ITK  4.9.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Private Attributes | List of all members
itk::bio::CellularAggregate< NSpaceDimension > Class Template Reference

#include <itkBioCellularAggregate.h>

+ Inheritance diagram for itk::bio::CellularAggregate< NSpaceDimension >:
+ Collaboration diagram for itk::bio::CellularAggregate< NSpaceDimension >:

Detailed Description

template<unsigned int NSpaceDimension = 3>
class itk::bio::CellularAggregate< NSpaceDimension >

Base class for different types of cellular groups, including bacterial colonies and pluricellular organisms.

This class represents an aggregation of bio::Cell objects.

Examples:
Examples/Segmentation/CellularSegmentation1.cxx, and Examples/Segmentation/CellularSegmentation2.cxx.

Definition at line 43 of file itkBioCellularAggregate.h.

Public Types

typedef Cell< NSpaceDimension > BioCellType
 
typedef MeshType::CellAutoPointer CellAutoPointer
 
typedef CellInterface
< typename
MeshType::CellPixelType,
typename MeshType::CellTraits
CellInterfaceType
 
typedef double CellPixelType
 
typedef
PointDataContainer::ConstIterator 
CellsConstIterator
 
typedef
PointDataContainer::Iterator 
CellsIterator
 
typedef SmartPointer< const SelfConstPointer
 
typedef float ImagePixelType
 
typedef MeshType::ConstPointer MeshConstPointer
 
typedef MeshType::Pointer MeshPointer
 
typedef
DefaultDynamicMeshTraits
< PointPixelType,
NSpaceDimension,
NSpaceDimension, double,
double, CellPixelType
MeshTraits
 
typedef Mesh< PointPixelType,
NSpaceDimension, MeshTraits
MeshType
 
typedef
MeshType::PointDataContainer 
PointDataContainer
 
typedef SmartPointer< SelfPointer
 
typedef BioCellTypePointPixelType
 
typedef
PointsContainer::ConstIterator 
PointsConstIterator
 
typedef MeshType::PointsContainer PointsContainer
 
typedef PointsContainer::Iterator PointsIterator
 
typedef MeshType::PointType PointType
 
typedef CellularAggregate Self
 
typedef SubstrateType::Pointer SubstratePointer
 
typedef std::vector
< SubstratePointer
SubstratesVector
 
typedef Image< ImagePixelType,
NSpaceDimension > 
SubstrateType
 
typedef ImagePixelType SubstrateValueType
 
typedef CellularAggregateBase Superclass
 
typedef BioCellType::VectorType VectorType
 
typedef
VoronoiRegionsContainer::ConstIterator 
VoronoiConstIterator
 
typedef
VoronoiRegionsContainer::Iterator 
VoronoiIterator
 
typedef
VoronoiRegionType::SelfAutoPointer 
VoronoiRegionAutoPointer
 
typedef MeshType::CellsContainer VoronoiRegionsContainer
 
typedef PolygonCell
< CellInterfaceType
VoronoiRegionType
 
- Public Types inherited from itk::bio::CellularAggregateBase
typedef SmartPointer< const SelfConstPointer
 
typedef float ImagePixelType
 
typedef SmartPointer< SelfPointer
 
typedef CellularAggregateBase Self
 
typedef ImagePixelType SubstrateValueType
 
typedef Object Superclass
 
- Public Types inherited from itk::Object
typedef SmartPointer< const SelfConstPointer
 
typedef SmartPointer< SelfPointer
 
typedef Object Self
 
typedef LightObject Superclass
 
- Public Types inherited from itk::LightObject
typedef SmartPointer< const SelfConstPointer
 
typedef SmartPointer< SelfPointer
 
typedef LightObject Self
 

Public Member Functions

virtual void Add (CellBase *cell)
 
virtual void Add (CellBase *cell, const VectorType &perturbation)
 
virtual void Add (CellBase *cellA, CellBase *cellB, double perturbationLength) override
 
virtual void AddSubstrate (SubstrateType *substrate)
 
virtual void AdvanceTimeStep ()
 
virtual ::itk::LightObject::Pointer CreateAnother () const
 
void DumpContent (std::ostream &os) const
 
virtual const MeshTypeGetMesh () const
 
virtual MeshTypeGetModifiableMesh ()
 
virtual const char * GetNameOfClass () const
 
unsigned int GetNumberOfCells () const
 
virtual SubstratesVectorGetSubstrates ()
 
virtual SubstrateValueType GetSubstrateValue (IdentifierType cellId, unsigned int substrateId) const override
 
virtual void GetVoronoi (IdentifierType cellId, VoronoiRegionAutoPointer &) const
 
virtual void KillAll ()
 
virtual void Remove (CellBase *cell) override
 
virtual void SetEgg (BioCellType *cell, const PointType &position)
 
void SetGrowthRadiusIncrement (double value)
 
void SetGrowthRadiusLimit (double value)
 
