FarhadifarTypeModifier.cpp

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*/

#include "FarhadifarTypeModifier.hpp"

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

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

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

    if (pCell->HasCellProperty<ApoptoticCellProperty>())
    {
        // 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();

        // Get the combined duration of the cell's M, G1 and S phases
        AbstractCellCycleModel* p_model = pCell->GetCellCycleModel();
        double growth_start_time = p_model->GetMDuration() + p_model->GetG1Duration() + p_model->GetSDuration();

        // The target area of a proliferating cell increases linearly from A to 2A over the course of the G2 phase
        if (cell_age > growth_start_time)
        {
            double g2_duration = p_model->GetG2Duration();
            cell_target_area *= (1 + (cell_age-growth_start_time)/g2_duration);
        }

        if (pCell->ReadyToDivide())
        {
            cell_target_area = this->mReferenceTargetArea;
        }
    }

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

template<unsigned DIM>
void FarhadifarTypeModifier<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 FarhadifarTypeModifier<1>;
template class FarhadifarTypeModifier<2>;
template class FarhadifarTypeModifier<3>;

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