ITK  4.1.0
Insight Segmentation and Registration Toolkit
itkBioCellularAggregate.h
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00001 /*=========================================================================
00002  *
00003  *  Copyright Insight Software Consortium
00004  *
00005  *  Licensed under the Apache License, Version 2.0 (the "License");
00006  *  you may not use this file except in compliance with the License.
00007  *  You may obtain a copy of the License at
00008  *
00009  *         http://www.apache.org/licenses/LICENSE-2.0.txt
00010  *
00011  *  Unless required by applicable law or agreed to in writing, software
00012  *  distributed under the License is distributed on an "AS IS" BASIS,
00013  *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
00014  *  See the License for the specific language governing permissions and
00015  *  limitations under the License.
00016  *
00017  *=========================================================================*/
00018 #ifndef __itkBioCellularAggregate_h
00019 #define __itkBioCellularAggregate_h
00020 
00021 #include "itkDefaultDynamicMeshTraits.h"
00022 #include "itkMesh.h"
00023 #include "itkImage.h"
00024 #include "itkBioCell.h"
00025 #include "itkPolygonCell.h"
00026 
00027 #include <iostream>
00028 #include <vector>
00029 
00030 namespace itk
00031 {
00032 namespace bio
00033 {
00042 template< unsigned int NSpaceDimension = 3 >
00043 class ITK_EXPORT CellularAggregate:public CellularAggregateBase
00044 {
00045 public:
00047   typedef CellularAggregate          Self;
00048   typedef CellularAggregateBase      Superclass;
00049   typedef SmartPointer< Self >       Pointer;
00050   typedef SmartPointer< const Self > ConstPointer;
00051 
00052 /*** Run-time type information (and related methods). */
00053   itkTypeMacro(BioCellularAggregate, CellularAggregateBase);
00054 
00056   itkNewMacro(Self);
00057 
00058   itkStaticConstMacro(SpaceDimension, unsigned int, NSpaceDimension);
00059 
00060 /*** Type to be used for data associated with each point in the mesh. */
00061   typedef    Cell< NSpaceDimension > BioCellType;
00062   typedef    BioCellType *           PointPixelType;
00063   typedef    double                  CellPixelType;
00064 
00066   typedef DefaultDynamicMeshTraits<
00067     PointPixelType,                     // PixelType
00068     NSpaceDimension,                    // Points Dimension
00069     NSpaceDimension,                    // Max.Topological Dimension
00070     double,                             // Type for coordinates
00071     double,                             // Type for interpolation
00072     CellPixelType                       // Type for values in the cells
00073     >  MeshTraits;
00074 
00076   typedef Mesh<  PointPixelType,
00077                  NSpaceDimension,
00078                  MeshTraits  >               MeshType;
00079 
00081   typedef typename MeshType::Pointer       MeshPointer;
00082   typedef typename MeshType::ConstPointer  MeshConstPointer;
00083   typedef typename MeshType::PointType     PointType;
00084   typedef typename BioCellType::VectorType VectorType;
00085 
00086   typedef typename MeshType::PointsContainer              PointsContainer;
00087   typedef typename MeshType::PointDataContainer           PointDataContainer;
00088   typedef typename MeshType::CellsContainer               VoronoiRegionsContainer;
00089   typedef typename PointsContainer::Iterator              PointsIterator;
00090   typedef typename PointDataContainer::Iterator           CellsIterator;
00091   typedef typename VoronoiRegionsContainer::Iterator      VoronoiIterator;
00092   typedef typename PointsContainer::ConstIterator         PointsConstIterator;
00093   typedef typename PointDataContainer::ConstIterator      CellsConstIterator;
00094   typedef typename VoronoiRegionsContainer::ConstIterator VoronoiConstIterator;
00095   typedef typename MeshType::CellAutoPointer              CellAutoPointer;
00096 
00098   typedef CellInterface<
00099     typename MeshType::CellPixelType,
00100     typename MeshType::CellTraits >      CellInterfaceType;
00101 
00102   typedef PolygonCell<  CellInterfaceType >           VoronoiRegionType;
00103   typedef typename VoronoiRegionType::SelfAutoPointer VoronoiRegionAutoPointer;
00104 
00106   typedef float                                    ImagePixelType;
00107   typedef Image< ImagePixelType, NSpaceDimension > SubstrateType;
00108   typedef typename SubstrateType::Pointer          SubstratePointer;
00109   typedef ImagePixelType                           SubstrateValueType;
00110   typedef std::vector< SubstratePointer >          SubstratesVector;
00111 public:
00112   unsigned int GetNumberOfCells(void) const;
00113 
00114   static unsigned int GetDimension() { return SpaceDimension; }
00115 
00116   void SetGrowthRadiusLimit(double value);
00117 
00118   void SetGrowthRadiusIncrement(double value);
00119 
00120   itkGetObjectMacro(Mesh, MeshType);
00121   itkGetConstObjectMacro(Mesh, MeshType);
00122 
00123   virtual void AdvanceTimeStep(void);
00124 
00125   virtual void SetEgg(BioCellType *cell, const PointType & position);
00126 
00127   virtual void Add(CellBase *cell);
00128 
00129   virtual void Add(CellBase *cell, const VectorType & perturbation);
00130 
00131   virtual void Add(CellBase *cellA, CellBase *cellB, double perturbationLength);
00132 
00133   virtual void Remove(CellBase *cell);
00134 
00135   virtual void GetVoronoi(IdentifierType cellId, VoronoiRegionAutoPointer &) const;
00136 
00137   void DumpContent(std::ostream & os) const;
00138 
00139   virtual void AddSubstrate(SubstrateType *substrate);
00140 
00141   virtual SubstratesVector & GetSubstrates(void);
00142 
00143   virtual SubstrateValueType GetSubstrateValue(IdentifierType cellId,
00144                                                unsigned int substrateId) const;
00145 
00146   virtual void KillAll(void);
00147 
00148 protected:
00149   CellularAggregate();
00150   virtual ~CellularAggregate();
00151   CellularAggregate(const Self &);
00152   void operator=(const Self &);
00153 
00154   void PrintSelf(std::ostream & os, Indent indent) const;
00155 
00156   virtual void ComputeForces(void);
00157 
00158   virtual void UpdatePositions(void);
00159 
00160   virtual void ComputeClosestPoints(void);
00161 
00162   virtual void ClearForces(void);
00163 
00164 private:
00165 
00166   MeshPointer      m_Mesh;
00167   SubstratesVector m_Substrates;
00168   double           m_FrictionForce;
00169   SizeValueType    m_Iteration;
00170   SizeValueType    m_ClosestPointComputationInterval;
00171 };
00172 } // end namespace bio
00173 } // end namespace itk
00174 
00175 #ifndef ITK_MANUAL_INSTANTIATION
00176 #include "itkBioCellularAggregate.hxx"
00177 #endif
00178 
00179 #endif
00180