AbstractCryptStatistics.cpp

/*

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*/
#include "AbstractCryptStatistics.hpp"
#include "CellPropertyRegistry.hpp"
#include "AbstractPhaseBasedCellCycleModel.hpp"
#include "CellLabel.hpp"
#include "WildTypeCellMutationState.hpp"

AbstractCryptStatistics::AbstractCryptStatistics(MeshBasedCellPopulation<2>& rCrypt)
    : mrCrypt(rCrypt)
{
}

AbstractCryptStatistics::~AbstractCryptStatistics()
{
}

void AbstractCryptStatistics::LabelSPhaseCells()
{
    for (AbstractCellPopulation<2>::Iterator cell_iter = mrCrypt.Begin();
         cell_iter != mrCrypt.End();
         ++cell_iter)
    {
        if (static_cast <AbstractPhaseBasedCellCycleModel*>(cell_iter->GetCellCycleModel())->GetCurrentCellCyclePhase()== S_PHASE)
        {
            // This should only be done for wild type cells (at the moment anyway)
            assert(cell_iter->GetMutationState()->IsType<WildTypeCellMutationState>());

            // Label this cell
            if (!cell_iter->HasCellProperty<CellLabel>())
            {
                /*
                 * This method is usually called after mrCrypt has called CellPropertyRegistry::TakeOwnership().
                 * This means that were we to call CellPropertyRegistry::Instance() here when adding the CellLabel,
                 * we would be creating a new CellPropertyRegistry. In this case the CellLabel's cell count would
                 * be incorrect. We therefore access the CellLabel via mrCrypt.GetCellPropertyRegistry().
                 */
                cell_iter->AddCellProperty(mrCrypt.GetCellPropertyRegistry()->Get<CellLabel>());
            }
        }
    }
}

void AbstractCryptStatistics::LabelAllCellsAsHealthy()
{
    for (AbstractCellPopulation<2>::Iterator cell_iter = mrCrypt.Begin();
         cell_iter != mrCrypt.End();
         ++cell_iter)
    {
        cell_iter->SetMutationState(mrCrypt.GetCellPropertyRegistry()->Get<WildTypeCellMutationState>());
        cell_iter->RemoveCellProperty<CellLabel>();
    }
}

std::vector<bool> AbstractCryptStatistics::AreCryptSectionCellsLabelled(std::vector<CellPtr>& rCryptSection)
{
    std::vector<bool> crypt_section_labelled(rCryptSection.size());

    for (unsigned vector_index=0; vector_index<rCryptSection.size(); vector_index++)
    {
        if (rCryptSection[vector_index]->HasCellProperty<CellLabel>())
        {
            crypt_section_labelled[vector_index] = true;
        }
        else
        {
            crypt_section_labelled[vector_index] = false;
        }
    }

    return crypt_section_labelled;
}