forked from InsightSoftwareConsortium/ITK
-
Notifications
You must be signed in to change notification settings - Fork 0
/
itkBioCellBase.h
175 lines (120 loc) · 4.76 KB
/
itkBioCellBase.h
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkBioCellBase.h
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) 2002 Insight 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 __itk_Bio_Cell_Base_H
#define __itk_Bio_Cell_Base_H
#include "itkRGBPixel.h"
#include "itkVector.h"
#include "itkPoint.h"
#include "itkBioGenome.h"
namespace itk {
namespace bio {
/** \class CellBase
* \brief non-templated Base class from which the templated Cell classes will be derived.
* Derived classes are instantiated for a specific space dimension.
*/
class CellBase
{
public:
typedef itk::RGBPixel<float> ColorType;
typedef unsigned long int IdentifierType;
typedef itk::bio::Genome GenomeType;
typedef GenomeType::GeneIdType GeneIdType;
virtual ColorType GetColor(void) const;
double GetRadius(void) const;
IdentifierType GetSelfIdentifier(void) const;
IdentifierType GetParentIdentifier(void) const;
enum CellCycleState {
M = 1UL,
Gap1,
S,
Gap2,
Gap0,
Apop
};
protected:
CellBase();
virtual ~CellBase();
virtual void Grow(void);
virtual void DNAReplication(void);
virtual void Apoptosis(void);
virtual void EnergyIntake(void);
virtual void NutrientsIntake(void);
virtual void ComputeGeneNetwork(void);
virtual void SecreteProducts(void);
virtual bool CheckPointGrowth(void);
virtual bool CheckPointDNAReplication(void);
virtual bool CheckPointMitosis(void);
virtual bool CheckPointApoptosis(void);
void MarkForRemoval(void);
// Static Members
static double DefaultRadius;
static ColorType DefaultColor;
static GeneIdType BlueGene; // Pigment genes
static GeneIdType RedGene;
static GeneIdType GreenGene;
static GeneIdType Cdk2E; // cell cycle control genes
static GeneIdType Caspase; // cleavage enzyme: apoptosis effector
static GeneIdType Pressurin; // signal from micro-tubules subject to stress
static double GrowthRadiusLimit;
static double GrowthRadiusIncrement;
static unsigned long MaximumGenerationLimit;
static unsigned long GrowthMaximumLatencyTime;
static unsigned long DivisionMaximumLatencyTime;
static double EnergySelfRepairLevel;
static double NutrientSelfRepairLevel;
static double DefaultEnergyIntake;
static double DefaultNutrientsIntake;
static unsigned long Counter;
static ColorType WellNourishedColor;
static ColorType HopefullColor;
static ColorType StarvingColor;
static double ChemoAttractantLowThreshold;
static double ChemoAttractantHighThreshold;
GenomeType * m_Genome;
GenomeType * m_GenomeCopy;
public:
virtual bool MarkedForRemoval(void) const;
static void SetGrowthRadiusLimit( double );
static void SetGrowthRadiusIncrement( double );
static void SetEnergySelfRepairLevel( double );
static void SetNutrientSelfRepairLevel( double );
static void SetDefaultColor( const ColorType & color );
static void SetChemoAttractantHighThreshold( double );
static void SetChemoAttractantLowThreshold( double );
static void SetGrowthMaximumLatencyTime( unsigned long latency );
static unsigned long GetGrowthMaximumLatencyTime( void );
static double GetGrowthRadiusLimit( void );
static void SetMaximumGenerationLimit( unsigned long );
static void SetDivisionMaximumLatencyTime( unsigned long );
static unsigned long GetDivisionMaximumLatencyTime(void);
static void ResetCounter(void);
static void Initialize(void); // define values in static variables.
protected:
double m_Pressure;
ColorType m_Color;
double m_Radius;
double m_EnergyReserveLevel;
double m_NutrientsReserveLevel;
unsigned long m_GrowthLatencyTime;
IdentifierType m_ParentIdentifier;
IdentifierType m_SelfIdentifier;
unsigned long m_Generation;
CellCycleState m_CycleState;
bool m_MarkedForRemoval;
unsigned long m_DivisionLatencyTime;
bool m_ScheduleApoptosis;
double m_ChemoAttractantLevel;
};
} // end namespace bio
} // end namespace itk
#endif