Checkpoint: Converted the previous version of the code to a more seperable versi…

…on with each function doing a seperate job. Renamed the series of 'sample' methods and changed what they do. The vector arrays are now owned by the spider class, and the previously-named 'sample' functions fill in the arrays with vectors. Update() has been renamed into genTemplate and now maps from the TissueSpace to bufferSpace. Some new comments for the documentation

Checkpoint: Converted the previous version of the code to a more seperable versi…
…on with each function doing a seperate job. Renamed the series of 'sample' methods and changed what they do. The vector arrays are now owned by the spider class, and the previously-named 'sample' functions fill in the arrays with vectors. Update() has been renamed into genTemplate and now maps from the TissueSpace to bufferSpace. Some new comments for the documentation
Pavel Govyadinov
1 parent 5f81932b
Showing 5 changed files with 220 additions and 201 deletions Show diff stats
stim/cuda/cost.h
stim/gl/gl_spider.h
stim/gl/gl_texture.h
stim/grids/grid.h
stim/grids/image_stack.h
@@ -2,8 +2,6 @@
 #include <cuda.h>
 #include <cuda_runtime.h>
 #include <cublas_v2.h>
-//#include "cuPrintf.cu"
-//#include "cuPrintf.cuh"
 #include <stdio.h>
 #include "../visualization/colormap.h"
 #include <sstream>
@@ -11,9 +9,6 @@
 #define DIM_Y 10890
 #define DIM_X 20
 typedef unsigned char uchar;
-//surface<void, 2> texOut; ///// maybe just do a normal array instead of a surface.
-		//we may not need a surface at all.
-//texture<float, cudaTextureType2D, cudaReadModeElementType> texTemplate 
 texture<uchar, cudaTextureType2D, cudaReadModeElementType> texIn;
 float *result;
 float* v_dif;
@@ -66,11 +61,9 @@ void get_diff (float *result)
 	float valIn		= tex2D(texIn, x, y)/255.0;
 	float valTemp		= Template(x);
 	result[idx] 		= abs(valIn-valTemp);
-	//result[idx] 		= abs(valTemp);
 //	#if __CUDA_ARCH__>=200
 //		printf("Value is : %f\n and the result is : %f\n", valIn, result[idx]);
 //	#endif
-	//cuPrintf("Value is : %f\n and the result is : %f\n", valIn, result[idx]);
 }
@@ -128,7 +121,6 @@ int get_cost(cudaGraphicsResource_t src, int inter)
 	initArray(src);
 	dim3 grid(20, 10890);
 	dim3 block(1, 1);
-	//texIn.normalized = 1;	
 	get_diff <<< grid, block >>> (result);
 	stim::gpu2image<float>(result, "test.bmp", 20,10890,0,1);
 	for (int i = 0; i < 1089; i++){
@@ -136,19 +128,11 @@ int get_cost(cudaGraphicsResource_t src, int inter)
 		if(output[i] <= mini){
 			mini = output[i];
 			idx = i;
-//		if(!testing)
-		
-//		testing = true;
-		}	//float* out = (float*) malloc(sizeof(float));
+		}
 	}	
 	name << "sample_" << inter << "_" << idx << ".bmp";
 	output[idx] = get_sum(result+(20*10*idx));
 	stim::gpu2image<float>(v_dif, name.str(), 20,10,0,1);
-	std::cout << output[0] << std::endl;
-	std::cout << output[100] << std::endl;
-	std::cout << output[500] << std::endl;
-	std::cout << output[1000] << std::endl;
-	std::cout << idx << std::endl;
 	cleanUP(src);
 	return idx;
 }
@@ -14,6 +14,7 @@
 #include "../math/rect.h"
 #include "../cuda/cost.h"
 #include "../cuda/glbind.h"
+#include <vector>
 #include <iostream>
 #include <fstream>
@@ -33,8 +34,11 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		stim::vec<float> magnitude;	//magnitude of the direction vector.
 						//mag[0] = length.
 						//mag[1] = width.