- Public Member Functions inherited from itk::bio::CellularAggregateBase
virtual ::itk::LightObject::Pointer CreateAnother () const
 
- Public Member Functions inherited from itk::Object
unsigned long AddObserver (const EventObject &event, Command *)
 
unsigned long AddObserver (const EventObject &event, Command *) const
 
virtual void DebugOff () const
 
virtual void DebugOn () const
 
CommandGetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionaryGetMetaDataDictionary ()
 
const MetaDataDictionaryGetMetaDataDictionary () const
 
virtual ModifiedTimeType GetMTime () const
 
virtual const TimeStampGetTimeStamp () const
 
bool HasObserver (const EventObject &event) const
 
void InvokeEvent (const EventObject &)
 
void InvokeEvent (const EventObject &) const
 
virtual void Modified () const
 
virtual void Register () const override
 
void RemoveAllObservers ()
 
void RemoveObserver (unsigned long tag)
 
void SetDebug (bool debugFlag) const
 
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
virtual void SetReferenceCount (int) override
 
virtual void UnRegister () const noexceptoverride
 
virtual void SetObjectName (std::string _arg)
 
virtual const std::string & GetObjectName () const
 
- Public Member Functions inherited from itk::LightObject
virtual void Delete ()
 
virtual int GetReferenceCount () const
 
 itkCloneMacro (Self)
 
void Print (std::ostream &os, Indent indent=0) const
 

Static Public Member Functions

static unsigned int GetDimension ()
 
static Pointer New ()
 
- Static Public Member Functions inherited from itk::bio::CellularAggregateBase
static Pointer New ()
 
- Static Public Member Functions inherited from itk::Object
static bool GetGlobalWarningDisplay ()
 
static void GlobalWarningDisplayOff ()
 
static void GlobalWarningDisplayOn ()
 
static Pointer New ()
 
static void SetGlobalWarningDisplay (bool flag)
 
- Static Public Member Functions inherited from itk::LightObject
static void BreakOnError ()
 
static Pointer New ()
 

Static Public Attributes

static const unsigned int SpaceDimension = NSpaceDimension
 

Protected Member Functions

 CellularAggregate ()
 
 CellularAggregate (const Self &)
 
virtual void ClearForces ()
 
virtual void ComputeClosestPoints ()
 
virtual void ComputeForces ()
 
void operator= (const Self &)
 
virtual void PrintSelf (std::ostream &os, Indent indent) const override
 
virtual void UpdatePositions ()
 
virtual ~CellularAggregate ()
 
- Protected Member Functions inherited from itk::bio::CellularAggregateBase
 CellularAggregateBase ()
 
 CellularAggregateBase (const Self &)
 
virtual ~CellularAggregateBase ()
 
- Protected Member Functions inherited from itk::Object
 Object ()
 
bool PrintObservers (std::ostream &os, Indent indent) const
 
virtual void SetTimeStamp (const TimeStamp &time)
 
virtual ~Object ()
 
- Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer InternalClone () const
 
 LightObject ()
 
virtual void PrintHeader (std::ostream &os, Indent indent) const
 
virtual void PrintTrailer (std::ostream &os, Indent indent) const
 
virtual ~LightObject ()
 

Private Attributes

SizeValueType m_ClosestPointComputationInterval
 
double m_FrictionForce
 
SizeValueType m_Iteration
 
MeshPointer m_Mesh
 
SubstratesVector m_Substrates
 

Additional Inherited Members

- Protected Attributes inherited from itk::LightObject
AtomicInt< int > m_ReferenceCount
 

Member Typedef Documentation

template<unsigned int NSpaceDimension = 3>
typedef Cell< NSpaceDimension > itk::bio::CellularAggregate< NSpaceDimension >::BioCellType

Definition at line 61 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef MeshType::CellAutoPointer itk::bio::CellularAggregate< NSpaceDimension >::CellAutoPointer

Definition at line 95 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef CellInterface< typename MeshType::CellPixelType, typename MeshType::CellTraits > itk::bio::CellularAggregate< NSpaceDimension >::CellInterfaceType

Voronoi region around a bio::Cell

Definition at line 100 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef double itk::bio::CellularAggregate< NSpaceDimension >::CellPixelType

Definition at line 63 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef PointDataContainer::ConstIterator itk::bio::CellularAggregate< NSpaceDimension >::CellsConstIterator

Definition at line 93 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef PointDataContainer::Iterator itk::bio::CellularAggregate< NSpaceDimension >::CellsIterator

Definition at line 90 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef SmartPointer< const Self > itk::bio::CellularAggregate< NSpaceDimension >::ConstPointer

Definition at line 50 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef float itk::bio::CellularAggregate< NSpaceDimension >::ImagePixelType

Convenient typedefs.

