void VertexBasedCellPopulation<DIM>::Update(bool hasHadBirthsOrDeaths)
{
VertexElementMap element_map(mpMutableVertexMesh->GetNumAllElements());
mpMutableVertexMesh->ReMesh(element_map);
if (!element_map.IsIdentityMap())
{
// Fix up the mappings between CellPtrs and VertexElements
///\todo We want to make these maps private, so we need a better way of doing the code below.
std::map<Cell*, unsigned> old_map = this->mCellLocationMap;
this->mCellLocationMap.clear();
this->mLocationCellMap.clear();
for (std::list<CellPtr>::iterator cell_iter = this->mCells.begin();
cell_iter != this->mCells.end();
++cell_iter)
{
// The cell vector should only ever contain living cells
unsigned old_elem_index = old_map[(*cell_iter).get()];
assert(!element_map.IsDeleted(old_elem_index));
unsigned new_elem_index = element_map.GetNewIndex(old_elem_index);
this->SetCellUsingLocationIndex(new_elem_index, *cell_iter);
}
// Check that each VertexElement has only one CellPtr associated with it in the updated cell population
Validate();
}
element_map.ResetToIdentity();
}
void T2SwapCellKiller<DIM>::CheckAndLabelCellsForApoptosisOrDeath()
{
/*
* This killer is different to other killers: it does not only check and label
* cells for apoptosis or death, it actually carries out vertex rearrangements
* and removes elements from the vertex mesh.
*
* We start with carrying out T2 swaps. Get the mesh and an element map.
* The static_cast will work since we already know it's a VertexBasedCellPopulation.
*/
MutableVertexMesh<DIM,DIM>& mesh = static_cast<MutableVertexMesh<DIM,DIM>&>(this->mpCellPopulation->rGetMesh());
VertexBasedCellPopulation<DIM>* p_vertex_population = static_cast<VertexBasedCellPopulation<DIM>*>(this->mpCellPopulation);
VertexElementMap element_map(mesh.GetNumAllElements());
bool recheck_mesh = true;
while (recheck_mesh == true)
{
// Note that whenever we call CheckForT2Swaps(), the element indices must run from zero up to mElements.size()-1
recheck_mesh = mesh.CheckForT2Swaps(element_map);
/*
* There might have maximally one T2 swap happened above, where a vertex element was removed from the
* mesh but the associated cell is still there. Here we check whether a new cell
* underwent a T2 swap and label it as dead as well as record its location and ID.
*/
for (unsigned elem_index = 0; elem_index < element_map.Size(); elem_index++)
{
CellPtr p_cell = this->mpCellPopulation->GetCellUsingLocationIndex(elem_index);
if (element_map.IsDeleted(elem_index) && !(p_cell->IsDead()))
{
p_vertex_population->AddLocationOfT2Swap(mesh.GetLastT2SwapLocation());
p_vertex_population->AddCellIdOfT2Swap(p_cell->GetCellId());
p_cell->Kill();
// There can't have been more than one new cell death, so leave the for loop here.
break;
}
}
}
}
CRCFile::element_map* CRCFile::GetElementMap(UINT uiGroup)
{
// insert menu if does not exist
element_map* pElementMap = NULL;
group_map::iterator itGroup = m_mapOutputLanguage.find(uiGroup);
if(itGroup == m_mapOutputLanguage.end())
{
std::pair<group_map::iterator, bool> pairGroup = m_mapOutputLanguage.insert(std::make_pair(uiGroup, element_map()));
if(!pairGroup.second)
{
_ASSERTE(false);
return NULL;
}
pElementMap = &(*(pairGroup.first)).second;
}
else
pElementMap = &((*itGroup).second);
if(!pElementMap)
{
_ASSERTE(false);
return NULL;
}
return pElementMap;
}
