NodeBasedCellPopulation.cpp

/*

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*/

#include "NodeBasedCellPopulation.hpp"
#include "VtkMeshWriter.hpp"

template<unsigned DIM>
NodeBasedCellPopulation<DIM>::NodeBasedCellPopulation(NodesOnlyMesh<DIM>& rMesh,
                                      std::vector<CellPtr>& rCells,
                                      const std::vector<unsigned> locationIndices,
                                      bool deleteMesh,
                                      bool validate)
    : AbstractCentreBasedCellPopulation<DIM>(rMesh, rCells, locationIndices),
      mDeleteMesh(deleteMesh),
      mMechanicsCutOffLength(DBL_MAX),
      mUseVariableRadii(false)
{
    mpNodesOnlyMesh = static_cast<NodesOnlyMesh<DIM>* >(&(this->mrMesh));
    if (validate)
    {
        Validate();
    }
}

template<unsigned DIM>
NodeBasedCellPopulation<DIM>::NodeBasedCellPopulation(NodesOnlyMesh<DIM>& rMesh)
    : AbstractCentreBasedCellPopulation<DIM>(rMesh),
      mDeleteMesh(true),
      mMechanicsCutOffLength(DBL_MAX), // will be set by serialize() method
      mUseVariableRadii(false) // will be set by serialize() method
{
    mpNodesOnlyMesh = static_cast<NodesOnlyMesh<DIM>* >(&(this->mrMesh));
    // No Validate() because the cells are not associated with the cell population yet in archiving
}

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

template<unsigned DIM>
NodesOnlyMesh<DIM>& NodeBasedCellPopulation<DIM>::rGetMesh()
{
    return *mpNodesOnlyMesh;
}

template<unsigned DIM>
const NodesOnlyMesh<DIM>& NodeBasedCellPopulation<DIM>::rGetMesh() const
{
    return *mpNodesOnlyMesh;
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::Clear()
{
    mNodePairs.clear();
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::Validate()
{
    std::vector<bool> validated_node(GetNumNodes());
    for (unsigned i=0; i<validated_node.size(); i++)
    {
        validated_node[i] = false;
    }

    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter=this->Begin(); cell_iter!=this->End(); ++cell_iter)
    {
        unsigned node_index = this->GetLocationIndexUsingCell((*cell_iter));
        validated_node[node_index] = true;
    }

    for (unsigned i=0; i<validated_node.size(); i++)
    {
        if (!validated_node[i])
        {
            EXCEPTION("Node " << i << " does not appear to have a cell associated with it");
        }
    }
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::SplitUpIntoBoxes(double cutOffLength, c_vector<double, 2*DIM> domainSize)
{
    mpNodesOnlyMesh->SetUpBoxCollection(cutOffLength, domainSize);
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::FindMaxAndMin()
{
    c_vector<double, DIM> min_posn;
    c_vector<double, DIM> max_posn;
    for (unsigned i=0; i<DIM; i++)
    {
        min_posn(i) = DBL_MAX;
        max_posn(i) = -DBL_MAX;
    }

    for (unsigned i=0; i<this->mrMesh.GetNumNodes(); i++)
    {
        c_vector<double, DIM> posn = this->GetNode(i)->rGetLocation();

        for (unsigned j=0; j<DIM; j++)
        {
            if (posn(j) > max_posn(j))
            {
                max_posn(j) = posn(j);
            }
            if (posn(j) < min_posn(j))
            {
                min_posn(j) = posn(j);
            }
        }
    }

    for (unsigned i=0; i<DIM; i++)
    {
        assert(min_posn(i) != DBL_MAX);
        mMinSpatialPositions(i) = min_posn(i);

        assert(max_posn(i) != -DBL_MAX);
        mMaxSpatialPositions(i) = max_posn(i);
    }
}

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

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::SetNode(unsigned nodeIndex, ChastePoint<DIM>& rNewLocation)
{
    mpNodesOnlyMesh->GetNode(nodeIndex)->SetPoint(rNewLocation);
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::Update(bool hasHadBirthsOrDeaths)
{
    NodeMap map(this->mrMesh.GetNumAllNodes());
    mpNodesOnlyMesh->ReMesh(map);

    if (!map.IsIdentityMap())
    {
        UpdateParticlesAfterReMesh(map);

        // Update the mappings between cells and location indices
        std::map<Cell*, unsigned> old_map = this->mCellLocationMap;