+		std::vector<stim::vec<float> > dirVectors;
+		std::vector<stim::vec<float> > posVectors;
+		std::vector<stim::vec<float> > magVectors;
 		using gl_texture<T>::texID;
-		//using image_stack<T>::S;
+		using gl_texture<T>::S;
 		cudaArray* c_Array;
 		//void** devPtr;
 		//size_t size;
@@ -49,6 +53,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			/* Method for finding the best direction for the spider.
 			   Not sure if necessary since the next position for the spider
 			   will be at direction * magnitude. */
+			genTemplate(posVectors, 1);
+			int best = getCost();
 		}
 		void
@@ -57,20 +63,20 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			/* Method for finding the best scale for the spider.
 			   changes the x, y, z size of the spider to minimize the cost
 			   function. */
+			genTemplate(magVectors, 1);
+			int best = getCost();
 		}
 		void
-		Evaluate()
-		{	
-			/* Uses uniform sampler2D in order to take a difference between
-			   the colors of two textures. 1st texture is the spider template,
-			   the 2nd is the location of the spider's overlap with the
-			   gl_template 
-	
-			   does the spider need to track it's location? Prob not since
-			   position can be set with gl_texture coordinates */
-		
+		findOptimalDirection()
+		{
+			/* Method for finding the best scale for the spider.
+			   changes the x, y, z size of the spider to minimize the cost
+			   function. */
+			genTemplate(dirVectors, 1);
+			int best = getCost();
 		}
+
 		void
 		Optimize()
@@ -120,6 +126,10 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			p4 = hor.p(0,1);
 			glBegin(GL_QUADS);
 				glTexCoord3f(
+				//	p1[0]/S[1],
+				//	p1[1]/S[2],
+				//	p1[2]/S[3]
+				//	);
 					p1[0],
 					p1[1],
 					p1[2]
@@ -127,6 +137,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 				//glVertex2f(0.0,0.0);
 				glVertex2f(v_x,v_y);
 				glTexCoord3f(
+				//	p2[0]/S[1],
+				//	p2[1]/S[2],
+				//	p2[2]/S[3]
 					p2[0],
 					p2[1],
 					p2[2]
@@ -134,6 +147,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 				//glVertex2f(1.0, 0.0);
 				glVertex2f(v_x+len, v_y);
 				glTexCoord3f(
+				//	p2[0]/S[1],
+				//	p2[1]/S[2],
+				//	p2[2]/S[3]
 					p3[0],
 					p3[1],
 					p3[2]
@@ -141,6 +157,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 				//glVertex2f(1.0, 2.0);
 				glVertex2f(v_x+len, v_y+len);
 				glTexCoord3f(
+				//	p4[0]/S[1],
+				//	p4[1]/S[2],
+				//	p4[2]/S[3]
 					p4[0],
 					p4[1],
 					p4[2]
@@ -154,6 +173,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			 p4 = ver.p(0,1);
 		 	 glBegin(GL_QUADS);
 				glTexCoord3f(
+				//	p1[0]/S[1],
+				//	p1[1]/S[2],
+				//	p1[2]/S[3]
 					p1[0],
 					p1[1],
 					p1[2]
@@ -161,6 +183,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 				//glVertex2f(1.0, 0.0);
 				glVertex2f(v_x+len, v_y);
 				glTexCoord3f(
+				//	p2[0]/S[1],
+				//	p2[1]/S[2],
+				//	p2[2]/S[3]
 					p2[0],
 					p2[1],
 					p2[2]
@@ -168,6 +193,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 				//glVertex2f(2.0, 0.0);
 				glVertex2f(v_x+2*len, v_y);
 				glTexCoord3f(
+				//	p3[0]/S[1],
+				//	p3[1]/S[2],
+				//	p3[2]/S[3]
 					p3[0],
 					p3[1],
 					p3[2]
@@ -175,6 +203,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 				//glVertex2f(2.0, 2.0);
 				glVertex2f(v_x+2*len, v_y+len);
 				glTexCoord3f(
+				//	p4[0]/S[1],
+				//	p4[1]/S[2],
+				//	p4[2]/S[3]
 					p4[0],
 					p4[1],
 					p4[2]
@@ -185,35 +216,60 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		}
 		void
-		UpdatePlanes(float v_x, float v_y, vec<float> vctr, int type = 0)
