fixed majority of the merge conflicts, edited vector.h and vec3.h and spider.h i…

…n order to accomplish this. added copy constructors and additional necessary methods.

fixed majority of the merge conflicts, edited vector.h and vec3.h and spider.h i…
…n order to accomplish this. added copy constructors and additional necessary methods.
Pavel Govyadinov
1 parent 03c403fa
Showing 4 changed files with 133 additions and 121 deletions Show diff stats
stim/gl/gl_spider.h
stim/math/vec3.h
stim/math/vector.h
stim/visualization/cylinder.h
@@ -7,13 +7,14 @@
 #include <cuda_gl_interop.h>
 #include <cudaGL.h>
 #include <math.h>
-#include "stim/gl/gl_texture.h"
-#include "stim/visualization/camera.h"
-#include "stim/gl/error.h"
-#include "stim/math/vector.h"
-#include "stim/math/rect.h"
-#include "stim/math/matrix.h"
-#include "stim/cuda/spider_cost.cuh"
+#include <stim/gl/gl_texture.h>
+#include <stim/visualization/camera.h>
+#include <stim/gl/error.h>
+#include <stim/math/vector.h>
+#include <stim/math/vec3.h>
+#include <stim/math/rect.h>
+#include <stim/math/matrix.h>
+#include <stim/cuda/spider_cost.cuh>
 #include <stim/cuda/cudatools/glbind.h>
 #include <stim/cuda/arraymath.cuh>
 #include <stim/cuda/cudatools.h>
@@ -48,15 +49,15 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 	private:
 		//
-		stim::vec<float> p;  	//vector designating the position of the spider.
-		stim::vec<float> d;	//vector designating the orientation of the spider
+		stim::vec3<float> p;  	//vector designating the position of the spider.
+		stim::vec3<float> d;	//vector designating the orientation of the spider
 						//always a unit vector.
-		stim::vec<float> m;	//magnitude of the spider vector.
+		stim::vec3<float> m;	//magnitude of the spider vector.
 						//mag[0] = length.
 						//mag[1] = width.
-		std::vector<stim::vec<float> > dV;	//A list of all the direction vectors.
-		std::vector<stim::vec<float> > pV;	//A list of all the position vectors.
-		std::vector<stim::vec<float> > mV;	//A list of all the size vectors.
+		std::vector<stim::vec3<float> > dV;	//A list of all the direction vectors.
+		std::vector<stim::vec3<float> > pV;	//A list of all the position vectors.
+		std::vector<stim::vec3<float> > mV;	//A list of all the size vectors.
 		stim::matrix<float, 4> cT;		//current Transformation matrix
 							//From tissue space to texture space.
@@ -88,21 +89,21 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		//Tracing variables.
-		std::stack< stim::vec<float> > 	seeds;		//seed positions.
-		std::stack< stim::vec<float> > 	seedsvecs;	//seed directions.
+		std::stack< stim::vec3<float> > seeds;		//seed positions.
+		std::stack< stim::vec3<float> > seedsvecs;	//seed directions.
 		std::stack< float > 		seedsmags;	//seed magnitudes.
-		std::vector< stim::vec<float> > cL;	//Positions of line currently being traced.
-		std::vector< stim::vec<float> > cD;	//Direction of line currently being traced.
+		std::vector< stim::vec3<float> > cL;	//Positions of line currently being traced.