        // Remove any dead pointers from the maps (needed to avoid archiving errors)
        this->mLocationCellMap.clear();
        this->mCellLocationMap.clear();

        for (std::list<CellPtr>::iterator it = this->mCells.begin();
             it != this->mCells.end();
             ++it)
        {
            unsigned old_node_index = old_map[(*it).get()];

            // This shouldn't ever happen, as the cell vector only contains living cells
            assert(!map.IsDeleted(old_node_index));

            unsigned new_node_index = map.GetNewIndex(old_node_index);
            this->SetCellUsingLocationIndex(new_node_index,*it);
        }

        this->Validate();
    }

    mpNodesOnlyMesh->SetMeshHasChangedSinceLoading();

    mpNodesOnlyMesh->ClearBoxCollection();

    FindMaxAndMin();

    // Something here to set up the domain size (max and min of each node position dimension)
    c_vector<double, 2*DIM> domain_size;
    for (unsigned i=0; i<DIM; i++)
    {
        domain_size(2*i) = mMinSpatialPositions(i);
        domain_size(2*i+1) = mMaxSpatialPositions(i);
    }

    if (mMechanicsCutOffLength == DBL_MAX)
    {
        std::string error =  std::string("NodeBasedCellPopulation cannot create boxes if the cut-off length has not been set - ")
                           + std::string("Call SetMechanicsCutOffLength on the CellPopulation ensuring it is larger than GetCutOffLength() on the force law");
        EXCEPTION(error);
    }

    /*
     * Add this parameter and suggest that mechanics systems set it.
     * Allocates memory for mpBoxCollection and does the splitting
     * and putting nodes into boxes.
     */

    mpNodesOnlyMesh->SetUpBoxCollection(mMechanicsCutOffLength, domain_size);

    mpNodesOnlyMesh->CalculateNodePairs(mNodePairs, mNodeNeighbours);

    /*
     * Update cell radii based on CellData
     */
    if (mUseVariableRadii)
    {
        for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
             cell_iter != this->End();
             ++cell_iter)
        {
            double cell_radius = cell_iter->GetCellData()->GetItem("Radius");
            unsigned node_index = this->GetLocationIndexUsingCell(*cell_iter);
            mpNodesOnlyMesh->SetCellRadius(node_index, cell_radius);
        }
    }
}

template<unsigned DIM>
unsigned NodeBasedCellPopulation<DIM>::RemoveDeadCells()
{
    unsigned num_removed = 0;
    for (std::list<CellPtr>::iterator cell_iter = this->mCells.begin();
         cell_iter != this->mCells.end();
         ++cell_iter)
    {
        if ((*cell_iter)->IsDead())
        {
            // Remove the node from the mesh
            num_removed++;
            mpNodesOnlyMesh->DeleteNodePriorToReMesh(this->GetLocationIndexUsingCell((*cell_iter)));

            // Update mappings between cells and location indices
            unsigned location_index_of_removed_node = this->GetLocationIndexUsingCell((*cell_iter));
            this->RemoveCellUsingLocationIndex(location_index_of_removed_node, (*cell_iter));

            // Update vector of cells
            cell_iter = this->mCells.erase(cell_iter);
            --cell_iter;
        }
    }

    return num_removed;
}

template<unsigned DIM>
unsigned NodeBasedCellPopulation<DIM>::AddNode(Node<DIM>* pNewNode)
{
    return mpNodesOnlyMesh->AddNode(pNewNode);
}

template<unsigned DIM>
unsigned NodeBasedCellPopulation<DIM>::GetNumNodes()
{
    return mpNodesOnlyMesh->GetNumAllNodes();
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::UpdateParticlesAfterReMesh(NodeMap& rMap)
{
}

template<unsigned DIM>
BoxCollection<DIM>* NodeBasedCellPopulation<DIM>::GetBoxCollection()
{
    return mpNodesOnlyMesh->GetBoxCollection();
}

template<unsigned DIM>
std::set< std::pair<Node<DIM>*, Node<DIM>* > >& NodeBasedCellPopulation<DIM>::rGetNodePairs()
{
//    if (mNodePairs.empty())
//    {
//        EXCEPTION("No node pairs set up, rGetNodePairs probably called before Update");
//    }
    return mNodePairs;
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::OutputCellPopulationParameters(out_stream& rParamsFile)
{
    *rParamsFile << "\t\t<MechanicsCutOffLength>" << mMechanicsCutOffLength << "</MechanicsCutOffLength>\n";
    *rParamsFile << "\t\t<UseVariableRadii>" << mUseVariableRadii <<
"</UseVariableRadii>\n";

