added more detailed comments, rewrote the m to be a float value instead of a vec…

…tor. remanded some variable for clarity fixed a couple of inconcistencies.

added more detailed comments, rewrote the m to be a float value instead of a vec…
…tor. remanded some variable for clarity fixed a couple of inconcistencies.
Pavel Govyadinov
1 parent 34ec8a82
Showing 2 changed files with 209 additions and 318 deletions Show diff stats
stim/biomodels/centerline.h
stim/gl/gl_spider.h
@@ -163,25 +163,25 @@ public:
 	/// Return the point on the fiber closest to q
 	/// @param q is the query point used to locate the nearest point on the fiber centerline
-	stim::vec<T> nearest(stim::vec<T> q){
-
-		stim::vec<double> temp( (double) q[0], (double) q[1], (double) q[2]);
-
-		unsigned int idx = ann(temp);		//determine the index of the nearest neighbor
-
-		return stim::vec<T>((T) c[idx][0], (T) c[idx][1], (T) c[idx][2]);	//return the nearest centerline point
-	}
+//	stim::vec<T> nearest(stim::vec<T> q){
+//
+//		stim::vec<double> temp( (double) q[0], (double) q[1], (double) q[2]);
+//
+//		unsigned int idx = ann(temp);		//determine the index of the nearest neighbor
+//
+//		return stim::vec<T>((T) c[idx][0], (T) c[idx][1], (T) c[idx][2]);	//return the nearest centerline point
+//	}
 	/// Return the point index on the fiber closest to q
 	/// @param q is the query point used to locate the nearest point on the fiber centerline
-	unsigned int nearest_idx(stim::vec<T> q){
-
-		stim::vec<double> temp((double) q[0], (double) q[1], (double) q[2]);
-
-		unsigned int idx = ann(temp);		//determine the index of the nearest neighbor
-
-		return idx;	//return the nearest centerline point index
-	}
+//	unsigned int nearest_idx(stim::vec<T> q){
+//
+//		stim::vec<double> temp((double) q[0], (double) q[1], (double) q[2]);
+//
+//		unsigned int idx = ann(temp);		//determine the index of the nearest neighbor
+//
+//		return idx;	//return the nearest centerline point index
+//	}
 	/// Returns the fiber centerline as an array of stim::vec points
 	std::vector< stim::vec<T> > get_centerline(){
@@ -28,9 +28,6 @@
 #include "../../../volume-spider/glnetwork.h"
 #include <stim/visualization/cylinder.h>
 #include <stim/cuda/testKernel.cuh>
-
-//#include <stim/cuda/testKernel.cuh>
-
 #include <iostream>
 #include <fstream>
 #ifdef TIMING
@@ -39,7 +36,6 @@
 #endif
 #ifdef TESTING
-	#include <iostream>
 	#include <cstdio>
 	#include <ctime>
 #endif
@@ -67,16 +63,16 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		stim::vec3<float> p;  	//vector designating the position of the spider.
 		stim::vec3<float> d;	//normalized direction of travel
-		stim::vec<float> m;		//size of the spider in tissue space
+		float m;			//size of the spider in tissue space.
 		std::vector<stim::vec3<float> > dV;	//A list of all the direction vectors.
 		std::vector<stim::vec3<float> > pV;	//A list of all test positions (relative to p)
-		std::vector<stim::vec3<float> > mV;	//A list of all the size vectors.
+		std::vector<float> mV;	//A list of all the size vectors.
 		stim::matrix<float, 4> cT;			//current Transformation matrix (tissue)->(texture)
 		GLuint texID;						//OpenGL ID for the texture to be traced
-		stim::vec<float> S;					//Size of a voxel in the volume.
-		stim::vec<float> R;					//Dimensions of the volume.
+		stim::vec3<float> S;					//Size of a voxel in the volume.
+		stim::vec3<float> R;					//Dimensions of the volume.
 		//GL and Cuda variables
@@ -88,15 +84,17 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		GLuint fboID;				//framebuffer ID for direction templates
 		GLuint texbufferID;			//texture ID for direction templates
+		GLuint direction_buffID;				//framebuffer ID, position templates
+		GLuint direction_texID;		//texture ID, position templates
-		GLuint pfboID;				//framebuffer ID, position templates
-		GLuint ptexbufferID;		//texture ID, position templates
+		GLuint position_buffID;				//framebuffer ID, position templates
+		GLuint position_texID;		//texture ID, position templates
-		GLuint mfboID;				//framebuffer ID, radius templates
-		GLuint mtexbufferID;		//texture ID, radius templates
+		GLuint radius_buffID;				//framebuffer ID, radius templates
+		GLuint radius_texID;		//texture ID, radius templates
-		GLuint bfboID;				//framebuffer ID, cylinder (surrounding fiber)
-		GLuint btexbufferID;		//texture ID, cylinder
+		GLuint cylinder_buffID;				//framebuffer ID, cylinder (surrounding fiber)
+		GLuint cylinder_texID;		//texture ID, cylinder
 		int numSamples;				//The number of templates in the buffer.
 		int numSamplesPos;
@@ -114,7 +112,7 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		std::vector< stim::vec3<float> > cL;	//centerline up to the current point
 		std::vector< stim::vec3<float> > cD;	//directions up to the current point (debugging)
-		std::vector< stim::vec<float> > cM;		//radius up to the current point
+		std::vector< float > cM;		//radius up to the current point
 		stim::glnetwork<float> nt;				//network object holding the currently traced centerlines
 		stim::glObj<float> sk;					//OBJ file storing the network (identical to above)
@@ -128,12 +126,12 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		stim::vec3<float> ups;					//up direction for the selection camera
 		stim::vec3<float> ds;					//direction for the selection camera
-		float t_length;							//length of the template (in pixels)
+		float n_pixels;							//length of the template (in pixels)
 		//cuda texture variables that keep track of the binding.