+		genTemplate(std::vector<stim::vec<float> > in, int type = 0)
 		{
+			float x = 0.0;
 			vec<float> Y(1.0,0.0,0.0);
-			if(cos(Y.dot(vctr))< 0.087){                                                                             Y[0] = 0.0; Y[1] = 1.0;}
+			Bind();	
                         switch(type) {
-				case 0:
-                                         hor = stim::rect<float>(magnitude, position, vctr.norm(),
-                        			((Y.cross(vctr)).cross(vctr)).norm());
-              				 ver = stim::rect<float>(magnitude, position, vctr.norm(),
-                        			hor.n());
+				case 0:          //Direction
+					for(int i = 0; i < in.size(); i++)
+					{
+					 	if(cos(Y.dot(in[i]))< 0.087){                                                                             Y[0] = 0.0; Y[1] = 1.0;}
+						else{Y[0] = 1.0; Y[1] = 0.0;}
+
+                                         	hor = stim::rect<float>(magnitude,
+							 position, in[i],
+                        				((Y.cross(in[i])).cross(in[i])).norm());
+              				 	ver = stim::rect<float>(magnitude,
+							 position, in[i],
+                        				hor.n());
+						UpdateBuffer(x, x+i*10.0);
+					 }
                				 break;
-        			case 1:
-                			 hor = stim::rect<float>(magnitude, vctr, direction,
-                      				((Y.cross(direction)).cross(direction)).norm());
-                			 ver = stim::rect<float>(magnitude, vctr, direction,
-                        			hor.n());
+        			case 1:		 //Position
+					if(cos(Y.dot(direction))< 0.087){                                                                             Y[0] = 0.0; Y[1] = 1.0;}
+					else{Y[0] = 1.0; Y[1] = 0.0;}
+
+					for(int i = 0; i < in.size(); i++)
+					{
+                				hor = stim::rect<float>(magnitude, in[i], direction,
+                      					((Y.cross(direction)).cross(direction))
+							.norm());
+                				ver = stim::rect<float>(magnitude, in[i], direction,
+                        				hor.n());
+						UpdateBuffer(x, x+i*10.0);
+					 }
                 			 break;
-        			case 2:
-                			 hor = stim::rect<float>(vctr, position, direction,
-                      				((Y.cross(direction)).cross(direction)).norm());
-                			 ver = stim::rect<float>(vctr, position, direction,
-                        			hor.n());
-					 break;
+        			case 2:		  //Scale
+					if(cos(Y.dot(direction))< 0.087){                                                                             Y[0] = 0.0; Y[1] = 1.0;}
+					else{Y[0] = 1.0; Y[1] = 0.0;}
+
+                			for(int i = 0; i < in.size(); i++)
+					{
+						hor = stim::rect<float>(in[i], position, direction,
+                      					((Y.cross(direction)).cross(direction))
+							.norm());
+                				ver = stim::rect<float>(in[i], position, direction,
+                        				hor.n());
+					}
+					break;
         			default:
                 			 std::cout << "unknown case have been passed"
                          			<< std::endl;
 					 break;
 			}               
-			UpdateBuffer(v_x, v_y);
+		Unbind();
 		}
 		/*
@@ -247,6 +303,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			glBindTexture(GL_TEXTURE_3D, texID);
 		}
+		/*
+		Method for Unbinding all of the texture resources
+		*/	
 		void
 		Unbind()
 		{
@@ -256,83 +315,46 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			glBindFramebuffer(GL_FRAMEBUFFER,0);
 			glBindTexture(GL_TEXTURE_2D, 0);
 		}
+
 		/*
 		Method for populating the buffer with the sampled texture.
