SimpleTargetAreaModifier.cpp

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*/

#include "SimpleTargetAreaModifier.hpp"

template<unsigned DIM>
SimpleTargetAreaModifier<DIM>::SimpleTargetAreaModifier()
    : AbstractTargetAreaModifier<DIM>()
{
}

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

template<unsigned DIM>
void SimpleTargetAreaModifier<DIM>::UpdateTargetAreaOfCell(CellPtr pCell)
{
    // Get target area A of a healthy cell in S, G2 or M phase
    double cell_target_area = this->mReferenceTargetArea;

    double g1_duration = pCell->GetCellCycleModel()->GetG1Duration();

    // If the cell is differentiated then its G1 duration is infinite
    if (g1_duration == DBL_MAX) // don't use magic number, compare to DBL_MAX
    {
        // This is just for fixed cell-cycle models, need to work out how to find the g1 duration
        g1_duration = pCell->GetCellCycleModel()->GetTransitCellG1Duration();
    }

    if (pCell->HasCellProperty<ApoptoticCellProperty>())
    {
        // Age of cell when apoptosis begins
        if (pCell->GetStartOfApoptosisTime() - pCell->GetBirthTime() < g1_duration)
        {
            cell_target_area *= 0.5*(1 + (pCell->GetStartOfApoptosisTime() - pCell->GetBirthTime())/g1_duration);
        }

        // The target area of an apoptotic cell decreases linearly to zero (and past it negative)
        cell_target_area = cell_target_area - 0.5*cell_target_area/(pCell->GetApoptosisTime())*(SimulationTime::Instance()->GetTime()-pCell->GetStartOfApoptosisTime());

        // Don't allow a negative target area
        if (cell_target_area < 0)
        {
            cell_target_area = 0;
        }
    }
    else
    {
        double cell_age = pCell->GetAge();

        // The target area of a proliferating cell increases linearly from A/2 to A over the course of the G1 phase
        if (cell_age < g1_duration)
        {
            cell_target_area *= 0.5*(1 + cell_age/g1_duration);
        }
        else
        {
            if (pCell->ReadyToDivide())
            {
                cell_target_area = 0.5*this->mReferenceTargetArea;
            }
        }
    }

    // Set cell data
    pCell->GetCellData()->SetItem("target area", cell_target_area);
}

template<unsigned DIM>
void SimpleTargetAreaModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    // No parameters to output, so just call method on direct parent class
    AbstractTargetAreaModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}

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

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