-		stim::cuda::cuda_texture t_dir;
-		stim::cuda::cuda_texture t_pos;
-		stim::cuda::cuda_texture t_mag;
+		stim::cuda::cuda_texture t_dir;				//cuda_texture object used as an interface between OpenGL and cuda for direction vectors.
+		stim::cuda::cuda_texture t_pos;				//cuda_texture object used as an interface between OpenGL and cuda for position vectors.
+		stim::cuda::cuda_texture t_mag;				//cuda_texture object used as an interface between OpenGL and cuda for size vectors.
 //--------------------------------------------------------------------------//
@@ -147,30 +145,29 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		findOptimalDirection()
 		{
 			#ifdef TIMING
-				gpuStartTimer();
+				gpuStartTimer();	//Timer for profiling
 			#endif
 			setMatrix();			//create the transformation matrix.
 			glCallList(dList);		//move the templates to p, d, m.
-			glFinish();
+			glFinish();			//flush the pipeline
 			#ifdef TIMING
-				direction_time += gpuStopTimer();
+				direction_time += gpuStopTimer();	//profiling
 			#endif
 			#ifdef TESTING
-//				test(texbufferID, GL_TEXTURE_2D,2*t_length,numSamples*t_length, "Final_Cost_Direction.bmp");
+//				test(texbufferID, GL_TEXTURE_2D,2*n_pixels,numSamples*n_pixels, "Final_Cost_Direction.bmp");
 			#endif
 			int best = getCost(t_dir.getTexture(), t_dir.getAuxArray() ,numSamples);		//find min cost.
-			stim::vec<float> next(		//find next vector.
+			stim::vec<float> next(		///calculate the next vector.
 			dV[best][0]*S[0]*R[0],
 			dV[best][1]*S[1]*R[1],
 			dV[best][2]*S[2]*R[2],
 			0);
-			next = (cT*next).norm();	//find next vector.
-			setPosition(	p[0]+next[0]*m[0]/stepsize,
-					p[1]+next[1]*m[0]/stepsize,
-					p[2]+next[2]*m[0]/stepsize);
-			setDirection(next[0], next[1], next[2]);
-							//move forward and change direction.
+			next = (cT*next).norm();	///transform the next vector into Tissue space.
+			setPosition(	p[0]+next[0]*m/stepsize,
+					p[1]+next[1]*m/stepsize,
+					p[2]+next[2]*m/stepsize);	
+			setDirection(next[0], next[1], next[2]);		//move forward and change direction.
 		}
 		/// Method for finding the best d (direction) for the spider.
@@ -180,17 +177,18 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		findOptimalPosition()
 		{
 			#ifdef TIMING
-				gpuStartTimer();
+				gpuStartTimer();	//timer for profiling
 			#endif
 			setMatrix();			//create the transformation matrix.
 			glCallList(dList+1);		//move the templates to p, d, m.
-			glFinish();
+			glFinish();			//flush the pipeline
 //			glFlush();
 			#ifdef TIMING
-				position_time += gpuStopTimer();
+				position_time += gpuStopTimer();		///timer for profiling
 			#endif
 			#ifdef TESTING
+//				test(texbufferID, GL_TEXTURE_2D,2*n_pixels,numSamples*n_pixels, "Final_Cost_Direction.bmp");
 			#endif
 			int best = getCost(t_pos.getTexture(), t_pos.getAuxArray(), numSamplesPos);		//find min cost.
 			stim::vec<float> next(		//find next position.
@@ -198,7 +196,7 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 				pV[best][1],
 				pV[best][2],
 				1);
-			next = cT*next;			//find next position.
+			next = cT*next;			//transform the next position vector into tissue space.
 			setPosition(
 					next[0]*S[0]*R[0],
 					next[1]*S[1]*R[1],
@@ -217,14 +215,14 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 			#endif
 			setMatrix();			//create the transformation.
 			glCallList(dList+2);		//move the templates to p, d, m.
-			glFinish();
+			glFinish();			//flush the drawing pipeline.
 			#ifdef TIMING
 				size_time += gpuStopTimer();
 			#endif
 			#ifdef TESTING
 			#endif
 			int best = getCost(t_mag.getTexture(), t_mag.getAuxArray(), numSamplesMag);		//get best cost.
-			setMagnitude(m[0]*mV[best][0]);	//adjust the magnitude.
+			setMagnitude(m*mV[best]);	//adjust the magnitude.
 		}
@@ -236,80 +234,78 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		branchDetection2(int n = 8, int l_template = 8, int l_square = 8)
 		{
 			#ifdef TIMING
-				gpuStartTimer();
+				gpuStartTimer();		///timer for performance analysis
 			#endif
-			if(cL.size() < 4){}
+			if(cL.size() < 4){}		///if the size of the fiber is less then 4 we do nothing.
 			else{
-			setMatrix(1);
-			DrawLongCylinder(n, l_template, l_square);
+			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(btexbufferID, GL_TEXTURE_2D, n*l_square, (cL.size()-1)*l_template);
-			stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);
-			float pval;
-			if(!result.empty())
+			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
+			stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);			///the borders of the texture.
