Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
CryptCellsGenerator.hpp
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35
36#ifndef CRYPTCELLSGENERATOR_HPP_
37#define CRYPTCELLSGENERATOR_HPP_
38
39#include <boost/mpl/integral_c.hpp>
40#include <boost/type_traits/is_same.hpp>
41#include <boost/mpl/if.hpp>
42
43#include "CellsGenerator.hpp"
44
45#include "CellPropertyRegistry.hpp"
46#include "TetrahedralMesh.hpp"
47#include "VertexMesh.hpp"
48#include "PottsMesh.hpp"
49
50#include "UniformG1GenerationalCellCycleModel.hpp"
51#include "FixedG1GenerationalCellCycleModel.hpp"
52#include "TysonNovakCellCycleModel.hpp"
53#include "WntCellCycleModel.hpp"
54#include "SimpleWntCellCycleModel.hpp"
55#include "StochasticWntCellCycleModel.hpp"
56#include "VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp"
57#include "VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.hpp"
58#include "Exception.hpp"
59#include "StemCellProliferativeType.hpp"
60#include "TransitCellProliferativeType.hpp"
61#include "DifferentiatedCellProliferativeType.hpp"
62
63
68template<class T1, class T2>
69bool ClassesAreSame()
70{
71 using namespace boost::mpl;
72 using namespace boost;
73 typedef typename if_< is_same<T1, T2>, integral_c<unsigned, 1>, integral_c<unsigned, 0> >::type selector_t;
74 return (selector_t()==1);
75}
76
82template<class CELL_CYCLE_MODEL>
83class CryptCellsGenerator : public CellsGenerator<CELL_CYCLE_MODEL,2>
84{
85public:
86
104 void Generate(std::vector<CellPtr>& rCells,
105 AbstractMesh<2,2>* pMesh,
106 const std::vector<unsigned> locationIndices,
107 bool randomBirthTimes,
108 double y0 = 0.3,
109 double y1 = 2.0,
110 double y2 = 3.0,
111 double y3 = 4.0,
112 bool initialiseCells = false);
113};
114
115template<class CELL_CYCLE_MODEL>
117 std::vector<CellPtr>& rCells,
118 AbstractMesh<2,2>* pMesh,
119 const std::vector<unsigned> locationIndices,
120 bool randomBirthTimes,
121 double y0,
122 double y1,
123 double y2,
124 double y3,
125 bool initialiseCells)
126{
127 rCells.clear();
128
130
131 unsigned mesh_size;
132 if (dynamic_cast<TetrahedralMesh<2,2>*>(pMesh))
133 {
134 mesh_size = pMesh->GetNumNodes();
135 unsigned num_cells = locationIndices.empty() ? pMesh->GetNumNodes() : locationIndices.size();
136 rCells.reserve(num_cells);
137 }
138 else if (dynamic_cast<PottsMesh<2>*>(pMesh))
139 {
140 mesh_size = static_cast<PottsMesh<2>*>(pMesh)->GetNumElements();
141 rCells.reserve(mesh_size);
142 }
143 else
144 {
145 // Note the double brackets, to stop the macro thinking is has two arguments.
146 assert((dynamic_cast<VertexMesh<2,2>*>(pMesh)));
147 mesh_size = static_cast<VertexMesh<2,2>*>(pMesh)->GetNumElements();
148 rCells.reserve(mesh_size);
149 }
150
151 boost::shared_ptr<AbstractCellProperty> p_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());
152
153 // Loop over the mesh and populate rCells
154 for (unsigned i=0; i<mesh_size; i++)
155 {
156 // Find the location of this cell
157 double y = 0.0;
158 if (dynamic_cast<TetrahedralMesh<2,2>*>(pMesh))
159 {
160 if (locationIndices.empty())
161 {
162 y = pMesh->GetNode(i)->GetPoint().rGetLocation()[1];
163
164 }
165 else if (std::find(locationIndices.begin(), locationIndices.end(), i) != locationIndices.end())
166 {
167 y = pMesh->GetNode(i)->GetPoint().rGetLocation()[1];
168 }
169 }
170 else if (dynamic_cast<PottsMesh<2>*>(pMesh))
171 {
172 y = static_cast<PottsMesh<2>*>(pMesh)->GetCentroidOfElement(i)[1];
173 }
174 else
175 {
176 // Note the double brackets, to stop the macro thinking is has two arguments.