 		usually uses the default direction vector and then
 		*/
 		void
-		sampleDirection(int numSamples = 1089, float solidAngle = M_PI)
+		genDirectionVectors(int numSamples = 1089, float solidAngle = M_PI/1.5)
 		{
-			//ofstream file;
-			//file.open("samples.txt", std::ios_base::app);
-			float samples[numSamples][3];    	//Set up the variables
-							 	//necessary for sample generation
 			vec<float> d_s = direction.cart2sph();
+			dirVectors.resize(1089);
 			vec<float> temp;
 			int dim = (sqrt(numSamples)-1)/2;
-			//std::cout << dim << std::endl;
-			float y_0 	= 0.0;
 			float p0  	= M_PI/3;
 			float dt  	= solidAngle/(1.0 * dim);
 			float dp  	= p0/(1.0*dim);
-			Bind();	
-			//file << "Step: Direction" << "\n";
-			//file << "iteration: " << iter << "\n";
-			//file << "starting pos and dir:" << "[" << position[0] << "," <<position[1] << "," << position[2] << "]" << ":" << "["  << direction[0] << "," << direction[1] << "," << direction[2] << "]\n"; 
-			//Loop over the samples such that the original orientation is in the
-			//center of the resulting texture index (544)
-			//file << position[0] << "," <<position[1] << "," << position[2] << "\n"; 
-			int idx;
 			for(int i = -dim; i <= dim; i++){
 				for(int j = -dim; j <= dim; j++){
 					//Create linear index
-					idx = (i+dim)*(dim*2+1) + (j+dim);
-
+					
 					temp[0] = d_s[0]; 			//rotate vector
 					temp[1] = d_s[1]+dt*i;
 					temp[2] = d_s[2]+dp*j;
 					temp = (temp.sph2cart()).norm();		//back to cart
-					samples[idx][0] = temp[0];	//save sample vector
-					samples[idx][1] = temp[1];
-					samples[idx][2] = temp[2];
-	
-			//		file << idx << ":"  <<"[" << samples[idx][0] << "," << samples[idx][1] << "," << samples[idx][2] << "]" << "\n";
-
-					UpdatePlanes(0.0, y_0+(idx)*10, temp); 
+					dirVectors.push_back(temp);
 				}
 			}
-			Unbind();
-			int nxt = getCost();
-			stim::vec<float> next(samples[nxt][0], samples[nxt][1], samples[nxt][2]);
-			//next[0] = samples[nxt][0];
-			//next[1] = samples[nxt][1];
-			//next[2] = samples[nxt][2];
-			next.norm();	
-			//file << "next direction" << "[" << next[0] << "," << next[1] << "," << next[2] << "]\n\n"; 
-			setPosition(position[0] + next[0]*magnitude[0]/2,
-					 position[1]+next[1]*magnitude[0]/2,
-						position[2]+next[2]*magnitude[0]/2);
-			setDirection(next[0], next[1], next[2]);
-			//file.close();
-			setDirection(next);
-			//file << "ending pos and dir:" << "[" << position[0] << "," <<position[1] << "," << position[2] << "]" << ":" << "["  << direction[0] << "," << direction[1] << "," << direction[2] << "]\n"; 
 		}
 		void
-		samplePosition(int numSamples = 1089, float delta = 0.2)
+		genPositionVectors(int numSamples = 1089, float delta = 0.2)
 		{
-			float samples[numSamples][3];    	//Set up the variables
 			vec<float> temp;
 			int dim = (sqrt(numSamples)-1)/2;
-			float y_0 	= 0.0;			//location of the first sample in the buffer
 			stim::rect<float> samplingPlane =
 				 stim::rect<float>(magnitude[0]*delta, position, direction);
 			float step = 1.0/(dim);
-			Bind();	
 			//Loop over the samples, keeping the original position sample
 			//in the center of the resulting texture.
