added support for exporting stim::network to stim::obj

David Mayerich
1 parent fa737592
Showing 3 changed files with 158 additions and 6 deletions Show diff stats
stim/biomodels/network.h
stim/math/vector.h
stim/visualization/obj.h
@@ -18,7 +18,7 @@ namespace stim{
 template<typename T>
 class network{
  
-	//helper classes
+	//-------------------HELPER CLASSES-----------------------
 	/// Stores information about a geometric point on the network centerline (including point position and radius)
 	//template<typename T>
 	class point : public stim::vec<T>{
@@ -113,6 +113,24 @@ class network{
 				return radius_sum / length;					//return the average radius of the fiber
 		}
  
+		std::vector< stim::vec<T> > geometry(){
+
+			std::vector< stim::vec<T> > result;				//create an array to store the fiber geometry
+			result.resize( P.size() );					//pre-allocate the array
+
+			typename std::list< point >::iterator p;				//create a list iterator
+			unsigned int pi = 0;						//create an index into the result array
+
+			//for each geometric point on the fiber centerline
+			for(p = P.begin(); p != P.end(); p++){
+				result[pi] = *p;
+				pi++;
+			}
+
+			return result;			//return the geometry array
+
+		}
+
 		std::string str(){
 			std::stringstream ss;
  
@@ -177,7 +195,7 @@ class network{
 	};
  
  
-
+//---------------NETWORK CLASS-----------------------------
  
 protected:
  
@@ -236,6 +254,8 @@ public:
 	}
  
 	/// Load a network from an OBJ object
+
+	/// @param object is the object file to be used as the basis for the network
 	void load( stim::obj<T> object){
  
 		//get the number of vertices in the object
@@ -302,6 +322,95 @@ public:
  
 	}	//end load()
  
+	/// Returns an array of node positions
+	std::vector< stim::vec<T> > get_node_positions(){
+
+		std::vector< stim::vec<T> > result;				//create an array to store the result
+		result.resize(N.size());						//set the array size
+
+		t_node_i ni;									//create a terminal node iterator
+		unsigned int vi = 0;							//vertex index into the result array
+
+		//for every terminal node
+		for(ni = N.begin(); ni != N.end(); ni++){
+
+			//create a vector based on the node position
+
+			//if the number of outgoing nodes is nonzero
+			if(ni->out.size() != 0)
+				result[vi] = ni->out.front()->P.front();
+			else if(ni->in.size() != 0)
+				result[vi] = ni->in.front()->P.back();
+
+			vi++;										//increment the array index
+		}
+
+		//return the resulting array
+		return result;
+	}
+
+	std::vector< stim::vec<T> > get_fiber_geometry( fiber_i f ){
+		return f->geometry();
+	}
+
+	/// Generate an OBJ file from the network
+
+	stim::obj<T> obj(){
+
+		//create an OBJ object
+		stim::obj<T> object;
+
+		//name the nodes
+		set_names();
+
+		//retrieve a list of terminal node positions
+		std::vector< stim::vec<T> > node_pos = get_node_positions();
+
+		//add the nodes to the obj file
+		object.addV(node_pos);
+
+		//counter for vertex indices in the object class
+		unsigned int nP;
+
+		//for each fiber
+		fiber_i fi;						//create a fiber iterator
+		for(fi = F.begin(); fi != F.end(); fi++){
+
+			//get an array of fiber points
+			std::vector< stim::vec<T> > fiber_p = get_fiber_geometry(fi);
+
+			//create a subset of this array
+			typename std::vector< stim::vec<T> >::iterator start = fiber_p.begin() + 1;
+			typename std::vector< stim::vec<T> >::iterator end = fiber_p.end() - 1;
+			typename std::vector< stim::vec<T> > fiber_subset(start, end);
+
+			//add this subset to the geometry object
+			nP = object.addV(fiber_subset);
+
+			//create an array to hold vertex indices for a line
+			std::vector<unsigned int> line;
+			line.resize(fiber_p.size());
+
+			//add the terminal nodes to the line list (make sure to add 1 to make them compatible with the OBJ)
+			line[0] = fi->n[0]->id + 1;
+			line[line.size() - 1] = fi->n[1]->id + 1;
+
+			//add the intermediate vertex indices to the line array
+			for(unsigned int i = 0; i < fiber_subset.size(); i++){
+				line[1 + i] = nP + i;
+			}
+
+			//add the line list to the object class
+			object.addLine(line);
+
+		}
+
+		return object;
+
+
+
+	}
+
 	/// This function returns the information necessary for a simple graph-based physical (ex. fluid) simulation.
  
 	/// @param n0 is a array which will contain the list of source nodes
@@ -59,7 +59,7 @@ struct vec : public std::vector&lt;T&gt;
 	//copy constructor
 	vec( const vec<T>& other){
 		unsigned int N = other.size();
-		for(int i=0; i<N; i++)
+		for(unsigned int i=0; i<N; i++)
 			push_back(other[i]);
 	}
  
@@ -112,7 +112,7 @@ struct vec : public std::vector&lt;T&gt;
  
         //compute and return the vector length
         T sum_sq = (T)0;
-        for(int i=0; i<N; i++)
+        for(unsigned int i=0; i<N; i++)
         {
             sum_sq += pow( at(i), 2 );
         }
@@ -231,7 +231,7 @@ struct vec : public std::vector&lt;T&gt;
  
         vec<T> result(N);
  
-        for(int i=0; i<N; i++)
+        for(unsigned int i=0; i<N; i++)
             result[i] = at(i) - rhs[i];
  
         return result;
@@ -340,7 +340,7 @@ struct vec : public std::vector&lt;T&gt;
 		unsigned int N = size();
  
 		ss<<"[";
-		for(int i=0; i<N; i++)
+		for(unsigned int i=0; i<N; i++)
 		{
 			ss<<at(i);
 			if(i != N-1)
@@ -52,6 +52,8 @@ protected:
 		vertex(T x, T y, T z) : stim::vec<T>(x, y, z){}
 		vertex(T x, T y, T z, T w) : stim::vec<T>(x, y, z, w){}
  
+		vertex(stim::vec<T> rhs) : stim::vec<T>(rhs){}
+
 		//constructor creates a vertex from a line string
 		vertex(std::string line){
  
@@ -631,6 +633,47 @@ public:
 		}
  
 		return l;
+	}
+
+	/// Add an array of vertices to the vertex list
+	unsigned int addV(std::vector< stim::vec<T> > vertices){
+
+		unsigned int NV = vertices.size();			//get the total number of new vertices
+
+		unsigned int currentV = V.size() + 1;			//store the index to the first submitted point
+		
+		//for each vertex
+		for(unsigned int vi = 0; vi < NV; vi++){
+			vertex v(vertices[vi]);
+			V.push_back(v);
+		}
+
+		//return the index to the first point
+		return currentV;
+
+	}
+
+	/// Add a line to the object
+	void addLine(std::vector<unsigned> v, std::vector<unsigned> vt = std::vector<unsigned>(), std::vector<unsigned> vn = std::vector<unsigned>()){
+
+		//create a new line geometry
+		geometry new_line;
+
+		unsigned int v_i, vt_i, vn_i;
+		for(unsigned int i = 0; i < v.size(); i++){
+			v_i = vt_i = vn_i = 0;
+
+			v_i = v[i];
+			if(vt.size() != 0)
+				vt_i = vt[i];
+			if(vn.size() != 0)
+				vn_i = vn[i];
+
+			new_line.push_back(triplet(v_i, vt_i, vn_i));
+		}
+
+		//push the new geometry to the line list
+		L.push_back(new_line);
  
 	}