CaBasedCellPopulation.cpp

/*

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 * Redistributions of source code must retain the above copyright notice,
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*/

#include "CaBasedCellPopulation.hpp"

#include <boost/scoped_array.hpp>

#include "RandomNumberGenerator.hpp"
#include "Warnings.hpp"

// Needed to convert mesh in order to write nodes to VTK (visualize as glyphs)
#include "VtkMeshWriter.hpp"

// Cell writers
#include "CellAgesWriter.hpp"
#include "CellAncestorWriter.hpp"
#include "CellLocationWriter.hpp"
#include "CellProliferativePhasesWriter.hpp"
#include "CellProliferativeTypesWriter.hpp"

// Cell population writers
#include "CellMutationStatesWriter.hpp"

#include "NodesOnlyMesh.hpp"
#include "Exception.hpp"

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::Validate()
{
    NEVER_REACHED;
}

template<unsigned DIM>
CaBasedCellPopulation<DIM>::CaBasedCellPopulation(PottsMesh<DIM>& rMesh,
                                                        std::vector<CellPtr>& rCells,
                                                        const std::vector<unsigned> locationIndices,
                                                        unsigned latticeCarryingCapacity,
                                                        bool deleteMesh,
                                                        bool validate)
    : AbstractOnLatticeCellPopulation<DIM>(rMesh, rCells, locationIndices, deleteMesh),
      mLatticeCarryingCapacity(latticeCarryingCapacity)
{
    mAvailableSpaces = std::vector<unsigned>(this->GetNumNodes(), latticeCarryingCapacity);

    // This must always be true
    assert(this->mCells.size() <= this->mrMesh.GetNumNodes()*latticeCarryingCapacity);

    if (locationIndices.empty())
    {
        EXCEPTION("No location indices being passed. Specify where cells lie before creating the cell population.");
    }
    else
    {
        // Create a set of node indices corresponding to empty sites.
        // Note iterating over mCells is OK as it has the same order as location indices at this point (its just coppied from rCells)
        std::list<CellPtr>::iterator it = this->mCells.begin();
        for (unsigned i=0; it != this->mCells.end(); ++it, ++i)
        {
            assert(i<locationIndices.size());
            if (!IsSiteAvailable(locationIndices[i],*it))
            {
                EXCEPTION("One of the lattice sites has more cells than the carrying capacity. Check the initial cell locations.");
            }
            mAvailableSpaces[locationIndices[i]]--;
        }
    }
    if (validate)
    {
        EXCEPTION("There is no validation for CaBasedCellPopulation.");
    }
}

template<unsigned DIM>
CaBasedCellPopulation<DIM>::CaBasedCellPopulation(PottsMesh<DIM>& rMesh)
    : AbstractOnLatticeCellPopulation<DIM>(rMesh)
{
}

template<unsigned DIM>
CaBasedCellPopulation<DIM>::~CaBasedCellPopulation()
{
    if (this->mDeleteMesh)
    {
        delete &this->mrMesh;
    }
}

template<unsigned DIM>
std::vector<unsigned>& CaBasedCellPopulation<DIM>::rGetAvailableSpaces()
{
    return mAvailableSpaces;
}

template<unsigned DIM>
bool CaBasedCellPopulation<DIM>::IsSiteAvailable(unsigned index, CellPtr pCell)
{
    return (mAvailableSpaces[index] != 0);
}

template<unsigned DIM>
PottsMesh<DIM>& CaBasedCellPopulation<DIM>::rGetMesh()
{
    return static_cast<PottsMesh<DIM>& >((this->mrMesh));
}

template<unsigned DIM>
const PottsMesh<DIM>& CaBasedCellPopulation<DIM>::rGetMesh() const
{
    return static_cast<PottsMesh<DIM>& >((this->mrMesh));
}

template<unsigned DIM>
Node<DIM>* CaBasedCellPopulation<DIM>::GetNode(unsigned index)
{
    return this->mrMesh.GetNode(index);
}

template<unsigned DIM>
unsigned CaBasedCellPopulation<DIM>::GetNumNodes()
{
    return this->mrMesh.GetNumNodes();
}

template<unsigned DIM>
c_vector<double, DIM> CaBasedCellPopulation<DIM>::GetLocationOfCellCentre(CellPtr pCell)
{
    return this->mrMesh.GetNode(this->GetLocationIndexUsingCell(pCell))->rGetLocation();
}