@@ -340,52 +362,34 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			for(int i = -dim; i <= dim; i++){
 				for(int j = -dim; j <= dim; j++){
 					//Create linear index
-					idx = (i+dim)*(dim*2+1) + (j+dim);
 					temp = samplingPlane.p(
 							0.5+step*i,
 								 0.5+step*j
 										);
-
-					samples[idx][0] = temp[0];	//save sample vector
-					samples[idx][1] = temp[1];
-					samples[idx][2] = temp[2];
-	
-					UpdatePlanes(0.0, y_0+(idx)*10, temp, 1); 
+					dirVectors.push_back(temp);
 				}
 			}
-			Unbind();
-			int nxt = getCost();
-			setPosition(samples[nxt][0], samples[nxt][1], samples[nxt][2]);
 		}
 		void
-		sampleMagnitude(int numSamples = 1089, float delta = 0.5)
+		genMagnitudeVectors(int numSamples = 1089, float delta = 0.5)
 		{
-			ofstream file;
-			file.open("samples.txt", std::ios_base::app);
-			float samples[numSamples];    	//Set up the variables
 			int dim = (sqrt(numSamples)-1)/2;
-			float y_0 	= 0.0;			//location of the first sample in the buffer
 			float min 	= 1.0-delta;
 			float max 	= 1.0+delta;
 			float step	= (max-min)/(numSamples-1);
 			float factor;
 			vec<float> temp;
-			Bind();	
 			for(int i = 0; i < numSamples; i++){
-					//Create linear index
-					factor = (min+step*i)*magnitude[0];
-					samples[i] = factor;	//save sample vector
-					stim::vec<float> temp(factor);
-					UpdatePlanes(0.0, y_0+(i)*10, temp, 2); 
+				//Create linear index
+				factor = (min+step*i)*magnitude[0];
+				temp[0] = factor;
+				temp[1] = factor;
+				magVectors.push_back(temp);	
 			}
-			Unbind();
-			int nxt = getCost();
-			setMagnitude(samples[nxt]);
-			file << position[0] << "," <<position[1] << "," << position[2] << "\n"; 
 		}
 //--------------------------------------------------------------------------//
@@ -433,36 +437,40 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		stim::rect<float> hor;
 		stim::rect<float> ver;	
-		//Default Constructor
+		///Default Constructor
 		gl_spider
 		()
 		{
 			setPosition(0.0,0.0,0.0);
 			setDirection(0.0,0.0,1.0);
-			setMagnitude(0.03);
+			setMagnitude(1.0);
 		}
-		//temporary constructor for convenience, will be removed in further updates.	
+		///temporary constructor for convenience, will be removed in further updates.	
 		gl_spider
 		(float pos_x, float pos_y, float pos_z, float dir_x, float dir_y, float dir_z,
 			float mag_x)
 		{
-			setPosition(pos_x, pos_y, pos_z);
-			setDirection(dir_x, dir_y, dir_z);
-			setMagnitude(mag_x);
-		}
-		
-		//Attached the spider to the texture with the given GLuint ID.
-		//Samples in the default direction acting as the init method.	
+			//setPosition(pos_x, pos_y, pos_z);
+			//setDirection(dir_x, dir_y, dir_z);
+			//setMagnitude(mag_x);
+		}
+		///@param GLuint id texture that is going to be sampled.
+		///@param numSamples number of samples per operation.
+		///Attached the spider to the texture with the given GLuint ID.
+		///Samples in the default direction acting as the init method.	
 		void
 		attachSpider(GLuint id, int numSamples = 1089)
 		{
 			texID = id;
 			GenerateFBO(20, numSamples*10);
-			sampleDirection();
+			//sampleDirection();
+			genDirectionVectors();
+			gl_texture<T>::setDims(0.6, 0.6, 1.0);
+			//gl_texture<T>::setDims(1.0, 1.0,1.0);
 		}
-		//temporary Method necessary for visualization and testing.
+		///temporary Method necessary for visualization and testing.
 		void
 		Update()
 		{
@@ -475,35 +483,39 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 				 hor.n());
 		}
-		//Returns the position vector.
+		///Returns the position vector.
 		vec<float>
 		getPosition()
 		{
 			return position;
 		}
-		//Returns the direction vector.
+		///Returns the direction vector.
 		vec<float>
 		getDirection()
 		{
 			return direction;
 		}
-		//Returns the magnitude vector.
+		///Returns the magnitude vector.
 		vec<float>
 		getMagnitude()
 		{
 			return magnitude;
 		}
-		//Sets the position vector to input vector pos
+		///@param vector pos, the new position.
+		///Sets the position vector to input vector pos.
 		void
 		setPosition(vec<float> pos)
 		{
 			position = pos;
 		}
-		
-		//Sets the position vector to the input float coordinates x,y,z
+
+		///@param x x-coordinate.
+		///@param y y-coordinate.
+		///@param z z-coordinate.
+		///Sets the position vector to the input float coordinates x,y,z.
 		void
 		setPosition(float x, float y, float z)
 		{
@@ -513,14 +525,18 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		}
-		//Sets the direction vector to input vector dir
+		///@param vector dir, the new direction.
