CryptSimulationBoundaryCondition.cpp

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*/

#include "CryptSimulationBoundaryCondition.hpp"
#include "WntConcentration.hpp"
#include "AbstractCentreBasedCellPopulation.hpp"
#include "RandomNumberGenerator.hpp"
#include "StemCellProliferativeType.hpp"

template<unsigned DIM>
CryptSimulationBoundaryCondition<DIM>::CryptSimulationBoundaryCondition(AbstractCellPopulation<DIM>* pCellPopulation)
    : AbstractCellPopulationBoundaryCondition<DIM>(pCellPopulation),
      mUseJiggledBottomCells(false)
{
}

template<unsigned DIM>
void CryptSimulationBoundaryCondition<DIM>::ImposeBoundaryCondition(const std::map<Node<DIM>*, c_vector<double, DIM> >& rOldLocations)
{
    // We only allow jiggling of bottom cells in 2D
    if (DIM == 1)
    {
        mUseJiggledBottomCells = false;
    }

    // Check whether a WntConcentration singleton has been set up
    bool is_wnt_included = WntConcentration<DIM>::Instance()->IsWntSetUp();
    if (!is_wnt_included)
    {
        WntConcentration<DIM>::Destroy();
    }

    // We iterate differently depending on whether we are using a centre- or vertex-based model
    if (dynamic_cast<AbstractCentreBasedCellPopulation<DIM>*>(this->mpCellPopulation))
    {
        // Iterate over all nodes associated with real cells to update their positions
        for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->mpCellPopulation->Begin();
             cell_iter != this->mpCellPopulation->End();
             ++cell_iter)
        {
            // Get index of node associated with cell
            unsigned node_index = this->mpCellPopulation->GetLocationIndexUsingCell(*cell_iter);

            // Get pointer to this node
            Node<DIM>* p_node = this->mpCellPopulation->GetNode(node_index);

            if (!is_wnt_included)
            {
                /*
                 * If WntConcentration is not set up then stem cells must be pinned,
                 * so we reset the location of each stem cell.
                 */
                if (cell_iter->GetCellProliferativeType()->template IsType<StemCellProliferativeType>())
                {
                    // Get old node location
                    c_vector<double, DIM> old_node_location = rOldLocations.find(p_node)->second;

                    // Return node to old location
                    p_node->rGetModifiableLocation() = old_node_location;
                }
            }

            // Any cell that has moved below the bottom of the crypt must be moved back up
            if (p_node->rGetLocation()[DIM-1] < 0.0)
            {
                p_node->rGetModifiableLocation()[DIM-1] = 0.0;

                if (mUseJiggledBottomCells)
                {
                   /*
                    * Here we give the cell a push upwards so that it doesn't
                    * get stuck on the bottom of the crypt (as per #422).
                    *
                    * Note that all stem cells may get moved to the same height, so
                    * we use a random perturbation to help ensure we are not simply
                    * faced with the same problem at a different height!
                    */
                    p_node->rGetModifiableLocation()[DIM-1] = 0.05*RandomNumberGenerator::Instance()->ranf();
                }
            }
            assert(p_node->rGetLocation()[DIM-1] >= 0.0);
        }
    }
    else
    {
        // Iterate over all nodes to update their positions
        for (unsigned node_index=0; node_index<this->mpCellPopulation->GetNumNodes(); node_index++)
        {
            // Get pointer to this node
            Node<DIM>* p_node = this->mpCellPopulation->GetNode(node_index);

            if (!is_wnt_included)
            {
                /*
                 * If WntConcentration is not set up then stem cells must be pinned,
                 * so we reset the location of each node whose height was close to zero.
                 */
                double node_height = rOldLocations.find(p_node)->second[DIM-1];
                if (node_height < DBL_EPSILON)
                {
                    // Return node to its old height, but allow it to slide left or right
                    p_node->rGetModifiableLocation()[DIM-1] = node_height;
                }
            }

            // Any node that has moved below the bottom of the crypt must be moved back up
            if (p_node->rGetLocation()[DIM-1] < 0.0)
            {
                p_node->rGetModifiableLocation()[DIM-1] = 0.0;

                if (mUseJiggledBottomCells)
                {
                   /*
                    * Here we give the node a push upwards so that it doesn't
                    * get stuck on the bottom of the crypt.
                    */
                    p_node->rGetModifiableLocation()[DIM-1] = 0.05*RandomNumberGenerator::Instance()->ranf();
                }
            }
            assert(p_node->rGetLocation()[DIM-1] >= 0.0);
        }
    }
}

template<unsigned DIM>
bool CryptSimulationBoundaryCondition<DIM>::VerifyBoundaryCondition()
{
    bool boundary_condition_satisfied = true;

    /*
     * Here we verify that the boundary condition is still satisfied by simply
     * checking that no cells lies below the y=0 boundary.
     */
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->mpCellPopulation->Begin();
         cell_iter != this->mpCellPopulation->End();
         ++cell_iter)
    {
        // Get index of node associated with cell
        unsigned node_index = this->mpCellPopulation->GetLocationIndexUsingCell(*cell_iter);

        // Get pointer to this node
        Node<DIM>* p_node = this->mpCellPopulation->GetNode(node_index);

        // If this node lies below the y=0 boundary, break and return false
        if (p_node->rGetLocation()[DIM-1] < 0.0)
        {
            boundary_condition_satisfied = false;
            break;
        }
    }

    return boundary_condition_satisfied;
}

template<unsigned DIM>
void CryptSimulationBoundaryCondition<DIM>::SetUseJiggledBottomCells(bool useJiggledBottomCells)
{
    mUseJiggledBottomCells = useJiggledBottomCells;
}

template<unsigned DIM>
bool CryptSimulationBoundaryCondition<DIM>::GetUseJiggledBottomCells()
{
    return mUseJiggledBottomCells;
}

template<unsigned DIM>
void CryptSimulationBoundaryCondition<DIM>::OutputCellPopulationBoundaryConditionParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t<UseJiggledBottomCells>" << mUseJiggledBottomCells << "</UseJiggledBottomCells>\n";
    // Call method on direct parent class
    AbstractCellPopulationBoundaryCondition<DIM>::OutputCellPopulationBoundaryConditionParameters(rParamsFile);
}

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

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