template<unsigned DIM>
Node<DIM>* CaBasedCellPopulation<DIM>::GetNodeCorrespondingToCell(CellPtr pCell)
{
    return this->mrMesh.GetNode(this->GetLocationIndexUsingCell(pCell));
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::AddCellUsingLocationIndex(unsigned index, CellPtr pCell)
{
    if (!IsSiteAvailable(index, pCell))
    {
        EXCEPTION("No available spaces at location index " << index << ".");
    }

    mAvailableSpaces[index]--;
    AbstractCellPopulation<DIM,DIM>::AddCellUsingLocationIndex(index, pCell);
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::RemoveCellUsingLocationIndex(unsigned index, CellPtr pCell)
{
    AbstractCellPopulation<DIM,DIM>::RemoveCellUsingLocationIndex(index, pCell);

    mAvailableSpaces[index]++;

    assert(mAvailableSpaces[index] <= mLatticeCarryingCapacity);
}

template<unsigned DIM>
bool CaBasedCellPopulation<DIM>::IsRoomToDivide(CellPtr pCell)
{
    bool is_room = false;

    // Get node index corresponding to this cell
    unsigned node_index = this->GetLocationIndexUsingCell(pCell);

    // Get the set of neighbouring node indices
    std::set<unsigned> neighbouring_node_indices = static_cast<PottsMesh<DIM>& >((this->mrMesh)).GetMooreNeighbouringNodeIndices(node_index);

    // Iterate through the neighbours to see if there are any available sites
    for (std::set<unsigned>::iterator neighbour_iter = neighbouring_node_indices.begin();
         neighbour_iter != neighbouring_node_indices.end();
         ++neighbour_iter)
    {
        if (IsSiteAvailable(*neighbour_iter, pCell))
        {
            is_room = true;
            break;
        }
    }

    return is_room;
}

template<unsigned DIM>
CellPtr CaBasedCellPopulation<DIM>::AddCell(CellPtr pNewCell, const c_vector<double,DIM>& rCellDivisionVector, CellPtr pParentCell)
{
    // Get node index corresponding to the parent cell
    unsigned parent_node_index = this->GetLocationIndexUsingCell(pParentCell);

    // Get the set of neighbouring node indices
    std::set<unsigned> neighbouring_node_indices = static_cast<PottsMesh<DIM>& >((this->mrMesh)).GetMooreNeighbouringNodeIndices(parent_node_index);
    unsigned num_neighbours = neighbouring_node_indices.size();

    // Each node must have at least one neighbour
    assert(!neighbouring_node_indices.empty());

    std::vector<double> neighbouring_node_propensities;
    std::vector<unsigned> neighbouring_node_indices_vector;

    double total_propensity = 0.0;

    for (std::set<unsigned>::iterator neighbour_iter = neighbouring_node_indices.begin();
            neighbour_iter != neighbouring_node_indices.end();
         ++neighbour_iter)
    {
        neighbouring_node_indices_vector.push_back(*neighbour_iter);

        double propensity_dividing_into_neighbour = EvaluateDivisionPropensity(parent_node_index,*neighbour_iter,pParentCell);

        if (!IsSiteAvailable(*neighbour_iter, pParentCell))
        {
            propensity_dividing_into_neighbour = 0.0;
        }
        neighbouring_node_propensities.push_back(propensity_dividing_into_neighbour);
        total_propensity += propensity_dividing_into_neighbour;
    }

    assert(total_propensity>0); // if this trips the cell cant divided so need to include this in the IsSiteAvailable method

    for (unsigned i=0; i<num_neighbours; i++)
    {
        neighbouring_node_propensities[i] /= total_propensity;
    }

     // Sample random number to specify which move to make
    RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();
    double random_number = p_gen->ranf();

    double total_probability = 0.0;
    unsigned daughter_node_index = UNSIGNED_UNSET;

    unsigned counter;
    for (counter=0; counter < num_neighbours; counter++)
    {
        total_probability += neighbouring_node_propensities[counter];
        if (total_probability >= random_number)
        {
            // Divide the parent cell to this neighbour location
            daughter_node_index = neighbouring_node_indices_vector[counter];
            break;
        }
    }
    // This loop should always break as sum(neighbouring_node_propensities) = 1

    assert(daughter_node_index != UNSIGNED_UNSET);
    assert(daughter_node_index < this->mrMesh.GetNumNodes());

    // Associate the new cell with the element
    this->mCells.push_back(pNewCell);