+			float pval;									//pvalue associated with the points on the cylinder.
+			if(!result.empty())								///if we have any points
 			{
-				for(int i = 0; i < result.size(); i++)
+				for(int i = 0; i < result.size(); i++)					///for each point
 				{
 					int id = result[i][2];
-					if(fmod(result[i][2], id) != 0 && id != 0)
+					if(fmod(result[i][2], id) != 0 && id != 0)			///if the remainer is odd
 					{
 						pval = ((cyl.getl(id+1)-cyl.getl(id))*
-							(fmod(result[i][2], id))+cyl.getl(id))/cyl.getl(cL.size()-1);
+							(fmod(result[i][2], id))+cyl.getl(id))/cyl.getl(cL.size()-1);		///calculate pvalue
 					}
-					else if(id == 0)
+					else if(id == 0)									///if the point is on the edge
 					{
-						pval = (cyl.getl(id+1)*result[i][2])/cyl.getl(cL.size()-1);
+						pval = (cyl.getl(id+1)*result[i][2])/cyl.getl(cL.size()-1);			
 					}
 					else
 					{
-						pval = (cyl.getl(id)/cyl.getl(cL.size()-1));
+						pval = (cyl.getl(id)/cyl.getl(cL.size()-1));					///if the point is somewhere on the surface of the cylinder other than the edge
 					}
-					stim::vec3<float> v = cyl.surf(pval, result[i][0]);
-					stim::vec3<float> di = cyl.p(pval);
-					float rad = cyl.r(pval);
-
-					std::cout << v.str() << " " << di.str() << " " << rad << std::endl;
+					stim::vec3<float> v = cyl.surf(pval, result[i][0]);					///find the coordinates of the point at pval on the surface in tissue space.
+					stim::vec3<float> di = cyl.p(pval);							///find the coord of v in tissue space projected on the centerline.
+					float rad = cyl.r(pval);								///find the radius at the pvalue's location
 					if(
 					 !(v[0] > size[0] || v[1] > size[1]
 					 || v[2] > size[2] || v[0] < 0
-					 || v[1] < 0 || v[2] < 0))
+					 || v[1] < 0 || v[2] < 0))								///if the v point is INSIDE the volume
 					{
-						setSeed(v);
-						setSeedVec((v-di).norm());
-						setSeedMag(rad);
+						setSeed(v);									///add a seedpoint's position.
+						setSeedVec((v-di).norm());							///add a seedpoints direction
+						setSeedMag(rad);								///add the starting radius.
 					}
 				}
 			}
 			}
 			#ifdef TIMING
-				branch_time += gpuStopTimer();
+				branch_time += gpuStopTimer();									///timer for performance.
 			#endif
 		}
 		float uniformRandom()
 		{
-			return (  (float)(rand()))/(  (float)(RAND_MAX));
+			return (  (float)(rand()))/(  (float)(RAND_MAX));							///generates a random number between 0 and 1 using the uniform distribution.
 		}
 		float normalRandom()
 		{
 			float u1 = uniformRandom();
 			float u2 = uniformRandom();
-			return cos(2.0*atan(1.0)*u2)*sqrt(-1.0*log(u1));
+			return cos(2.0*atan(1.0)*u2)*sqrt(-1.0*log(u1));							///generate a random number using the normal distribution between 0 and 1.
 		}
 		stim::vec3<float> uniformRandVector()
 		{
-			stim::vec3<float> r(uniformRandom(), uniformRandom(), 1.0);
+			stim::vec3<float> r(uniformRandom(), uniformRandom(), 1.0);						///generate a random vector using the uniform distribution between 0 and 1.
 			return r;
 		}
 		stim::vec3<float> normalRandVector()
 		{
-			stim::vec3<float> r(normalRandom(), normalRandom(), 1.0);
+			stim::vec3<float> r(normalRandom(), normalRandom(), 1.0);						///generate a random vector using the normal distribution between 0 and 1.
 			return r;
 		}
@@ -332,44 +328,44 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 			//Set up the vectors necessary for Rectangle creation.
 			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);
+			stim::vec3<float> pos(0.0,0.0,0.0);		//center point of a rectangle
+			float mag = 1.0;				//size of the generated rectangle.
+			stim::vec3<float> dir(0.0, 0.0, 1.0);		//normal of the rectangle
-			float PHI[2], Z[2], range;
-			PHI[0] = solidAngle/2;
+			float PHI[2], Z[2], range;			
+			PHI[0] = solidAngle/2;				///Project the solid angle into spherical coordinates
 			PHI[1] = asin(0);
-			Z[0] = cos(PHI[0]);
+			Z[0] = cos(PHI[0]);				///Project the z into spherical coordinates
 			Z[1] = cos(PHI[1]);
-			range = Z[0] - Z[1];
+			range = Z[0] - Z[1];				///The range the possible values can be.
 			float z, theta, phi;
-			glNewList(dList, GL_COMPILE); 		
-			for(int i = 0; i < numSamples; i++)
+			glNewList(dList, GL_COMPILE); 			///create a display list of all the direction templates.
