fixed merge conflicts

Pavel Govyadinov
2 parents 2e0f052a 52b09bd9
Showing 1 changed file with 250 additions and 6 deletions Show diff stats
stim/biomodels/network.h
@@ -93,6 +93,7 @@ class network{
 				return ss.str();
 			}
  
+
 	};
  
 protected:
@@ -124,6 +125,150 @@ public:
 		return V.size();
 	}
  
+	std::vector<vertex> operator*(T s){
+		for (unsigned i=0; i< vertices; i ++ ){
+			V[i] = V[i] * s;
+		}
+		return V;
+	}
+
+	std::vector<vertex> operator*(vec<T> s){
+		for (unsigned i=0; i< vertices; i ++ ){
+			for (unsigned dim = 0 ; dim< 3; dim ++){
+				V[i][dim] = V[i][dim] * s[dim];
+			}
+		}
+		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 number of branch points in thenetwork
+
+	unsigned int BranchP(){
+		unsigned int B=0;
+		unsigned int c;
+		for(unsigned v=0; v < V.size(); v ++){
+			c = ((V[v].e[0].size()) + (V[v].e[1].size()));
+			if (c > 2){
+			B += 1;}
+		}		
+		return B;
+
+	}
+
+	// Returns number of end points (tips) in thenetwork
+
+	unsigned int EndP(){
+		unsigned int B=0;
+		unsigned int c;
+		for(unsigned v=0; v < V.size(); v ++){
+			c = ((V[v].e[0].size()) + (V[v].e[1].size()));
+			if (c == 1){
+			B += 1;}
+		}		
+		return B;
+
+	}
+
+	//// Returns a dictionary with the key as the vertex
+	//std::map<std::vector<vertex>,unsigned int> DegreeDict(){
+	//	std::map<std::vector<vertex>,unsigned int> dd;
+	//	unsigned int c = 0;
+	//	for(unsigned v=0; v < V.size(); v ++){
+	//		c = ((V[v].e[0].size()) + (V[v].e[1].size()));
+	//		dd[V[v]] = c;
+	//	}
+	//	return dd;
+	//}
+
+	//// Return number of branching stems
+	//unsigned int Stems(){
+	//	unsigned int s = 0;
+	//	std::map<std::vector<vertex>,unsigned int> dd;
+	//	dd = DegreeDict();
+	//	//for(unsigned v=0; v < V.size(); v ++){
+	//	//	V[v].e[0].
+	//	return s;
+	//}
+
+
+	// Returns an average of fiber/edge lengths in the network
+	double Lengths(){
+		stim::vec<T> L;double sumLength = 0;
+		for(unsigned e = 0; e < E.size(); e++){				//for each edge in the network
+			L.push_back(E[e].length());						//append the edge length
+			sumLength = sumLength + E[e].length();
+		}
+		double avg = sumLength / E.size();
+		return avg;
+	}
+
+
+	// Returns an average of tortuosities in the network
+	double Tortuosities(){
+		stim::vec<T> t;
+		stim::vec<T> id1, id2;                        // starting and ending vertices of the edge
+		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
+			if(distance > 0){
+				tortuosity = E[e].length()/	distance	;		// tortuoisty = edge length / edge displacement
+			}
+			else{
+				tortuosity = 0;}
+			t.push_back(tortuosity);
+			sumTortuosity += tortuosity;
+		}
+		double avg = sumTortuosity / E.size();
+		return avg;
+	}
+
+	// Returns average contraction of the network
+	double Contractions(){
+	stim::vec<T> t;
+	stim::vec<T> id1, id2;                        // starting and ending vertices of the edge
+	double distance;double contraction;double sumContraction = 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
+		contraction = distance / E[e].length();		// tortuoisty = edge length / edge displacement
+		t.push_back(contraction);
+		sumContraction += contraction;
+	}
+	double avg = sumContraction / E.size();
+	return avg;
+	}
+
+	// returns average fractal dimension of the branches of the network
+	double FractalDimensions(){
+	stim::vec<T> t;
+	stim::vec<T> id1, id2;                        // starting and ending vertices of the edge
+	double distance;double fract;double sumFractDim = 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
+		fract = std::log(distance) / std::log(E[e].length());		// tortuoisty = edge length / edge displacement