    // Update location cell map
    CellPtr p_created_cell = this->mCells.back();
    AddCellUsingLocationIndex(daughter_node_index,p_created_cell);

    return p_created_cell;
}

template<unsigned DIM>
double CaBasedCellPopulation<DIM>:: EvaluateDivisionPropensity(unsigned currentNodeIndex,
                                                                       unsigned targetNodeIndex,
                                                                       CellPtr pCell)
{
    return 1.0;
}

template<unsigned DIM>
unsigned CaBasedCellPopulation<DIM>::RemoveDeadCells()
{
    unsigned num_removed = 0;

    for (std::list<CellPtr>::iterator cell_iter = this->mCells.begin();
         cell_iter != this->mCells.end();
         )
    {
        if ((*cell_iter)->IsDead())
        {
            // Get the index of the node corresponding to this cell
            unsigned node_index = this->GetLocationIndexUsingCell(*cell_iter);

            RemoveCellUsingLocationIndex(node_index, (*cell_iter));

            // Erase cell and update counter
            num_removed++;
            cell_iter = this->mCells.erase(cell_iter);
        }
        else
        {
            ++cell_iter;
        }
    }
    return num_removed;
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::UpdateCellLocations(double dt)
{
    // Iterate over cells
    for (std::list<CellPtr>::iterator cell_iter = this->mCells.begin();
         cell_iter != this->mCells.end();
         ++cell_iter)
    {
        // Loop over neighbours and calculate probability of moving (make sure all probabilities are <1)
        unsigned node_index = this->GetLocationIndexUsingCell(*cell_iter);

        // Find a random available neighbouring node to overwrite current site
        std::set<unsigned> neighbouring_node_indices = static_cast<PottsMesh<DIM>& >((this->mrMesh)).GetMooreNeighbouringNodeIndices(node_index);
        std::vector<double> neighbouring_node_propensities;
        std::vector<unsigned> neighbouring_node_indices_vector;

        if (!neighbouring_node_indices.empty())
        {
            unsigned num_neighbours = neighbouring_node_indices.size();
            double probability_of_not_moving = 1.0;

            for (std::set<unsigned>::iterator iter = neighbouring_node_indices.begin();
                 iter != neighbouring_node_indices.end();
                 ++iter)
            {
                double probability_of_moving = 0.0;

                neighbouring_node_indices_vector.push_back(*iter);

                if (IsSiteAvailable(*iter, *cell_iter))
                {
                    // Iterating over the update rule
                    for (typename std::vector<boost::shared_ptr<AbstractCaUpdateRule<DIM> > >::iterator iterRule = mUpdateRuleCollection.begin();
                         iterRule != mUpdateRuleCollection.end();
                         ++iterRule)
                    {
                        probability_of_moving += (*iterRule)->EvaluateProbability(node_index, *iter, *this, dt, 1, *cell_iter);
                        if (probability_of_moving < 0)
                        {
                            EXCEPTION("The probability of cellular movement is smaller than zero. In order to prevent it from happening you should change your time step and parameters");
                        }

                        if (probability_of_moving > 1)
                        {
                            EXCEPTION("The probability of the cellular movement is bigger than one. In order to prevent it from happening you should change your time step and parameters");
                        }
                    }

                    probability_of_not_moving -= probability_of_moving;
                    neighbouring_node_propensities.push_back(probability_of_moving);
                }
                else
                {
                    neighbouring_node_propensities.push_back(0.0);
                }
            }
            if (probability_of_not_moving < 0)
            {
                EXCEPTION("The probability of the cell not moving is smaller than zero. In order to prevent it from happening you should change your time step and parameters");
            }

            // Sample random number to specify which move to make
            RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();
            double random_number = p_gen->ranf();

            double total_probability = 0.0;
            for (unsigned counter=0; counter<num_neighbours; counter++)
            {
                total_probability += neighbouring_node_propensities[counter];
                if (total_probability >= random_number)
                {
                    //Move the cell to this neighbour location
                    unsigned chosen_neighbour_location_index = neighbouring_node_indices_vector[counter];
                    this->MoveCellInLocationMap((*cell_iter), node_index, chosen_neighbour_location_index);
                    break;
                }
            }
            // If loop completes with total_probability < random_number then stay in the same location
        }
        else
        {
            // Each node in the mesh must have at least one neighbour
            NEVER_REACHED;
        }
    }
}

