void DeltaNotchTrackingModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
// Make sure the cell population is updated
rCellPopulation.Update();
// First recover each cell's Notch and Delta concentrations from the ODEs and store in CellData
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
DeltaNotchCellCycleModel* p_model = static_cast<DeltaNotchCellCycleModel*>(cell_iter->GetCellCycleModel());
double this_delta = p_model->GetDelta();
double this_notch = p_model->GetNotch();
// Note that the state variables must be in the same order as listed in DeltaNotchOdeSystem
cell_iter->GetCellData()->SetItem("notch", this_notch);
cell_iter->GetCellData()->SetItem("delta", this_delta);
}
// Next iterate over the population to compute and store each cell's neighbouring Delta concentration in CellData
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
// Get the set of neighbouring location indices
std::set<unsigned> neighbour_indices = rCellPopulation.GetNeighbouringLocationIndices(*cell_iter);
// Compute this cell's average neighbouring Delta concentration and store in CellData
if (!neighbour_indices.empty())
{
double mean_delta = 0.0;
for (std::set<unsigned>::iterator iter = neighbour_indices.begin();
iter != neighbour_indices.end();
++iter)
{
CellPtr p_cell = rCellPopulation.GetCellUsingLocationIndex(*iter);
double this_delta = p_cell->GetCellData()->GetItem("delta");
mean_delta += this_delta/neighbour_indices.size();
}
cell_iter->GetCellData()->SetItem("mean delta", mean_delta);
}
else
{
// If this cell has no neighbours, such as an isolated cell in a CaBasedCellPopulation, store 0.0 for the cell data
cell_iter->GetCellData()->SetItem("mean delta", 0.0);
}
}
}