+		std::vector< stim::vec3<float> > cD;	//Direction of line currently being traced.
 		std::vector< stim::vec<float> > cM;	//Magnitude of line currently being traced.
 		stim::glnetwork<float> nt;		//object for storing the network.
 		stim::vec<float> rev;			//reverse vector;
 		stim::camera camSel;
-		stim::vec<float> ps;
-		stim::vec<float> ups;
-		stim::vec<float> ds;
+		stim::vec3<float> ps;
+		stim::vec3<float> ups;
+		stim::vec3<float> ds;
 		static const float t_length = 16.0;
@@ -188,7 +189,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			glCallList(dList+3);
 			std::vector< stim::vec<float> > result = find_branch(
 					btexbufferID, GL_TEXTURE_2D, 16, 216);
-			stim::vec<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
+			stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
 			if(!result.empty())
 			{
 				for(int i = 1; i < result.size(); i++)
@@ -200,11 +201,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 						1.0);
 					cylp = cT*cylp;
-					stim::vec<float> vec(
+					stim::vec3<float> vec(
 						cylp[0]*S[0]*R[0],
 						cylp[1]*S[1]*R[1],
 						cylp[2]*S[2]*R[2]);
-					stim::vec<float> seeddir(-p[0] + cylp[0]*S[0]*R[0],
+					stim::vec3<float> seeddir(-p[0] + cylp[0]*S[0]*R[0],
 						   -p[1] + cylp[1]*S[1]*R[1],
 						   -p[2] + cylp[2]*S[2]*R[2]);
 						seeddir = seeddir.norm();
@@ -236,7 +237,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			DrawLongCylinder(n, l_template, l_square);
 			stim::cylinder<float> cyl(cL, cM);
 			std::vector< stim::vec<float> > result = find_branch(btexbufferID, GL_TEXTURE_2D, n*l_square, (cL.size()-1)*l_template);
-			stim::vec<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
+			stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
 			float pval;
 			if(!result.empty())
 			{
@@ -257,8 +258,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 					{
 						pval = (cyl.getl(id)/cyl.getl(cL.size()-1));
 					}
-					stim::vec<float> v = cyl.surf(pval, result[i][0]);
-					stim::vec<float> di = cyl.p(pval);
+					stim::vec3<float> v = cyl.surf(pval, result[i][0]);
+					stim::vec3<float> di = cyl.p(pval);
 					float rad = cyl.r(pval);
 					if(
 					 !(v[0] > size[0] || v[1] > size[1]
@@ -287,15 +288,15 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			return cos(2.0*atan(1.0)*u2)*sqrt(-1.0*log(u1));
 		}
-		stim::vec<float> uniformRandVector()
+		stim::vec3<float> uniformRandVector()
 		{
-			stim::vec<float> r(uniformRandom(), uniformRandom(), 1.0);
+			stim::vec3<float> r(uniformRandom(), uniformRandom(), 1.0);
 			return r;
 		}
-		stim::vec<float> normalRandVector()
+		stim::vec3<float> normalRandVector()
 		{
-			stim::vec<float> r(normalRandom(), normalRandom(), 1.0);
+			stim::vec3<float> r(normalRandom(), normalRandom(), 1.0);
 			return r;
 		}
@@ -339,10 +340,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			float z, theta, phi;
-			std::vector<stim::vec<float> > vecsUni;
+			std::vector<stim::vec3<float> > vecsUni;
 			for(int i = 0; i < numSamplesPos; i++)
 			{
-				stim::vec<float> a(uniformRandom()*0.8, uniformRandom()*0.8, 0.0);
+				stim::vec3<float> a(uniformRandom()*0.8, uniformRandom()*0.8, 0.0);
 				a[0] = a[0]-0.4;
 				a[1] = a[1]-0.4;
 				vecsUni.push_back(a);
@@ -369,10 +370,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		{
 			//Set up the vectors necessary for Rectangle creation.
-			vec<float> Y(1.0,0.0,0.0);		//orthogonal vec.
-			vec<float> pos(0.0,0.0,0.0);
-			vec<float> mag(1.0, 1.0, 1.0);
-			vec<float> dir(0.0, 0.0, 1.0);
+			stim::vec3<float> Y(1.0,0.0,0.0);		//orthogonal vec.