+			for(int i = 0; i < numSamples; i++)		///for each sample
 			{
-				z = uniformRandom()*range + Z[1];
-				theta = uniformRandom()*stim::TAU;
-				phi = acos(z);
-				stim::vec3<float> sph(1, theta, phi);
-				stim::vec3<float> cart = sph.sph2cart();
-				dV.push_back(cart);
-				if(cos(Y.dot(cart)) < 0.087)
+				z = uniformRandom()*range + Z[1];	///generate a z coordinate
+				theta = uniformRandom()*stim::TAU;	///generate a theta coordinate
+				phi = acos(z);				///generate a phi from the z.
+				stim::vec3<float> sph(1, theta, phi);	///combine into a vector in spherical coordinates.
+				stim::vec3<float> cart = sph.sph2cart();///convert to cartesian.	
+				dV.push_back(cart);			///save the generated vector for further use.
+				if(cos(Y.dot(cart)) < 0.087)		///make sure that the Y is not parallel to the new vector.
 				{
 						Y[0] = 0.0; Y[1] = 1.0;
 				}else{
 					Y[0] = 1.0; Y[1] = 0.0;
 				}
-                                hor = stim::rect<float>(mag,
+                                hor = stim::rect<float>(mag,		///generate a rectangle with the new vectro as a normal.
 					 pos, cart,
                        			((Y.cross(cart)).cross(cart)).norm());
-       				ver = stim::rect<float>(mag,
+       				ver = stim::rect<float>(mag,		///generate another rectangle that's perpendicular the first but parallel to the cart vector.
 					 pos, cart,
                        			hor.n());
-				UpdateBuffer(0.0, 0.0+i*t_length);
+				UpdateBuffer(0.0, 0.0+i*n_pixels);	///Put the necessary points into the diplaylist.
 			}
-			glEndList();
+			glEndList();					///finilize the display list.
 		}
 		///@param float delta, How much the rectangles vary in position.
@@ -383,28 +379,28 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		{
 			//Set up the vectors necessary for Rectangle creation.
 			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);
+			stim::vec3<float> pos(0.0,0.0,0.0);		//center point of a rectangle
+			float mag = 1.0;				///size of each rectangle
+			stim::vec3<float> dir(0.0, 0.0, 1.0);		///normal of the rectangle plane.
 			//Set up the variable necessary for vector creation.
-			glNewList(dList+1, GL_COMPILE);
-			for(int i = 0; i < numSamplesPos; i++)
+			glNewList(dList+1, GL_COMPILE);			///generate a new display list.
+			for(int i = 0; i < numSamplesPos; i++)		///for the number of position samples
 			{
-				stim::vec3<float> temp = uniformRandVector();
-				temp = temp*delta*2.0 - delta/2.0;
+				stim::vec3<float> temp = uniformRandVector();	///generate a random point on a plane.
+				temp = temp*delta*2.0 - delta/2.0;		///scale the point
 				temp[2] = 0.0;
-				pV.push_back(temp);
-                		hor = stim::rect<float>(mag,
+				pV.push_back(temp);				///save the point for further use.
+                		hor = stim::rect<float>(mag,			///generate a rectangle with the new vector as a normal.
 					 temp, dir,
                       			((Y.cross(d)).cross(d))
 					.norm());
-                		ver = stim::rect<float>(mag,
+                		ver = stim::rect<float>(mag,			///generate another rectangle that's perpendicular the first but parallel to the cart vector.
 					 temp, dir,
                         		hor.n());
-				UpdateBuffer(0.0, 0.0+i*t_length);
+				UpdateBuffer(0.0, 0.0+i*n_pixels);		///sample the necessary points and put them into a display list.
 			}
-			glEndList();
+			glEndList();					///finilize the display list.
 		}
 		///@param float delta, How much the rectangles are allowed to expand.
@@ -419,35 +415,32 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 			//Set up the vectors necessary for Rectangle creation.
 			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);
+			stim::vec3<float> pos(0.0, 0.0, 0.0);		//center of the future rect.
+			float mag = 1.0;				///size of the rectangle
+			stim::vec3<float> dir(0.0, 0.0, 1.0);		///normal of the rectangle plane.
 			//Set up the variable necessary for vector creation.
-			int dim = (sqrt(numSamplesMag)-1)/2;
-			float min 	= 1.0-delta;
-			float max 	= 1.0+delta;
-			float step	= (max-min)/(numSamplesMag-1);
+			float min 	= 1.0-delta;			///smallest size
+			float max 	= 1.0+delta;			///largers size.
+			float step	= (max-min)/(numSamplesMag-1);	///the size variation from one rect to the next.
 			float factor;
-			stim::vec3<float> temp(0.0,0.0,0.0);
 			glNewList(dList+2, GL_COMPILE);
-			for(int i = 0; i < numSamplesMag; i++){
+			for(int i = 0; i < numSamplesMag; i++){		///for the number of position samples
 				//Create linear index
-				factor = (min+step*i)*mag[0];
-				temp = factor;
-				mV.push_back(temp);	
-				hor = stim::rect<float>(temp,
+				factor = (min+step*i)*mag;		///scaling factor
+				mV.push_back(factor);			///save the size factor for further use.
+				hor = stim::rect<float>(factor,		///generate a rectangle with the new vector as a normal.
 					 pos, dir, 
        	       				((Y.cross(d)).cross(d))
 					.norm());
-               			ver = stim::rect<float>(temp,
+               			ver = stim::rect<float>(factor,		///generate another rectangle that's perpendicular the first but parallel to the cart vector.
 					 pos, dir,
                        			hor.n());
-				UpdateBuffer(0.0, 0.0+i*t_length);
+				UpdateBuffer(0.0, 0.0+i*n_pixels);	///sample the necessary points and put them into a display list.
