fixed GCC errors and warnings associated with NetMets

David Mayerich
1 parent 6e9cf1ac
Showing 2 changed files with 16 additions and 15 deletions Show diff stats
stim/biomodels/network.h
stim/structures/kdtree.cuh
@@ -35,7 +35,7 @@ class network{
 		// default constructor
 		edge() : cylinder<T>()
 		{
-			v[1] = -1; v[0] = -1;
+			v[1] = (unsigned)(-1); v[0] = (unsigned)(-1);
 		}
 		/// Constructor - creates an edge from a list of points by calling the stim::fiber constructor
  
@@ -421,7 +421,7 @@ public:
 		R = (*this);									//initialize the result with the current network
  
 		//generate a KD-tree for network A
-		float metric = 0.0;                               				// initialize metric to be returned after comparing the networks
+		//float metric = 0.0;                               				// initialize metric to be returned after comparing the networks
 		stim::cuda_kdtree<T, 3> kdt;								// initialize a pointer to a kd tree
 		size_t MaxTreeLevels = 3;									// max tree level
  
@@ -447,8 +447,8 @@ public:
  
 		stim::vec3<T> p0, p1;
 		float m1;
-		float M = 0;									//stores the total metric value
-		float L = 0;									//stores the total network length
+		//float M = 0;									//stores the total metric value
+		//float L = 0;									//stores the total network length
 		float* queryPt = new float[3];
 		for(unsigned e = 0; e < R.E.size(); e++){					//for each edge in A
 			R.E[e].add_mag(0);							//add a new magnitude for the metric
@@ -488,7 +488,7 @@ public:
 	void load_txt(std::string filename)
 	{
 		std::vector <std::string> file_contents;
-		std::ifstream file(filename);
+		std::ifstream file(filename.c_str());
 		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
@@ -553,8 +553,8 @@ public:
 	void
 	to_txt(std::string filename)
 	{
-		std::ofstream ofs(filename, std::ofstream::out | std::ofstream::app);
-		int num;
+		std::ofstream ofs(filename.c_str(), std::ofstream::out | std::ofstream::app);
+		//int num;
 		ofs << (E.size()).str() << "\n";
 		for(unsigned int i = 0; i < E.size(); i++)
 		{
@@ -567,7 +567,8 @@ public:
 		{
 			std::string str;
 			str = V[i].str();
-			removeCharsFromString(str, "[],");
+			char temp[4] = "[],";
+			removeCharsFromString(str, temp);
 			ofs << str << "\n";
 		}
 		ofs.close();
@@ -52,7 +52,7 @@ namespace stim {
 		int current_axis;													// current judging axis
 		int cmps;															// count how many time of comparisons (just for cpu-kdtree)
 		int n_id;															// store the total number of nodes
-		std::vector <kdtree::point<T, D>> *tmp_points;						// transfer or temp points
+		std::vector < typename kdtree::point<T, D> > *tmp_points;						// transfer or temp points
 		kdtree::kdnode<T> *root;											// root node
 		static cpu_kdtree<T, D> *cur_tree_ptr;
 	public:
@@ -78,7 +78,7 @@ namespace stim {
 			}
 			root = NULL;
 		}
-		void Create(std::vector <kdtree::point<T, D>> &reference_points, size_t max_levels) {
+		void Create(std::vector < typename kdtree::point<T, D> > &reference_points, size_t max_levels) {
 			tmp_points = &reference_points;												
 			root = new kdtree::kdnode<T>();									// initializing the root node
 			root->idx = n_id++;												// the index of root is 0
@@ -119,11 +119,11 @@ namespace stim {
 			}
 		}
 		static bool SortPoints(const size_t a, const size_t b) {						// create functor for std::sort
-			std::vector <kdtree::point<T, D>> &pts = *cur_tree_ptr->tmp_points;			// put cur_tree_ptr to current input points' pointer
+			std::vector < typename kdtree::point<T, D> > &pts = *cur_tree_ptr->tmp_points;			// put cur_tree_ptr to current input points' pointer
 			return pts[a].dim[cur_tree_ptr->current_axis] < pts[b].dim[cur_tree_ptr->current_axis];
 		}
 		void Split(kdtree::kdnode<T> *cur, kdtree::kdnode<T> *left, kdtree::kdnode<T> *right) {
-			std::vector <kdtree::point<T, D>> &pts = *tmp_points;
+			std::vector < typename kdtree::point<T, D> > &pts = *tmp_points;
 			current_axis = cur->level % D;												// indicate the judicative dimension or axis
 			std::sort(cur->indices.begin(), cur->indices.end(), SortPoints);			// using SortPoints as comparison function to sort the data
 			size_t mid_value = cur->indices[cur->indices.size() / 2];                   // odd in the mid_value, even take the floor
@@ -317,7 +317,7 @@ namespace stim {
 				std::cout<<"The max_tree_levels should be smaller!"<<std::endl;
 				exit(1);
 			}
-			std::vector <kdtree::point<T, D>> reference_points(reference_count);																				// restore the reference points in particular way
+			std::vector < typename kdtree::point<T, D> > reference_points(reference_count);																				// restore the reference points in particular way
 			for (size_t j = 0; j < reference_count; j++)
 				for (size_t i = 0; i < dim_count; i++)
 					reference_points[j].dim[i] = h_reference_points[j * dim_count + i];
@@ -331,7 +331,7 @@ namespace stim {
 			HANDLE_ERROR(cudaMalloc((void**)&d_index, sizeof(size_t) * d_reference_count));
 			HANDLE_ERROR(cudaMalloc((void**)&d_reference_points, sizeof(kdtree::point<T, D>) * d_reference_count));
  
-			std::vector <cuda_kdnode<T>> tmp_nodes(num_nodes);																									
+			std::vector < cuda_kdnode<T> > tmp_nodes(num_nodes);																									
 			std::vector <size_t> indices(d_reference_count);
 			std::vector <kdtree::kdnode<T>*> next_nodes;
 			size_t cur_pos = 0;
@@ -372,7 +372,7 @@ namespace stim {
 			HANDLE_ERROR(cudaMemcpy(d_reference_points, &reference_points[0], sizeof(kdtree::point<T, D>) * reference_points.size(), cudaMemcpyHostToDevice));
 		}
 		void Search(T *h_query_points, size_t query_count, size_t dim_count, T *dists, size_t *indices) {
-			std::vector <kdtree::point<T, D>> query_points(query_count);
+			std::vector < typename kdtree::point<T, D> > query_points(query_count);
 			for (size_t j = 0; j < query_count; j++)
 				for (size_t i = 0; i < dim_count; i++)
 					query_points[j].dim[i] = h_query_points[j * dim_count + i];