+			stim::vec3<float> pos(0.0,0.0,0.0);
+			stim::vec3<float> mag(1.0, 1.0, 1.0);
+			stim::vec3<float> dir(0.0, 0.0, 1.0);
 			float PHI[2], Z[2], range;
 			PHI[0] = solidAngle/2;
@@ -390,8 +391,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 				z = uniformRandom()*range + Z[1];
 				theta = uniformRandom()*2*M_PI;
 				phi = acos(z);
-				stim::vec<float> sph(1, theta, phi);
-				stim::vec<float> cart = sph.sph2cart();
+				stim::vec3<float> sph(1, theta, phi);
+				stim::vec3<float> cart = sph.sph2cart();
 				dV.push_back(cart);
 				if(cos(Y.dot(cart)) < 0.087)
 				{
@@ -420,16 +421,16 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		genPositionVectors(float delta = 0.4)
 		{
 			//Set up the vectors necessary for Rectangle creation.
-			vec<float> Y(1.0,0.0,0.0);		//orthogonal vec.
-			vec<float> pos(0.0,0.0,0.0);
-			vec<float> mag(1.0, 1.0, 1.0);
-			vec<float> dir(0.0, 0.0, 1.0);
+			stim::vec3<float> Y(1.0,0.0,0.0);		//orthogonal vec.
+			stim::vec3<float> pos(0.0,0.0,0.0);
+			stim::vec3<float> mag(1.0, 1.0, 1.0);
+			stim::vec3<float> dir(0.0, 0.0, 1.0);
 			//Set up the variable necessary for vector creation.
 			glNewList(dList+1, GL_COMPILE);
 			for(int i = 0; i < numSamplesPos; i++)
 			{
-				stim::vec<float> temp = uniformRandVector();
+				stim::vec3<float> temp = uniformRandVector();
 				temp = temp*delta*2.0 - delta/2.0;
 				temp[2] = 0.0;
 				pV.push_back(temp);
@@ -456,10 +457,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		{
 			//Set up the vectors necessary for Rectangle creation.
-			vec<float> Y(1.0, 0.0, 0.0);		//orthogonal vec.
-			vec<float> pos(0.0, 0.0, 0.0);
-			vec<float> mag(1.0, 1.0, 1.0);
-			vec<float> dir(0.0, 0.0, 1.0);
+			stim::vec3<float> Y(1.0, 0.0, 0.0);		//orthogonal vec.
+			stim::vec3<float> pos(0.0, 0.0, 0.0);
+			stim::vec3<float> mag(1.0, 1.0, 1.0);
+			stim::vec3<float> dir(0.0, 0.0, 1.0);
 			//Set up the variable necessary for vector creation.
 			int dim = (sqrt(numSamplesMag)-1)/2;
@@ -467,7 +468,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			float max 	= 1.0+delta;
 			float step	= (max-min)/(numSamplesMag-1);
 			float factor;
-			vec<float> temp(0.0,0.0,0.0);
+			stim::vec3<float> temp(0.0,0.0,0.0);
 			glNewList(dList+2, GL_COMPILE);
 			for(int i = 0; i < numSamplesMag; i++){
@@ -495,10 +496,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		void
 		UpdateBuffer(float v_x, float v_y)
 		{	
-			stim::vec<float>p1; 
-        	        stim::vec<float>p2; 
-	                stim::vec<float>p3; 
-                	stim::vec<float>p4;	
+			stim::vec3<float>p1; 
+        	        stim::vec3<float>p2; 
+	                stim::vec3<float>p3; 
+                	stim::vec3<float>p4;	
 			p1 = hor.p(1,1);
 			p2 = hor.p(1,0);
 			p3 = hor.p(0,0);
@@ -712,10 +713,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		Bind(GLuint &textureID, GLuint &framebufferID, int nSamples, float len = 8.0)
 		{
-//			std::cout << glGetIntegerv(GL_MAX_TEXTURE_SIZE) << std::endl;
-			GLint max;
-			glGetIntegerv(GL_MAX_TEXTURE_SIZE, &max);
-//			std::cout << max << std::endl;
 			glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);//set up GL buffer
 			glFramebufferTexture2D(
 				GL_FRAMEBUFFER,
@@ -727,8 +724,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};
 			glDrawBuffers(1, DrawBuffers);
 			glBindTexture(GL_TEXTURE_2D, textureID);
-//			glClearColor(1,1,1,1);
-//			glClear(GL_COLOR_BUFFER_BIT);
 			glMatrixMode(GL_PROJECTION);
 			glLoadIdentity();
 			glMatrixMode(GL_MODELVIEW);
@@ -837,10 +832,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		initCuda()
 		{	
 			stim::cudaSetDevice();
-			MonteCarloDirectionVectors(500);
-			//GLint max;
-			//glGetIntegerv(GL_MAX_TEXTURE_SIZE, &max);
-			//std::cout << max << std::endl;
 		}
 		//horizonal rectangle forming the spider.