template<unsigned DIM>
bool CaBasedCellPopulation<DIM>::IsCellAssociatedWithADeletedLocation(CellPtr pCell)
{
    return false;
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::Update(bool hasHadBirthsOrDeaths)
{
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::AcceptPopulationWriter(boost::shared_ptr<AbstractCellPopulationWriter<DIM, DIM> > pPopulationWriter)
{
    pPopulationWriter->Visit(this);
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::AcceptCellWriter(boost::shared_ptr<AbstractCellWriter<DIM, DIM> > pCellWriter, CellPtr pCell)
{
    pCellWriter->VisitCell(pCell, this);
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::OpenWritersFiles(const std::string& rDirectory)
{
    if (this->mOutputResultsForChasteVisualizer)
    {
        if (!this-> template HasWriter<CellLocationWriter>())
        {
            this-> template AddCellWriter<CellLocationWriter>();
        }
    }

    AbstractCellPopulation<DIM>::OpenWritersFiles(rDirectory);
}

template<unsigned DIM>
double CaBasedCellPopulation<DIM>::GetVolumeOfCell(CellPtr pCell)
{
    double cell_volume = 1.0;
    return cell_volume;
}

template<unsigned DIM>
double CaBasedCellPopulation<DIM>::GetWidth(const unsigned& rDimension)
{
    double width = this->mrMesh.GetWidth(rDimension);
    return width;
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::AddUpdateRule(boost::shared_ptr<AbstractCaUpdateRule<DIM> > pUpdateRule)
{
    mUpdateRuleCollection.push_back(pUpdateRule);
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::RemoveAllUpdateRules()
{
    mUpdateRuleCollection.clear();
}

template<unsigned DIM>
const std::vector<boost::shared_ptr<AbstractCaUpdateRule<DIM> > >& CaBasedCellPopulation<DIM>::rGetUpdateRuleCollection() const
{
    return mUpdateRuleCollection;
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::OutputCellPopulationParameters(out_stream& rParamsFile)
{
    // Call method on direct parent class
    AbstractOnLatticeCellPopulation<DIM>::OutputCellPopulationParameters(rParamsFile);
}

template<unsigned DIM>
void CaBasedCellPopulation<DIM>::WriteVtkResultsToFile(const std::string& rDirectory)
{
#ifdef CHASTE_VTK
    unsigned num_timesteps = SimulationTime::Instance()->GetTimeStepsElapsed();
    std::stringstream time;
    time << num_timesteps;

    VtkMeshWriter<DIM, DIM> mesh_writer(rDirectory, "results_"+time.str(), false);

    unsigned num_cells = this->GetNumRealCells();
    std::vector<double> cell_types(num_cells, -1.0);
    std::vector<double> cell_mutation_states(num_cells, -1.0);
    std::vector<double> cell_ids(num_cells, -1.0);
    std::vector<double> cell_ancestors(num_cells, -1.0);
    std::vector<double> cell_ages(num_cells, -1.0);
    std::vector<double> cell_cycle_phases(num_cells, -1.0);
    std::vector<Node<DIM>*> nodes;

    // When outputting any CellData, we assume that the first cell is representative of all cells
    unsigned num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
    std::vector<std::string> cell_data_names = this->Begin()->GetCellData()->GetKeys();

    std::vector<std::vector<double> > cell_data;
    for (unsigned var=0; var<num_cell_data_items; var++)
    {
        std::vector<double> cell_data_var(num_cells);
        cell_data.push_back(cell_data_var);
    }

    unsigned cell = 0;

    // Counter to keep track of how many cells are at a lattice site
    unsigned num_sites = this->mrMesh.GetNumNodes();
    boost::scoped_array<unsigned> number_of_cells_at_site(new unsigned[num_sites]);
    for (unsigned i=0; i<num_sites; i++)
    {
        number_of_cells_at_site[i] = 0;
    }

    for (std::list<CellPtr>::iterator iter = this->mCells.begin();
         iter != this->mCells.end();
         ++iter)
    {
        CellPtr cell_ptr = *iter;
        cell_ids[cell] = cell_ptr->GetCellId();

        unsigned location_index = this->GetLocationIndexUsingCell(*iter);

        number_of_cells_at_site[location_index]++;
        assert(number_of_cells_at_site[location_index]<=mLatticeCarryingCapacity);

        // Note that we define this vector before setting it as otherwise the profiling build will break (see #2367)
        c_vector<double, DIM> coords;
        coords = this->mrMesh.GetNode(location_index)->rGetLocation();

