CryptSimulation2d.cpp

/*

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*/

#include "CryptSimulation2d.hpp"
#include "CellAncestor.hpp"
#include "CellBetaCateninWriter.hpp"
#include "MeshBasedCellPopulation.hpp"
#include "SmartPointers.hpp"
#include "StemCellProliferativeType.hpp"
#include "VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp"
#include "VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.hpp"
#include "WntConcentration.hpp"

CryptSimulation2d::CryptSimulation2d(AbstractCellPopulation<2>& rCellPopulation,
                                     bool deleteCellPopulationInDestructor,
                                     bool initialiseCells)
    : OffLatticeSimulation<2>(rCellPopulation,
                             deleteCellPopulationInDestructor,
                             initialiseCells),
      mUsingMeshBasedCellPopulation(false)
{
    /* Throw an exception message if not using a  MeshBasedCellPopulation or a VertexBasedCellPopulation.
     * This is to catch NodeBasedCellPopulations as AbstactOnLatticeBasedCellPopulations are caught in
     * the OffLatticeSimulation constructor.
     */
    if ((dynamic_cast<VertexBasedCellPopulation<2>*>(&rCellPopulation) == nullptr)
        && (dynamic_cast<MeshBasedCellPopulation<2>*>(&rCellPopulation) == nullptr))
    {
        EXCEPTION("CryptSimulation2d is to be used with MeshBasedCellPopulation or VertexBasedCellPopulation (or subclasses) only");
    }

    if (dynamic_cast<MeshBasedCellPopulation<2>*>(&mrCellPopulation))
    {
        mUsingMeshBasedCellPopulation = true;

        MAKE_PTR(CryptCentreBasedDivisionRule<2>, p_centre_div_rule);
        static_cast<MeshBasedCellPopulation<2>*>(&mrCellPopulation)->SetCentreBasedDivisionRule(p_centre_div_rule);
    }
    else // VertexBasedCellPopulation
    {
        MAKE_PTR(CryptVertexBasedDivisionRule<2>, p_vertex_div_rule);
        static_cast<VertexBasedCellPopulation<2>*>(&mrCellPopulation)->SetVertexBasedDivisionRule(p_vertex_div_rule);
    }

    if (!mDeleteCellPopulationInDestructor)
    {
        // Pass a CryptSimulationBoundaryCondition object into mBoundaryConditions
        MAKE_PTR_ARGS(CryptSimulationBoundaryCondition<2>, p_bc, (&rCellPopulation));
        AddCellPopulationBoundaryCondition(p_bc);
    }
}

CryptSimulation2d::~CryptSimulation2d()
{
}

void CryptSimulation2d::SetupSolve()
{
    // First call method on base class
    OffLatticeSimulation<2>::SetupSolve();

    /*
     * To check if beta-catenin results will be written to file, we test if the first
     * cell has a cell-cycle model that is a subclass of AbstractVanLeeuwen2009WntSwatCellCycleModel.
     * In doing so, we assume that all cells in the simulation have the same cell-cycle
     * model.
     */
    if (dynamic_cast<AbstractVanLeeuwen2009WntSwatCellCycleModel*>(this->mrCellPopulation.Begin()->GetCellCycleModel()))
    {
        mrCellPopulation.AddCellWriter<CellBetaCateninWriter>();
    }

    if (dynamic_cast<AbstractVanLeeuwen2009WntSwatCellCycleModel*>(mrCellPopulation.Begin()->GetCellCycleModel()))
    {
        *mpVizSetupFile << "BetaCatenin\n";
    }
}

void CryptSimulation2d::UseJiggledBottomCells()
{
    // The CryptSimulationBoundaryCondition object is the first element of mBoundaryConditions
    boost::static_pointer_cast<CryptSimulationBoundaryCondition<2> >(mBoundaryConditions[0])->SetUseJiggledBottomCells(true);
}

void CryptSimulation2d::SetBottomCellAncestors()
{
    /*
     * We use a different height threshold depending on which type of cell
     * population we are using, a MeshBasedCellPopulationWithGhostNodes or
     * a VertexBasedCellPopulation.
     *
     * \todo Make this threshold height a member variable and set it in the constructor,
     *       depending on the cell population type; this would allow us to remove mUsingMeshBasedCellPopulation
     */
    double threshold_height = 1.0;
    if (mUsingMeshBasedCellPopulation)
    {
        threshold_height = 0.5;
    }

    unsigned index = 0;
    for (AbstractCellPopulation<2>::Iterator cell_iter = mrCellPopulation.Begin();
         cell_iter != mrCellPopulation.End();
         ++cell_iter)
    {
        if (mrCellPopulation.GetLocationOfCellCentre(*cell_iter)[1] < threshold_height)
        {
            MAKE_PTR_ARGS(CellAncestor, p_cell_ancestor, (index++));
            cell_iter->SetAncestor(p_cell_ancestor);
        }
    }
}

void CryptSimulation2d::OutputSimulationParameters(out_stream& rParamsFile)
{
    double width = mrCellPopulation.GetWidth(0);
    bool use_jiggled_bottom_cells = boost::static_pointer_cast<CryptSimulationBoundaryCondition<2> >(mBoundaryConditions[0])->GetUseJiggledBottomCells();

    *rParamsFile << "\t\t<CryptCircumference>" << width << "</CryptCircumference>\n";
    *rParamsFile << "\t\t<UseJiggledBottomCells>" << use_jiggled_bottom_cells << "</UseJiggledBottomCells>\n";

    // Call method on direct parent class
    OffLatticeSimulation<2>::OutputSimulationParameters(rParamsFile);
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(CryptSimulation2d)