@@ -869,11 +860,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		(int samples = 1089, int samplespos = 441,int samplesmag = 144)
 		{
 //			std::cout << "I ran this constructor" << std::endl;
-			p = vec<float>(0.0, 0.0, 0.0);
-			d = vec<float>(0.0, 0.0, 1.0);
-			m = vec<float>(1.0, 1.0);
-			S = vec<float>(1.0, 1.0, 1.0);
-			R = vec<float>(1.0, 1.0, 1.0);
+			p = stim::vec3<float>(0.0, 0.0, 0.0);
+			d = stim::vec3<float>(0.0, 0.0, 1.0);
+			m = stim::vec<float>(1.0, 1.0);
+			S = stim::vec3<float>(1.0, 1.0, 1.0);
+			R = stim::vec3<float>(1.0, 1.0, 1.0);
 //			std::cout << samples << std::endl;
 			numSamples = samples;
 //			std::cout << numSamples << std::endl;
@@ -894,11 +885,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		(float pos_x, float pos_y, float pos_z, float dir_x, float dir_y, float dir_z,
 			float mag_x, int numsamples = 1089, int numsamplespos = 441, int numsamplesmag =144)
 		{
-			p = vec<float>(pos_x, pos_y, pos_z);
-			d = vec<float>(dir_x, dir_y, dir_z);
-			m = vec<float>(mag_x, mag_x, mag_x);
-			S = vec<float>(1.0,1.0,1.0);
-			R = vec<float>(1.0,1.0,1.0);
+			p = stim::vec3<float>(pos_x, pos_y, pos_z);
+			d = stim::vec3<float>(dir_x, dir_y, dir_z);
+			m = stim::vec<float>(mag_x, mag_x, mag_x);
+			S = stim::vec3<float>(1.0,1.0,1.0);
+			R = stim::vec3<float>(1.0,1.0,1.0);
 			numSamples = numsamples;
 			numSamplesPos = numsamplespos;
 			numSamplesMag = numsamplesmag;
@@ -910,13 +901,13 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		///@param float mag, size of the vector.
 		///@param int 	samples, number of templates this spider is going to use.
 		gl_spider
-		(stim::vec<float> pos, stim::vec<float> dir, float mag, int samples = 1089, int samplesPos = 441, int samplesMag = 144)
+		(stim::vec3<float> pos, stim::vec3<float> dir, float mag, int samples = 1089, int samplesPos = 441, int samplesMag = 144)
 		{
 			p = pos;
 			d = dir;
 			m = vec<float>(mag, mag, mag);
-			S = vec<float>(1.0,1.0,1.0);
-			R = vec<float>(1.0,1.0,1.0);
+			S = vec3<float>(1.0,1.0,1.0);
+			R = vec3<float>(1.0,1.0,1.0);
 			numSamples = samples;
 			numSamplesPos = samplesPos;
 			numSamplesMag = samplesMag;
@@ -978,14 +969,14 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 //-----------------------------ACCESS METHODS-------------------------------//
 //--------------------------------------------------------------------------//
 		///Returns the p vector.
