Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
ParallelCellsGenerator.hpp
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35
36#ifndef PARALLELCELLSGENERATOR_HPP_
37#define PARALLELCELLSGENERATOR_HPP_
38
39#include <vector>
40#include "Cell.hpp"
41#include "WildTypeCellMutationState.hpp"
42#include "AbstractCellProperty.hpp"
43#include "NodesOnlyMesh.hpp"
44
49template<class CELL_CYCLE_MODEL, unsigned DIM>
51{
52 friend class TestParallelCellsGenerator; // For testing.
53
54private:
55
62 c_vector<double, 2*DIM> GetArchiveBoundingBox(std::string archivePath);
63
64public:
65
73 void GenerateParallelCells( std::string archivePath,
74 std::vector<CellPtr>& cells,
76 boost::shared_ptr<AbstractCellProperty> pCellProliferativeType=boost::shared_ptr<AbstractCellProperty>());
77};
78
79// Implementation
80template<class CELL_CYCLE_MODEL, unsigned DIM>
81void ParallelCellsGenerator<CELL_CYCLE_MODEL, DIM>::GenerateParallelCells(std::string archivePath, std::vector<CellPtr>& cells, NodesOnlyMesh<DIM>& mesh, boost::shared_ptr<AbstractCellProperty> pCellProliferativeType)
82{
83 // Get a bounding box for the archived nodes
84 c_vector<double, 2*DIM> base_bounding_box = GetArchiveBoundingBox(archivePath);
85
86 // Add small factor to make sure the box is big enough to contain the initial population.
87 for (unsigned i=0; i<DIM; i++)
88 {
89 base_bounding_box[2*i] -= 1e-14;
90 base_bounding_box[2*i + 1] += 1e-14;
91 }
92
93 // Construct box collection of NodesOnlyMesh
94 mesh.SetInitialBoxCollection(base_bounding_box, mesh.GetMaximumInteractionDistance());
95
96 unsigned node_index = 0;
97
98 std::ifstream infile(archivePath.c_str(), std::ios::in);
99
100 std::string line;
101 std::getline(infile, line); // Get first line which is ignored as it is a header.
102
103 while (std::getline(infile, line))
104 {
105 // Get line in archive file.
106 std::istringstream iss(line);
107
108 // Extract a location.
109 c_vector<double, DIM> location;
110 for (unsigned k=0; k<DIM; k++)
111 {
112 iss >> location[k];
113 }
114
115 // Add it to the mesh and make an appropriate cell if it is owned.
116 if (mesh.IsOwned(location))
117 {
118 // Make a node at this point.
119 Node<DIM>* p_node = new Node<DIM>(node_index, location); // Memory is managed by NodesOnlyMesh.
120 mesh.AddNode(p_node);
121
122 // Make cell
123 CELL_CYCLE_MODEL* p_cell_cycle_model = new CELL_CYCLE_MODEL;
124 p_cell_cycle_model->SetDimension(DIM);
125
126 // Wild type hard-coded for now.
127 boost::shared_ptr<AbstractCellProperty> p_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());
128 CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));
129 p_cell->SetCellProliferativeType(pCellProliferativeType);
130 cells.push_back(p_cell);
131
132 node_index++;
133 }
134 }
135
136 infile.close();
137
138 // Tidy up the mesh.
139 NodeMap map(mesh.GetMaximumNodeIndex()+1);
140 mesh.ReMesh(map);
141}
142
143template<class CELL_CYCLE_MODEL, unsigned DIM>
144c_vector<double, 2*DIM> ParallelCellsGenerator<CELL_CYCLE_MODEL, DIM>::GetArchiveBoundingBox(std::string archivePath)
145{
146 c_vector<double, 2*DIM> bounding_box;
147 for (unsigned i=0; i<DIM; i++)
148 {
149 bounding_box[2*i] = DBL_MAX;
150 bounding_box[2*i + 1] = -DBL_MAX;
151 }
152
153 std::ifstream infile(archivePath.c_str());
154
155 std::string line;
156 std::getline(infile, line);
157
158 std::istringstream iss(line);
159
160 // Check file dimensions and template dimensions match.
161 unsigned num_lines;
162 unsigned file_dimension;
163
164 iss >> num_lines >> file_dimension;
165
166 if (file_dimension != DIM)
167 {
168 EXCEPTION("Space dimension of ParallelCellsGenerator and archive file do not match");
169 }
170
171 while (std::getline(infile, line))
172 {
173 std::stringstream new_iss(line);
174 for (unsigned i=0; i<DIM; i++)
175 {
176 double point;
177 new_iss >> point;
178 bounding_box[2*i] = (point < bounding_box[2*i]) ? point : bounding_box[2*i];
179 bounding_box[2*i+1] = (point > bounding_box[2*i+1]) ? point : bounding_box[2*i+1];
180 }
181 }
182
183 infile.close();
184
185 return bounding_box;
186}
187#endif /* PARALLELCELLSGENERATOR_HPP_ */
#define EXCEPTION(message)
static CellPropertyRegistry * Instance()
Definition Cell.hpp:92
Definition Node.hpp:59
c_vector< double, 2 *DIM > GetArchiveBoundingBox(std::string archivePath)
void GenerateParallelCells(std::string archivePath, std::vector< CellPtr > &cells, NodesOnlyMesh< DIM > &mesh, boost::shared_ptr< AbstractCellProperty > pCellProliferativeType=boost::shared_ptr< AbstractCellProperty >())