DeltaNotchTrackingModifier.cpp

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*/

#include "DeltaNotchTrackingModifier.hpp"
#include "NodeBasedCellPopulation.hpp"
#include "VertexBasedCellPopulation.hpp"
#include "MeshBasedCellPopulation.hpp"
#include "MeshBasedCellPopulationWithGhostNodes.hpp"
#include "PottsBasedCellPopulation.hpp"
#include "DeltaNotchCellCycleModel.hpp"

template<unsigned DIM>
DeltaNotchTrackingModifier<DIM>::DeltaNotchTrackingModifier()
    : AbstractCellBasedSimulationModifier<DIM>()
{
}

template<unsigned DIM>
DeltaNotchTrackingModifier<DIM>::~DeltaNotchTrackingModifier()
{
}

template<unsigned DIM>
void DeltaNotchTrackingModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    UpdateCellData(rCellPopulation);
}

template<unsigned DIM>
void DeltaNotchTrackingModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
{
    /*
     * We must update CellData in SetupSolve(), otherwise it will not have been
     * fully initialised by the time we enter the main time loop.
     */
    UpdateCellData(rCellPopulation);
}

template<unsigned DIM>
void DeltaNotchTrackingModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
    // Make sure the cell population is updated
    rCellPopulation.Update();

    // First recover each cell's Notch and Delta concentrations from the ODEs and store in CellData
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        DeltaNotchCellCycleModel* p_model = static_cast<DeltaNotchCellCycleModel*>(cell_iter->GetCellCycleModel());
        double this_delta = p_model->GetDelta();
        double this_notch = p_model->GetNotch();

        // Note that the state variables must be in the same order as listed in DeltaNotchOdeSystem
        cell_iter->GetCellData()->SetItem("notch", this_notch);
        cell_iter->GetCellData()->SetItem("delta", this_delta);
    }

    // Next iterate over the population to compute and store each cell's neighbouring Delta concentration in CellData
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
         cell_iter != rCellPopulation.End();
         ++cell_iter)
    {
        // Get the location index corresponding to this cell
        unsigned index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);

        // Get the set of neighbouring location indices
        std::set<unsigned> neighbour_indices;

        if(dynamic_cast<MeshBasedCellPopulationWithGhostNodes<DIM>*>(&rCellPopulation))
        {
            MeshBasedCellPopulationWithGhostNodes<DIM> * p_cell_population = static_cast<MeshBasedCellPopulationWithGhostNodes<DIM>*>(&rCellPopulation);

            neighbour_indices = rCellPopulation.GetNeighbouringNodeIndices(index);

            // Remove ghost nodes from the neighbour indices
            for(std::set<unsigned>::iterator iter = neighbour_indices.begin();
                    iter != neighbour_indices.end();)
            {
               if(p_cell_population->IsGhostNode(*iter))
               {
                   neighbour_indices.erase(iter++);
               }
               else
               {
                  ++iter;
               }
            }

        }
        else if (dynamic_cast<AbstractCentreBasedCellPopulation<DIM>*>(&rCellPopulation))
        {
            neighbour_indices = rCellPopulation.GetNeighbouringNodeIndices(index);
        }
        else if (dynamic_cast<VertexBasedCellPopulation<DIM>*>(&rCellPopulation))
        {
            neighbour_indices = static_cast<VertexBasedCellPopulation<DIM>*>(&rCellPopulation)->rGetMesh().GetNeighbouringElementIndices(index);
        }
        else if(dynamic_cast<PottsBasedCellPopulation<DIM>*>(&rCellPopulation))
        {
            neighbour_indices = static_cast<PottsBasedCellPopulation<DIM>*>(&rCellPopulation)->rGetMesh().GetNeighbouringElementIndices(index);
        }
        else
        {
            NEVER_REACHED;
        }

        // Compute this cell's average neighbouring Delta concentration and store in CellData
        if (!neighbour_indices.empty())
        {
            double mean_delta = 0.0;
            for (std::set<unsigned>::iterator iter = neighbour_indices.begin();
                 iter != neighbour_indices.end();
                 ++iter)
            {
                CellPtr p_cell = rCellPopulation.GetCellUsingLocationIndex(*iter);
                double this_delta = p_cell->GetCellData()->GetItem("delta");
                mean_delta += this_delta/neighbour_indices.size();
            }
            cell_iter->GetCellData()->SetItem("mean delta", mean_delta);
        }
        else
        {
            // If simulation trips at this assertion it is because at least one of the cells has no neighbours (as defined by mesh/population/interaction distance)
            NEVER_REACHED;
        }
    }
}

// Explicit instantiation
template class DeltaNotchTrackingModifier<1>;
template class DeltaNotchTrackingModifier<2>;
template class DeltaNotchTrackingModifier<3>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(DeltaNotchTrackingModifier)