-		vec<float>
+		vec3<float>
 		getPosition()
 		{
 			return p;
 		}
 		///Returns the d vector.
-		vec<float>
+		vec3<float>
 		getDirection()
 		{
 			return d;
@@ -1001,7 +992,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		///@param stim::vec<float> pos, the new p.
 		///Sets the p vector to input vector pos.
 		void
-		setPosition(vec<float> pos)
+		setPosition(stim::vec3<float> pos)
 		{
 			p = pos;
 		}
@@ -1021,7 +1012,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		///@param stim::vec<float> dir, the new d.
 		///Sets the d vector to input vector dir.
 		void
-		setDirection(vec<float> dir)
+		setDirection(stim::vec3<float> dir)
 		{
 			d = dir;
 		}
@@ -1041,7 +1032,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		///@param stim::vec<float> dir, the new d.
 		///Sets the m vector to the input vector mag.	
 		void
-		setMagnitude(vec<float> mag)
+		setMagnitude(stim::vec<float> mag)
 		{
 			m[0] = mag[0];
 			m[1] = mag[0];
@@ -1071,7 +1062,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		///@param stim::vec<float> Dims, voxel size.
 		///Sets the voxel sizes in each direction. necessary for non-standard data.
 		void
-		setDims(stim::vec<float> Dims)
+		setDims(stim::vec3<float> Dims)
 		{
 			S = Dims;
 		}
@@ -1091,7 +1082,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		///@param stim::vec<float> Dims, size of the volume.
 		///Sets the data volume sizes in each direction.
 		void
-		setSize(stim::vec<float> Siz)
+		setSize(stim::vec3<float> Siz)
 		{
 			S = Siz;
 		}
@@ -1125,7 +1116,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		///Adds a seed to the seed list.
 		///Assumes that the coordinates passes are in tissue space.
 		void
-		setSeed(stim::vec<float> pos)
+		setSeed(stim::vec3<float> pos)
 		{
 			seeds.push(pos);
 		}
@@ -1133,7 +1124,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		///@param stim::vec<float> dir, the direction of the seed to be added.
 		///Adds a seed to the seed directions list.
 		void
-		setSeedVec(stim::vec<float> dir)
+		setSeedVec(stim::vec3<float> dir)
 		{
 			seedsvecs.push(dir);
 		}
@@ -1173,18 +1164,18 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		}
 		///Method to get the top of the seed positions stack.
-		stim::vec<float> 
+		stim::vec3<float> 
 		getLastSeed()
 		{
-			stim::vec<float> tp = seeds.top();
+			stim::vec3<float> tp = seeds.top();
 			return tp;
 		}
 		///Method to get the top of the seed direction stack.
-		stim::vec<float> 
+		stim::vec3<float> 
 		getLastSeedVec()
 		{
-			stim::vec<float> tp = seedsvecs.top();
+			stim::vec3<float> tp = seedsvecs.top();
 			return tp;
 		}
@@ -1206,7 +1197,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		}
 		///returns the seeds position stack.
-		std::stack<stim::vec<float> >
+		std::stack<stim::vec3<float> >
 		getSeeds()
 		{
 			return seeds;
@@ -1252,7 +1243,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			for(int i = 0; i < nt.sizeE(); i++)
 			{
 				std::vector<stim::vec< float > > cm = nt.getEdgeCenterLineMag(i);
-                 		std::vector<stim::vec< float > > ce = nt.getEdgeCenterLine(i);
+                 		std::vector<stim::vec3< float > > ce = nt.getEdgeCenterLine(i);
 				sk.Begin(stim::OBJ_LINE);
 				for(int j = 0; j < ce.size(); j++)
 				{
@@ -1269,7 +1260,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		stim::glObj<float>
 		getNetwork()
 		{
-//			return sk;
+
 		}
 		///returns a COPY of the entire stim::glnetwork object.
