From 8495a970270ff4fc04982ab2b510408f9a1b5cf3 Mon Sep 17 00:00:00 2001
From: pgovyadi <pgovyadi@gmail.com>
Date: Thu, 4 Feb 2016 14:43:07 -0600
Subject: [PATCH] added comments to cylinder

---
 stim/visualization/cylinder.h | 36 ++++++++++++++++++++++++++++++------
 1 file changed, 30 insertions(+), 6 deletions(-)

diff --git a/stim/visualization/cylinder.h b/stim/visualization/cylinder.h
index 31524d2..49e3dec 100644
--- a/stim/visualization/cylinder.h
+++ b/stim/visualization/cylinder.h
@@ -11,22 +11,26 @@ template<typename T>
 class cylinder
 {
 	private:
-		stim::circle<T> s;
-		std::vector< stim::vec<T> > pos;
-		std::vector< stim::vec<T> > mags;
-		std::vector< T > L;
+		stim::circle<T> s;			//an arbitrary circle
+		std::vector< stim::vec<T> > pos;	//positions of the cylinder.
+		std::vector< stim::vec<T> > mags;	//radii at each position
+		std::vector< T > L;			//length of the cylinder at each position.
 	
+		///default init	
 		void
 		init()
 		{
 
 		}
 
+		///inits the cylinder from a list of points (inP) and radii (inM)
 		void
 		init(std::vector<stim::vec<T> > inP, std::vector<stim::vec<T> > inM)
 		{
 			pos = inP;
 			mags = inM;
+
+			//calculate each L.
 			L.resize(pos.size()-1);
 			T temp = (T)0;
 			for(int i = 0; i < L.size()-1; i++)
@@ -36,6 +40,7 @@ class cylinder
 			}
 		}
 		
+		///returns the direction vector at point idx.
 		stim::vec<T>
 		d(int idx)
 		{
@@ -43,6 +48,7 @@ class cylinder
 			
 		}
 
+		///returns the total length of the line at index j.
 		T
 		getl(int j)
 		{
@@ -53,6 +59,8 @@ class cylinder
 			}
 		}
 
+		///finds the index of the point closest to the length l on the lower bound.
+		///binary search.
 		int
 		findIdx(T l)
 		{
@@ -76,13 +84,13 @@ class cylinder
 		}
 
 	public:
+		///default constructor
 		cylinder()
 		{
 
 		}
 
 		///constructor to create a cylinder from a set of points, radii, and the number of sides for the cylinder.
-		///The higher the number of sides, the more rectangeles compose the surface of the cylinder.
 		///@param inP:  Vector of stim vecs composing the points of the centerline.
 		///@param inM:  Vector of stim vecs composing the radii of the centerline.
 		cylinder(std::vector<stim::vec<T> > inP, std::vector<stim::vec<T> > inM)
@@ -92,6 +100,8 @@ class cylinder
 
 
 		///Returns a position vector at the given p-value (p value ranges from 0 to 1).
+		///interpolates the position along the line.
+		///@param pvalue: the location of the in the cylinder, from 0 (beginning to 1).
 		stim::vec<T>
 		p(T pvalue)
 		{
@@ -102,6 +112,10 @@ class cylinder
 			return (pos[idx] + (pos[idx+1]-pos[idx])*((l-L[idx])/(L[idx+1]- L[idx])));
 		}
 
+		///Returns a position vector at the given length into the fiber (based on the pvalue).
+		///Interpolates the radius along the line.
+		///@param l: the location of the in the cylinder.
+		///@param idx: integer location of the point closest to l but prior to it.
 		stim::vec<T>
 		p(T l, int idx)
 		{
@@ -109,6 +123,8 @@ class cylinder
 		}
 
 		///Returns a radius at the given p-value (p value ranges from 0 to 1).
+		///interpolates the radius along the line.
+		///@param pvalue: the location of the in the cylinder, from 0 (beginning to 1).
 		T
 		r(T pvalue)
 		{
@@ -119,6 +135,10 @@ class cylinder
 			return (mags[idx] + (mags[idx+1]-mags[idx])*((l-L[idx])/(L[idx+1]- L[idx])));
 		}
 
+		///Returns a radius at the given length into the fiber (based on the pvalue).
+		///Interpolates the position along the line.
+		///@param l: the location of the in the cylinder.
+		///@param idx: integer location of the point closest to l but prior to it.
 		T
 		r(T l, int idx)
 		{
@@ -127,7 +147,9 @@ class cylinder
 
 
 		///returns the position of the point with a given pvalue and theta on the surface
-		///in x, y, z coordinates. Theta is in degrees from 0 to 360
+		///in x, y, z coordinates. Theta is in degrees from 0 to 360.
+		///@param pvalue: the location of the in the cylinder, from 0 (beginning to 1).
+		///@param theta: the angle to the point of a circle.
 		stim::vec<T>
 		surf(T pvalue, T theta)
 		{
@@ -142,6 +164,8 @@ class cylinder
 			return(s.p(theta));
 		}
 
+		///returns a vector of points necessary to create a circle at every position in the fiber.
+		///@param sides: the number of sides of each circle.	
 		std::vector<std::vector<vec<T> > >
 		getPoints(int sides)
 		{
--
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