ParallelCellsGenerator.hpp

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*/

#ifndef PARALLELCELLSGENERATOR_HPP_
#define PARALLELCELLSGENERATOR_HPP_

#include <vector>
#include "Cell.hpp"
#include "WildTypeCellMutationState.hpp"
#include "AbstractCellProperty.hpp"
#include "NodesOnlyMesh.hpp"

template<class CELL_CYCLE_MODEL, unsigned DIM>
class ParallelCellsGenerator
{
    friend class TestParallelCellsGenerator;    // For testing.

private:

    c_vector<double, 2*DIM> GetArchiveBoundingBox(std::string archivePath);

public:

    void GenerateParallelCells( std::string archivePath,
                                std::vector<CellPtr>& cells,
                                NodesOnlyMesh<DIM>& mesh,
                                boost::shared_ptr<AbstractCellProperty> pCellProliferativeType=boost::shared_ptr<AbstractCellProperty>());
};

// Implementation
template<class CELL_CYCLE_MODEL, unsigned DIM>
void ParallelCellsGenerator<CELL_CYCLE_MODEL, DIM>::GenerateParallelCells(std::string archivePath, std::vector<CellPtr>& cells, NodesOnlyMesh<DIM>& mesh, boost::shared_ptr<AbstractCellProperty> pCellProliferativeType)
{
    // Get a bounding box for the archived nodes
    c_vector<double, 2*DIM> base_bounding_box = GetArchiveBoundingBox(archivePath);

    // Add small factor to make sure the box is big enough to contain the initial population.
    for (unsigned i=0; i<DIM; i++)
    {
        base_bounding_box[2*i] -= 1e-14;
        base_bounding_box[2*i + 1] += 1e-14;
    }

    // Construct box collection of NodesOnlyMesh
    mesh.SetInitialBoxCollection(base_bounding_box, mesh.GetMaximumInteractionDistance());

    unsigned node_index = 0;

    std::ifstream infile(archivePath.c_str(), std::ios::in);

    std::string line;
    std::getline(infile, line);    // Get first line which is ignored as it is a header.

    while (std::getline(infile, line))
    {
        // Get line in archive file.
        std::istringstream iss(line);

        // Extract a location.
        c_vector<double, DIM> location;
        for (unsigned k=0; k<DIM; k++)
        {
            iss >> location[k];
        }

        // Add it to the mesh and make an appropriate cell if it is owned.
        if (mesh.IsOwned(location))
        {
            // Make a node at this point.
            Node<DIM>* p_node = new Node<DIM>(node_index, location);    // Memory is managed by NodesOnlyMesh.
            mesh.AddNode(p_node);

            // Make cell
            CELL_CYCLE_MODEL* p_cell_cycle_model = new CELL_CYCLE_MODEL;
            p_cell_cycle_model->SetDimension(DIM);

            // Wild type hard-coded for now.
            boost::shared_ptr<AbstractCellProperty> p_state(CellPropertyRegistry::Instance()->Get<WildTypeCellMutationState>());
            CellPtr p_cell(new Cell(p_state, p_cell_cycle_model));
            p_cell->SetCellProliferativeType(pCellProliferativeType);
            cells.push_back(p_cell);

            node_index++;
        }
    }

    infile.close();

    // Tidy up the mesh.
    NodeMap map(mesh.GetMaximumNodeIndex()+1);
    mesh.ReMesh(map);
}

template<class CELL_CYCLE_MODEL, unsigned DIM>
c_vector<double, 2*DIM> ParallelCellsGenerator<CELL_CYCLE_MODEL, DIM>::GetArchiveBoundingBox(std::string archivePath)
{
    c_vector<double, 2*DIM> bounding_box;
    for (unsigned i=0; i<DIM; i++)
    {
        bounding_box[2*i] = DBL_MAX;
        bounding_box[2*i + 1] = -DBL_MAX;
    }

    std::ifstream infile(archivePath.c_str());

    std::string line;
    std::getline(infile, line);

    std::istringstream iss(line);

    // Check file dimensions and template dimensions match.
    unsigned num_lines;
    unsigned file_dimension;

    iss >> num_lines >> file_dimension;

    if (file_dimension != DIM)
    {
        EXCEPTION("Space dimension of ParallelCellsGenerator and archive file do not match");
    }

    while (std::getline(infile, line))
    {
        std::stringstream new_iss(line);
        for (unsigned i=0; i<DIM; i++)
        {
            double point;
            new_iss >> point;
            bounding_box[2*i] = (point < bounding_box[2*i]) ? point : bounding_box[2*i];
            bounding_box[2*i+1] = (point > bounding_box[2*i+1]) ? point : bounding_box[2*i+1];
        }
    }

    infile.close();

    return bounding_box;
}
#endif /* PARALLELCELLSGENERATOR_HPP_ */