void CryptProjectionForce::UpdateNode3dLocationMap(AbstractCellPopulation<2>& rCellPopulation)
{
mNode3dLocationMap.clear();
c_vector<double, 2> node_location_2d;
c_vector<double, 3> node_location_3d;
// Only consider nodes corresponding to real cells
for (AbstractCellPopulation<2>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
// Get node index
unsigned node_index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);
// Get 3D location
node_location_2d = rCellPopulation.GetLocationOfCellCentre(*cell_iter);
node_location_3d[0] = node_location_2d[0];
node_location_3d[1] = node_location_2d[1];
node_location_3d[2] = CalculateCryptSurfaceHeightAtPoint(node_location_2d);
// Add to map
mNode3dLocationMap[node_index] = node_location_3d;
}
}
/*
* 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);
}
}
/* The second public method overrides {{{AddForceContribution()}}}.
* This method takes in one argument, a reference to the cell population itself.
*/
void AddForceContribution(AbstractCellPopulation<2>& rCellPopulation)
{
/* Inside the method, we loop over cells, and add a vector to
* each node associated with cells with the {{{MotileCellProperty}}}, which is proportional (with constant {{{mStrength}}}) to the negative of the position. Causing
* cells to move inwards towards the origin. Note that this will currently only work with subclasses of {{{AbstractCentreBasedCellPopulation}}}s as
* we associate cells with nodes in the force calculation. However, this could easily be modified to make it work for {{{VertexBasedCellPopulation}}}s.
*/
for (AbstractCellPopulation<2>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
if (cell_iter->HasCellProperty<MotileCellProperty>())
{
unsigned node_index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);
c_vector<double, 2> location = rCellPopulation.GetLocationOfCellCentre(*cell_iter);
c_vector<double, 2> force = -1.0 * mStrength * location;
rCellPopulation.GetNode(node_index)->AddAppliedForceContribution(force);
}
}
}