        // Move the coordinate slightly so that we can visualise all cells in a lattice site if there is more than one per site
        if (mLatticeCarryingCapacity > 1)
        {
            c_vector<double, DIM> offset;

            if (DIM == 2)
            {
                double angle = (double)number_of_cells_at_site[location_index]*2.0*M_PI/(double)mLatticeCarryingCapacity;
                offset[0] = 0.2*sin(angle);
                offset[1] = 0.2*cos(angle);
            }
            else
            {
                RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();

                for (unsigned i=0; i<DIM; i++)
                {
                    offset[i] = p_gen->ranf(); // This assumes that all sites are 1 apart
                }
            }

            for (unsigned i=0; i<DIM; i++)
            {
                coords[i] += offset[i];
            }
        }

        nodes.push_back(new Node<DIM>(cell, coords, false));

        if (this-> template HasWriter<CellAncestorWriter>())
        {
            double ancestor_index = (cell_ptr->GetAncestor() == UNSIGNED_UNSET) ? (-1.0) : (double)cell_ptr->GetAncestor();
            cell_ancestors[cell] = ancestor_index;
        }
        if (this-> template HasWriter<CellProliferativeTypesWriter>())
        {
            cell_types[cell] = cell_ptr->GetCellProliferativeType()->GetColour();
        }
        if (this-> template HasWriter<CellMutationStatesWriter>())
        {
            cell_mutation_states[cell] = cell_ptr->GetMutationState()->GetColour();

            CellPropertyCollection collection = cell_ptr->rGetCellPropertyCollection();
            CellPropertyCollection label_collection = collection.GetProperties<CellLabel>();

            if (label_collection.GetSize() == 1)
            {
                boost::shared_ptr<CellLabel> p_label = boost::static_pointer_cast<CellLabel>(label_collection.GetProperty());
                cell_mutation_states[cell] = p_label->GetColour();
            }

        }
        if (this-> template HasWriter<CellAgesWriter>())
        {
            cell_ages[cell] = cell_ptr->GetAge();
        }
        if (this-> template HasWriter<CellProliferativePhasesWriter>())
        {
            cell_cycle_phases[cell] = cell_ptr->GetCellCycleModel()->GetCurrentCellCyclePhase();
        }
        for (unsigned var=0; var<num_cell_data_items; var++)
        {
            cell_data[var][cell] = cell_ptr->GetCellData()->GetItem(cell_data_names[var]);
        }

        cell ++;
    }

    // Cell IDs can be used to threshold out the empty lattice sites (which have ID=-1)
    mesh_writer.AddPointData("Cell ids", cell_ids);

    if (this-> template HasWriter<CellProliferativeTypesWriter>())
    {
        mesh_writer.AddPointData("Cell types", cell_types);
    }
    if (this-> template HasWriter<CellMutationStatesWriter>())
    {
        mesh_writer.AddPointData("Mutation states", cell_mutation_states);
    }
    if (this-> template HasWriter<CellAncestorWriter>())
    {
        mesh_writer.AddPointData("Ancestors", cell_ancestors);
    }
    if (this-> template HasWriter<CellAgesWriter>())
    {
        mesh_writer.AddPointData("Ages", cell_ages);
    }
    if (this-> template HasWriter<CellProliferativePhasesWriter>())
    {
        mesh_writer.AddPointData("Cycle phases", cell_cycle_phases);
    }
    if (num_cell_data_items > 0)
    {
        for (unsigned var=0; var<cell_data.size(); var++)
        {
            mesh_writer.AddPointData(cell_data_names[var], cell_data[var]);
        }
    }

    /*
     * The current VTK writer can only write things which inherit from AbstractTetrahedralMeshWriter.
     * For now, we do an explicit conversion to NodesOnlyMesh. This can be written to VTK then visualized as glyphs.
     */
    NodesOnlyMesh<DIM> temp_mesh;
    temp_mesh.ConstructNodesWithoutMesh(nodes, 1.5);  // Arbitrary cut off as connectivity not used.
    mesh_writer.WriteFilesUsingMesh(temp_mesh);

    *(this->mpVtkMetaFile) << "        <DataSet timestep=\"";
    *(this->mpVtkMetaFile) << num_timesteps;
    *(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
    *(this->mpVtkMetaFile) << num_timesteps;
    *(this->mpVtkMetaFile) << ".vtu\"/>\n";

    // Tidy up
    for (unsigned i=0; i<nodes.size(); i++)
    {
        delete nodes[i];
    }
#endif //CHASTE_VTK
}

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

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