void VolumeTrackingModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
// Make sure the cell population is updated
rCellPopulation.Update();
/**
* This hack is needed because in the case of a MeshBasedCellPopulation in which
* multiple cell divisions have occurred over one time step, the Voronoi tessellation
* (while existing) is out-of-date. Thus, if we did not regenerate the Voronoi
* tessellation here, an assertion may trip as we try to access a Voronoi element
* whose index exceeds the number of elements in the out-of-date tessellation.
*
* \todo work out how to properly fix this (#1986)
*/
if (bool(dynamic_cast<MeshBasedCellPopulation<DIM>*>(&rCellPopulation)))
{
static_cast<MeshBasedCellPopulation<DIM>*>(&(rCellPopulation))->CreateVoronoiTessellation();
}
// Iterate over cell population
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
// Get the volume of this cell
double cell_volume = rCellPopulation.GetVolumeOfCell(*cell_iter);
// Store the cell's volume in CellData
cell_iter->GetCellData()->SetItem("volume", cell_volume);
}
}
/*
* Next, we define the {{{UpdateCellData()}}} method itself. This is a helper
* method that computes the height (y coordinate) of each cell in the population
* and stores this in the {{{CellData}}} property.
*/
void UpdateCellData(AbstractCellPopulation<2,2>& rCellPopulation)
{
/*
* We begin by calling {{{Update()}}} on the cell population, which ensures that
* it is in a coherent state.
*/
rCellPopulation.Update();
/*
* Next, we iterate over the cell population...
*/
for (AbstractCellPopulation<2>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
/*
* ...find its height...
*/
double cell_height = rCellPopulation.GetLocationOfCellCentre(*cell_iter)[1];
/*
* ...and store this in the {{{CellData}}} item "height".
*/
cell_iter->GetCellData()->SetItem("height", cell_height);
}
}
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);
}
}
}