Definition at line 106 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef MeshType::ConstPointer itk::bio::CellularAggregate< NSpaceDimension >::MeshConstPointer

Definition at line 82 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef MeshType::Pointer itk::bio::CellularAggregate< NSpaceDimension >::MeshPointer

Mesh Associated types

Definition at line 81 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef DefaultDynamicMeshTraits< PointPixelType, NSpaceDimension, NSpaceDimension, double, double, CellPixelType > itk::bio::CellularAggregate< NSpaceDimension >::MeshTraits

Mesh Traits

Definition at line 73 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef Mesh< PointPixelType, NSpaceDimension, MeshTraits > itk::bio::CellularAggregate< NSpaceDimension >::MeshType

Mesh Traits

Definition at line 78 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef MeshType::PointDataContainer itk::bio::CellularAggregate< NSpaceDimension >::PointDataContainer

Definition at line 87 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef SmartPointer< Self > itk::bio::CellularAggregate< NSpaceDimension >::Pointer

Definition at line 49 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef BioCellType* itk::bio::CellularAggregate< NSpaceDimension >::PointPixelType

Definition at line 62 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef PointsContainer::ConstIterator itk::bio::CellularAggregate< NSpaceDimension >::PointsConstIterator

Definition at line 92 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef MeshType::PointsContainer itk::bio::CellularAggregate< NSpaceDimension >::PointsContainer

Definition at line 86 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef PointsContainer::Iterator itk::bio::CellularAggregate< NSpaceDimension >::PointsIterator

Definition at line 89 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef MeshType::PointType itk::bio::CellularAggregate< NSpaceDimension >::PointType

Definition at line 83 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef CellularAggregate itk::bio::CellularAggregate< NSpaceDimension >::Self

Standard class typedefs.

Definition at line 47 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef SubstrateType::Pointer itk::bio::CellularAggregate< NSpaceDimension >::SubstratePointer

Definition at line 108 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef std::vector< SubstratePointer > itk::bio::CellularAggregate< NSpaceDimension >::SubstratesVector

Definition at line 110 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef Image< ImagePixelType, NSpaceDimension > itk::bio::CellularAggregate< NSpaceDimension >::SubstrateType

Definition at line 107 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef ImagePixelType itk::bio::CellularAggregate< NSpaceDimension >::SubstrateValueType

Definition at line 109 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef CellularAggregateBase itk::bio::CellularAggregate< NSpaceDimension >::Superclass

Definition at line 48 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef BioCellType::VectorType itk::bio::CellularAggregate< NSpaceDimension >::VectorType

Definition at line 84 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef VoronoiRegionsContainer::ConstIterator itk::bio::CellularAggregate< NSpaceDimension >::VoronoiConstIterator

Definition at line 94 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef VoronoiRegionsContainer::Iterator itk::bio::CellularAggregate< NSpaceDimension >::VoronoiIterator

Definition at line 91 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef VoronoiRegionType::SelfAutoPointer itk::bio::CellularAggregate< NSpaceDimension >::VoronoiRegionAutoPointer

Definition at line 103 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef MeshType::CellsContainer itk::bio::CellularAggregate< NSpaceDimension >::VoronoiRegionsContainer

Definition at line 88 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
typedef PolygonCell< CellInterfaceType > itk::bio::CellularAggregate< NSpaceDimension >::VoronoiRegionType

Definition at line 102 of file itkBioCellularAggregate.h.