@@ -1295,7 +1286,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		void
 		Update()
 		{
-			vec<float> Y(1.0,0.0,0.0);
+			vec3<float> Y(1.0,0.0,0.0);
 			if(cos(Y.dot(d))< 0.087){
 				Y[0] = 0.0; Y[1] = 1.0;}
 			hor = stim::rect<float>(m, p, d.norm(),
@@ -1389,7 +1380,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			GenerateFBO(n*l_square, cylLen*l_template, btexbufferID, bfboID);
 			Bind(btexbufferID, bfboID, cylLen, l_template*l_square/2.0);
 			stim::cylinder<float> cyl(cL, cM);
-			std::vector<std::vector<stim::vec<float> > > p = cyl.getPoints(n);
+			std::vector<std::vector<stim::vec3<float> > > p = cyl.getPoints(n);
 			for(int i = 0; i < p.size()-1; i++)	///number of circles
 			{
 				for(int j = 0; j < p[0].size()-1; j++)		///points in the circle
@@ -1418,11 +1409,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		void
 		trace(int min_cost)
 		{	
-//			rev = stim::vec<float>(0.0,0.0,1.0);
 			bool sEmpty = true;
 			float lastmag = 16.0;;
-			stim::vec<float> curSeed; 
-			stim::vec<float> curSeedVec;			
+			stim::vec3<float> curSeed; 
+			stim::vec3<float> curSeedVec;			
 			float curSeedMag;
 			while(!Empty())
 			{
@@ -1448,7 +1438,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		}
 		int
-		selectObject(stim::vec<float> loc, stim::vec<float> dir, float mag) 
+		selectObject(stim::vec3<float> loc, stim::vec3<float> dir, float mag) 
 		{
 		//Define the varibles and turn on Selection Mode
@@ -1554,10 +1544,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		}	
 		void
-		addToNetwork(pair<stim::fiber<float>, int> in, stim::vec<float> spos, 
-				stim::vec<float> smag, stim::vec<float> sdir)
+		addToNetwork(pair<stim::fiber<float>, int> in, stim::vec3<float> spos, 
+				stim::vec<float> smag, stim::vec3<float> sdir)
 		{
-                        std::vector<stim::vec<float> > ce = in.first.centerline();                
+                        std::vector<stim::vec3<float> > ce = in.first.centerline();                
                         std::vector<stim::vec<float> > cm = in.first.centerlinemag();
 			//if the fiber is longer than 2 steps (the number it takes to diverge)
 			if(ce.size() > 3)
@@ -1602,12 +1592,12 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		}
 		std::pair<stim::fiber<float>, int >
-		traceLine(stim::vec<float> pos, stim::vec<float> mag, int min_cost)
+		traceLine(stim::vec3<float> pos, stim::vec<float> mag, int min_cost)
 		{
 			//starting (seed) position and magnitude.
-			stim::vec<float> spos = getPosition();
+			stim::vec3<float> spos = getPosition();
 			stim::vec<float> smag = getMagnitude();
-			stim::vec<float> sdir = getDirection();	
+			stim::vec3<float> sdir = getDirection();	
 			Bind();
 //			sk.Begin(stim::OBJ_LINE);
@@ -1624,7 +1614,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			int h;
 			bool started = false;
 			bool running = true;
-			stim::vec<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
+			stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
 			while(running)
 			{
 				int cost = Step();
@@ -1684,7 +1674,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 							break;
 						}
 						else {  
-							cL.push_back(stim::vec<float>(p[0], p[1],p[2]));
+							cL.push_back(stim::vec3<float>(p[0], p[1],p[2]));
 							cM.push_back(stim::vec<float>(m[0], m[0]));
 //							Bind(btexbufferID, bfboID, 27);
 							Unbind();
@@ -37,10 +37,14 @@ public:
 	}
 	//access an element using an index
-	CUDA_CALLABLE T& operator[](int idx){
+	CUDA_CALLABLE T& operator[](size_t idx){
 		return ptr[idx];
 	}
+	CUDA_CALLABLE T* data(){
+		return ptr;
+	}
+
 /// Casting operator. Creates a new vector with a new type U.