 			CHECK_OPENGL_ERROR
 			}
-			glEndList();
+			glEndList();					///finilize the displaylist.
 		}
 		///@param float v_x x-coordinate in buffer-space,
@@ -457,15 +450,15 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		void
 		UpdateBuffer(float v_x, float v_y)
 		{	
-			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);
-			p4 = hor.p(0,1);
-			glBegin(GL_QUADS);
+			stim::vec3<float>p1; 				///first point.
+        	        stim::vec3<float>p2; 				///second point.
+	                stim::vec3<float>p3; 				///third point.
+                	stim::vec3<float>p4;				///fourth point.
+			p1 = hor.p(1,1);				///generate the top right point from the horizontal template.
+			p2 = hor.p(1,0);				///generate the bottom right point from the horizonatal template.
+			p3 = hor.p(0,0);				///generate the bottom left point from the horizontal template.
+			p4 = hor.p(0,1);				///generate the top left point from the horizonatal template.
+			glBegin(GL_QUADS);				///generate the Quad from the 4 points.
 				glTexCoord3f(
 					p1[0],
 					p1[1],
@@ -477,51 +470,51 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 					p2[1],
 					p2[2]
 					);
-				glVertex2f(v_x+t_length, v_y);
+				glVertex2f(v_x+n_pixels, v_y);
 				glTexCoord3f(
 					p3[0],
 					p3[1],
 					p3[2]
 					);
-				glVertex2f(v_x+t_length, v_y+t_length);
+				glVertex2f(v_x+n_pixels, v_y+n_pixels);
 				glTexCoord3f(
 					p4[0],
 					p4[1],
 					p4[2]
 					);
-				glVertex2f(v_x, v_y+t_length);
-			 glEnd();
-
-			 p1 = ver.p(1,1);
-			 p2 = ver.p(1,0);
-			 p3 = ver.p(0,0);
-			 p4 = ver.p(0,1);
-		 	 glBegin(GL_QUADS);
+				glVertex2f(v_x, v_y+n_pixels);
+			 glEnd();					///finish the quad.
+
+			 p1 = ver.p(1,1);				///generate the top right point from the vertical template.
+			 p2 = ver.p(1,0);                               ///generate the bottom right point from the vertical template.
+			 p3 = ver.p(0,0);                               ///generate the bottom left point from the vertical template.
+			 p4 = ver.p(0,1);                               ///generate the top left point from the vertical template.
+		 	 glBegin(GL_QUADS);				///generate the Quad from the 4 points.
 				glTexCoord3f(
 					p1[0],
 					p1[1],
 					p1[2]
 					);
-				glVertex2f(v_x+t_length, v_y);
+				glVertex2f(v_x+n_pixels, v_y);
 				glTexCoord3f(
 					p2[0],
 					p2[1],
 					p2[2]
 					);
-				glVertex2f(v_x+2.0*t_length, v_y);
+				glVertex2f(v_x+2.0*n_pixels, v_y);
 				glTexCoord3f(
 					p3[0],
 					p3[1],
 					p3[2]
 					);
-				glVertex2f(v_x+2.0*t_length, v_y+t_length);
+				glVertex2f(v_x+2.0*n_pixels, v_y+n_pixels);
 				glTexCoord3f(
 					p4[0],
 					p4[1],
 					p4[2]
 					);
-				glVertex2f(v_x+t_length, v_y+t_length);
-			glEnd(); 
+				glVertex2f(v_x+n_pixels, v_y+n_pixels);
+			glEnd(); 					///finish the quad.
 		}
@@ -539,50 +532,24 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		void
 		GenerateFBO(unsigned int width, unsigned int height, GLuint &textureID, GLuint &framebufferID)
 		{
-			glDeleteFramebuffers(1, &framebufferID);
-			glGenFramebuffers(1, &framebufferID);
-			glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);
+			glDeleteFramebuffers(1, &framebufferID);				///clear the framebuffer.
+			glGenFramebuffers(1, &framebufferID);					///generate a clean buffer.
+			glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);			///bind the new buffer.
 //			int numChannels = 1;
 //			unsigned char* texels = new unsigned char[width * height * numChannels];
-			glGenTextures(1, &textureID);
+			glGenTextures(1, &textureID);						///generate a texture that will attach to the buffer.
 			glBindTexture(GL_TEXTURE_2D, textureID);
 			//Textures repeat and use linear interpolation, luminance format.
-			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_REPEAT);
-			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_REPEAT);
-			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);
+			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_REPEAT);		///Set up the texture to repeat at edges.
+			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_REPEAT);		
+			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);	///Set up the texture to use Linear interpolation
 			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
-			glTexImage2D(GL_TEXTURE_2D, 0, GL_LUMINANCE,
+			glTexImage2D(GL_TEXTURE_2D, 0, GL_LUMINANCE,				///Create the texture with no data.
 				 width, height, 0, GL_LUMINANCE, GL_UNSIGNED_BYTE, NULL);   
 //			delete[] texels;
-			glBindFramebuffer(GL_FRAMEBUFFER, 0); 
-			glBindTexture(GL_TEXTURE_2D, 0);
-		}
-
-		///@param uint width sets the width of the buffer.
