filled in the rest of the code necessary for reading the writing .nwt files. fully functional

Pavel Govyadinov
1 parent 66d1c0ff
Showing 1 changed file with 80 additions and 23 deletions Show diff stats
stim/biomodels/network.h
@@ -112,6 +112,7 @@ class network{
 			}
 			return E;
 		}
+
 		/// operator for writing the edge information into a binary .nwt file.
 		friend std::ofstream& operator<<(std::ofstream& out, const edge& e)
 		{
@@ -122,10 +123,11 @@ class network{
 			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));
+				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
+				out.write(reinterpret_cast<const char*>(&e.R[i]), sizeof(T));	///write the radius
+				std::cout << point.str() << " " << e.R[i] << std::endl;
 			//	}
 			}
 			return out;	//return stream
@@ -134,13 +136,13 @@ class network{
 		/// operator for reading an edge from a binary .nwt file.
 		friend std::ifstream& operator>>(std::ifstream& in, edge& e)
 		{
-//			unsigned int v0, v1, sz;
-			unsigned int sz;
-			in.read(reinterpret_cast<char*>(&e.v[0]), sizeof(unsigned int));	//read the staring point.
-			in.read(reinterpret_cast<char*>(&e.v[1]), sizeof(unsigned int));	//read the ending point
+			unsigned int v0, v1, sz;
+			in.read(reinterpret_cast<char*>(&v0), sizeof(unsigned int));	//read the staring point.
+			in.read(reinterpret_cast<char*>(&v1), sizeof(unsigned int));	//read the ending point
 			in.read(reinterpret_cast<char*>(&sz), sizeof(unsigned int));	//read the number of points in the edge
 			stim::centerline<T> temp = stim::centerline<T>(sz);		//allocate the new edge
 			e = edge(temp);		
+			e.v[0] = v0; e.v[1] = v1;
 			for(int i = 0; i < sz; i++)		//set the points and radii to the newly read values
 			{
 				stim::vec3<T> point;
@@ -150,7 +152,8 @@ class network{
 		//				for(int j = 0; j < nmags(); j++)		///future code for mags
 		//				{
 				in.read(reinterpret_cast<char*>(&mag), sizeof(T));	
-				set_r(0, mag);
+				e.set_r(0, mag);
+				std::cout << point.str() << " " << mag << std::endl;
 		//				}
 			}
 			return in;
@@ -164,7 +167,10 @@ class network{
 			//std::vector<unsigned int> edges;					//indices of edges connected to this node.
 			std::vector<unsigned int> e[2];						//indices of edges going out (e[0]) and coming in (e[1])
 			//stim::vec3<T> p;							//position of this node in physical space.
-
+			//default constructor
+			vertex() : stim::vec3<T>()
+			{
+			}
 			//constructor takes a stim::vec
 			vertex(stim::vec3<T> p) : stim::vec3<T>(p){}
@@ -193,27 +199,27 @@ class network{
 				unsigned int s0, s1;
 				s0 = v.e[0].size();
 				s1 = v.e[1].size();
-				out.write(reinterpret_cast<const char*>(&v[0]), 3*sizeof(T));
-				out.write(reinterpret_cast<const char*>(&s0), sizeof(unsigned int));	
-				out.write(reinterpret_cast<const char*>(&s1), 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());
+				out.write(reinterpret_cast<const char*>(&v.ptr[0]), 3*sizeof(T));	///write physical vertex location
+				out.write(reinterpret_cast<const char*>(&s0), sizeof(unsigned int));	///write the number of "incoming edges"
+				out.write(reinterpret_cast<const char*>(&s1), sizeof(unsigned int));	///write the number of "outgoing edges"	
+				out.write(reinterpret_cast<const char*>(&v.e[0][0]), sizeof(unsigned int)*v.e[0].size());	///write the "incoming edges"
+				out.write(reinterpret_cast<const char*>(&v.e[1][0]), sizeof(unsigned int)*v.e[1].size());	///write the "outgoing edges"
 				return out;
 			}
 			///operator for reading the edge out of the stream;
 			friend std::ifstream& operator>>(std::ifstream& in, vertex& v)
 			{
-				in.read(reinterpret_cast<char*>(&v[0]), 3*sizeof(T));
-				unsigned int s[2];
-				in.read(reinterpret_cast<char*>(&s[0]), 2*sizeof(unsigned int));
+				in.read(reinterpret_cast<char*>(&v[0]), 3*sizeof(T));	///read the physical position
+				unsigned int s[2];					
+				in.read(reinterpret_cast<char*>(&s[0]), 2*sizeof(unsigned int));	///read the sizes of incoming and outgoing edge arrays
 				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<char*>(&v.e[0][0]),s[0]*sizeof(unsigned int));
-				in.read(reinterpret_cast<char*>(&v.e[1][0]),s[1]*sizeof(unsigned int));
+				in.read(reinterpret_cast<char*>(&v.e[0][0]),s[0]*sizeof(unsigned int));		///read the arrays of "incoming edges"
+				in.read(reinterpret_cast<char*>(&v.e[1][0]),s[1]*sizeof(unsigned int));		///read the arrays of "outgoing edges"
 				return in;
 			}
@@ -529,23 +535,48 @@ public:
 	void
 	loadNwt(std::string filename)
 	{
+		int dims[2];		///number of vertex, number of edges
+		readHeader(filename, &dims[0]);		//read header
+		std::ifstream file;
+		file.open(filename, std::ios::in | std::ios::binary);		///skip header information.