177 assert((dynamic_cast<VertexMesh<2,2>*>(pMesh)));
178 y = static_cast<VertexMesh<2,2>*>(pMesh)->GetCentroidOfElement(i)[1];
179 }
180
181 // Create a cell-cycle model and set the spatial dimension
182 CELL_CYCLE_MODEL* p_cell_cycle_model = new CELL_CYCLE_MODEL;
183 p_cell_cycle_model->SetDimension(2);
184
185 double typical_transit_cycle_time = p_cell_cycle_model->GetAverageTransitCellCycleTime();
186 double typical_stem_cycle_time = p_cell_cycle_model->GetAverageStemCellCycleTime();
187
188 double birth_time = 0.0;
189 if (randomBirthTimes)
190 {
191 birth_time = -p_random_num_gen->ranf();
192 }
193
194 // Set the cell-cycle model's generation if required
195 unsigned generation = 4;
196 if (y <= y0)
197 {
198 generation = 0;
199 }
200 else if (y < y1)
201 {
202 generation = 1;
203 }
204 else if (y < y2)
205 {
206 generation = 2;
207 }
208 else if (y < y3)
209 {
210 generation = 3;
211 }
212 if (dynamic_cast<AbstractSimpleGenerationalCellCycleModel*>(p_cell_cycle_model))
213 {
214 dynamic_cast<AbstractSimpleGenerationalCellCycleModel*>(p_cell_cycle_model)->SetGeneration(generation);
215 }
216
217 // Create a cell
218 CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));
219
220 // Set the cell's proliferative type, dependent on its height up the crypt and whether it can terminally differentiate
221 if (y <= y0)
222 {
223 p_cell->SetCellProliferativeType(CellPropertyRegistry::Instance()->Get<StemCellProliferativeType>());
224 }
225 else
226 {
227 p_cell->SetCellProliferativeType(CellPropertyRegistry::Instance()->Get<TransitCellProliferativeType>());
228 if (y >= y3 && p_cell_cycle_model->CanCellTerminallyDifferentiate())
229 {
230 p_cell->SetCellProliferativeType(CellPropertyRegistry::Instance()->Get<DifferentiatedCellProliferativeType>());
231 }
232 }
233
234 // Initialise the cell-cycle model if this is required
235 if (initialiseCells)
236 {
237 p_cell->InitialiseCellCycleModel();
238 }
239
240 // Set the cell's birth time
241 if (y <= y0)
242 {
243 birth_time *= typical_stem_cycle_time; // hours
244 }
245 else
246 {
247 birth_time *= typical_transit_cycle_time; // hours
248 }
249 p_cell->SetBirthTime(birth_time);
250
251 if (locationIndices.empty())
252 {
253 rCells.push_back(p_cell);
254 }
255 else if (std::find(locationIndices.begin(), locationIndices.end(), i) != locationIndices.end())
256 {
257 rCells.push_back(p_cell);
258 }
259 }
260}
261
262#endif /* CRYPTCELLSGENERATOR_HPP_ */
virtual unsigned GetNumNodes() const
Node< SPACE_DIM > * GetNode(unsigned index) const
static CellPropertyRegistry * Instance()
Definition Cell.hpp:92
void Generate(std::vector< CellPtr > &rCells, AbstractMesh< 2, 2 > *pMesh, const std::vector< unsigned > locationIndices, bool randomBirthTimes, double y0=0.3, double y1=2.0, double y2=3.0, double y3=4.0, bool initialiseCells=false)
static RandomNumberGenerator * Instance()