CellPopulationAreaWriter.cpp

/*

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*/

#include "CellPopulationAreaWriter.hpp"
#include "AbstractCellPopulation.hpp"
#include "MeshBasedCellPopulation.hpp"
#include "CaBasedCellPopulation.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "PottsBasedCellPopulation.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "ApoptoticCellProperty.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellPopulationAreaWriter<ELEMENT_DIM, SPACE_DIM>::CellPopulationAreaWriter()
    : AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM>("cellpopulationareas.dat")
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellPopulationAreaWriter<ELEMENT_DIM, SPACE_DIM>::Visit(MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
{
    assert(SPACE_DIM==2 || SPACE_DIM==3); // LCOV_EXCL_LINE

    VertexMesh<ELEMENT_DIM, SPACE_DIM>* voronoi_tessellation = pCellPopulation->GetVoronoiTessellation();

    assert (voronoi_tessellation != nullptr);

    // Don't use the Voronoi tessellation to calculate the total area of the mesh because it gives huge areas for boundary cells
    double total_area = static_cast<MutableMesh<ELEMENT_DIM,SPACE_DIM>&>((pCellPopulation->rGetMesh())).GetVolume();
    double apoptotic_area = 0.0;

    // Loop over elements of mpVoronoiTessellation
    for (typename VertexMesh<ELEMENT_DIM,SPACE_DIM>::VertexElementIterator elem_iter = voronoi_tessellation->GetElementIteratorBegin();
         elem_iter != voronoi_tessellation->GetElementIteratorEnd();
         ++elem_iter)
    {
        // Get index of this element in mpVoronoiTessellation
        unsigned elem_index = elem_iter->GetIndex();

        // Get the index of the corresponding node in mrMesh
        unsigned node_index = voronoi_tessellation->GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(elem_index);

        // Discount ghost nodes
        if (!pCellPopulation->IsGhostNode(node_index))
        {
            // Get the cell corresponding to this node
            CellPtr p_cell =  pCellPopulation->GetCellUsingLocationIndex(node_index);

            // Only bother calculating the area/volume of apoptotic cells
            bool cell_is_apoptotic = p_cell->HasCellProperty<ApoptoticCellProperty>();
            if (cell_is_apoptotic)
            {
                double cell_volume = voronoi_tessellation->GetVolumeOfElement(elem_index);
                apoptotic_area += cell_volume;
            }
        }
    }
    *this->mpOutStream << total_area << " " << apoptotic_area;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellPopulationAreaWriter<ELEMENT_DIM, SPACE_DIM>::Visit(CaBasedCellPopulation<SPACE_DIM>* pCellPopulation)
{
    EXCEPTION("CellPopulationAreaWriter cannot be used with a CaBasedCellPopulation");
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellPopulationAreaWriter<ELEMENT_DIM, SPACE_DIM>::Visit(NodeBasedCellPopulation<SPACE_DIM>* pCellPopulation)
{
    EXCEPTION("CellPopulationAreaWriter cannot be used with a NodeBasedCellPopulation");
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellPopulationAreaWriter<ELEMENT_DIM, SPACE_DIM>::Visit(PottsBasedCellPopulation<SPACE_DIM>* pCellPopulation)
{
    EXCEPTION("CellPopulationAreaWriter cannot be used with a PottsBasedCellPopulation");
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellPopulationAreaWriter<ELEMENT_DIM, SPACE_DIM>::Visit(VertexBasedCellPopulation<SPACE_DIM>* pCellPopulation)
{
    EXCEPTION("CellPopulationAreaWriter cannot be used with a VertexBasedCellPopulation");
}

// Explicit instantiation
template class CellPopulationAreaWriter<1,1>;
template class CellPopulationAreaWriter<1,2>;
template class CellPopulationAreaWriter<2,2>;
template class CellPopulationAreaWriter<1,3>;
template class CellPopulationAreaWriter<2,3>;
template class CellPopulationAreaWriter<3,3>;

#include "SerializationExportWrapperForCpp.hpp"
// Declare identifier for the serializer
EXPORT_TEMPLATE_CLASS_ALL_DIMS(CellPopulationAreaWriter)