T2SwapCellKiller.cpp

/*

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*/

#include "T2SwapCellKiller.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) == NULL)
    {
        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());
    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);
    }

    /*
     * In the T2 swaps that happened above, vertex elements were removed from the
     * mesh but the associated cells are still there. Here we check which cells
     * underwent a T2 swap and label them as dead.
     */
    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->Kill();
        }
    }
}

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)