-		///@param uint height sets the height of the buffer.
-		///Function for setting up the 2D buffer that stores the samples.
-		void
-		GenerateFBO(unsigned int width, unsigned int height)
-		{
-			glGenFramebuffers(1, &fboID);
-			glBindFramebuffer(GL_FRAMEBUFFER, fboID);
-//			int numChannels = 1;
-//			unsigned char* texels = new unsigned char[width * height * numChannels];
-			glGenTextures(1, &texbufferID);
-			glBindTexture(GL_TEXTURE_2D, texbufferID);
-
-			//Textures repeat and use linear interpolation, luminance format.
-			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_REPEAT);
-			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_REPEAT);
-			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);
-			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
-			glTexImage2D(GL_TEXTURE_2D, 0, GL_LUMINANCE,
-				 width, height, 0, GL_LUMINANCE, GL_UNSIGNED_BYTE, NULL);   
-//			delete[] texels;
-			glBindFramebuffer(GL_FRAMEBUFFER, 0); 
-			glBindTexture(GL_TEXTURE_2D, 0);
-			CHECK_OPENGL_ERROR
+			glBindFramebuffer(GL_FRAMEBUFFER, 0); 					///Bind the frontbuffer
+			glBindTexture(GL_TEXTURE_2D, 0);					///Unbind the texture.
 		}
@@ -614,9 +581,9 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 				//rotate to the current direction of the spider.
 				glRotatef(rot[0], rot[1], rot[2], rot[3]);
 				//scale to the magnitude of the spider.
-				glScalef(m[0],
-					 m[0],
-					 m[0]);
+				glScalef(m,
+					 m,
+					 m);
 				//get and store the current transformation matrix for later use.
 				glGetFloatv(GL_TEXTURE_MATRIX, curTrans);
 				cT.set(curTrans);
@@ -636,36 +603,6 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		///Method for controling the buffer and texture binding.
 		///Clears the buffer upon binding.
-		void
-		Bind()
-		{
-			glBindFramebuffer(GL_FRAMEBUFFER, fboID);//set up GL buffer		
-			glFramebufferTexture2D(
-				GL_FRAMEBUFFER,
-				GL_COLOR_ATTACHMENT0,
-				GL_TEXTURE_2D,
-				texbufferID,
-				0);
-			glBindFramebuffer(GL_FRAMEBUFFER, fboID);
-			GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};
-			glDrawBuffers(1, DrawBuffers);
-			glBindTexture(GL_TEXTURE_2D, texbufferID);
-			glClearColor(1,1,1,1);
-			glClear(GL_COLOR_BUFFER_BIT);
-			glMatrixMode(GL_PROJECTION);
-			glLoadIdentity();
-			glMatrixMode(GL_MODELVIEW);
-			glLoadIdentity();
-			glViewport(0,0,2.0*t_length, numSamples*t_length);
-			gluOrtho2D(0.0,2.0*t_length,0.0,numSamples*t_length);
-			glEnable(GL_TEXTURE_3D);
-			glBindTexture(GL_TEXTURE_3D, texID);
-
-			CHECK_OPENGL_ERROR
-		}
-		
-		///Method for controling the buffer and texture binding.
-		///Clears the buffer upon binding.
 		///@param GLuint &textureID, texture to be bound.
 		///@param GLuint &framebufferID, framebuffer used for storage.
 		///@param int nSamples, number of rectanges to create. 
@@ -673,25 +610,25 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		Bind(GLuint &textureID, GLuint &framebufferID, int nSamples, float len = 8.0)
 		{
-			glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);//set up GL buffer
-			glFramebufferTexture2D(
+			glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);	///Bind the framebuffer.
+			glFramebufferTexture2D(					///associate it with the texture
 				GL_FRAMEBUFFER,
 				GL_COLOR_ATTACHMENT0,
 				GL_TEXTURE_2D,
 				textureID,
 				0);
-			glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);
-			GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};
-			glDrawBuffers(1, DrawBuffers);
-			glBindTexture(GL_TEXTURE_2D, textureID);
-			glMatrixMode(GL_PROJECTION);
+			glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);	///Bind the framebuffer.
+			GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};		///generate the drawbuffer.
+			glDrawBuffers(1, DrawBuffers);				///set the drawbuffer.
+			glBindTexture(GL_TEXTURE_2D, textureID);		///Bind the texture passed.
+			glMatrixMode(GL_PROJECTION);				///clear out the draw matrices
 			glLoadIdentity();
 			glMatrixMode(GL_MODELVIEW);
 			glLoadIdentity();
-			glViewport(0,0,2.0*len, nSamples*len);
-			gluOrtho2D(0.0,2.0*len,0.0,nSamples*len);
-			glEnable(GL_TEXTURE_3D);
-			glBindTexture(GL_TEXTURE_3D, texID);
+			glViewport(0,0,2.0*len, nSamples*len);			///set up viewport
+			gluOrtho2D(0.0,2.0*len,0.0,nSamples*len);		///Set up ortho
+			glEnable(GL_TEXTURE_3D);				
+			glBindTexture(GL_TEXTURE_3D, texID);			///bind the main texture (return to original state).
