unsigned AbstractCellBasedSimulation<ELEMENT_DIM,SPACE_DIM>::DoCellBirth()
{
if (mNoBirth)
{
return 0;
}
unsigned num_births_this_step = 0;
// Iterate over all cells, seeing if each one can be divided
for (typename AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>::Iterator cell_iter = mrCellPopulation.Begin();
cell_iter != mrCellPopulation.End();
++cell_iter)
{
// Check if this cell is ready to divide
double cell_age = cell_iter->GetAge();
if (cell_age > 0.0)
{
if (cell_iter->ReadyToDivide())
{
// Check if there is room into which the cell may divide
if (mrCellPopulation.IsRoomToDivide(*cell_iter))
{
// Create a new cell
CellPtr p_new_cell = cell_iter->Divide();
// Call method that determines how cell division occurs and returns a vector
c_vector<double, SPACE_DIM> new_location = CalculateCellDivisionVector(*cell_iter);
// If required, output this location to file
/**
* \todo (#2441)
*
* For consistency with the rest of the output code, consider removing the
* AbstractCellBasedSimulation member mOutputDivisionLocations, adding a new
* member mAgesAndLocationsOfDividingCells to AbstractCellPopulation, adding
* a new class CellDivisionLocationsWriter to the CellPopulationWriter hierarchy
* to output the content of mAgesAndLocationsOfDividingCells to file (remembering
* to clear mAgesAndLocationsOfDividingCells at each timestep), and replacing the
* following conditional statement with something like
*
* if (mrCellPopulation.HasWriter<CellDivisionLocationsWriter>())
* {
* mCellDivisionLocations.push_back(new_location);
* }
*/
if (mOutputDivisionLocations)
{
*mpDivisionLocationFile << SimulationTime::Instance()->GetTime() << "\t";
for (unsigned i=0; i<SPACE_DIM; i++)
{
*mpDivisionLocationFile << new_location[i] << "\t";
}
*mpDivisionLocationFile << "\t" << cell_age << "\n";
}
// Add new cell to the cell population
mrCellPopulation.AddCell(p_new_cell, new_location, *cell_iter);
// Update counter
num_births_this_step++;
}
}
}
}
return num_births_this_step;
}
void NodeBasedCellPopulation<DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
std::stringstream time;
time << SimulationTime::Instance()->GetTimeStepsElapsed();
VtkMeshWriter<DIM, DIM> mesh_writer(rDirectory, "results_"+time.str(), false);
// Make sure the nodes are ordered contiguously in memory.
NodeMap map(1 + this->mpNodesOnlyMesh->GetMaximumNodeIndex());
this->mpNodesOnlyMesh->ReMesh(map);
mesh_writer.SetParallelFiles(*mpNodesOnlyMesh);
unsigned num_nodes = GetNumNodes();
std::vector<double> cell_types(num_nodes);
std::vector<double> cell_ancestors(num_nodes);
std::vector<double> cell_mutation_states(num_nodes);
std::vector<double> cell_ages(num_nodes);
std::vector<double> cell_cycle_phases(num_nodes);
std::vector<double> cell_radii(num_nodes);
std::vector<std::vector<double> > cellwise_data;
std::vector<double> rank(num_nodes);
unsigned num_cell_data_items = 0;
std::vector<std::string> cell_data_names;
// We assume that the first cell is representative of all cells
if (num_nodes > 0)
{
num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
cell_data_names = this->Begin()->GetCellData()->GetKeys();
}
for (unsigned var=0; var<num_cell_data_items; var++)
{
std::vector<double> cellwise_data_var(num_nodes);
cellwise_data.push_back(cellwise_data_var);
}
// Loop over cells
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
cell_iter != this->End();
++cell_iter)
{
// Get the node index corresponding to this cell
unsigned global_index = this->GetLocationIndexUsingCell(*cell_iter);
Node<DIM>* p_node = this->GetNode(global_index);
unsigned node_index = this->rGetMesh().SolveNodeMapping(global_index);
if (this-> template HasWriter<CellAncestorWriter>())
{
double ancestor_index = (cell_iter->GetAncestor() == UNSIGNED_UNSET) ? (-1.0) : (double)cell_iter->GetAncestor();
cell_ancestors[node_index] = ancestor_index;
}
if (this-> template HasWriter<CellProliferativeTypesWriter>())
{
double cell_type = cell_iter->GetCellProliferativeType()->GetColour();
cell_types[node_index] = cell_type;
}
if (this-> template HasWriter<CellMutationStatesCountWriter>())
{
double mutation_state = cell_iter->GetMutationState()->GetColour();
CellPropertyCollection collection = cell_iter->rGetCellPropertyCollection();
CellPropertyCollection label_collection = collection.GetProperties<CellLabel>();
if (label_collection.GetSize() == 1)
{
boost::shared_ptr<CellLabel> p_label = boost::static_pointer_cast<CellLabel>(label_collection.GetProperty());
mutation_state = p_label->GetColour();
}
cell_mutation_states[node_index] = mutation_state;
}
if (this-> template HasWriter<CellAgesWriter>())
{
double age = cell_iter->GetAge();
cell_ages[node_index] = age;
}
if (this-> template HasWriter<CellProliferativePhasesWriter>())
{
double cycle_phase = cell_iter->GetCellCycleModel()->GetCurrentCellCyclePhase();
cell_cycle_phases[node_index] = cycle_phase;
}
if (this-> template HasWriter<CellVolumesWriter>())
{
double cell_radius = p_node->GetRadius();
cell_radii[node_index] = cell_radius;
}
for (unsigned var=0; var<num_cell_data_items; var++)
{
cellwise_data[var][node_index] = cell_iter->GetCellData()->GetItem(cell_data_names[var]);
}
rank[node_index] = (PetscTools::GetMyRank());
}
mesh_writer.AddPointData("Process rank", rank);
if (this-> template HasWriter<CellProliferativeTypesWriter>())
{
mesh_writer.AddPointData("Cell types", cell_types);
}
if (this-> template HasWriter<CellAncestorWriter>())
{
mesh_writer.AddPointData("Ancestors", cell_ancestors);
}
if (this-> template HasWriter<CellMutationStatesCountWriter>())
{
mesh_writer.AddPointData("Mutation states", cell_mutation_states);
}
if (this-> template HasWriter<CellAgesWriter>())
{
mesh_writer.AddPointData("Ages", cell_ages);
}
if (this-> template HasWriter<CellProliferativePhasesWriter>())
{
mesh_writer.AddPointData("Cycle phases", cell_cycle_phases);
}
if (this-> template HasWriter<CellVolumesWriter>())
{
mesh_writer.AddPointData("Cell radii", cell_radii);
}
if (num_cell_data_items > 0)
{
for (unsigned var=0; var<cellwise_data.size(); var++)
{
mesh_writer.AddPointData(cell_data_names[var], cellwise_data[var]);
}
}
mesh_writer.WriteFilesUsingMesh(*mpNodesOnlyMesh);
*(this->mpVtkMetaFile) << " <DataSet timestep=\"";
*(this->mpVtkMetaFile) << SimulationTime::Instance()->GetTimeStepsElapsed();
*(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
*(this->mpVtkMetaFile) << SimulationTime::Instance()->GetTimeStepsElapsed();
*(this->mpVtkMetaFile) << ".vtu\"/>\n";
#endif //CHASTE_VTK
}
