Modified centerline, cylinder and network to have std::vector constructors

Pavel Govyadinov
1 parent 43865a41
Showing 4 changed files with 62 additions and 36 deletions Show diff stats
stim/biomodels/centerline.h
stim/biomodels/network.h
stim/parser/table.h
stim/visualization/cylinder.h
@@ -32,6 +32,21 @@ protected:
 		return ab.norm();
 	}
  
+	//initializes the integrated length vector to make parameterization easier, starting with index idx (all previous indices are assumed to be correct)
+	void update_L(size_t start = 0) {
+		L.resize(size());									//allocate space for the L array
+		if (start == 0) {
+			L[0] = 0;											//initialize the length value for the first point to zero (0)
+			start++;
+		}
+
+		stim::vec3<T> d;
+		for (size_t i = start; i < size(); i++) {		//for each line segment in the centerline
+			d = at(i) - at(i - 1);
+			L[i] = L[i - 1] + d.len();				//calculate the running length total
+		}
+	}
+
 	void init() {
 		if (size() == 0) return;								//return if there aren't any points
 		update_L();
@@ -93,7 +108,12 @@ public:
 	centerline(size_t n) : std::vector< stim::vec3<T> >(n){
 		init();
 	}
-
+	centerline(std::vector<stim::vec3<T> > pos) :
+		std::vector<stim::vec3<T> > (pos)
+	{
+		init();
+	}
+	
 	//overload the push_back function to update the length vector
 	void push_back(stim::vec3<T> p) {
 		std::vector< stim::vec3<T> >::push_back(p);
@@ -121,20 +141,6 @@ public:
 		return L.back();
 	}
  
-	//initializes the integrated length vector to make parameterization easier, starting with index idx (all previous indices are assumed to be correct)
-	void update_L(size_t start = 0) {
-		L.resize(size());									//allocate space for the L array
-		if (start == 0) {
-			L[0] = 0;											//initialize the length value for the first point to zero (0)
-			start++;
-		}
-
-		stim::vec3<T> d;
-		for (size_t i = start; i < size(); i++) {		//for each line segment in the centerline
-			d = at(i) - at(i - 1);
-			L[i] = L[i - 1] + d.len();				//calculate the running length total
-		}
-	}
  
 	/// stitch two centerlines
 	///@param c1, c2: two centerlines
@@ -79,6 +79,10 @@ class network{
  
 		}
 */
+		edge(std::vector<stim::vec3<T> p, std::vector<T> s)
+			: cylinder<T>(p,s)
+		{
+		}
 		///@param p is an array of positions in space
 		edge(stim::centerline<T> p) : cylinder<T>(p){}
  
@@ -141,24 +145,25 @@ class network{
 			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;
+//			stim::centerline<T> temp = stim::centerline<T>(sz);		//allocate the new edge
+//			e = edge(temp);
+			std::vector<stim::vec3<T> > p(sz);
+			std::vector<T> r(sz);
 			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<char*>(&point[0]), 3*sizeof(T));
-				e[i] = point;
+				p[i] = point;
 				T mag;
 		//				for(int j = 0; j < nmags(); j++)		///future code for mags
 		//				{
 				in.read(reinterpret_cast<char*>(&mag), sizeof(T));	
-				e.set_r(i, mag);
+				r[i] = mag;
 				//std::cout << point.str() << " " << mag << std::endl;
 		//				}
 			}
-			e.init();
-			e.update();
+			e = edge(p,r);
+			e.v[0] = v0; e.v[1] = v1;
 			return in;
 		}
 	};
 #ifndef STIM_CSV_H
 #define STIM_CSV_H
  
+#include <type_traits>
 #include <vector>
 #include <sstream>
 #include <fstream>
@@ -105,4 +106,4 @@ namespace stim{
 };
  
  
-#endif
 \ No newline at end of file
+#endif
@@ -18,6 +18,20 @@ protected:
 	std::vector< T > R;				//stores a list of magnitudes for each point in the centerline (assuming mags[0] is the radius)
  
 	using stim::centerline<T>::findIdx;
+
+	void init() {
+		U.resize(size());			//allocate space for the frenet frame vectors
+//		if (R.size() != 0)
+		R.resize(size());
+
+		stim::circle<T> c;								//create a circle
+		stim::vec3<T> d0, d1;
+		for (size_t i = 0; i < size() - 1; i++) {		//for each line segment in the centerline
+			c.rotate(d(i));								//rotate the circle to match that normal
+			U[i] = c.U;									//save the U vector from the circle
+		}
+		U[size() - 1] = c.U;							//for the last point, duplicate the final frenet frame vector
+	}
  
 	//calculates the U values for each point to initialize the frenet frame
 	//	this function assumes that the centerline has already been set
@@ -34,6 +48,19 @@ public:
 	cylinder(centerline<T>c) : centerline<T>(c) {
 		init();
 	}
+
+	cylinder(std::vector<stim::vec3<T> > p, std::vector<T> s)
+		: centerline<T>(p)
+	{
+		R = s;
+		init();
+	{
+
+	cylinder(stim::centerline<T> p, std::vector<T> s)
+	{
+		d = s;
+		init();
+	{
  
 	//cylinder(centerline<T>c, T r) : centerline(c) {
 	//	init();
@@ -82,19 +109,6 @@ public:
 		return R[i];
 	}
  
-	void init() {
-		U.resize(size());			//allocate space for the frenet frame vectors
-//		if (R.size() != 0)
-		R.resize(size());
-
-		stim::circle<T> c;								//create a circle
-		stim::vec3<T> d0, d1;
-		for (size_t i = 0; i < size() - 1; i++) {		//for each line segment in the centerline
-			c.rotate(d(i));								//rotate the circle to match that normal
-			U[i] = c.U;									//save the U vector from the circle
-		}
-		U[size() - 1] = c.U;							//for the last point, duplicate the final frenet frame vector
-	}
  
 	///adds a magnitude to each point in the cylinder
 	/*void add_mag(V val = 0) {