    // Call method on direct parent class
    AbstractCentreBasedCellPopulation<DIM>::OutputCellPopulationParameters(rParamsFile);
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::SetMechanicsCutOffLength(double mechanicsCutOffLength)
{
    assert(mechanicsCutOffLength > 0.0);
    mMechanicsCutOffLength = mechanicsCutOffLength;
}

template<unsigned DIM>
double NodeBasedCellPopulation<DIM>::GetMechanicsCutOffLength()
{
    return mMechanicsCutOffLength;
}

template<unsigned DIM>
bool NodeBasedCellPopulation<DIM>::GetUseVariableRadii()
{
    return mUseVariableRadii;
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::SetUseVariableRadii(bool useVariableRadii)
{
    mUseVariableRadii = useVariableRadii;
}

template<unsigned DIM>
double NodeBasedCellPopulation<DIM>::GetWidth(const unsigned& rDimension)
{
    // Update the member variables mMinSpatialPositions and mMaxSpatialPositions
    FindMaxAndMin();

    // Compute the maximum distance between any nodes in this dimension
    double width = mMaxSpatialPositions(rDimension) - mMinSpatialPositions(rDimension);

    return width;
}

template<unsigned DIM>
std::set<unsigned> NodeBasedCellPopulation<DIM>::GetNeighbouringNodeIndices(unsigned index)
{
    // Check the mNodeNeighbours has been set up correctly
    if (mNodeNeighbours.empty())
    {
        EXCEPTION("mNodeNeighbours not set up. Call Update() before GetNeighbouringNodeIndices()");
    }

    std::set<unsigned> neighbouring_node_indices;

    // Get location and radius of node
    c_vector<double, DIM> node_i_location = this->GetNode(index)->rGetLocation();
    double radius_of_cell_i = mpNodesOnlyMesh->GetCellRadius(index);

    // Make sure that the max_interaction distance is smaller than the box collection size
    if (!(radius_of_cell_i * 2.0 < mMechanicsCutOffLength))
    {
        EXCEPTION("mMechanicsCutOffLength is smaller than twice the radius of cell " << index << " (" << radius_of_cell_i << ") so interactions may be missed. Make the cut-off larger to avoid errors.");
    }


    // Get set of 'candidate' neighbours.
    std::set<unsigned> near_nodes = mNodeNeighbours.find(index)->second;

    // Find which ones are actually close
    for (std::set<unsigned>::iterator iter = near_nodes.begin();
            iter != near_nodes.end();
            ++iter)
    {
        // Be sure not to return the index itself.
        if ((*iter) != index)
        {
            // Get the location of this node
            c_vector<double, DIM> node_j_location = this->GetNode((*iter))->rGetLocation();

            // Get the vector the two nodes (assuming no periodicities etc.)
            c_vector<double, DIM> node_to_node_vector = node_i_location - node_j_location;

            // Calculate the distance between the two nodes
            double distance_between_nodes = norm_2(node_to_node_vector);

            // Get the radius of the cell corresponding to this node
            double radius_of_cell_j = mpNodesOnlyMesh->GetCellRadius((*iter));

            // If the cells are close enough to exert a force on each other...
            double max_interaction_distance = radius_of_cell_i + radius_of_cell_j;

            // Make sure that the max_interaction distance is smaller than the box collection size
            if (!(max_interaction_distance < mMechanicsCutOffLength))
            {
                EXCEPTION("mMechanicsCutOffLength is smaller than the sum of radius of cell " << index << " (" << radius_of_cell_i << ") and cell " << (*iter) << " (" << radius_of_cell_j <<"). Make the cut-off larger to avoid errors.");
            }
            if (distance_between_nodes <= max_interaction_distance)// + DBL_EPSILSON) //Assumes that max_interaction_distance is of over 1
            {
                // ...then add this node index to the set of neighbouring node indices
                neighbouring_node_indices.insert((*iter));
            }
        }
    }

    return neighbouring_node_indices;
}

template<unsigned DIM>
double NodeBasedCellPopulation<DIM>::GetVolumeOfCell(CellPtr pCell)
{
    // Get node index corresponding to this cell
    unsigned node_index = this->GetLocationIndexUsingCell(pCell);

    // Get cell radius
    double cell_radius = mpNodesOnlyMesh->GetCellRadius(node_index);

