VesselNetworkGraphCalculator.cpp

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#include <boost/graph/graphviz.hpp>
#include <boost/graph/visitors.hpp>
#include <boost/graph/adjacency_list.hpp>
#include <boost/graph/breadth_first_search.hpp>
#include <boost/pending/indirect_cmp.hpp>
#include "Exception.hpp"
#include "VesselNetworkGraphCalculator.hpp"
#include "PetscTools.hpp"

template<typename TimeMap> class bfs_time_visitor : public boost::default_bfs_visitor
{
    typedef typename boost::property_traits<TimeMap>::value_type T;

public:

    TimeMap m_timemap;

    T& m_time;

    bfs_time_visitor(TimeMap tmap, T& t)
    :m_timemap(tmap),
     m_time(t)
    {
    }

    template<typename Vertex, typename Graph>
    void discover_vertex(Vertex u, const Graph& g) const
    {
        put(m_timemap, u, m_time++);
    }
};

template <unsigned DIM>
VesselNetworkGraphCalculator<DIM>::VesselNetworkGraphCalculator() :
    mpVesselNetwork()
{

}

template <unsigned DIM>
VesselNetworkGraphCalculator<DIM>::~VesselNetworkGraphCalculator()
{

}

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

template <unsigned DIM>
std::vector<std::vector<unsigned> > VesselNetworkGraphCalculator<DIM>::GetNodeNodeConnectivity()
{
    if(!mpVesselNetwork)
    {
        EXCEPTION("Vessel network not set in graph calculator");
    }

    std::vector<boost::shared_ptr<VesselNode<DIM> > > nodes = mpVesselNetwork->GetVesselEndNodes();
    std::vector<boost::shared_ptr<Vessel<DIM> > > vessels = mpVesselNetwork->GetVessels();
    std::vector<std::vector<unsigned> > node_vessel_connectivity = GetNodeVesselConnectivity();

    std::vector<std::vector<unsigned> > connectivity;
    for (unsigned node_index = 0; node_index < nodes.size(); node_index++)
    {
        std::vector<unsigned> node_indexes;
        boost::shared_ptr<VesselNode<DIM> > p_node = nodes[node_index];
        unsigned num_branches = node_vessel_connectivity[node_index].size();
        for (unsigned vessel_index = 0; vessel_index < num_branches; vessel_index++)
        {
            boost::shared_ptr<Vessel<DIM> > p_vessel = vessels[node_vessel_connectivity[node_index][vessel_index]];

            // Get the node at the other end of the vessel
            boost::shared_ptr<VesselNode<DIM> > p_other_node = p_vessel->GetNodeAtOppositeEnd(p_node);
            typename std::vector<boost::shared_ptr<VesselNode<DIM> > >::iterator node_iter = std::find(nodes.begin(), nodes.end(), p_other_node);
            unsigned other_node_index = std::distance(nodes.begin(), node_iter);
            node_indexes.push_back(other_node_index);
        }
        connectivity.push_back(node_indexes);
    }
    return connectivity;
}

template <unsigned DIM>
std::vector<std::vector<unsigned> > VesselNetworkGraphCalculator<DIM>::GetNodeVesselConnectivity()
{
    if(!mpVesselNetwork)
    {
        EXCEPTION("Vessel network not set in graph calculator");
    }

    std::vector<boost::shared_ptr<VesselNode<DIM> > > nodes = mpVesselNetwork->GetVesselEndNodes();
    std::vector<boost::shared_ptr<Vessel<DIM> > > vessels = mpVesselNetwork->GetVessels();
    unsigned num_nodes = nodes.size();
    std::vector<std::vector<unsigned> > connectivity;
    for (unsigned node_index = 0; node_index < num_nodes; node_index++)
    {
        boost::shared_ptr<VesselNode<DIM> > p_node = nodes[node_index];
        std::vector<unsigned> vessel_indexes;

        unsigned num_segments_on_node = p_node->GetNumberOfSegments();
        for (unsigned segment_index = 0; segment_index < num_segments_on_node; segment_index++)
        {
            boost::shared_ptr<Vessel<DIM> > p_vessel = p_node->GetSegments()[segment_index]->GetVessel();

            typename std::vector<boost::shared_ptr<Vessel<DIM> > >::iterator vessel_iter =
                    std::find(vessels.begin(), vessels.end(), p_vessel);
            unsigned vessel_index = std::distance(vessels.begin(), vessel_iter);
            vessel_indexes.push_back(vessel_index);
        }
        connectivity.push_back(vessel_indexes);
    }
    return connectivity;
}