 			CHECK_OPENGL_ERROR
 		}
@@ -701,32 +638,14 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		Unbind()
 		{
 			//Finalize GL_buffer
-			glBindTexture(GL_TEXTURE_3D, 0);                      
-			CHECK_OPENGL_ERROR
-			glBindTexture(GL_TEXTURE_2D, 0);                      
+			glBindTexture(GL_TEXTURE_3D, 0);                      ///Bind the front buffer.
 			CHECK_OPENGL_ERROR
-			glBindFramebuffer(GL_FRAMEBUFFER, 0);
+			glBindTexture(GL_TEXTURE_2D, 0);                      ///Bind the default GL texture.
 			CHECK_OPENGL_ERROR
-			glDisable(GL_TEXTURE_3D);
+			glBindFramebuffer(GL_FRAMEBUFFER, 0);		      ///Bind the defautl framebuffer.
 			CHECK_OPENGL_ERROR
-		}
-
-		///Makes the spider take a step.
-		///starting with the current p, d, m, find the next optimal p, d, m.
-		///Performs the branch detection on each step.
-		int
-		StepP()
-		{
-			Bind();
+			glDisable(GL_TEXTURE_3D);			      ///Turn off texturing.
 			CHECK_OPENGL_ERROR
-			findOptimalDirection();
-			findOptimalPosition();
-			findOptimalScale();
-			Unbind();
-			Bind(btexbufferID, bfboID, 27);
-			branchDetection2();
-			Unbind();
-			return current_cost;
 		}
@@ -741,27 +660,17 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		///finds the minimum cost and sets the current_cost to that value.
 		/// and returns the index of the template with the minimal cost. 
 		int
-		getCost()
-		{
-			stim::vec<int> cost = 
-//				stim::cuda::get_cost(texbufferID, GL_TEXTURE_2D, numSamples);
-			cudaDeviceSynchronize();
-			current_cost = cost[1];
-			return cost[0];
-		}
-
-		int
 		getCost(cudaTextureObject_t tObj, float* result, int n)
 		{
 			#ifdef TIMING
 				gpuStartTimer();
 			#endif
 			stim::vec<int> cost = 
-				stim::cuda::get_cost(tObj, result, n, 2*t_length, t_length);
+				stim::cuda::get_cost(tObj, result, n, 2*n_pixels, n_pixels);	///call the cuda function with the appropriate texture buffer.
 			#ifdef TIMING
 				cost_time += gpuStopTimer();
 			#endif
-			current_cost = cost[1];
+			current_cost = cost[1];							///current cost.
 			return cost[0];
 		}
@@ -798,7 +707,7 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 //			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 = stim::vec<float>(1.0, 1.0);
+			m = 1.0;
 			S = stim::vec3<float>(1.0, 1.0, 1.0);
 			R = stim::vec3<float>(1.0, 1.0, 1.0);
 			numSamples = samples;
@@ -821,7 +730,7 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		{
 			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);
+			m = mag_x;
 			S = stim::vec3<float>(1.0,1.0,1.0);
 			R = stim::vec3<float>(1.0,1.0,1.0);
 			numSamples = numsamples;
@@ -839,7 +748,7 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		{
 			p = pos;
 			d = dir;
-			m = vec<float>(mag, mag, mag);
+			m = mag;
 			S = vec3<float>(1.0,1.0,1.0);
 			R = vec3<float>(1.0,1.0,1.0);
 			numSamples = samples;
@@ -852,14 +761,14 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		(void)
 		{
 			Unbind();
-			glDeleteTextures(1, &texbufferID);
-			glDeleteBuffers(1, &fboID);
-			glDeleteTextures(1, &ptexbufferID);
-			glDeleteBuffers(1, &pfboID);
-			glDeleteTextures(1, &mtexbufferID);
-			glDeleteBuffers(1, &mfboID);     
-			glDeleteTextures(1, &btexbufferID);
-			glDeleteBuffers(1, &bfboID);
+			glDeleteTextures(1, &direction_texID);
+			glDeleteBuffers(1, &direction_buffID);
+			glDeleteTextures(1, &position_texID);
+			glDeleteBuffers(1, &position_buffID);
+			glDeleteTextures(1, &radius_texID);
+			glDeleteBuffers(1, &radius_buffID);     
+			glDeleteTextures(1, &cylinder_texID);
+			glDeleteBuffers(1, &cylinder_buffID);
 		}
 		///@param GLuint id, texture that is going to be sampled.