+		t.push_back(sumFractDim);
+		sumFractDim += fract;
+	}
+	double avg = sumFractDim / E.size();
+	return avg;
+	}
 	stim::cylinder<T> get_cylinder(unsigned f){
 		return E[f];									//return the specified edge (casting it to a fiber)
 	}
@@ -164,9 +309,8 @@ public:
 			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
+			it = find(id2vert.begin(), id2vert.end(), i[0]);	//look for the first node
+			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 edge to the edge
@@ -174,20 +318,21 @@ public:
 				id2vert.push_back(i[0]);					//add the ID to the ID->vertex conversion list
 			}
 			else{									//if the vertex already exists
+				it_idx = std::distance(id2vert.begin(), it);
 				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[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
 			}
 			else{									//if the vertex already exists
+				it_idx = std::distance(id2vert.begin(), it);
 				V[it_idx].e[1].push_back(E.size());				//add the current edge as incoming
 				new_edge.v[1] = it_idx;
 			}
@@ -326,8 +471,107 @@ public:
 	unsigned nmags(){
 		return E[0].nmags();
 	}
+	// split a string in text by the character sep
+	stim::vec<T> split(std::string &text, char sep) 
+	{
+		stim::vec<T> tokens;
+		std::size_t start = 0, end = 0;
+		while ((end = text.find(sep, start)) != std::string::npos) {
+		tokens.push_back(atof(text.substr(start, end - start).c_str()));
+		start = end + 1;
+		}
+		tokens.push_back(atof(text.substr(start).c_str()));
+		return tokens;
+	}
+	// load a network in text file to a network class
+	void load_txt(std::string filename)
+	{
+		std::vector <std::string> file_contents;
+		std::ifstream file(filename);
+		std::string line;
+		std::vector<unsigned> id2vert;	//this list stores the vertex ID associated with each network vertex
+		//for each line in the text file, store them as strings in file_contents
+		while (std::getline(file, line))
+		{
+			std::stringstream ss(line);
+			file_contents.push_back(ss.str());
+		}
+		unsigned int numEdges = atoi(file_contents[0].c_str()); //number of edges in the network
+		unsigned int I = atoi(file_contents[1].c_str()) ;		//calculate the number of points3d on the first edge
+		unsigned int count = 1; unsigned int k = 2; // count is global counter through the file contents, k is for the vertices on the edges
+		// for each edge in the network.
+		for (unsigned int i = 0; i < numEdges; i ++ )
+		{
+			// pre allocate a position vector p with number of points3d on the edge p
+			std::vector< stim::vec<T> > p(0, I);
+			// for each point on the nth edge
+		  for (unsigned int j = k; j < I + k; j++)
+		  {
+			 // split the points3d of floats with separator space and form a float3 position vector out of them
+			  p.push_back(split(file_contents[j], ' '));
+		  }
+			count += p.size() + 1; // increment count to point at the next edge in the network
+			I = atoi(file_contents[count].c_str()); // read in the points3d at the next edge and convert it to an integer
+			k = count + 1;
+			edge new_edge = p; // create an edge with a vector of points3d  on the edge
+			E.push_back(new_edge); // push the edge into the network
+		}
+		unsigned int numVertices = atoi(file_contents[count].c_str()); // this line in the text file gives the number of distinct vertices
+		count = count + 1; // this line of text file gives the first verrtex
+		// push each vertex into V
+		for (unsigned int i = 0; i < numVertices; i ++)
+		{
+			vertex new_vertex = split(file_contents[count], ' ');
+			V.push_back(new_vertex);
+			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