Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
SimpleTargetAreaModifier.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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15 this list of conditions and the following disclaimer.
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19 * Neither the name of the University of Oxford nor the names of its
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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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33
34*/
35
36#include "SimpleTargetAreaModifier.hpp"
37#include "AbstractPhaseBasedCellCycleModel.hpp"
38#include "ApoptoticCellProperty.hpp"
39
40template<unsigned DIM>
46
47template<unsigned DIM>
51
52template<unsigned DIM>
54{
55 // Get target area A of a healthy cell in S, G2 or M phase
56 double cell_target_area = this->mReferenceTargetArea;
57
58 double growth_duration = mGrowthDuration;
59 if (growth_duration == DOUBLE_UNSET)
60 {
61
62 if (dynamic_cast<AbstractPhaseBasedCellCycleModel*>(pCell->GetCellCycleModel()) == nullptr)
63 {
64 EXCEPTION("If SetGrowthDuration() has not been called, a subclass of AbstractPhaseBasedCellCycleModel must be used");
65 }
66 AbstractPhaseBasedCellCycleModel* p_model = static_cast<AbstractPhaseBasedCellCycleModel*>(pCell->GetCellCycleModel());
67
68 growth_duration = p_model->GetG1Duration();
69
70 // If the cell is differentiated then its G1 duration is infinite
71 if (growth_duration == DBL_MAX)
72 {
73 // This is just for fixed cell-cycle models, need to work out how to find the g1 duration
74 growth_duration = p_model->GetTransitCellG1Duration();
75 }
76 }
77
78 if (pCell->HasCellProperty<ApoptoticCellProperty>())
79 {
80
81 // Age of cell when apoptosis begins
82 if (pCell->GetStartOfApoptosisTime() - pCell->GetBirthTime() < growth_duration)
83 {
84 cell_target_area *= 0.5*(1 + (pCell->GetStartOfApoptosisTime() - pCell->GetBirthTime())/growth_duration);
85 }
86
87 // The target area of an apoptotic cell decreases linearly to zero
88 double time_spent_apoptotic = SimulationTime::Instance()->GetTime() - pCell->GetStartOfApoptosisTime();
89
90 cell_target_area *= 1.0 - 0.5/(pCell->GetApoptosisTime())*time_spent_apoptotic;
91 if (cell_target_area < 0)
92 {
93 cell_target_area = 0;
94 }
95
96 }
97 else
98 {
99 double cell_age = pCell->GetAge();
100 // The target area of a proliferating cell increases linearly from A/2 to A over the course of the prescribed duration
101 if (cell_age < growth_duration)
102 {
103 cell_target_area *= 0.5*(1 + cell_age/growth_duration);
104 }
105 else
106 {
114 if (pCell->ReadyToDivide())
115 {
116 cell_target_area = 0.5*this->mReferenceTargetArea;
117 }
118 }
119 }
120 // Set cell data
121 pCell->GetCellData()->SetItem("target area", cell_target_area);
122}
123
124template<unsigned DIM>
126{
127 return mGrowthDuration;
128}
129
130template<unsigned DIM>
132{
133 assert(growthDuration >= 0.0);
134 mGrowthDuration = growthDuration;
135}
136
137template<unsigned DIM>
139{
140 *rParamsFile << "\t\t\t<GrowthDuration>" << mGrowthDuration << "</GrowthDuration>\n";
141
142 // Next, call method on direct parent class
144}
145
146// Explicit instantiation
147template class SimpleTargetAreaModifier<1>;
148template class SimpleTargetAreaModifier<2>;
149template class SimpleTargetAreaModifier<3>;
150
151// Serialization for Boost >= 1.36
const double DOUBLE_UNSET
Definition Exception.hpp:57
#define EXCEPTION(message)
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void OutputSimulationModifierParameters(out_stream &rParamsFile)
void SetGrowthDuration(double growthDuration)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
virtual void UpdateTargetAreaOfCell(const CellPtr pCell)
double GetTime() const
static SimulationTime * Instance()