fixed some cuda compilation errors regarding operator<< & operator>> for edge and vertex classes.

Pavel Govyadinov
1 parent 3b14b0f5
Showing 1 changed file with 56 additions and 33 deletions Show diff stats
stim/biomodels/network.h
@@ -12,10 +12,9 @@
 #include <stim/visualization/obj.h>
 #include <stim/visualization/swc.h>
 #include <stim/visualization/cylinder.h>
-#include <stim/structures/kdtree.cuh>
 #include <stim/cuda/cudatools/timer.h>
 #include <stim/cuda/cudatools/callable.h>
-
+#include <stim/structures/kdtree.cuh>
 //********************help function********************
 // gaussian_function
 CUDA_CALLABLE float gaussianFunction(float x, float std = 25) { return exp(-x / (2 * std*std)); }  // std default sigma value is 25
@@ -64,13 +63,13 @@ class network{
 	class edge : public cylinder<T>
 	{
 		public:
-		unsigned v[2];		//unique id's designating the starting and ending
+		unsigned int v[2];		//unique id's designating the starting and ending
 		// default constructor
 		edge() : cylinder<T>() {
 			v[1] = (unsigned)(-1); v[0] = (unsigned)(-1);
 		}
 		/// 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.
@@ -78,7 +77,7 @@ class network{
 		{
 		}
-
+*/
 		///@param p is an array of positions in space
 		edge(stim::centerline<T> p) : cylinder<T>(p){}
@@ -114,11 +113,11 @@ 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)
+		friend std::ofstream& operator<<(std::ofstream& out, const edge& 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.
+			unsigned int sz = e.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
 			{
@@ -133,25 +132,26 @@ class network{
 		}
 		/// operator for reading an edge from a binary .nwt file.
-		std::ofstream& operator>>(std::ofstream& in, edge<T>& e)
+		friend std::ifstream& operator>>(std::ifstream& in, edge& 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
+//			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
+			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);		
 			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));
+				in.read(reinterpret_cast<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));	
+		//				for(int j = 0; j < nmags(); j++)		///future code for mags
+		//				{
+				in.read(reinterpret_cast<char*>(&mag), sizeof(T));	
 				set_r(0, mag);
-//				}
+		//				}
 			}
 			return in;
 		}
@@ -169,7 +169,8 @@ class network{
 			vertex(stim::vec3<T> p) : stim::vec3<T>(p){}
 			/// Output the vertex information as a string
-			std::string	str(){
+			std::string 
+			str(){
 				std::stringstream ss;
 				ss<<"\t(x, y, z) = "<<stim::vec3<T>::str();
@@ -187,31 +188,35 @@ class network{
 				return ss.str();
 			}
 			///operator for writing the edge into the stream;
-			std::ofstream& operator<<(std::ofstream& out, const vertex& v)
+			friend std::ofstream& operator<<(std::ofstream& out, const vertex& v)
 			{
+				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*>(&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*>(&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());
 				return out;
 			}
 			///operator for reading the edge out of the stream;
-			std::ofstream& operator<<(std::ofstream& in, vertex& v)
+			friend std::ifstream& operator>>(std::ifstream& in, vertex& v)
 			{
-				in.read(reinterpret_cast<const char*>(&v[0]), 3*sizeof(T))
+				in.read(reinterpret_cast<char*>(&v[0]), 3*sizeof(T));
 				unsigned int s[2];
-				in.read(reinterpret_cast<const char*>(&s[0]), 2*sizeof(unsigned int));
+				in.read(reinterpret_cast<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));
+				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));
 				return in;
 			}
+
 	};
 protected:
@@ -519,27 +524,45 @@ public:
 		}
 	}
+
 	///loads a .nwt file. Reads the header and loads the data into the network according to the header.
-/*	void
+	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)
 	{
-
+		std::ofstream file;
+		file.open(filename, std::ios::out | std::ios::binary);	
+		for(int i = 0; i < V.size(); i++)
+		{
+			file << V[i];
+		}
+		for(int i = 0; i < E.size(); i++)
+		{
+			file << E[i];
+		}
 	}
+
+	///Writes the header information to a .nwt file.
 	void
 	writeHeader(std::string filename)
 	{
 	}
-*/
+
+	///Reads the header information from a .nwt file.
+	void
+	readHeader(std::string filename, unsigned int &dims)
+	{
+		
+	}
+
 	//load a network from an SWC file
 	void load_swc(std::string filename) {
 		stim::swc<T> S;										// create swc variable
@@ -819,7 +842,7 @@ public:
 			T* query = new T[3 * n];
 			T* m1 = new T[n];
 			T* dists = new T[n];
-			size* nnIdx = new size_t[n];
+			size_t* nnIdx = new size_t[n];
 			edge2array(query, R.E[e]);
@@ -1097,7 +1120,7 @@ public:
 		stim::vec3<T> p0, p1;
 		T* queryPt = new T[3];
-		for(unsigned e = 0; e < R.E.size(); e++){			// for each edge in A
+		for(unsigned int e = 0; e < R.E.size(); e++){			// for each edge in A
 			T M;											// the sum of metrics of current edge
 			for(unsigned p = 0; p < R.E[e].size(); p++)
 				M += A.E[e].r(p);