added code to subdivide networks

David Mayerich
1 parent 7c43b7f9
Showing 2 changed files with 60 additions and 36 deletions Show diff stats
stim/biomodels/fiber.h
stim/biomodels/network.h
@@ -5,7 +5,7 @@
 #include <ANN/ANN.h>
 namespace stim{
-		
+
 /**	This class stores information about a single fiber represented as a set of geometric points
  *	between two branch or end points. This class is used as a fundamental component of the stim::network
  *	class to describe an interconnected (often biological) network.
@@ -39,7 +39,7 @@ protected:
 		for(unsigned int i = 0; i < N; i++)					//allocate space for each point
 			c[i] = (double*) malloc(sizeof(double) * 3);
-		
+
 		r = (T*) malloc(sizeof(T) * N);			//allocate space for the radii
 	}
@@ -62,7 +62,7 @@ protected:
 		gen_kdtree();							//generate the kd tree for the new fiber
 	}
-	/// generate a KD tree for points on fiber 
+	/// generate a KD tree for points on fiber
 	void gen_kdtree()
 	{
 		int n_data = N; //create an array of data points
@@ -123,7 +123,7 @@ public:
 		copy(obj);
 	}
-	
+
 	//temp constructor for graph visualization
 	fiber(int n)
 	{
@@ -218,7 +218,7 @@ public:
 		return l;									//return the length
 	}
-	
+
 	/// Calculates the length and average radius of the fiber
 	/// @param length is filled with the fiber length
@@ -267,7 +267,7 @@ public:
 		T r_sum = 0.;
 		for(unsigned int i = 0; i < N; i++)
 		{
-			r_sum = r_sum + r[i];	
+			r_sum = r_sum + r[i];
 		}
 		return r_sum/((T) N);
 	}
@@ -282,16 +282,16 @@ public:
 	T radius(int idx){
 		return r[idx];
 	}
-	/// get index of a node on a fiber 
+	/// get index of a node on a fiber
 	// by matching the node on fiber to already set vertices (both strings)
 	// used in obj file conversion
-	int 
-	getIndexes(std::string* input, std::string searched, int sizeV) 
+	int
+	getIndexes(std::string* input, std::string searched, int sizeV)
 	{
 		int result = 0;
 		for (int i = 0; i < sizeV; i++)
 		{
-			if (input[i] == searched) 
+			if (input[i] == searched)
 			{
 				result = i + 1;
 			}
@@ -453,7 +453,7 @@ public:
 	/// @param i is the index of the element to be returned as a stim::vec
 	stim::vec<T> operator[](unsigned i){
-		return get_vec(i);		
+		return get_vec(i);
 	}
 	/// Back method returns the last point in the fiber
@@ -461,14 +461,14 @@ public:
 		return get_vec(N-1);
 	}
 		////resample a fiber in the network
-	stim::fiber<T> Resample(T spacing=25.0)
+	stim::fiber<T> resample(T spacing=25.0)
 	{
 		std::vector<T> v(3);    //v-direction vector of the segment
 		stim::vec<T> p(3);      //- intermediate point to be added
-		std::vector<T> p1(3);   // p1 - starting point of an segment on the fiber, 
-		std::vector<T> p2(3);   // p2 - ending point, 
+		std::vector<T> p1(3);   // p1 - starting point of an segment on the fiber,
+		std::vector<T> p2(3);   // p2 - ending point,
 		double sum=0;  //distance summation
 		std::vector<stim::vec<T> > fiberPositions = centerline();
 		std::vector<stim::vec<T> > newPointList; // initialize list of new resampled points on the fiber
@@ -483,7 +483,7 @@ public:
 				v[d] = p2[d] - p1[d];            //direction vector
 				sum +=v[d] * v[d];               //length of segment-distance between starting and ending point
 			}
-			newPointList.push_back(fiberPositions[f]); //always push the starting point
+			//newPointList.push_back(fiberPositions[f]); //always push the starting point
 			T lengthSegment = sqrt(sum);  //find Length of the segment as distance between the starting and ending points of the segment
@@ -37,8 +37,20 @@ class network{
 		/// Constructor - creates an edge from a list of points by calling the stim::fiber constructor
-		///@param p is a position in space
+		///@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(){
@@ -98,15 +110,16 @@ class network{
 		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
-		//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
@@ -117,7 +130,7 @@ class network{
 			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
+			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
@@ -132,36 +145,32 @@ class network{
 			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
+				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
-				e.v[0] = it_idx;
+				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 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
+				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
-				e.v[1] = it_idx;
+				new_edge.v[1] = it_idx;
 			}
-			stim::fiber<T> f = e.Resample(25.0);
-			std::cout<<"resampled fiber length"<<std::endl;
-			std::cout<<f.length()<<std::endl;
-			std::cout<<"resampled fiber--"<<std::endl;
-			std::cout<<f.str()<<std::endl;
-			E.push_back(e);										//push the edge to the list
+			
+			E.push_back(new_edge);										//push the edge to the list
 		}
 	}
@@ -182,6 +191,21 @@ class network{
 		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