+		///Sets the direction vector to input vector dir.
 		void
 		setDirection(vec<float> dir)
 		{
 			direction = dir;
 		}
-		//Sets the direction vector to the input float coordinates x,y,z
+		///@param x x-coordinate.
+		///@param y y-coordinate.
+		///@param z z-coordinate.
+		///Sets the direction vector to the input float coordinates x,y,z.
 		void
 		setDirection(float x, float y, float z)
 		{
@@ -528,8 +544,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			direction[1] = y;
 			direction[2] = z;
 		}
-		
-		//Sets the magnitude vector to the input vector mag.	
+			
+		///@param vector dir, the new direction.
+		///Sets the magnitude vector to the input vector mag.	
 		void
 		setMagnitude(vec<float> mag)
 		{
@@ -537,6 +554,8 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			magnitude[1] = mag[0];
 		}
+		///@param mag size of the sampled region.
+		///Sets the magnitude vector to the input mag for both templates.
 		void
 		setMagnitude(float mag)
 		{
@@ -544,7 +563,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			magnitude[1] = mag;
 		}
-		//temporary method for visualization.
+		///temporary method for visualization.
 		GLuint
 		getFB()
 		{
@@ -564,9 +583,9 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			/* Method for finding the best direction for the spider.
 			   Uses the camera to rotate. Then Calls Evaluate to find new cost.
 			*/
-			sampleDirection();
-			samplePosition();
-			sampleMagnitude();
+			//sampleDirection();
+			//samplePosition();
+			//sampleMagnitude();
 		}
 		/* Method for initializing the cuda devices, necessary only
@@ -31,13 +31,10 @@ template&lt;typename T&gt;
 class gl_texture : public virtual image_stack<T>
 {
 	private:
-		/*
-		Method: setTextureType
-		Inputs:
-		Outputs:
-			Sets the internal texture_type, based on the data
-			size. Either 3D, 2D, 1D textures.
-		*/
+		
+		///Method: setTextureType
+		///	Sets the internal texture_type, based on the data
+		///	size. Either 3D, 2D, 1D textures.
 		void
 		setTextureType()
@@ -54,28 +51,22 @@ class gl_texture : public virtual image_stack&lt;T&gt;
 		GLuint texID;				//OpenGL object
 		GLenum texture_type;			//1D, 2D, 3D
 		using image_stack<T>::R;
+		using image_stack<T>::S;
 		using image_stack<T>::ptr;
 		using image_stack<T>::samples;
 	public:
-		/*
-		Method: Basic Constructor
-		Inputs:
-		Outputs:
-			Creates an instance of the gl_texture object.
-		*/
+		///Method: Basic Constructor
+		///	Creates an instance of the gl_texture object.
 		gl_texture()
 		{
 		}
-		/*
-		Method: Path Constructor
-		Inputs: string file_path
-		Outputs:
-			Creates an instance of the gl_texture object with a path to the data.
-		*/
+		///Method: Path Constructor
+		///@param string file_path path to the directory with the files.
+		///	Creates an instance of the gl_texture object with a path to the data.
 		gl_texture(std::string file_path)
 		{
@@ -84,13 +75,34 @@ class gl_texture : public virtual image_stack&lt;T&gt;
 			setTextureType();
 		}
-		/*
-		Method: setPath
-		Inputs:string file_Path
-		Outputs:
-			sets the protected path variable of an instance of the gl_texture class
-			to the method input.
-		*/
+
+		///Method:setDims
+		///@param x size of the voxel in x direction
+		///@param y size of the voxel in y direction
+		///@param z size of the voxel in z direction
+		///	Sets the dimenstions of the voxels.
+		void
+		setDims(float x, float y, float z)
+		{
+			S[1] = x;
+			S[2] = y;
+			S[3] = z;
+		}
+
+		///Method:getDims
+		///	get the dimenstions of the voxels.
+
+		vec<float>
+		getDims()
+		{
+			vec<float> dims(S[1], S[2], S[3]);
+			return dims;
+		}	
+
+		///Method:setPath
+		///@param file_Path location of the directory with the files
+		///	Sets the path and calls the loader on that path.
