ITK  4.1.0
Insight Segmentation and Registration Toolkit
itkBioCellBase.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 __itkBioCellBase_h
00019 #define __itkBioCellBase_h
00020 
00021 #include "itkRGBPixel.h"
00022 #include "itkPoint.h"
00023 #include "itkIntTypes.h"
00024 #include "itkBioGenome.h"
00025 
00026 namespace itk
00027 {
00028 namespace bio
00029 {
00036 class ITK_EXPORT CellBase
00037 {
00038 public:
00039   typedef   itk::RGBPixel< float > ColorType;
00040   typedef   itk::IdentifierType    IdentifierType;
00041   typedef   itk::bio::Genome       GenomeType;
00042   typedef   GenomeType::GeneIdType GeneIdType;
00043 
00044   virtual ColorType GetColor(void) const;
00045 
00046   double GetRadius(void) const;
00047 
00048   IdentifierType GetSelfIdentifier(void) const;
00049 
00050   IdentifierType GetParentIdentifier(void) const;
00051 
00052   enum CellCycleState
00053   {
00054     M = 1UL,
00055     Gap1,
00056     S,
00057     Gap2,
00058     Gap0,
00059     Apop
00060   };
00061 protected:
00062   CellBase();
00063   virtual ~CellBase();
00064 
00065   virtual void Grow(void);
00066 
00067   virtual void DNAReplication(void);
00068 
00069   virtual void Apoptosis(void);
00070 
00071   virtual void EnergyIntake(void);
00072 
00073   virtual void NutrientsIntake(void);
00074 
00075   virtual void ComputeGeneNetwork(void);
00076 
00077   virtual void SecreteProducts(void);
00078 
00079   virtual bool CheckPointGrowth(void);
00080 
00081   virtual bool CheckPointDNAReplication(void);
00082 
00083   virtual bool CheckPointMitosis(void);
00084 
00085   virtual bool CheckPointApoptosis(void);
00086 
00087   void MarkForRemoval(void);
00088 
00089   // Static Members
00090   static ColorType DefaultColor;
00091 
00092   static GeneIdType BlueGene;        // Pigment genes
00093   static GeneIdType RedGene;
00094   static GeneIdType GreenGene;
00095   static GeneIdType Cdk2E;           // cell cycle control  genes
00096   static GeneIdType Caspase;         // cleavage enzyme: apoptosis effector
00097   static GeneIdType Pressurin;       // signal from micro-tubules subject to
00098                                      // stress
00099 
00100   static SizeValueType MaximumGenerationLimit;
00101   static SizeValueType GrowthMaximumLatencyTime;
00102   static SizeValueType DivisionMaximumLatencyTime;
00103 
00104   static double EnergySelfRepairLevel;
00105   static double NutrientSelfRepairLevel;
00106 
00107   static double DefaultEnergyIntake;
00108   static double DefaultNutrientsIntake;
00109 
00110   static SizeValueType Counter;
00111 
00112   static ColorType WellNourishedColor;
00113   static ColorType HopefullColor;
00114   static ColorType StarvingColor;
00115 
00116   static double ChemoAttractantLowThreshold;
00117   static double ChemoAttractantHighThreshold;
00118 
00119   GenomeType *m_Genome;
00120   GenomeType *m_GenomeCopy;
00121 
00122   static double DefaultRadius;
00123   static double GrowthRadiusLimit;
00124   static double GrowthRadiusIncrement;
00125 public:
00126 
00127   virtual bool MarkedForRemoval(void) const;
00128 
00129   static void SetDefaultRadius(double);
00130 
00131   static void SetGrowthRadiusLimit(double);
00132 
00133   static void SetGrowthRadiusIncrement(double);
00134 
00135   static void SetEnergySelfRepairLevel(double);
00136 
00137   static void SetNutrientSelfRepairLevel(double);
00138 
00139   static void SetDefaultColor(const ColorType & color);
00140 
00141   static void SetChemoAttractantHighThreshold(double);
00142 
00143   static void SetChemoAttractantLowThreshold(double);
00144 
00145   static void SetGrowthMaximumLatencyTime(SizeValueType latency);
00146 
00147   static SizeValueType GetGrowthMaximumLatencyTime(void);
00148 
00149   static double GetGrowthRadiusLimit(void);
00150 
00151   static void SetMaximumGenerationLimit(SizeValueType);
00152 
00153   static void SetDivisionMaximumLatencyTime(SizeValueType);
00154 
00155   static SizeValueType GetDivisionMaximumLatencyTime(void);
00156 
00157   static void ResetCounter(void);
00158 
00159   static void Initialize(void); // define values in static variables.
00160 
00161 protected:
00162   double m_Pressure;
00163 
00164   ColorType m_Color;
00165 
00166   double m_Radius;
00167   double m_EnergyReserveLevel;
00168   double m_NutrientsReserveLevel;
00169 
00170   SizeValueType m_GrowthLatencyTime;
00171 
00172   IdentifierType m_ParentIdentifier;
00173   IdentifierType m_SelfIdentifier;
00174 
00175   SizeValueType m_Generation;
00176 
00177   CellCycleState m_CycleState;
00178 
00179   bool          m_MarkedForRemoval;
00180   SizeValueType m_DivisionLatencyTime;
00181 
00182   bool   m_ScheduleApoptosis;
00183   double m_ChemoAttractantLevel;
00184 };
00185 } // end namespace bio
00186 } // end namespace itk
00187 
00188 #endif
00189