Constructor & Destructor Documentation

template<unsigned int NSpaceDimension = 3>
itk::bio::CellularAggregate< NSpaceDimension >::CellularAggregate ( )
protected
template<unsigned int NSpaceDimension = 3>
virtual itk::bio::CellularAggregate< NSpaceDimension >::~CellularAggregate ( )
protectedvirtual
template<unsigned int NSpaceDimension = 3>
itk::bio::CellularAggregate< NSpaceDimension >::CellularAggregate ( const Self )
protected

Member Function Documentation

template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::Add ( CellBase cell)
virtual
template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::Add ( CellBase cell,
const VectorType perturbation 
)
virtual
template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::Add ( CellBase cellA,
CellBase cellB,
double  perturbationLength 
)
overridevirtual

Reimplemented from itk::bio::CellularAggregateBase.

template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::AddSubstrate ( SubstrateType substrate)
virtual
template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::AdvanceTimeStep ( )
virtual
template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::ClearForces ( )
protectedvirtual
template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::ComputeClosestPoints ( )
protectedvirtual
template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::ComputeForces ( )
protectedvirtual
template<unsigned int NSpaceDimension = 3>
virtual::itk::LightObject::Pointer itk::bio::CellularAggregate< NSpaceDimension >::CreateAnother ( ) const
virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

template<unsigned int NSpaceDimension = 3>
void itk::bio::CellularAggregate< NSpaceDimension >::DumpContent ( std::ostream &  os) const
template<unsigned int NSpaceDimension = 3>
static unsigned int itk::bio::CellularAggregate< NSpaceDimension >::GetDimension ( void  )
inlinestatic
template<unsigned int NSpaceDimension = 3>
virtual const MeshType* itk::bio::CellularAggregate< NSpaceDimension >::GetMesh ( ) const
virtual
template<unsigned int NSpaceDimension = 3>
virtual MeshType* itk::bio::CellularAggregate< NSpaceDimension >::GetModifiableMesh ( )
virtual
template<unsigned int NSpaceDimension = 3>
virtual const char* itk::bio::CellularAggregate< NSpaceDimension >::GetNameOfClass ( ) const
virtual

Standard part of all itk objects.

Reimplemented from itk::bio::CellularAggregateBase.

template<unsigned int NSpaceDimension = 3>
unsigned int itk::bio::CellularAggregate< NSpaceDimension >::GetNumberOfCells ( ) const
template<unsigned int NSpaceDimension = 3>
virtual SubstratesVector& itk::bio::CellularAggregate< NSpaceDimension >::GetSubstrates ( )
virtual
template<unsigned int NSpaceDimension = 3>
virtual SubstrateValueType itk::bio::CellularAggregate< NSpaceDimension >::GetSubstrateValue ( IdentifierType  cellId,
unsigned int  substrateId 
) const
overridevirtual

Reimplemented from itk::bio::CellularAggregateBase.

template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::GetVoronoi ( IdentifierType  cellId,
VoronoiRegionAutoPointer  
) const
virtual
template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::KillAll ( )
virtual
template<unsigned int NSpaceDimension = 3>
static Pointer itk::bio::CellularAggregate< NSpaceDimension >::New ( )
static

Method for creation through the object factory.

template<unsigned int NSpaceDimension = 3>
void itk::bio::CellularAggregate< NSpaceDimension >::operator= ( const Self )
protected
template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
overrideprotectedvirtual

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::bio::CellularAggregateBase.

template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::Remove ( CellBase cell)
overridevirtual

Reimplemented from itk::bio::CellularAggregateBase.

template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::SetEgg ( BioCellType cell,
const PointType position 
)
virtual
template<unsigned int NSpaceDimension = 3>
void itk::bio::CellularAggregate< NSpaceDimension >::SetGrowthRadiusIncrement ( double  value)
template<unsigned int NSpaceDimension = 3>
void itk::bio::CellularAggregate< NSpaceDimension >::SetGrowthRadiusLimit ( double  value)
template<unsigned int NSpaceDimension = 3>
virtual void itk::bio::CellularAggregate< NSpaceDimension >::UpdatePositions ( )
protectedvirtual

Member Data Documentation

template<unsigned int NSpaceDimension = 3>
SizeValueType itk::bio::CellularAggregate< NSpaceDimension >::m_ClosestPointComputationInterval
private

Definition at line 170 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
double itk::bio::CellularAggregate< NSpaceDimension >::m_FrictionForce
private

Definition at line 168 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
SizeValueType itk::bio::CellularAggregate< NSpaceDimension >::m_Iteration
private

Definition at line 169 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
MeshPointer itk::bio::CellularAggregate< NSpaceDimension >::m_Mesh
private

Definition at line 166 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
SubstratesVector itk::bio::CellularAggregate< NSpaceDimension >::m_Substrates
private

Definition at line 167 of file itkBioCellularAggregate.h.

template<unsigned int NSpaceDimension = 3>
const unsigned int itk::bio::CellularAggregate< NSpaceDimension >::SpaceDimension = NSpaceDimension
static

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