    // Begin code to approximate cell volume
    double averaged_cell_radius = 0.0;
    unsigned num_cells = 0;

    // Get the location of this node
    c_vector<double, DIM> node_i_location = GetNode(node_index)->rGetLocation();

    // Get the set of node indices corresponding to this cell's neighbours
    std::set<unsigned> neighbouring_node_indices = GetNeighbouringNodeIndices(node_index);

    // Loop over this set
    for (std::set<unsigned>::iterator iter = neighbouring_node_indices.begin();
         iter != neighbouring_node_indices.end();
         ++iter)
    {
        // Get the location of the neighbouring node
        c_vector<double, DIM> node_j_location = GetNode(*iter)->rGetLocation();

        double neighbouring_cell_radius = mpNodesOnlyMesh->GetCellRadius( *iter);

        // If this throws then you may not be considering all cell interactions use a larger cut off length
        assert(cell_radius+neighbouring_cell_radius<mMechanicsCutOffLength);

        // Calculate the distance between the two nodes and add to cell radius
        double separation = norm_2(node_j_location - node_i_location);

        if (separation < cell_radius+neighbouring_cell_radius)
        {
            // The effective radius is the mid point of the overlap
            averaged_cell_radius = averaged_cell_radius + cell_radius - (cell_radius+neighbouring_cell_radius-separation)/2.0;
            num_cells++;
        }
    }
    if (num_cells == 0)
    {
        averaged_cell_radius =  cell_radius;
    }
    else
    {
        averaged_cell_radius /= num_cells;
    }
    assert(averaged_cell_radius<mMechanicsCutOffLength/2.0);

    cell_radius = averaged_cell_radius;

    // End code to approximate cell volume

    // Calculate cell volume from radius of cell
    double cell_volume = 0.0;
    if (DIM == 2)
    {
        cell_volume = M_PI*cell_radius*cell_radius;
    }
    else if (DIM == 3)
    {
        cell_volume = (4.0/3.0)*M_PI*cell_radius*cell_radius*cell_radius;
    }

    return cell_volume;
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::WriteCellVolumeResultsToFile()
{
    assert(DIM==2 || DIM==3);

    // Write time to file
    *(this->mpCellVolumesFile) << SimulationTime::Instance()->GetTime() << " ";

    // Loop over cells
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
         cell_iter != this->End();
         ++cell_iter)
    {
        // Get the index of the corresponding node in mrMesh
        unsigned node_index = this->GetLocationIndexUsingCell(*cell_iter);

        // Write node index to file
        *(this->mpCellVolumesFile) << node_index << " ";

        // Write cell ID to file
        *(this->mpCellVolumesFile) << cell_iter->GetCellId() << " ";

        // Write node location to file
        c_vector<double, DIM> node_location = this->GetNode(node_index)->rGetLocation();
        for (unsigned i=0; i<DIM; i++)
        {
            *(this->mpCellVolumesFile) << node_location[i] << " ";
        }

        // Write cell volume (in 3D) or area (in 2D) to file
        double cell_volume = this->GetVolumeOfCell(*cell_iter);
        *(this->mpCellVolumesFile) << cell_volume << " ";
    }

    *(this->mpCellVolumesFile) << "\n";
}

template<unsigned DIM>
void NodeBasedCellPopulation<DIM>::WriteVtkResultsToFile()
{
#ifdef CHASTE_VTK
    std::stringstream time;
    time << SimulationTime::Instance()->GetTimeStepsElapsed();
    VtkMeshWriter<DIM, DIM> mesh_writer(this->mDirPath, "results_"+time.str(), false);

    unsigned num_nodes = GetNumNodes();
    std::vector<double> cell_types(num_nodes);
    std::vector<double> cell_ancestors(num_nodes);
    std::vector<double> cell_mutation_states(num_nodes);
    std::vector<double> cell_ages(num_nodes);
    std::vector<double> cell_cycle_phases(num_nodes);
    std::vector<double> cell_radii(num_nodes);
    std::vector<std::vector<double> > cellwise_data;

    unsigned num_cell_data_items = 0;
    std::vector<std::string> cell_data_names;
    //We assume that the first cell is representative of all cells
    num_cell_data_items = this->Begin()->GetCellData()->GetNumItems();
    cell_data_names = this->Begin()->GetCellData()->GetKeys();

    for (unsigned var=0; var<num_cell_data_items; var++)
    {
        std::vector<double> cellwise_data_var(num_nodes);
        cellwise_data.push_back(cellwise_data_var);
    }