@@ -878,42 +787,39 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 			network_time = 0;
 			hit_time = 0;
 #endif
-			stepsize = 2.5;
-			t_length = 16.0;
+			stepsize = 3.0;
+			n_pixels = 16.0;
 			srand(100);	
 			texID = id;
-			GenerateFBO(t_length*2, numSamples*t_length, texbufferID, fboID); 
-			std::cout << numSamples << std::endl;
+			GenerateFBO(n_pixels*2, numSamples*n_pixels, direction_texID, direction_buffID); 
 			CHECK_OPENGL_ERROR
-			GenerateFBO(t_length*2, numSamplesPos*t_length, ptexbufferID, pfboID); 
-			std::cout << numSamplesPos << std::endl;
+			GenerateFBO(n_pixels*2, numSamplesPos*n_pixels, position_texID, position_buffID); 
 			CHECK_OPENGL_ERROR
-			GenerateFBO(t_length*2, numSamplesMag*t_length, mtexbufferID, mfboID); 
-			std::cout << numSamplesMag << std::endl;
+			GenerateFBO(n_pixels*2, numSamplesMag*n_pixels, radius_texID, radius_buffID); 
 			CHECK_OPENGL_ERROR
-			GenerateFBO(16, 216, btexbufferID, bfboID); 
+			GenerateFBO(16, 216, cylinder_texID, cylinder_buffID); 
 			CHECK_OPENGL_ERROR
 			t_dir.MapCudaTexture(texbufferID, GL_TEXTURE_2D);
 			t_dir.Alloc(numSamples);
-			t_pos.MapCudaTexture(ptexbufferID, GL_TEXTURE_2D);
+			t_pos.MapCudaTexture(position_texID, GL_TEXTURE_2D);
 			t_pos.Alloc(numSamplesPos);
-			t_mag.MapCudaTexture(mtexbufferID, GL_TEXTURE_2D);
+			t_mag.MapCudaTexture(radius_texID, GL_TEXTURE_2D);
 			t_mag.Alloc(numSamplesMag);
 			setMatrix();
 			dList = glGenLists(3);
 			glListBase(dList);
-			Bind(texbufferID, fboID, numSamples, t_length);
+			Bind(direction_texID, direction_buffID, numSamples, n_pixels);
 				genDirectionVectors(5*stim::PI/4);
 			Unbind();
-			Bind(ptexbufferID, pfboID, numSamplesPos, t_length);
+			Bind(position_texID, position_buffID, numSamplesPos, n_pixels);
 				genPositionVectors();
 			Unbind();
-			Bind(mtexbufferID, mfboID, numSamplesMag, t_length);
+			Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
 				genMagnitudeVectors();
 			Unbind();
-			Bind(btexbufferID, bfboID, 27);
-			DrawCylinder();
+			Bind(cylinder_texID, cylinder_buffID, 27);
+				DrawCylinder();
 			Unbind();
 		}
@@ -981,22 +887,13 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 			d[2] = z;
 		}
-		///@param stim::vec<float> dir, the new d.
-		///Sets the m vector to the input vector mag.	
-		void
-		setMagnitude(stim::vec<float> mag)
-		{
-			m[0] = mag[0];
-			m[1] = mag[0];
-		}
 		///@param float mag, size of the sampled region.
 		///Sets the m vector to the input mag for both templates.
 		void
 		setMagnitude(float mag)
 		{
-			m[0] = mag;
-			m[1] = mag;
+			m = mag;
 		}
 		///@param float x, voxel size in the x direction.
@@ -1269,7 +1166,7 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		GLuint
 		getFB()
 		{
-			return bfboID;
+			return cylinder_buffID;
 		}
 //--------------------------------------------------------------------------//
@@ -1293,14 +1190,14 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		int
 		Step()
 		{
-			Bind(texbufferID, fboID, numSamples, t_length);
+			Bind(direction_texID, direction_buffID, numSamples, n_pixels);
 			CHECK_OPENGL_ERROR
 				findOptimalDirection();
 			Unbind();
-			Bind(ptexbufferID, pfboID, numSamplesPos, t_length);
+			Bind(position_texID, position_buffID, numSamplesPos, n_pixels);
 				findOptimalPosition();
 			Unbind();
-			Bind(mtexbufferID, mfboID, numSamplesMag, t_length);
+			Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
 				findOptimalScale();
 			Unbind();
 			CHECK_OPENGL_ERROR
@@ -1387,12 +1284,13 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		}
 ///need to return the cylinder.
+///SOMETHING MIGHT BE GOING ON HERE IN GENERATE BUFFER.
 		void
 		DrawLongCylinder(int n = 8, int l_template = 8,int l_square = 8)
 		{
 			int cylLen = cL.size()-1;
-			GenerateFBO(n*l_square, cylLen*l_template, btexbufferID, bfboID);
-			Bind(btexbufferID, bfboID, cylLen, l_template*l_square/2.0);
+			GenerateFBO(n*l_square, cylLen*l_template, cylinder_texID, cylinder_buffID);
+			Bind(cylinder_texID, cylinder_buffID, cylLen, l_template*l_square/2.0);
 			stim::cylinder<float> cyl(cL, cM);
 			std::vector<std::vector<stim::vec3<float> > > p = cyl.getPoints(n);
 			for(int i = 0; i < p.size()-1; i++)	///number of circles
@@ -1636,12 +1534,9 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 		{
 			//starting (seed) position and magnitude.
 			stim::vec3<float> spos = getPosition();
-//			std::cout << "I did this" << std::endl;
-//			findOptimalScale();
 			stim::vec<float> smag = getMagnitude();
 			stim::vec3<float> sdir = getDirection();	
-			Bind();
 //			sk.Begin(stim::OBJ_LINE);
@@ -1662,7 +1557,6 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 				int cost = Step();
 				if (cost > min_cost){
 					running = false;
-//					sk.End();
 					branchDetection2();
 					addToNetwork(cL, cM);
 					std::cout << "the cost of " << cost << " > " << min_cost << std::endl;
@@ -1698,7 +1592,7 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 					}
 					else
 					{
-						h = selectObject(p, getDirection(), m[0]);
+						h = selectObject(p, getDirection(), m);
 						//Have we hit something previously traced?
 						if(h != -1){
 							std::cout << "I hit the fiber " << h << std::endl;
@@ -1709,11 +1603,8 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
 						}
 						else {  
 							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();
+							cM.push_back(m);
 							CHECK_OPENGL_ERROR
-							
 						}
 				 	}
                  		}