Merged branch JACK into master

David Mayerich
2 parents b64c530d ee17b90b
Showing 5 changed files with 22 additions and 16 deletions Show diff stats
stim/biomodels/network.h
stim/math/circle.h
stim/structures/kdtree.cuh
stim/visualization/cylinder.h
stim/visualization/swc.h
@@ -71,7 +71,7 @@ class network{
 		/// Constructor - creates an edge from a list of points by calling the stim::fiber constructor
 		///@param p is an array of positions in space
-		edge(centerline p) : cylinder<T>(p){}
+		edge(stim::centerline<T> p) : cylinder<T>(p){}
 		/// Copy constructor creates an edge from a cylinder
 		edge(stim::cylinder<T> f) : cylinder<T>(f) {}
@@ -673,7 +673,7 @@ public:
 		//compare each point in the current network to the field produced by A
 		kdt.create(c, n_data, MaxTreeLevels);				// build a KD tree
-		std::vector<std::vector<unsigned>> relation;		// the relationship between GT and T corresponding to NN
+		std::vector<std::vector<unsigned> > relation;		// the relationship between GT and T corresponding to NN
 		relation.resize(A.E.size());										
 		for(unsigned e = 0; e < A.E.size(); e++){			//for each edge in A
@@ -35,6 +35,8 @@ public:
 	using stim::plane<T>::rotate;
 	using stim::plane<T>::setU;
+	using stim::plane<T>::init;
+
 	///base constructor
 	///@param th value of the angle of the starting point from 0 to 360.
 	CUDA_CALLABLE
@@ -137,7 +139,7 @@ public:
 	bool
 	operator==(const circle<T> & rhs)
 	{
-		if(P == rhs.P && U == rhs.U && Y == rhs.Y)
+		if(P == rhs.P && U == rhs.U)
 			return true;
 		else
 			return false;
@@ -360,7 +360,7 @@ namespace stim {
 			//bb.init(&h_reference_points[0]);
 			//aaboundingboxing<T, D>(bb, h_reference_points, reference_count);
-			std::vector < typename cpu_kdtree::point<T, D>> reference_points(reference_count);																				// restore the reference points in particular way
+			std::vector < typename cpu_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 < D; i++)
 					reference_points[j].dim[i] = h_reference_points[j * D + i];																																// creating a tree on cpu
@@ -11,6 +11,8 @@ namespace stim
 template<typename T>
 class cylinder : public centerline<T> {
 protected:
+	
+	using stim::centerline<T>::d;
 	std::vector< stim::vec3<T> > U;					//stores the array of U vectors defining the Frenet frame
 	std::vector< T > R;				//stores a list of magnitudes for each point in the centerline (assuming mags[0] is the radius)
@@ -36,23 +38,25 @@ public:
 	using stim::centerline<T>::size;
 	using stim::centerline<T>::at;
+	using stim::centerline<T>::L;
+	using stim::centerline<T>::length;
-	cylinder() : centerline(){}
-	
-	cylinder(centerline& c) : centerline(c) {
-		init();
-	}
+	cylinder() : centerline<T>(){}
-	cylinder(centerline& c, T r) : centerline(c) {
+	cylinder(centerline<T>c) : centerline<T>(c) {
 		init();
-		//add_mag(r);
 	}
+	//cylinder(centerline<T>c, T r) : centerline(c) {
+	//	init();
+	//	//add_mag(r);
+	//}
+
 	//initialize a cylinder with a list of points and magnitude values
-	cylinder(centerline& c, std::vector<T> r) : centerline(c){
-		init();
-		//add_mag(r);
-	}
+	//cylinder(centerline<T>c, std::vector<T> r) : centerline(c){
+	//	init();
+	//	//add_mag(r);
+	//}
 	//copy the original radius
 	void copy_r(std::vector<T> radius) {
@@ -85,7 +85,7 @@ namespace stim {
 	template <typename T>
 	class swc {
 	public:
-		std::vector< typename swc_tree::swc_node<T>> node;
+		std::vector< typename swc_tree::swc_node<T> > node;
 		swc() {};									// default constructor
 		// load the swc as tree nodes