network.h
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#ifndef STIM_NETWORK_H
#define STIM_NETWORK_H
#include <list>
#include <stdlib.h>
#include <sstream>
#include <fstream>
#include <algorithm>
#include <string.h>
#include <math.h>
#include <stim/math/vector.h>
#include <stim/visualization/obj.h>
#include <stim/biomodels/fiber.h>
#include <ANN/ANN.h>
#include <boost/tuple/tuple.hpp>
namespace stim{
/** This is the a class that interfaces with gl_spider in order to store the currently
* segmented network. The following data is stored and can be extracted:
* 1)Network geometry and centerline.
* 2)Network connectivity (a graph of nodes and edges), reconstructed using ANN library.
*/
template<typename T>
class network{
///Each edge is a fiber with two nodes.
///Each node is an in index to the endpoint of the fiber in the nodes array.
class edge : public fiber<T>
{
public:
unsigned v[2]; //unique id's designating the starting and ending
// default constructor
edge() : fiber<T>(){v[1] = -1; v[0] = -1;}
/// Constructor - creates an edge from a list of points by calling the stim::fiber constructor
///@param p is an array of positions in space
edge(std::vector< stim::vec<T> > p) : fiber<T>(p){}
/// Copy constructor creates an edge from a fiber
edge(stim::fiber<T> f) : fiber<T>(f) {}
/// Resamples an edge by calling the fiber resampling function
edge resample(T spacing){
edge e(fiber<T>::resample()); //call the fiber->edge constructor
e.v[0] = v[0]; //copy the vertex data
e.v[1] = v[1];
return e; //return the new edge
}
/// Output the edge information as a string
std::string str(){
std::stringstream ss;
ss<<"("<<fiber<T>::N<<")\tl = "<<length()<<"\t"<<v[0]<<"----"<<v[1];
return ss.str();
}
};
///Node class that stores the physical position of the node as well as the edges it is connected to (edges that connect to it), As well as any additional data necessary.
class vertex : public stim::vec<T>
{
public:
//std::vector<unsigned int> edges; //indices of edges connected to this node.
std::vector<unsigned int> e[2]; //indices of edges going out (e[0]) and coming in (e[1])
//stim::vec<T> p; //position of this node in physical space.
//constructor takes a stim::vec
vertex(stim::vec<T> p) : stim::vec<T>(p){}
/// Output the vertex information as a string
std::string str(){
std::stringstream ss;
ss<<"\t(x, y, z) = "<<stim::vec<T>::str();
if(e[0].size() > 0){
ss<<"\t> ";
for(unsigned int o = 0; o < e[0].size(); o++)
ss<<e[0][o]<<" ";
}
if(e[1].size() > 0){
ss<<"\t< ";
for(unsigned int i = 0; i < e[1].size(); i++)
ss<<e[1][i]<<" ";
}
return ss.str();
}
};
private:
std::vector<edge> E; //list of edges
std::vector<vertex> V; //list of vertices.
public:
///Returns the number of edges in the network.
unsigned int edges(){
return E.size();
}
///Returns the number of nodes in the network.
unsigned int vertices(){
return V.size();
}
stim::fiber<T> get_fiber(unsigned f){
return E[f]; //return the specified edge (casting it to a fiber)
}
//load a network from an OBJ file
void load_obj(std::string filename){
stim::obj<T> O; //create an OBJ object
O.load(filename); //load the OBJ file as an object
std::vector<unsigned> id2vert; //this list stores the OBJ vertex ID associated with each network vertex
unsigned i[2]; //temporary, IDs associated with the first and last points in an OBJ line
//for each line in the OBJ object
for(unsigned int l = 1; l <= O.numL(); l++){
std::vector< stim::vec<T> > c; //allocate an array of points for the vessel centerline
O.getLine(l, c); //get the fiber centerline
edge new_edge = c; //create an edge from the given centerline
//get the first and last vertex IDs for the line
std::vector< unsigned > id; //create an array to store the centerline point IDs
O.getLinei(l, id); //get the list of point IDs for the line
i[0] = id.front(); //get the OBJ ID for the first element of the line
i[1] = id.back(); //get the OBJ ID for the last element of the line
std::vector<unsigned>::iterator it; //create an iterator for searching the id2vert array
unsigned it_idx; //create an integer for the id2vert entry index
//find out if the nodes for this fiber have already been created
it = find(id2vert.begin(), id2vert.end(), i[0]); //look for the first node
it_idx = std::distance(id2vert.begin(), it);
if(it == id2vert.end()){ //if i[0] hasn't already been used
vertex new_vertex = new_edge[0]; //create a new vertex, assign it a position
new_vertex.e[0].push_back(E.size()); //add the current edge as outgoing
new_edge.v[0] = V.size(); //add the new vertex to the edge
V.push_back(new_vertex); //add the new vertex to the vertex list
id2vert.push_back(i[0]); //add the ID to the ID->vertex conversion list
}
else{ //if the vertex already exists
V[it_idx].e[0].push_back(E.size()); //add the current edge as outgoing
new_edge.v[0] = it_idx;
}
it = find(id2vert.begin(), id2vert.end(), i[1]); //look for the second ID
it_idx = std::distance(id2vert.begin(), it);
if(it == id2vert.end()){ //if i[1] hasn't already been used
vertex new_vertex = new_edge.back(); //create a new vertex, assign it a position
new_vertex.e[1].push_back(E.size()); //add the current edge as incoming
new_edge.v[1] = V.size();
V.push_back(new_vertex); //add the new vertex to the vertex list
id2vert.push_back(i[1]); //add the ID to the ID->vertex conversion list
}
else{ //if the vertex already exists
V[it_idx].e[1].push_back(E.size()); //add the current edge as incoming
new_edge.v[1] = it_idx;
}
E.push_back(new_edge); //push the edge to the list
}
}
/// Output the network as a string
std::string str(){
std::stringstream ss;
ss<<"Nodes ("<<V.size()<<")--------"<<std::endl;
for(unsigned int v = 0; v < V.size(); v++){
ss<<"\t"<<v<<V[v].str()<<std::endl;
}
ss<<"Edges ("<<E.size()<<")--------"<<std::endl;
for(unsigned e = 0; e < E.size(); e++){
ss<<"\t"<<e<<E[e].str()<<std::endl;
}
return ss.str();
}
/// This function resamples all fibers in a network given a desired minimum spacing
stim::network<T> resample(T spacing){
stim::network<T> n; //create a new network that will be an exact copy, with resampled fibers
n.V = V; //copy all vertices
n.E.resize(E.size()); //allocate space for the edge list
//copy all fibers, resampling them in the process
for(unsigned e = 0; e < E.size(); e++){ //for each edge in the edge list
n.E[e] = E[e].resample(spacing); //resample the edge and copy it to the new network
}
return n; //return the resampled network
}
}; //end stim::network class
}; //end stim namespace
#endif