template <unsigned DIM>
bool VesselNetworkGraphCalculator<DIM>::IsConnected(boost::shared_ptr<VesselNode<DIM> > pSourceNode, boost::shared_ptr<VesselNode<DIM> > pQueryNode)
{
    if(!mpVesselNetwork)
    {
        EXCEPTION("Vessel network not set in graph calculator");
    }

    if (!mpVesselNetwork->NodeIsInNetwork(pSourceNode))
    {
        EXCEPTION("Source node is not in network.");
    }
    if (!mpVesselNetwork->NodeIsInNetwork(pQueryNode))
    {
        EXCEPTION("Query node is not in network.");
    }

    if (pSourceNode == pQueryNode)
    {
        return true;
    }

    boost::shared_ptr<Vessel<DIM> > p_source_vessel = pSourceNode->GetSegments()[0]->GetVessel();
    boost::shared_ptr<Vessel<DIM> > p_query_vessel = pQueryNode->GetSegments()[0]->GetVessel();

    if (p_source_vessel == p_query_vessel || p_source_vessel->IsConnectedTo(p_query_vessel))
    {
        return true;
    }

    // Assign the vessel nodes unique IDs
    std::vector<boost::shared_ptr<VesselNode<DIM> > >  vessel_nodes = mpVesselNetwork->GetVesselEndNodes();
    typename std::vector<boost::shared_ptr<VesselNode<DIM> > >::iterator node_iter;
    unsigned counter = 0;
    for(node_iter = vessel_nodes.begin(); node_iter != vessel_nodes.end(); node_iter++)
    {
        (*node_iter)->SetId(counter);
        counter ++;
    }

    // Get the start nodes of the containing and query vessels
    boost::shared_ptr<VesselNode<DIM> > pEquivalentSourceNode = p_source_vessel->GetStartNode();
    boost::shared_ptr<VesselNode<DIM> > pEquivalentQueryNode = p_query_vessel->GetStartNode();

    // construct graph representation of vessel network
    typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS> Graph;

    Graph G;

    std::vector<boost::shared_ptr<Vessel<DIM> > >  vessels = mpVesselNetwork->GetVessels();
    for (unsigned i = 0; i < vessels.size(); i++)
    {
        add_edge(vessels[i]->GetStartNode()->GetId(), vessels[i]->GetEndNode()->GetId(), G);
    }

    // typedefs
    typedef boost::graph_traits<Graph>::vertices_size_type Size;

    // a vector to hold the discover time property for each vertex
    std::vector<Size> dtime(num_vertices(G));

    Size time = 0;
    bfs_time_visitor<Size*>vis(&dtime[0], time);

    // use breadth first search to establish discovery time of all nodes from node1
    // this assigns a discovery time to dTime for each node (index relates to nodeID)
    // dTime is zero for node1 and all other nodes that are not connected to node1
    // dTime is nonzero for all nodes that are connected to node1 (except node 1 itself)
    breadth_first_search(G,vertex(pEquivalentSourceNode->GetId(),G), boost::visitor(vis));

    return (dtime[pEquivalentQueryNode->GetId()] > 0);
}

template <unsigned DIM>
std::vector<bool > VesselNetworkGraphCalculator<DIM>::IsConnected(std::vector<boost::shared_ptr<VesselNode<DIM> > > sourceNodes,
        std::vector<boost::shared_ptr<VesselNode<DIM> > > queryNodes)
{
    if(!mpVesselNetwork)
    {
        EXCEPTION("Vessel network not set in graph calculator");
    }

    // Assign the vessel nodes unique IDs
    std::vector<boost::shared_ptr<VesselNode<DIM> > >  vessel_nodes = mpVesselNetwork->GetVesselEndNodes();

    typename std::vector<boost::shared_ptr<VesselNode<DIM> > >::iterator node_iter;
    unsigned counter = 0;
    for(node_iter = vessel_nodes.begin(); node_iter != vessel_nodes.end(); node_iter++)
    {
        (*node_iter)->SetId(counter);
        counter ++;
    }

    // construct graph representation of vessel network
    typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS> Graph;
    typedef boost::graph_traits<Graph>::vertices_size_type Size;

