T2SwapCellKiller.cpp

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*/
 
#include "T2SwapCellKiller.hpp"
#include "CellRemovalLocationsWriter.hpp"
 
template<unsigned DIM>
T2SwapCellKiller<DIM>::T2SwapCellKiller(AbstractCellPopulation<DIM>* pCellPopulation)
    : AbstractCellKiller<DIM>(pCellPopulation)
{
    // Throw an exception if the population is not a VertexBasedCellPopulation
    if (dynamic_cast<VertexBasedCellPopulation<DIM>*>(this->mpCellPopulation) == nullptr)
    {
        EXCEPTION("A T2SwapCellKiller should only be used together with a VertexBasedCellPopulation.");
    }
}
 
template<unsigned DIM>
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());
 
                /* Mark the cell as killed and store removal information if required.
                 * Note we can't use the KillCell() helper method here as it will fail as the
                 * element has already been deleted.
                 * this->mpCellPopulation->KillCell(p_cell, "T2SwapCellKiller");
                 */
                if (p_vertex_population->template HasWriter<CellRemovalLocationsWriter>())
                {
                    std::stringstream removal_info;
                    removal_info << SimulationTime::Instance()->GetTime() << "\t";
                    for (unsigned i = 0; i < DIM; i++)
                    {
                        removal_info << mesh.GetLastT2SwapLocation()[i] << "\t";
                    }
                    removal_info << "\t" << p_cell->GetAge() << "\t" << p_cell->GetCellId() << "\t"
                                 << "T2SwapCellKiller"
                                 << "\t";
 
                    p_vertex_population->AddRemovalInformation(removal_info.str());
                }
                p_cell->Kill();
 
                // There can't have been more than one new cell death, so leave the for loop here.
                break;
            }
        }
    }
 
}
 
template<unsigned DIM>
void T2SwapCellKiller<DIM>::OutputCellKillerParameters(out_stream& rParamsFile)
{
    // No parameters to output, so just call method on direct parent class
    AbstractCellKiller<DIM>::OutputCellKillerParameters(rParamsFile);
}
 
// Explicit instantiation
template class T2SwapCellKiller<1>;
template class T2SwapCellKiller<2>;
template class T2SwapCellKiller<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(T2SwapCellKiller)