From a36c385045865d354d3a9876fa97057fc194c2ae Mon Sep 17 00:00:00 2001
From: pgovyadi <pgovyadi@gmail.com>
Date: Mon, 29 Aug 2016 16:16:10 -0500
Subject: [PATCH] fixed the bug that cause the segfault

---
 stim/gl/gl_spider.h           | 16 ++++++----------
 stim/visualization/cylinder.h |  7 +------
 2 files changed, 7 insertions(+), 16 deletions(-)

diff --git a/stim/gl/gl_spider.h b/stim/gl/gl_spider.h
index b7524b8..53242a4 100644
--- a/stim/gl/gl_spider.h
+++ b/stim/gl/gl_spider.h
@@ -240,6 +240,7 @@ class gl_spider // : public virtual gl_texture<T>
 			if(cL.size() < 4){}		///if the size of the fiber is less then 4 we do nothing.
 			else{
 			setMatrix(1);			///finds the current transformation matrix
+
 			DrawLongCylinder(n, l_template, l_square);	///Draw the cylinder.
 			stim::cylinder<float> cyl(cL, cM);
 			std::vector< stim::vec<float> > result = find_branch(cylinder_texID, GL_TEXTURE_2D, n*l_square, (cL.size()-1)*l_template);		///find all the centers in cuda
@@ -734,7 +735,6 @@ class gl_spider // : public virtual gl_texture<T>
 		gl_spider
 		(int samples = 1089, int samplespos = 441,int samplesmag = 144)
 		{
-//			std::cout << "I ran this constructor" << std::endl;
 			p = stim::vec3<float>(0.0, 0.0, 0.0);
 			d = stim::vec3<float>(0.0, 0.0, 1.0);
 			m = 1.0;
@@ -1015,7 +1015,6 @@ class gl_spider // : public virtual gl_texture<T>
 		void
 		setSeedMag(float mag)
 		{
-//			std::cout << "sMag: " << mag << std::endl;
 			seedsmags.push(mag);
 		}
 
@@ -1028,7 +1027,6 @@ class gl_spider // : public virtual gl_texture<T>
 		void
 		setSeed(float x, float y, float z)
 		{
-//			std::cout << "sPos: " << x << " " << y << " " << z << std::endl;
 			seeds.push(stim::vec<float>(x, y, z));
 		}
 
@@ -1039,7 +1037,6 @@ class gl_spider // : public virtual gl_texture<T>
 		void
 		setSeedVec(float x, float y, float z)
 		{
-//			std::cout << "sDir: " << x << " " << y << " " << z << std::endl;
 			seedsvecs.push(stim::vec<float>(x, y, z));
 		}
 		
@@ -1375,7 +1372,6 @@ class gl_spider // : public virtual gl_texture<T>
 //				cL.push_back(curSeed);
 //				cM.push_back(curSeedMag);
 //				cD.push_back(curSeedMag);
-				std::cout << p << m << std::endl;
 				traceLine(p, m, min_cost);
 			}
 		}
@@ -1564,7 +1560,7 @@ class gl_spider // : public virtual gl_texture<T>
 		{
 			//starting (seed) position and magnitude.
 			stim::vec3<float> spos = getPosition();
-			stim::vec<float> smag = getMagnitude();
+			float smag = getMagnitude();
 			stim::vec3<float> sdir = getDirection();	
 
 			Bind();
@@ -1590,7 +1586,7 @@ class gl_spider // : public virtual gl_texture<T>
 					running = false;
 					branchDetection2();
 					addToNetwork(cL, cM);
-					std::cout << "the cost of " << cost << " > " << min_cost << std::endl;
+					std::cerr << "the cost of " << cost << " > " << min_cost << std::endl;
 					break;
 				} else {
 					//Have we found the edge of the map?
@@ -1602,7 +1598,7 @@ class gl_spider // : public virtual gl_texture<T>
 						running = false;
 						branchDetection2();
 						addToNetwork(cL, cM);
-						std::cout << "I hit and edge" << std::endl;
+						std::cerr << "I hit and edge" << std::endl;
 						break;
 					}
 					//If this is the first step in the trace,
@@ -1618,7 +1614,7 @@ class gl_spider // : public virtual gl_texture<T>
 						running = false;
 						branchDetection2();
 						addToNetwork(cL, cM);
-						std::cout << "The templates are too big" << std::endl;
+						std::cerr << "The templates are too big" << std::endl;
 						break;
 					}
 					else
@@ -1626,7 +1622,7 @@ class gl_spider // : public virtual gl_texture<T>
 						h = selectObject(p, getDirection(), m);
 						//Have we hit something previously traced?
 						if(h != -1){
-							std::cout << "I hit the fiber " << h << std::endl;
+							std::cerr << "I hit the fiber " << h << std::endl;
 							running = false;
 							branchDetection2();
 							addToNetwork(cL, cM);
diff --git a/stim/visualization/cylinder.h b/stim/visualization/cylinder.h
index 24bc778..3d5bc64 100644
--- a/stim/visualization/cylinder.h
+++ b/stim/visualization/cylinder.h
@@ -221,13 +221,8 @@ class cylinder
 			: centerline<T>(inP)
 		{
 			std::vector<stim::vec<T> > temp;
-			stim::vec<T> zero;
+			stim::vec<T> zero(0.0,0.0);
 			temp.resize(inM.size(), zero);
-			for(int i = 0; i < inM.size(); i++)
-			{
-				std::cerr << inP[i] << " " <<  inM[i] << std::endl;
-				temp[i][0] = inM[i];
-			}
 			init(inP, temp);
 		}
 
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