NormallyDistributedTargetAreaModifier.cpp

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#include "NormallyDistributedTargetAreaModifier.hpp"
#include "AbstractPhaseBasedCellCycleModel.hpp"
#include "ApoptoticCellProperty.hpp"
#include "RandomNumberGenerator.hpp"
 
#include <algorithm>
 
template<unsigned DIM>
NormallyDistributedTargetAreaModifier<DIM>::NormallyDistributedTargetAreaModifier()
    : AbstractTargetAreaModifier<DIM>(),
      mGrowthDuration(DOUBLE_UNSET)
{
}
 
template<unsigned DIM>
NormallyDistributedTargetAreaModifier<DIM>::~NormallyDistributedTargetAreaModifier()
{
}
 
template<unsigned DIM>
void NormallyDistributedTargetAreaModifier<DIM>::UpdateTargetAreaOfCell(CellPtr pCell)
{
    // Generate random numbers if needed
    while (pCell->GetCellId() >= mNormalRandomNumbers.size())
    {
        // Generate N(1, 0.4)
        double random_number = RandomNumberGenerator::Instance()->NormalRandomDeviate(1.0, 0.4);
 
        // Bound the result to be in [0.5, 1.5]
        random_number = std::min(1.5, random_number);
        random_number = std::max(0.5, random_number);
 
        mNormalRandomNumbers.push_back(random_number);
    }
 
    // Get target area A of a healthy cell in S, G2 or M phase
    double cell_target_area = this->mReferenceTargetArea;
 
    double growth_duration = mGrowthDuration;
    if (growth_duration == DOUBLE_UNSET)
    {
        if (dynamic_cast<AbstractPhaseBasedCellCycleModel*>(pCell->GetCellCycleModel()) == NULL)
        {
            EXCEPTION("If SetGrowthDuration() has not been called, a subclass of AbstractPhaseBasedCellCycleModel must be used");
        }
        AbstractPhaseBasedCellCycleModel* p_model = static_cast<AbstractPhaseBasedCellCycleModel*>(pCell->GetCellCycleModel());
 
        growth_duration = p_model->GetG1Duration();
 
        // If the cell is differentiated then its G1 duration is infinite
        if (growth_duration == DBL_MAX)
        {
            // This is just for fixed cell-cycle models, need to work out how to find the g1 duration
            growth_duration = p_model->GetTransitCellG1Duration();
        }
    }
 
    if (pCell->HasCellProperty<ApoptoticCellProperty>())
    {
        // Age of cell when apoptosis begins
        if (pCell->GetStartOfApoptosisTime() - pCell->GetBirthTime() < growth_duration)
        {
            cell_target_area *= 0.5*(1 + (pCell->GetStartOfApoptosisTime() - pCell->GetBirthTime())/growth_duration);
        }
 
        // The target area of an apoptotic cell decreases linearly to zero
        double time_spent_apoptotic = SimulationTime::Instance()->GetTime() - pCell->GetStartOfApoptosisTime();
 
        cell_target_area *= 1.0 - 0.5/(pCell->GetApoptosisTime())*time_spent_apoptotic;
        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 prescribed duration
        if (cell_age < growth_duration)
        {
            cell_target_area *= 0.5*(1 + cell_age/growth_duration);
        }
        else
        {
            if (pCell->ReadyToDivide())
            {
                cell_target_area = 0.5*this->mReferenceTargetArea;
            }
        }
    }
 
    // Set cell data
    pCell->GetCellData()->SetItem("target area", cell_target_area * mNormalRandomNumbers[pCell->GetCellId()]);
}
 
template<unsigned DIM>
double NormallyDistributedTargetAreaModifier<DIM>::GetGrowthDuration()
{
    return mGrowthDuration;
}
 
template<unsigned DIM>
void NormallyDistributedTargetAreaModifier<DIM>::SetGrowthDuration(double growthDuration)
{
    assert(growthDuration >= 0.0);
    mGrowthDuration = growthDuration;
}
 
template<unsigned DIM>
void NormallyDistributedTargetAreaModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t\t<GrowthDuration>" << mGrowthDuration << "</GrowthDuration>\n";
 
    // Next, call method on direct parent class
    AbstractTargetAreaModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
}
 
// Explicit instantiation
template class NormallyDistributedTargetAreaModifier<1>;
template class NormallyDistributedTargetAreaModifier<2>;
template class NormallyDistributedTargetAreaModifier<3>;
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(NormallyDistributedTargetAreaModifier)