average branching index of the network statistic added

pranathivemuri
1 parent 10b95d6e
Showing 1 changed file with 59 additions and 17 deletions Show diff stats
stim/biomodels/network.h
@@ -126,6 +126,18 @@ public:
 		return V;
 	}
+	// Returns an average of branching index in the network
+
+	double BranchingIndex(){
+		double B=0;
+		for(unsigned v=0; v < V.size(); v ++){
+			B += ((V[v].e[0].size()) + (V[v].e[1].size()));
+		}
+		B = B / V.size();
+		return B;
+
+	}
+
 	// Returns an average of fiber/edge lengths in the network
 	double Lengths(){
 		stim::vec<T> L;double sumLength = 0;
@@ -142,26 +154,11 @@ public:
 	double Tortuosities(){
 		stim::vec<T> t;
 		stim::vec<T> id1, id2;                        // starting and ending vertices of the edge
-		//std::vector< stim::vec<T> > vert;	             // list of visited vertices
-		//std::vector<stim::vec<T>>::iterator it;			//create an iterator for searching the id2vert array
-		//std::vector<unsigned> daughters;               // to count number of daughter vessels at branch points
-		//stim::vec<T> visitedVert;
-		//unsigned visited;
 		double distance;double tortuosity;double sumTortuosity = 0;
 		for(unsigned e = 0; e < E.size(); e++){				//for each edge in the network
 			id1 = E[e][0];									//get the edge starting point
 			id2 = E[e][E[e].size() - 1];					//get the edge ending point
 			distance = (id1 - id2).len();                   //displacement between the starting and ending points
-			//it = find(vert.begin(), vert.end(), id1);	    //look for the first node has a daughter vessel already
-			//visitedVert = std::distance(vert.begin(), it);    //index where it already exists
-			//if(visitedVert == id1){
-			//	visited += 1;
-			//	daughters[e] = visited;
-			//}
-			//else{
-			//	vert.push_back(id1);
-			//	daughters[e] = 1;
-			//}
 			if(distance > 0){
 				tortuosity = E[e].length()/	distance	;		// tortuoisty = edge length / edge displacement
 			}
@@ -171,7 +168,6 @@ public:
 			sumTortuosity += tortuosity;
 		}
 		double avg = sumTortuosity / E.size();
-		//std::cout<<"number of unique branch points"<<daughters.size()<<std::endl;
 		return avg;
 	}
@@ -228,7 +224,7 @@ public:
 			if(it == id2vert.end()){							//if i[1] hasn't already been used
 				vertex new_vertex = new_edge[I-1];							//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();
+				new_edge.v[1] = 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[1]);						//add the ID to the ID->vertex conversion list
 			}
@@ -427,6 +423,52 @@ public:
 			count += atoi(file_contents[count + 1].c_str()) + 2; // Skip number of edge ids + 2 to point to the next vertex
 		}
 	} // end load_txt function
+
+	// strTxt returns a string of edges
+	std::string
+	strTxt(std::vector< stim::vec<T> > p)
+	{
+		std::stringstream ss;
+		std::stringstream oss;
+		for(unsigned int i = 0; i < p.size(); i++){
+			ss.str(std::string());
+			for(unsigned int d = 0; d < 3; d++){
+				ss<<c[i][d];
+			}
+			ss < "\n"
+		}
+		return ss.str();
+	}
+	// removes specified character from string
+	void removeCharsFromString(std::string &str, char* charsToRemove ) {
+	   for ( unsigned int i = 0; i < strlen(charsToRemove); ++i ) {
+		  str.erase( remove(str.begin(), str.end(), charsToRemove[i]), str.end() );
+	   }
+	}
+	//exports network to txt file
+	void
+	to_txt(std::string filename)
+	{
+		std::ofstream ofs;
+		ofs.open(filename, std::ofstream::out | std::ofstream::app);
+		int num;
+		ofs << (E.size()).str() << "\n";
+		for(unsigned int i = 0; i < E.size(); i++)
+		{
+			 std::string str;
+			 ofs << (E[i].size()).str() << "\n";
+			 str = E[i].strTxt();
+             ofs << str << "\n";
+		} 
+		for(int i = 0; i < V.size(); i++)
+		{
+			std::string str;
+			str = V[i].str();
+			removeCharsFromString(str, "[],");
+			ofs << str << "\n";
+		}
+		ofs.close();
+	}
 };		//end stim::network class
 };		//end stim namespace
 #endif