 	template< typename U >
 	CUDA_CALLABLE operator vec3<U>(){
@@ -249,4 +253,4 @@ std::ostream&amp; operator&lt;&lt;(std::ostream&amp; os, stim::vec3&lt;T&gt; const&amp; rhs){
 	return os;
 }
-#endif
 \ No newline at end of file
+#endif
@@ -74,6 +74,13 @@ struct vec : public std::vector&lt;T&gt;
 			at(i) = other[i];
 		}
 	}
+
+	vec( vec3<T>& other){
+		resize(3);							//resize the current vector to match the copy
+		for(size_t i=0; i<3; i++){	//copy each element
+			at(i) = other[i];
+		}
+	}
 	//I'm not sure what these were doing here.
 	//Keep them now, we'll worry about it later.
@@ -328,15 +335,16 @@ struct vec : public std::vector&lt;T&gt;
 		return *this;
 	}
-	/// Cast to a vec3
-	operator stim::vec3<T>(){
-		stim::vec3<T> r;
-		size_t N = std::min<size_t>(size(), 3);
-		for(size_t i = 0; i < N; i++)
-			r[i] = at(i);
-		return r;
-	}
-
+	/// Cast to a vec3
+	operator stim::vec3<T>(){
+		stim::vec3<T> r;
+		size_t N = std::min<size_t>(size(), 3);
+		for(size_t i = 0; i < N; i++)
+			r[i] = at(i);
+		return r;
+	}
+
+
 	/// Casting and assignment
 	template<typename Y>
 	vec<T> & operator=(vec<Y> rhs){
@@ -347,6 +355,16 @@ struct vec : public std::vector&lt;T&gt;
 			at(i) = rhs[i];
 		return *this;
 	}
+
+	/// Assign a vec = vec3
+	template<typename Y>
+	vec<T> & operator=(vec3<Y> rhs)
+	{
+		resize(3);
+		for(size_t i=0; i<3; i++)
+			at(i) = rhs[i];
+		return *this;
+	}
 	/// Unary minus (returns the negative of the vector)
 	vec<T> operator-() const{
@@ -23,7 +23,7 @@ class cylinder
 		}
-		///inits the cylinder from a list of points (inP) and radii (inM)
+		///inits the cylinder from a list of points (std::vector of stim::vec3 --inP) and radii (inM)
 		void
 		init(std::vector<stim::vec3<T> > inP, std::vector<stim::vec<T> > inM)
 		{
@@ -142,14 +142,15 @@ class cylinder
 		}
 		///constructor to create a cylinder from a set of points, radii, and the number of sides for the cylinder.
-		///@param inP:  Vector of stim vecs composing the points of the centerline.
+		///@param inP:  Vector of stim vec3 composing the points of the centerline.
 		///@param inM:  Vector of stim vecs composing the radii of the centerline.
-		cylinder(std::vector<stim::vec3<T> > inP, std::vector<stim::vec3<T> > inM){
+		cylinder(std::vector<stim::vec3<T> > inP, std::vector<stim::vec<T> > inM){
 			init(inP, inM);
 		}
+
 		///Constructor defines a cylinder with centerline inP and magnitudes of zero
-		///@param inP: Vector of stim vecs composing the points of the centerline
+		///@param inP: Vector of stim vec3 composing the points of the centerline
 		cylinder(std::vector< stim::vec3<T> > inP){
 			std::vector< stim::vec<T> > inM;						//create an array of arbitrary magnitudes
@@ -160,7 +161,6 @@ class cylinder
 			init(inP, inM);
 		}
-
 		///Returns the number of points on the cylinder centerline
 		unsigned int size(){