CellPopulationElementWriter.cpp

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*/

#include "CellPopulationElementWriter.hpp"
#include "AbstractCellPopulation.hpp"
#include "MeshBasedCellPopulation.hpp"
#include "CaBasedCellPopulation.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "PottsBasedCellPopulation.hpp"
#include "VertexBasedCellPopulation.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellPopulationElementWriter<ELEMENT_DIM, SPACE_DIM>::CellPopulationElementWriter()
    : AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM>("results.vizelements")
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellPopulationElementWriter<ELEMENT_DIM, SPACE_DIM>::Visit(MeshBasedCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation)
{
    for (typename MutableMesh<ELEMENT_DIM,SPACE_DIM>::ElementIterator elem_iter = static_cast<MutableMesh<ELEMENT_DIM,SPACE_DIM>&>((pCellPopulation->rGetMesh())).GetElementIteratorBegin();
         elem_iter != static_cast<MutableMesh<ELEMENT_DIM,SPACE_DIM>&>((pCellPopulation->rGetMesh())).GetElementIteratorEnd();
         ++elem_iter)
    {
        bool element_contains_dead_cells_or_deleted_nodes = false;

        // Hack that covers the case where the element contains a node that is associated with a cell that has just been killed (#1129)
        for (unsigned i=0; i<ELEMENT_DIM+1; i++)
        {
            unsigned node_index = elem_iter->GetNodeGlobalIndex(i);

            if (pCellPopulation->GetNode(node_index)->IsDeleted())
            {
                element_contains_dead_cells_or_deleted_nodes = true;
                break;
            }
            else if (pCellPopulation->IsCellAttachedToLocationIndex(node_index))
            {
                if (pCellPopulation->GetCellUsingLocationIndex(node_index)->IsDead())
                {
                    element_contains_dead_cells_or_deleted_nodes = true;
                    break;
                }
            }
        }
        if (!element_contains_dead_cells_or_deleted_nodes)
        {
            for (unsigned i=0; i<ELEMENT_DIM+1; i++)
            {
                *this->mpOutStream << elem_iter->GetNodeGlobalIndex(i) << " ";
            }
        }
    }
}

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellPopulationElementWriter<ELEMENT_DIM, SPACE_DIM>::Visit(PottsBasedCellPopulation<SPACE_DIM>* pCellPopulation)
{
    // Loop over cells and find associated elements so in the same order as the cells in output files
    for (typename AbstractCellPopulation<SPACE_DIM, SPACE_DIM>::Iterator cell_iter = pCellPopulation->Begin();
         cell_iter != pCellPopulation->End();
         ++cell_iter)
    {
        unsigned elem_index = pCellPopulation->GetLocationIndexUsingCell(*cell_iter);

        // Hack that covers the case where the element is associated with a cell that has just been killed (#1129)
        bool elem_corresponds_to_dead_cell = false;

        if (pCellPopulation->IsCellAttachedToLocationIndex(elem_index))
        {
            elem_corresponds_to_dead_cell = pCellPopulation->GetCellUsingLocationIndex(elem_index)->IsDead();
        }

        // Write element data to file
        if (!(pCellPopulation->GetElement(elem_index)->IsDeleted()) && !elem_corresponds_to_dead_cell)
        {
            PottsElement<SPACE_DIM>* p_element = pCellPopulation->rGetMesh().GetElement(elem_index);
            unsigned num_nodes_in_element = p_element->GetNumNodes();

            // First write the number of Nodes belonging to this VertexElement
            *this->mpOutStream << num_nodes_in_element << " ";

            // Then write the global index of each Node in this element
            for (unsigned i=0; i<num_nodes_in_element; i++)
            {
                *this->mpOutStream << p_element->GetNodeGlobalIndex(i) << " ";
            }
        }
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellPopulationElementWriter<ELEMENT_DIM, SPACE_DIM>::Visit(VertexBasedCellPopulation<SPACE_DIM>* pCellPopulation)
{
    // Loop over cells and find associated elements so in the same order as the cells in output files
    for (typename AbstractCellPopulation<SPACE_DIM, SPACE_DIM>::Iterator cell_iter = pCellPopulation->Begin();
         cell_iter != pCellPopulation->End();
         ++cell_iter)
    {
        unsigned elem_index = pCellPopulation->GetLocationIndexUsingCell(*cell_iter);

        // Hack that covers the case where the element is associated with a cell that has just been killed (#1129)
        bool elem_corresponds_to_dead_cell = false;

        if (pCellPopulation->IsCellAttachedToLocationIndex(elem_index))
        {
            elem_corresponds_to_dead_cell = pCellPopulation->GetCellUsingLocationIndex(elem_index)->IsDead();
        }

        // Write element data to file
        if (!(pCellPopulation->GetElement(elem_index)->IsDeleted()) && !elem_corresponds_to_dead_cell)
        {
            VertexElement<SPACE_DIM, SPACE_DIM>* p_element = pCellPopulation->rGetMesh().GetElement(elem_index);
            unsigned num_nodes_in_element = p_element->GetNumNodes();

            // First write the number of Nodes belonging to this VertexElement
            *this->mpOutStream << num_nodes_in_element << " ";

            // Then write the global index of each Node in this element
            for (unsigned i=0; i<num_nodes_in_element; i++)
            {
                *this->mpOutStream << p_element->GetNodeGlobalIndex(i) << " ";
            }
        }
    }
}

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

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