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 "ImmersedBoundaryCellPopulation.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(
    [[maybe_unused]] MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation) // [[maybe_unused]] due to unused-but-set-parameter warning in GCC 7,8,9
{
    if constexpr ((SPACE_DIM == 2) || (SPACE_DIM == 3))
    {
        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;
    }
    else
    {
        NEVER_REACHED;
    }
}
 
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");
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellPopulationAreaWriter<ELEMENT_DIM, SPACE_DIM>::Visit(ImmersedBoundaryCellPopulation<SPACE_DIM>* pCellPopulation)
{
    EXCEPTION("CellPopulationAreaWriter cannot be used with a ImmersedBoundaryCellPopulation");
}
 
// 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)