CsvVesselNetworkReader.cpp

/*

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#include "Exception.hpp"
#include "CsvVesselNetworkReader.hpp"
#include <boost/tokenizer.hpp>
#include <boost/lexical_cast.hpp>
#include <fstream>

template<unsigned DIM>
CsvVesselNetworkReader<DIM>::CsvVesselNetworkReader()
    : mFileName(),
      mRadiusLabel()
{
}

template<unsigned DIM>
CsvVesselNetworkReader<DIM>::~CsvVesselNetworkReader()
{
}

template <unsigned DIM>
boost::shared_ptr<CsvVesselNetworkReader<DIM> > CsvVesselNetworkReader<DIM>::Create()
{
    MAKE_PTR(CsvVesselNetworkReader<DIM>, pSelf);
    return pSelf;
}

template<unsigned DIM>
boost::shared_ptr<VesselNetwork<DIM> > CsvVesselNetworkReader<DIM>::Read()
{
    if(mFileName.empty())
    {
        EXCEPTION("File name not set in vessel network reader");
    }

    std::ifstream in(mFileName.c_str());
    if(!in.is_open())
    {
        EXCEPTION("Problem during input file opening in vessel network reader.");
    }

    // Create an empty vessel network
    boost::shared_ptr<VesselNetwork<DIM> > p_network = VesselNetwork<DIM>::Create();

    typedef boost::tokenizer< boost::escaped_list_separator<char> > Tokenizer;
    std::vector<std::string> vec;
    std::string line;

    unsigned counter = 0;
    while (std::getline(in, line))
    {
        // Skip the header
        if(counter == 0)
        {
            counter ++;
            continue;
        }
        Tokenizer tok(line);
        vec.assign(tok.begin(),tok.end());

        if(vec.size()<10)
        {
            EXCEPTION("CSV File not in expected format");
        }

        double pos_x_1 = boost::lexical_cast<double>(vec[3]);
        double pos_y_1 = boost::lexical_cast<double>(vec[4]);
        double pos_z_1 = boost::lexical_cast<double>(vec[5]);
        double pos_x_2 = boost::lexical_cast<double>(vec[6]);
        double pos_y_2 = boost::lexical_cast<double>(vec[7]);
        double pos_z_2 = boost::lexical_cast<double>(vec[8]);

        p_network->AddVessel(Vessel<DIM>::Create(VesselNode<DIM>::Create(pos_x_1, pos_y_1 ,pos_z_1),
                                                 VesselNode<DIM>::Create(pos_x_2, pos_y_2 ,pos_z_2)));

        counter ++;
    }

    // Need to flip in 'y' direction for consistency with VTK tools
    std::pair<DimensionalChastePoint<DIM>, DimensionalChastePoint<DIM> > extents = p_network->GetExtents();
    units::quantity<unit::length> length_scale = extents.second.GetReferenceLengthScale();
    double y_max = extents.second.GetLocation(length_scale)[1];

    for(unsigned idx=0; idx<p_network->GetNumberOfNodes();idx++)
    {
        c_vector<double, DIM> current_location = p_network->GetNode(idx)->rGetLocation().GetLocation(length_scale);
        c_vector<double, DIM> new_location;
        new_location[0] = current_location[0];
        new_location[1] = y_max - current_location[1];
        if(DIM==3)
        {
            new_location[2] = current_location[2];
        }
        p_network->GetNode(idx)->SetLocation(DimensionalChastePoint<DIM>(new_location, length_scale));
    }
    return p_network;
}

template<unsigned DIM>
void CsvVesselNetworkReader<DIM>::SetFileName(const std::string& rFileName)
{
    mFileName = rFileName;
}

//Explicit instantiation
template class CsvVesselNetworkReader<2> ;
template class CsvVesselNetworkReader<3> ;