+
 		void
 		setPath(std::string file_path)
@@ -100,12 +112,9 @@ class gl_texture : public virtual image_stack&lt;T&gt;
 			setTextureType();
 		}
-		/*
-		Method: getPath
-		Inputs:
-		Outputs: string path
-			Returns the path associated with an instance of the gl_texture class.
-		*/
+		///Method: getPath
+		///Outputs: string path
+		///	Returns the path associated with an instance of the gl_texture class.
 		std::string
 		getPath()
@@ -113,27 +122,20 @@ class gl_texture : public virtual image_stack&lt;T&gt;
 			return path;
 		}
-		/*
-		Method: getTexture
-		Inputs:
-		Outputs: GLuint texID
-			Returns the id of the texture create by/associated with the 
-			instance of the gl_texture class.
-		*/
+		///Method: getTexture
+		///Outputs: GLuint texID
+		///	Returns the id of the texture create by/associated with the 
+		///	instance of the gl_texture class.
 		GLuint
 		getTexture()
 		{
 			return texID;
 		}
-	
-		/*
-		Method: createTexture
-		Inputs:
-		Outputs:
-			Creates a texture and from the data located at <path> and
-			assigns that texture to texID
-		*/
+		
+		///Method: createTexture
+		///	Creates a texture and from the loaded data and
+		///	assigns that texture to texID
 		//TO DO :::: 1D textures
 	        //TO DO:::add methods for handling the cases of T
 		// and convert them to GL equivalent.
@@ -154,11 +156,11 @@ class gl_texture : public virtual image_stack&lt;T&gt;
 			{
 				case GL_TEXTURE_3D:
 					glTexParameteri(texture_type,
-						 GL_TEXTURE_WRAP_S, GL_REPEAT);
+						 GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
 					glTexParameteri(texture_type,
-						 GL_TEXTURE_WRAP_T, GL_REPEAT);
+						 GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
 					glTexParameteri(texture_type,
-						 GL_TEXTURE_WRAP_R, GL_REPEAT);
+						 GL_TEXTURE_WRAP_R, GL_CLAMP_TO_EDGE);
 					glTexImage3D(texture_type,
 						0,
 					//	GL_RGB16,
@@ -190,15 +192,8 @@ class gl_texture : public virtual image_stack&lt;T&gt;
 					break;
 			}
 		}
-		/*
-			Temporary methods for debugging and testing are below.
-			Self-explanatory.
-		*/
-		stim::vec<unsigned long,4>
-		getDims()
-		{
-			return R;
-		}
+			///Temporary methods for debugging and testing are below.
+			///Self-explanatory.
 		T*
 		getData()
@@ -21,6 +21,7 @@ class grid{
 protected:
 	stim::vec<unsigned long, D> R;		//elements in each dimension
+	stim::vec<float, D> S;
 	T* ptr;									//pointer to the data (on the GPU or CPU)
 	///Return the total number of values in the binary file
@@ -63,6 +64,12 @@ public:
 		init();		
 	}
+	void
+	setDim(stim::vec<float, D> s)
+	{
+		S = s;
+	}
+
 	///Constructor used to specify the grid size as a set of parameters
 	/// @param X0... is a list of values describing the grid size along each dimension
@@ -156,6 +163,7 @@ public:
 		ptr[p] = value;
 	}
+
 	///Outputs grid data as a string
 	std::string str(){
@@ -17,6 +17,7 @@ class image_stack : public virtual stim::grid&lt;T, 4&gt;{
 	enum image_type {stimAuto, stimMono, stimRGB, stimRGBA};
 protected:
+	using stim::grid<T, 4>::S;
 	using stim::grid<T, 4>::R;
 	using stim::grid<T, 4>::ptr;
 	using stim::grid<T, 4>::samples;
@@ -83,7 +84,19 @@ public:
 		I.save(file_name);
 	}
-
+	///Sets the dimensions of the image in each direction
+	///Voxel-size.
+	/// @param x size in the x direction
+	/// @param y size in the y direction
+	/// @param z size in the z direction
+	void
+	set_dim(float x, float y, float z)
+	{
+		S[0] = 1;
+		S[1] = x;
+		S[2] = y;
+		S[3] = z;
+	}
 	///Saves the entire stack to a set of images
 	/// @param file_mask is the mask describing how the file names will be saved (ex. image????.bmp)