+		file.seekg(14+58+4+4, file.beg);
+		vertex v;
+		for(int i = 0; i < dims[0]; i++)		///for every vertex, read vertex, add to network.
+		{
+			file >> v;
+			V.push_back(v);
+//			std::cout << i << " " << v.str() << std::endl;
+		}
+		std::cout << std::endl;
+		for(int i = 0; i < dims[1]; i++)		///for every edge, read edge, add to network.
+		{
+			edge e;
+			file >> e;
+			E.push_back(e);
+			std::cout << i << " " << E[i].str() << std::endl;
+		}
+		file.close();
 	}
 	///saves a .nwt file. Writes the header in raw text format, then saves the network as a binary file.
 	void
 	saveNwt(std::string filename)
 	{
+		writeHeader(filename);
 		std::ofstream file;
-		file.open(filename, std::ios::out | std::ios::binary);	
-		for(int i = 0; i < V.size(); i++)
+		file.open(filename, std::ios::out | std::ios::binary | std::ios::app);	///since we have written the header we are not appending.
+		for(int i = 0; i < V.size(); i++)	///look through the Vertices and write each one.
 		{
+//			std::cout << i << " " << V[i].str() << std::endl;
 			file << V[i];
 		}
-		for(int i = 0; i < E.size(); i++)
+		for(int i = 0; i < E.size(); i++)	///loop through the Edges and write each one.
 		{
+			std::cout << i << " " << E[i].str() << std::endl;
 			file << E[i];
 		}
+		file.close();
 	}
@@ -553,14 +584,40 @@ public:
 	void
 	writeHeader(std::string filename)
 	{
+		std::string magicString = "nwtFileFormat ";		///identifier for the file.
+		std::string desc = "fileid(14B), desc(58B), #vertices(4B), #edges(4B): bindata";
+		int hNumVertices = V.size();		///int byte header storing the number of vertices in the file
+		int hNumEdges = E.size();		///int byte header storing the number of edges.
+		std::ofstream file;
+		file.open(filename, std::ios::out | std::ios::binary);
+		std::cout << hNumVertices << " " << hNumEdges << std::endl;
+		file.write(reinterpret_cast<const char*>(&magicString.c_str()[0]), 14);	//write the file id
+		file.write(reinterpret_cast<const char*>(&desc.c_str()[0]), 58);	//write the description
+		file.write(reinterpret_cast<const char*>(&hNumVertices), sizeof(int));	//write #vert.
+		file.write(reinterpret_cast<const char*>(&hNumEdges), sizeof(int));	//write #edges
+//		file << magicString.c_str() << desc.c_str() << hNumVertices << hNumEdges;
+		file.close();
 	}
 	///Reads the header information from a .nwt file.
 	void
-	readHeader(std::string filename, unsigned int &dims)
+	readHeader(std::string filename, int *dims)
 	{
-		
+		char magicString[14];		///id
+		char desc[58];			///description
+		int hNumVertices;		///#vert
+		int hNumEdges;			///#edges
+		std::ifstream file;		////create stream
+		file.open(filename, std::ios::in | std::ios::binary);
+		file.read(reinterpret_cast<char*>(&magicString[0]), 14);	///read the file id.
+		file.read(reinterpret_cast<char*>(&desc[0]), 58);		///read the description
+		file.read(reinterpret_cast<char*>(&hNumVertices), sizeof(int));	///read the number of vertices
+		file.read(reinterpret_cast<char*>(&hNumEdges), sizeof(int));	///read the number of edges
+//		std::cout << magicString << desc << hNumVertices << " " <<  hNumEdges << std::endl;
+		file.close();							///close the file.
+		dims[0] = hNumVertices;						///fill the returned reference.
+		dims[1] = hNumEdges;
 	}
 	//load a network from an SWC file