     }
   if (attr->m_DefinedCallbacks.DomainAddEvent == true)
     {
     typename MemberCommand< PSMAttribute<VDimension> >::Pointer tmpcmd
       = MemberCommand< PSMAttribute<VDimension> >::New();
     tmpcmd->SetCallbackFunction(attr, &PSMAttribute<VDimension>::DomainAddEventCallback);
     this->AddObserver(ParticleDomainAddEvent(), tmpcmd);
     }
   if (attr->m_DefinedCallbacks.TransformSetEvent == true)
     {
     typename MemberCommand< PSMAttribute<VDimension> >::Pointer tmpcmd
       = MemberCommand< PSMAttribute<VDimension> >::New();
     tmpcmd->SetCallbackFunction(attr, &PSMAttribute<VDimension>::TransformSetEventCallback);
     this->AddObserver(ParticleTransformSetEvent(), tmpcmd);
     }
   if (attr->m_DefinedCallbacks.PrefixTransformSetEvent == true)
     {
     typename MemberCommand< PSMAttribute<VDimension> >::Pointer tmpcmd
       = MemberCommand< PSMAttribute<VDimension> >::New();
     tmpcmd->SetCallbackFunction(attr, &PSMAttribute<VDimension>::PrefixTransformSetEventCallback);
     this->AddObserver(ParticlePrefixTransformSetEvent(), tmpcmd);
     }
   if (attr->m_DefinedCallbacks.NeighborhoodSetEvent == true)
     {
     typename MemberCommand< PSMAttribute<VDimension> >::Pointer tmpcmd
       = MemberCommand< PSMAttribute<VDimension> >::New();
     tmpcmd->SetCallbackFunction(attr, &PSMAttribute<VDimension>::NeighborhoodSetEventCallback);
     this->AddObserver(ParticleNeighborhoodSetEvent(), tmpcmd);
     }
   if (attr->m_DefinedCallbacks.PositionSetEvent == true)
     {
     typename MemberCommand< PSMAttribute<VDimension> >::Pointer tmpcmd
       = MemberCommand< PSMAttribute<VDimension> >::New();
     tmpcmd->SetCallbackFunction(attr, &PSMAttribute<VDimension>::PositionSetEventCallback);
     this->AddObserver(ParticlePositionSetEvent(), tmpcmd);
     }
   if (attr->m_DefinedCallbacks.PositionAddEvent == true)
     {
     typename MemberCommand< PSMAttribute<VDimension> >::Pointer tmpcmd
       = MemberCommand< PSMAttribute<VDimension> >::New();
     tmpcmd->SetCallbackFunction(attr, &PSMAttribute<VDimension>::PositionAddEventCallback);
     this->AddObserver(ParticlePositionAddEvent(), tmpcmd);
     }
   if (attr->m_DefinedCallbacks.PositionRemoveEvent == true)
     {
     typename MemberCommand< PSMAttribute<VDimension> >::Pointer tmpcmd
       = MemberCommand< PSMAttribute<VDimension> >::New();
     tmpcmd->SetCallbackFunction(attr, &PSMAttribute<VDimension>::PositionRemoveEventCallback);
     this->AddObserver(ParticlePositionRemoveEvent(), tmpcmd);
     }
 }

template<unsigned int VDimension>

void itk::PSMParticleSystem< VDimension >::SetFixedParticleFlag ( unsigned int i )

inline

The following methods provide functionality for specifying particle indices that are fixed landmarks. SetPosition() calls to these particle indices will silently fail. For simplicity, only one list of indices is maintained for all dimensions. If particle index n is flagged, for example, then particle index n in all domains is fixed.

Definition at line 418 of file itkPSMParticleSystem.h.

419 { if (i < m_FixedParticleFlags.size()) m_FixedParticleFlags[i] = true; }

template<unsigned int VDimension>

void itk::PSMParticleSystem< VDimension >::SetNeighborhood	(	unsigned int	i,
		NeighborhoodType *	N,
		int	threadId = `0`
	)

Set/Get the neighborhood object associated with domain k.

Definition at line 130 of file itkPSMParticleSystem.hxx.

 {
   m_Neighborhoods[i] = N;
   m_Neighborhoods[i]->SetDomain(m_Domains[i]);
   m_Neighborhoods[i]->SetPointContainer(m_Positions[i]);
   
   // Notify any observers.
   ParticleNeighborhoodSetEvent e;
   e.SetThreadID(threadId);
   e.SetDomainIndex(i);
   this->InvokeEvent(e);
 }

template<unsigned int VDimension>

void itk::PSMParticleSystem< VDimension >::SetNumberOfDomains ( unsigned int num )

protected

Set the number of domains. This method modifies the size of the m_Domains, m_Positions, and m_Transform lists.

Definition at line 35 of file itkPSMParticleSystem.hxx.

 {
   // in case nothing has changed.
   if (num == m_Domains.size())
     {
     return;
     }
   m_Domains.resize(num);
   m_Transforms.resize(num);
   m_InverseTransforms.resize(num);
   m_PrefixTransforms.resize(num);
   m_InversePrefixTransforms.resize(num);
   m_Positions.resize(num);
   m_IndexCounters.resize(num);
   m_Neighborhoods.resize(num);
   m_DomainFlags.resize(num);
   this->Modified();
 }

template<unsigned int VDimension>

void itk::PSMParticleSystem< VDimension >::SetTransform	(	unsigned int	i,
		const TransformType &	T,
		int	threadId = `0`
	)

Set the transform associated with domain i. This method will also compute and set the corresponding inverse transform if possible. If the inverse transform cannot be computed, the exception is quietly handled by this method and an identity transform is set in its place. The calling program is responsible for knowing when an inverse transform cannot be computed.