    Graph G;

    std::vector<boost::shared_ptr<Vessel<DIM> > >  vessels = mpVesselNetwork->GetVessels();
    for (unsigned i = 0; i < vessels.size(); i++)
    {
        add_edge(vessels[i]->GetStartNode()->GetId(), vessels[i]->GetEndNode()->GetId(), G);
    }

    std::vector<bool > connected(queryNodes.size(),false);

    for(unsigned i=0; i<sourceNodes.size(); i++)
    {
        if (!mpVesselNetwork->NodeIsInNetwork(sourceNodes[i]))
        {
            EXCEPTION("Source node is not in network.");
        }

        boost::shared_ptr<VesselNode<DIM> > pSourceNode = sourceNodes[i];
        boost::shared_ptr<Vessel<DIM> > p_source_vessel = pSourceNode->GetSegments()[0]->GetVessel();
        boost::shared_ptr<VesselNode<DIM> > pEquivalentSourceNode = p_source_vessel->GetStartNode();

        // a vector to hold the discover time property for each vertex
        std::vector<Size> dtime(num_vertices(G));

        Size time = 0;
        bfs_time_visitor<Size*>vis(&dtime[0], time);

        breadth_first_search(G,vertex(pEquivalentSourceNode->GetId(),G), boost::visitor(vis));

        for (unsigned j=0; j<queryNodes.size(); j++)
        {
            if (!mpVesselNetwork->NodeIsInNetwork(queryNodes[j]))
            {
                EXCEPTION("Query node is not in network.");
            }

            boost::shared_ptr<VesselNode<DIM> > pQueryNode = queryNodes[j];

            if (pSourceNode == pQueryNode)
            {
                connected[j] = true;
                continue;
            }

            boost::shared_ptr<Vessel<DIM> > p_query_vessel = pQueryNode->GetSegments()[0]->GetVessel();
            if (p_source_vessel == p_query_vessel || p_source_vessel->IsConnectedTo(p_query_vessel))
            {
                connected[j] = true;
                continue;
            }

            boost::shared_ptr<VesselNode<DIM> > pEquivalentQueryNode = p_query_vessel->GetStartNode();

            if (dtime[pEquivalentQueryNode->GetId()] > 0)
            {
                connected[j] = true;
            }
        }
    }

    return connected;
}

template <unsigned DIM>
void VesselNetworkGraphCalculator<DIM>::WriteConnectivity(const std::string& output_filename)
{
    if(!mpVesselNetwork)
    {
        EXCEPTION("Vessel network not set in graph calculator");
    }

    // construct graph representation of vessel network
    boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS> G;
    typename std::vector<boost::shared_ptr<VesselNode<DIM> > >::iterator node_iterator;
    std::vector<boost::shared_ptr<VesselNode<DIM> > > nodes = mpVesselNetwork->GetVesselEndNodes();

    for (node_iterator = nodes.begin(); node_iterator != nodes.end(); node_iterator++)
    {
        if ((*node_iterator)->GetSegments().size() > 1)
        {
            for (unsigned j = 1; j < (*node_iterator)->GetSegments().size(); j++)
            {
                add_edge(mpVesselNetwork->GetVesselIndex((*node_iterator)->GetSegments()[0]->GetVessel()),
                         mpVesselNetwork->GetVesselIndex((*node_iterator)->GetSegments()[j]->GetVessel()), G);
            }
        }
    }

    std::vector<boost::shared_ptr<Vessel<DIM> > >  vessels = mpVesselNetwork->GetVessels();
    typename std::vector<boost::shared_ptr<Vessel<DIM> > >::iterator vessel_iterator;
    for (vessel_iterator = vessels.begin(); vessel_iterator != vessels.end(); vessel_iterator++)
    {
        if ((*vessel_iterator)->GetStartNode()->GetNumberOfSegments() == 1 && (*vessel_iterator)->GetEndNode()->GetNumberOfSegments() == 1)
        {
            add_edge(mpVesselNetwork->GetVesselIndex((*vessel_iterator)),
                     mpVesselNetwork->GetVesselIndex((*vessel_iterator)), G);
        }
    }

    if(PetscTools::AmMaster())
    {
        std::ofstream outf(output_filename.c_str());
        boost::dynamic_properties dp;
        dp.property("node_id", get(boost::vertex_index, G));
        write_graphviz_dp(outf, G, dp);
    }
}

template <unsigned DIM>
void VesselNetworkGraphCalculator<DIM>::SetVesselNetwork(boost::shared_ptr<VesselNetwork<DIM> > pVesselNetwork)
{
    mpVesselNetwork = pVesselNetwork;
}

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