    // Loop over cells
    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = this->Begin();
         cell_iter != this->End();
         ++cell_iter)
    {
        // Get the node index corresponding to this cell
        unsigned node_index = this->GetLocationIndexUsingCell(*cell_iter);

        if (this->mOutputCellAncestors)
        {
            double ancestor_index = (cell_iter->GetAncestor() == UNSIGNED_UNSET) ? (-1.0) : (double)cell_iter->GetAncestor();
            cell_ancestors[node_index] = ancestor_index;
        }
        if (this->mOutputCellProliferativeTypes)
        {
            double cell_type = cell_iter->GetCellProliferativeType();
            cell_types[node_index] = cell_type;
        }
        if (this->mOutputCellMutationStates)
        {
            double mutation_state = cell_iter->GetMutationState()->GetColour();

            CellPropertyCollection collection = cell_iter->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());
                mutation_state = p_label->GetColour();
            }

            cell_mutation_states[node_index] = mutation_state;
        }
        if (this->mOutputCellAges)
        {
            double age = cell_iter->GetAge();
            cell_ages[node_index] = age;
        }
        if (this->mOutputCellCyclePhases)
        {
            double cycle_phase = cell_iter->GetCellCycleModel()->GetCurrentCellCyclePhase();
            cell_cycle_phases[node_index] = cycle_phase;
        }
        if (this->mOutputCellVolumes)
        {
            double cell_radius = mpNodesOnlyMesh->GetCellRadius(node_index);
            cell_radii[node_index] = cell_radius;
        }

        for (unsigned var=0; var<num_cell_data_items; var++)
        {
            cellwise_data[var][node_index] = cell_iter->GetCellData()->GetItem(cell_data_names[var]);
        }
    }

    if (this->mOutputCellProliferativeTypes)
    {
        mesh_writer.AddPointData("Cell types", cell_types);
    }
    if (this->mOutputCellAncestors)
    {
        mesh_writer.AddPointData("Ancestors", cell_ancestors);
    }
    if (this->mOutputCellMutationStates)
    {
        mesh_writer.AddPointData("Mutation states", cell_mutation_states);
    }
    if (this->mOutputCellAges)
    {
        mesh_writer.AddPointData("Ages", cell_ages);
    }
    if (this->mOutputCellCyclePhases)
    {
        mesh_writer.AddPointData("Cycle phases", cell_cycle_phases);
    }
    if (this->mOutputCellVolumes)
    {
        mesh_writer.AddPointData("Cell radii", cell_radii);
    }
    if (num_cell_data_items > 0)
    {
        for (unsigned var=0; var<cellwise_data.size(); var++)
        {
            mesh_writer.AddPointData(cell_data_names[var], cellwise_data[var]);
        }
    }

    mesh_writer.WriteFilesUsingMesh(*mpNodesOnlyMesh);

    *(this->mpVtkMetaFile) << "        <DataSet timestep=\"";
    *(this->mpVtkMetaFile) << SimulationTime::Instance()->GetTimeStepsElapsed();
    *(this->mpVtkMetaFile) << "\" group=\"\" part=\"0\" file=\"results_";
    *(this->mpVtkMetaFile) << SimulationTime::Instance()->GetTimeStepsElapsed();
    *(this->mpVtkMetaFile) << ".vtu\"/>\n";
#endif //CHASTE_VTK
}

template<unsigned DIM>
CellPtr NodeBasedCellPopulation<DIM>::AddCell(CellPtr pNewCell, const c_vector<double,DIM>& rCellDivisionVector, CellPtr pParentCell)
{
    assert(pNewCell);

    // Add new cell to cell population
    CellPtr p_created_cell = AbstractCentreBasedCellPopulation<DIM>::AddCell(pNewCell, rCellDivisionVector, pParentCell);
    assert(p_created_cell == pNewCell);

    // Then set the new cell radius in the NodesOnlyMesh
    unsigned parent_node_index = this->GetLocationIndexUsingCell(pParentCell);
    unsigned new_node_index = this->GetLocationIndexUsingCell(p_created_cell);
    mpNodesOnlyMesh->SetCellRadius(new_node_index, mpNodesOnlyMesh->GetCellRadius(parent_node_index));

    // Return pointer to new cell
    return p_created_cell;
}

// Explicit instantiation

template class NodeBasedCellPopulation<1>;
template class NodeBasedCellPopulation<2>;
template class NodeBasedCellPopulation<3>;

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