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itkBioCellularAggregate.h
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itkBioCellularAggregate.h
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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkBioCellularAggregate.h
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __itkBioCellularAggregate_h
#define __itkBioCellularAggregate_h
#include "itkBioCellularAggregateBase.h"
#include "itkDefaultDynamicMeshTraits.h"
#include "itkMesh.h"
#include "itkImage.h"
#include "itkBioCell.h"
#include "itkPolygonCell.h"
#include <iostream>
#include <vector>
namespace itk {
namespace bio {
/** \class CellularAggregate
* \brief This class represent an aggregation of bio::Cell objects
* This class is the base for different types of cellular groups
* including bacterial colonies and pluricellular organisms
*/
template<unsigned int NSpaceDimension=3>
class CellularAggregate : public CellularAggregateBase
{
public:
/** Standard class typedefs. */
typedef CellularAggregate Self;
typedef CellularAggregateBase Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/*** Run-time type information (and related methods). */
itkTypeMacro(BioCellularAggregate, CellularAggregateBase);
/** Method for creation through the object factory. */
itkNewMacro(Self);
itkStaticConstMacro( SpaceDimension, unsigned int, NSpaceDimension);
/*** Type to be used for data associated with each point in the mesh. */
typedef Cell<NSpaceDimension> BioCellType;
typedef BioCellType * PointPixelType;
typedef double CellPixelType;
/** Mesh Traits */
typedef DefaultDynamicMeshTraits<
PointPixelType, // PixelType
NSpaceDimension, // Points Dimension
NSpaceDimension, // Max.Topological Dimension
double, // Type for coordinates
double, // Type for interpolation
CellPixelType // Type for values in the cells
> MeshTraits;
/** Mesh Traits */
typedef Mesh< PointPixelType,
NSpaceDimension,
MeshTraits > MeshType;
/** Mesh Associated types */
typedef typename MeshType::Pointer MeshPointer;
typedef typename MeshType::ConstPointer MeshConstPointer;
typedef typename MeshType::PointType PointType;
typedef typename BioCellType::VectorType VectorType;
typedef typename MeshType::PointsContainer PointsContainer;
typedef typename MeshType::PointDataContainer PointDataContainer;
typedef typename MeshType::CellsContainer VoronoiRegionsContainer;
typedef typename PointsContainer::Iterator PointsIterator;
typedef typename PointDataContainer::Iterator CellsIterator;
typedef typename VoronoiRegionsContainer::Iterator VoronoiIterator;
typedef typename PointsContainer::ConstIterator PointsConstIterator;
typedef typename PointDataContainer::ConstIterator CellsConstIterator;
typedef typename VoronoiRegionsContainer::ConstIterator VoronoiConstIterator;
typedef typename MeshType::PointIdentifier IdentifierType;
typedef typename MeshType::CellAutoPointer CellAutoPointer;
/** Voronoi region around a bio::Cell */
typedef CellInterface<
typename MeshType::CellPixelType,
typename MeshType::CellTraits > CellInterfaceType;
typedef PolygonCell< CellInterfaceType > VoronoiRegionType;
typedef typename VoronoiRegionType::SelfAutoPointer VoronoiRegionAutoPointer;
/** Convenient typedefs. */
typedef float ImagePixelType;
typedef Image<ImagePixelType, NSpaceDimension > SubstrateType;
typedef typename SubstrateType::Pointer SubstratePointer;
typedef ImagePixelType SubstrateValueType;
typedef std::vector< SubstratePointer > SubstratesVector;
public:
unsigned int GetNumberOfCells(void) const;
static unsigned int GetDimension() { return SpaceDimension; }
void SetGrowthRadiusLimit( double value );
void SetGrowthRadiusIncrement( double value );
itkGetObjectMacro( Mesh, MeshType );
itkGetConstObjectMacro( Mesh, MeshType );
virtual void AdvanceTimeStep(void);
virtual void SetEgg( BioCellType * cell, const PointType & position );
virtual void Add( CellBase * cell );
virtual void Add( CellBase * cell, const VectorType & perturbation );
virtual void Add( CellBase * cellA, CellBase * cellB, double perturbationLength );
virtual void Remove( CellBase * cell );
virtual void GetVoronoi( unsigned long int cellId, VoronoiRegionAutoPointer & ) const;
void DumpContent( std::ostream & os ) const;
virtual void AddSubstrate( SubstrateType * substrate );
virtual SubstratesVector & GetSubstrates( void );
virtual SubstrateValueType GetSubstrateValue( unsigned long int cellId,
unsigned int substrateId ) const;
virtual void KillAll(void);
protected:
CellularAggregate();
virtual ~CellularAggregate();
CellularAggregate( const Self & );
void operator=(const Self&);
void PrintSelf(std::ostream& os, Indent indent) const;
virtual void ComputeForces(void);
virtual void UpdatePositions(void);
virtual void ComputeClosestPoints(void);
virtual void ClearForces(void);
private:
MeshPointer m_Mesh;
SubstratesVector m_Substrates;
double m_FrictionForce;
unsigned long m_Iteration;
unsigned long m_ClosestPointComputationInterval;
};
} // end namespace bio
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkBioCellularAggregate.txx"
#endif
#endif