Definition at line 102 of file itkPSMParticleSystem.hxx.

 {
   m_Transforms[i] = T;
   m_InverseTransforms[i] = this->InvertTransform(T);
 
   // Notify any observers.
   ParticleTransformSetEvent e;
   e.SetThreadID(threadId);
   e.SetDomainIndex(i);
   this->InvokeEvent(e);
 }

template<unsigned int VDimension>

void itk::PSMParticleSystem< VDimension >::SplitAllParticles	(	double	epsilon,
		int	threadId = `0`
	)

Doubles the number of particles of the system by splitting each particle into 2 particles. Each new particle position is added to the system at a random epsilon distance on the surface from the original particle. The new particles are added using the AddPosition method, so all appropriate callbacks are invoked.

Definition at line 288 of file itkPSMParticleSystem.hxx.

 {
   // Find a random direction.
   vnl_vector_fixed<double, VDimension> random;
   
   for (unsigned int i = 0; i < VDimension; i++)
     {        random[i] = static_cast<double>(rand());        }
   double norm = random.magnitude();
   
   // Normalize the random vector.
   random /= norm;
   
   // Loop through all particle positions in the domain and add a new position
   // at an epsilon distance and random direction.
   for (unsigned i = 0; i < this->GetNumberOfDomains(); i++)
     {
       this->SplitAllParticlesInDomain(random, epsilon, i, threadId);
     }
 }

template<unsigned int VDimension>

void itk::PSMParticleSystem< VDimension >::SynchronizePositions ( )

inline

Invokes the set event on all particle positions, resetting them to their current value. This method may be called to synchronize positional information among various observers which may have gone out of sync.

Definition at line 124 of file itkPSMParticleSystem.h.

   {
     for (unsigned int d = 0; d < this->GetNumberOfDomains(); d++)
       {
       for (unsigned int p = 0; p < this->GetNumberOfParticles(d); p++)
         {
         this->SetPosition(this->GetPosition(p,d), p, d);
         }
       } 
   }

template<>

PSMParticleSystem< 3 >::PointType itk::PSMParticleSystem< 3 >::TransformPoint	(	const PointType &	p,
		const TransformType &	T
	)		const

For efficiency, we specialize for 3D and 2D

Definition at line 26 of file itkPSMParticleSystem.cxx.

 {
   PointType ans;
 
   ans[0] = T[0][0] * p[0] + T[0][1] * p[1] + T[0][2] * p[2] + T[0][3];
   ans[1] = T[1][0] * p[0] + T[1][1] * p[1] + T[1][2] * p[2] + T[1][3];
   ans[2] = T[2][0] * p[0] + T[2][1] * p[1] + T[2][2] * p[2] + T[2][3];
 
   return ans;
 }

template<>

PSMParticleSystem< 2 >::PointType itk::PSMParticleSystem< 2 >::TransformPoint	(	const PointType &	p,
		const TransformType &	T
	)		const

For efficiency, we specialize for 3D and 2D

Definition at line 41 of file itkPSMParticleSystem.cxx.

 {
   PointType ans;
 
   ans[0] = T[0][0] * p[0] + T[0][1] * p[1] + T[0][2];
   ans[1] = T[1][0] * p[0] + T[1][1] * p[1] + T[1][2];
 
   return ans;
 }

template<unsigned int VDimension>

PointType itk::PSMParticleSystem< VDimension >::TransformPoint	(	const PointType &	,
		const TransformType &
	)		const

Transforms a point using the given transform. NOTE: Scaling is not currently implemented. (This method may be converted to virtual and overridden if tranform type is generalized.)

template<>

PSMParticleSystem< 3 >::VectorType itk::PSMParticleSystem< 3 >::TransformVector	(	const VectorType &	p,
		const TransformType &	T
	)		const

For efficiency, we specialize for 3D and 2D

Definition at line 56 of file itkPSMParticleSystem.cxx.

 {
   VectorType ans;
 
   ans[0] = T[0][0] * p[0] + T[0][1] * p[1] + T[0][2] * p[2];
   ans[1] = T[1][0] * p[0] + T[1][1] * p[1] + T[1][2] * p[2];
   ans[2] = T[2][0] * p[0] + T[2][1] * p[1] + T[2][2] * p[2];
 
   return ans;
 }

template<>

PSMParticleSystem< 2 >::VectorType itk::PSMParticleSystem< 2 >::TransformVector	(	const VectorType &	p,
		const TransformType &	T
	)		const

For efficiency, we specialize for 3D and 2D

Definition at line 71 of file itkPSMParticleSystem.cxx.

 {
   VectorType ans;
 
   ans[0] = T[0][0] * p[0] + T[0][1] * p[1];
   ans[1] = T[1][0] * p[0] + T[1][1] * p[1];
 
   return ans;
 }

template<unsigned int VDimension>

VectorType itk::PSMParticleSystem< VDimension >::TransformVector	(	const VectorType &	,
		const TransformType &
	)		const

Transforms a vector using the given transform. Only the rotational part of the transform is applied. NOTE: Scaling is not currently supported.

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

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

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

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

Member Typedef Documentation

Member Function Documentation

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