stim/biomodels/network.h

#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
		/// Constructor - creates an edge from a list of points by calling the stim::fiber constructor
		///@param p is a position in space
		edge(std::vector< stim::vec<T> > p) : fiber<T>(p){}
			
		/// 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();
	}
	//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
		//prints each line in the obj file - vertex positions and fibers
		std::cout<<O.str()<<std::endl;
		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 e = 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 v = e[0];								//create a new vertex, assign it a position
				v.e[0].push_back(E.size());						//add the current edge as outgoing
				e.v[0] = V.size();								//add the new vertex to the edge
				V.push_back(v);									//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
				e.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 v = e.back();							//create a new vertex, assign it a position
				v.e[1].push_back(E.size());						//add the current edge as incoming
				e.v[1] = V.size();
				V.push_back(v);									//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
				e.v[1] = it_idx;
			}
			/*lines to be added for resampling each fiber in the network class
			//std::vector< stim::vec<T> > newFiberPos, fiberPos;
			//fiberPos = e.centerline();
			//newFiberPos = e.Resample(fiberPos);
			//edge newEdge = newFiberPos;
			//E.push_back(newEdge);	
			*/
			
			E.push_back(e);										//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();
	}
};		//end stim::network class
};		//end stim namespace
#endif