CryptCellsGenerator.hpp

/*

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*/

#ifndef CRYPTCELLSGENERATOR_HPP_
#define CRYPTCELLSGENERATOR_HPP_

#include <boost/mpl/integral_c.hpp>
#include <boost/type_traits/is_same.hpp>
#include <boost/mpl/if.hpp>

#include "CellsGenerator.hpp"

#include "CellPropertyRegistry.hpp"
#include "TetrahedralMesh.hpp"
#include "VertexMesh.hpp"
#include "PottsMesh.hpp"

#include "StochasticDurationGenerationBasedCellCycleModel.hpp"
#include "FixedDurationGenerationBasedCellCycleModel.hpp"
#include "TysonNovakCellCycleModel.hpp"
#include "WntCellCycleModel.hpp"
#include "SimpleWntCellCycleModel.hpp"
#include "StochasticWntCellCycleModel.hpp"
#include "VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp"
#include "VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.hpp"
#include "Exception.hpp"


template<class T1, class T2>
bool ClassesAreSame()
{
    using namespace boost::mpl;
    using namespace boost;
    typedef typename if_< is_same<T1, T2>, integral_c<unsigned, 1>, integral_c<unsigned, 0> >::type selector_t;
    return  (selector_t()==1);
}

template<class CELL_CYCLE_MODEL>
class CryptCellsGenerator : public CellsGenerator<CELL_CYCLE_MODEL,2>
{
public:

    void Generate(std::vector<CellPtr>& rCells,
                  AbstractMesh<2,2>* pMesh,
                  const std::vector<unsigned> locationIndices,
                  bool randomBirthTimes,
                  double y0 = 0.3,
                  double y1 = 2.0,
                  double y2 = 3.0,
                  double y3 = 4.0,
                  bool initialiseCells = false);
};


template<class CELL_CYCLE_MODEL>
void CryptCellsGenerator<CELL_CYCLE_MODEL>::Generate(
                                      std::vector<CellPtr>& rCells,
                                      AbstractMesh<2,2>* pMesh,
                                      const std::vector<unsigned> locationIndices,
                                      bool randomBirthTimes,
                                      double y0,
                                      double y1,
                                      double y2,
                                      double y3,
                                      bool initialiseCells)
{
    CellPropertyRegistry::Instance()->Clear();

    RandomNumberGenerator* p_random_num_gen = RandomNumberGenerator::Instance();

    rCells.clear();

    unsigned mesh_size;
    if (dynamic_cast<TetrahedralMesh<2,2>*>(pMesh))
    {
        mesh_size = pMesh->GetNumNodes();
        unsigned num_cells = locationIndices.empty() ? pMesh->GetNumNodes() : locationIndices.size();
        rCells.reserve(num_cells);
    }
    else if (dynamic_cast<PottsMesh<2>*>(pMesh))
    {
        mesh_size = static_cast<PottsMesh<2>*>(pMesh)->GetNumElements();
        rCells.reserve(mesh_size);
    }
    else
    {
        /*
         * We cannot directly assert this dynamic cast. This is because the assert macro
         * doesn't understand the <2,2> and thinks that it is being passed two arguments.
         */
        bool is_vertex_mesh = (dynamic_cast<VertexMesh<2,2>*>(pMesh));
        if (!is_vertex_mesh)
        {
            NEVER_REACHED;
        }
        mesh_size = static_cast<VertexMesh<2,2>*>(pMesh)->GetNumElements();
        rCells.reserve(mesh_size);
    }

    for (unsigned i=0; i<mesh_size; i++)
    {
        CellProliferativeType cell_type;
        unsigned generation;

        double y = 0.0;

        if (dynamic_cast<TetrahedralMesh<2,2>*>(pMesh))
        {
            if (locationIndices.empty())
            {
                y = pMesh->GetNode(i)->GetPoint().rGetLocation()[1];

            }
            else if (std::find(locationIndices.begin(), locationIndices.end(), i) != locationIndices.end())
            {
                y = pMesh->GetNode(i)->GetPoint().rGetLocation()[1];
            }
        }
        else if (dynamic_cast<PottsMesh<2>*>(pMesh))
        {
            y = dynamic_cast<PottsMesh<2>*>(pMesh)->GetCentroidOfElement(i)[1];
        }
        else
        {
            /*
             * We cannot directly assert this dynamic cast. This is because the assert macro
             * doesn't understand the <2,2> and thinks that it is being passed two arguments.
             */
            bool is_vertex_mesh = (dynamic_cast<VertexMesh<2,2>*>(pMesh));
            if (!is_vertex_mesh)
            {
                NEVER_REACHED;
            }
            y = dynamic_cast<VertexMesh<2,2>*>(pMesh)->GetCentroidOfElement(i)[1];
        }

        CELL_CYCLE_MODEL* p_cell_cycle_model = new CELL_CYCLE_MODEL;
        p_cell_cycle_model->SetDimension(2);

        double typical_transit_cycle_time = p_cell_cycle_model->GetAverageTransitCellCycleTime();
        double typical_stem_cycle_time = p_cell_cycle_model->GetAverageStemCellCycleTime();

        double birth_time = 0.0;
        if (randomBirthTimes)
        {
            birth_time = -p_random_num_gen->ranf();
        }

        if (y <= y0)
        {
            cell_type = STEM;
            generation = 0;
            birth_time *= typical_stem_cycle_time; // hours
        }
        else if (y < y1)
        {
            cell_type = TRANSIT;
            generation = 1;
            birth_time *= typical_transit_cycle_time; // hours
        }
        else if (y < y2)
        {
            cell_type = TRANSIT;
            generation = 2;
            birth_time *= typical_transit_cycle_time; // hours
        }
        else if (y < y3)
        {
            cell_type = TRANSIT;
            generation = 3;
            birth_time *= typical_transit_cycle_time; // hours
        }
        else
        {
            cell_type = p_cell_cycle_model->CanCellTerminallyDifferentiate() ? DIFFERENTIATED : TRANSIT;
            generation = 4;
            birth_time *= typical_transit_cycle_time; // hours
        }

        if (dynamic_cast<AbstractSimpleGenerationBasedCellCycleModel*>(p_cell_cycle_model))
        {
            dynamic_cast<AbstractSimpleGenerationBasedCellCycleModel*>(p_cell_cycle_model)->SetGeneration(generation);
        }

        boost::shared_ptr<AbstractCellProperty> p_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());

        CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));
        p_cell->SetCellProliferativeType(cell_type);

        if (initialiseCells)
        {
            p_cell->InitialiseCellCycleModel();
        }

        p_cell->SetBirthTime(birth_time);

        if (locationIndices.empty())
        {
            rCells.push_back(p_cell);
        }
        else if (std::find(locationIndices.begin(), locationIndices.end(), i) != locationIndices.end())
        {
            rCells.push_back(p_cell);
        }
    }
}

#endif /* CRYPTCELLSGENERATOR_HPP_ */