added operators for reading and writing binary .nwt files::need to fill in the methods

Pavel Govyadinov
1 parent 4b9199d3
Showing 2 changed files with 98 additions and 3 deletions Show diff stats
stim/biomodels/network.h
stim/visualization/cylinder.h
@@ -71,6 +71,14 @@ class network{
 		}
 		/// Constructor - creates an edge from a list of points by calling the stim::fiber constructor
  
+		///@param v0, the starting index.
+		///@param v1, the ending index.
+		///@param sz, the number of point in the fiber.
+		edge(unsigned int v0, unsigned int v1, unsigned int sz) : cylinder<T>(
+		{
+
+		}
+
 		///@param p is an array of positions in space
 		edge(stim::centerline<T> p) : cylinder<T>(p){}
  
@@ -105,7 +113,48 @@ class network{
 			}
 			return E;
 		}
+		/// operator for writing the edge information into a binary .nwt file.
+		std::ofstream& operator<<(std::ofstream& out, const edge<T>& e)
+		{
+			out.write(reinterpret_cast<const char*>(&e.v[0]), sizeof(unsigned int));	///write the starting point.
+			out.write(reinterpret_cast<const char*>(&e.v[1]), sizeof(unsigned int));	///write the ending point.
+			unsigned int sz = size();	///write the number of point in the edge.
+			out.write(reinterpret_cast<const char*>(&sz), sizeof(unsigned int));
+			for(int i = 0; i < sz; i++)	///write each point
+			{
+				stim::vec3<T> point = e[i];
+				out.write(reinterpret_cast<const char*>(point[0]), 3*sizeof(T));
+			//	for(int j = 0; j < nmags(); j++)	//future code for multiple mags
+			//	{
+				out.write(reinterpret_cast<const char*>(e[i].R[0]), sizeof(T));	///write the radius
+			//	}
+			}
+			return out;	//return stream
+		}
  
+		/// operator for reading an edge from a binary .nwt file.
+		std::ofstream& operator>>(std::ofstream& in, edge<T>& e)
+		{
+			unsigned int v0, v1, sz;
+			in.read((reinterpret_cast<const char*>(&v[0]), sizeof(unsigned int));	//read the staring point.
+			in.read((reinterpret_cast<const char*>(&v[1]), sizeof(unsigned int));	//read the ending point
+			in.read((reinterpret_cast<const char*>(&sz), sizeof(unsigned int));	//read the number of points in the edge
+			stim::centerline temp = stim::centerline(sz)		//allocate the new edge
+			e = edge(temp);		
+			for(int i = 0; i < sz; i++)		//set the points and radii to the newly read values
+			{
+				stim::vec3<T> point;
+				in.read((reinterpret_cast<const char*>(&point[0]) 3*sizeof(T));
+				e[i] = point;
+				T mag;
+//				for(int j = 0; j < nmags(); j++)		///future code for mags
+//				{
+				in.read(reinterpret_cast<const char*>(&mag), sizeof(T));	
+				set_r(0, mag);
+//				}
+			}
+			return in;
+		}
 	};
  
 	///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.
@@ -137,6 +186,32 @@ class network{
  
 				return ss.str();
 			}
+			///operator for writing the edge into the stream;
+			std::ofstream& operator<<(std::ofstream& out, const vertex& v)
+			{
+				out.write(reinterpret_cast<const char*>(&v[0]), 3*sizeof(T));
+				out.write(reinterpret_cast<const char*>(&v.e[0].size()), sizeof(unsigned int));	
+				out.write(reinterpret_cast<const char*>(&v.e[1].size()), sizeof(unsigned int));	
+				out.write(reinterpret_cast<const char*>(&v.e[0][0]), sizeof(unsigned int)*v.e[0].size());
+				out.write(reinterpret_cast<const char*>(&v.e[1][0]), sizeof(unsigned int)*v.e[1].size());
+				return out;
+			}
+
+			///operator for reading the edge out of the stream;
+			std::ofstream& operator<<(std::ofstream& in, vertex& v)
+			{
+				in.read(reinterpret_cast<const char*>(&v[0]), 3*sizeof(T))
+				unsigned int s[2];
+				in.read(reinterpret_cast<const char*>(&s[0]), 2*sizeof(unsigned int));
+
+				std::vector<unsigned int> one(s[0]);
+				std::vector<unsigned int> two(s[1]);
+				v.e[0] = one;
+				v.e[1] = two;
+				in.read(reinterpret_cast<const char*>(&v.e[0][0]),s[0]*sizeof(unsigned int));
+				in.read(reinterpret_cast<const char*>(&v.e[1][0]),s[1]*sizeof(unsigned int));
+				return in;
+			}
 	};
  
 protected:
@@ -444,7 +519,27 @@ public:
  
 		}
 	}
+	///loads a .nwt file. Reads the header and loads the data into the network according to the header.
+/*	void
+	loadNwt(std::string filename)
+	{
  
+	}
+
+	///saves a .nwt file. Writes the header in raw text format, then saves the network as a binary file.
+	///
+	void
+	saveNwt(std::string filename)
+	{
+
+	}
+
+	void
+	writeHeader(std::string filename)
+	{
+		
+	}
+*/
 	//load a network from an SWC file
 	void load_swc(std::string filename) {
 		stim::swc<T> S;										// create swc variable
@@ -1136,4 +1231,4 @@ public:
 	}
 };		//end stim::network class
 };		//end stim namespace
-#endif
 \ No newline at end of file
+#endif
@@ -46,7 +46,7 @@ public:
 	cylinder(centerline<T>c) : centerline<T>(c) {
 		init();
 	}
-
+	
 	//cylinder(centerline<T>c, T r) : centerline(c) {
 	//	init();
 	//	//add_mag(r);
@@ -711,4 +711,4 @@ public:
 };
  
 }
-#endif
 \ No newline at end of file
+#endif