texture updates

David Mayerich
1 parent 278c622b
Showing 4 changed files with 139 additions and 240 deletions Show diff stats
stim/gl/gl_texture.h
stim/grids/grid.h
stim/grids/image_stack.h
stim/visualization/camera.h
 #ifndef STIM_GL_TEXTURE_H
 #define STIM_GL_TEXTURE_H
-
-
-
-/*
-includes not necessary (yet)
-
-#include <iterator>
-#include <algorithm>
-
-
-*/
-
 #include <math.h>
 #include <iostream>
 #include <vector>
 #include "../grids/image_stack.h"
 #include <GL/glut.h>
-//#include <GL/glext.h>
-#include "./error.h"	
+#include <GL/glext.h>
+#include <stim/gl/error.h>	
 namespace stim{
 /*
@@ -30,22 +18,8 @@ class gl_texture
 template<typename T>
 class gl_texture : public virtual image_stack<T>
 {
-	private:
-		///	Sets the internal texture_type, based on the data
-		///	size. Either 3D, 2D, 1D textures.
-		
-		void
-		setTextureType()
-		{
-			if (R[3] > 1)
-				texture_type = GL_TEXTURE_3D;
-			else if (R[3] == 1 && R[2] == 0)
-				texture_type = GL_TEXTURE_1D;
-			else if (R[3] == 1)
-				texture_type = GL_TEXTURE_2D;
-		}
 	protected:
-		std::string path;
+		//std::string path;
 		GLuint texID;				//OpenGL object
 		GLenum texture_type;			//1D, 2D, 3D
 		GLint interpType;
@@ -57,43 +31,56 @@ class gl_texture : public virtual image_stack&lt;T&gt;
 		using image_stack<T>::ptr;
 		using image_stack<T>::samples;
+		///	Sets the internal texture_type, based on the data dimensions
+		void setTextureType(){
+			if (R[3] > 1)						//if the third dimension is greater than 1
+				texture_type = GL_TEXTURE_3D;	//this is a 3D texture
+			else if (R[2] > 1)					//if the second dimension is greater than 1
+				texture_type = GL_TEXTURE_2D;	//this is a 2D texture
+			else if (R[1] > 1)					//if the dimension value is greater than 1
+				texture_type = GL_TEXTURE_1D;	//this is a 1D texture
+		}
+
+		//initializes important variables
+		void init() {
+			texID = 0;							//initialize texture ID to zero, default if OpenGL returns an error
+			memset(R, 0, sizeof)
+		}
+
 	public:
 		///default constructor
-		gl_texture()
-		{
+		gl_texture() : image_stack<T>() {
 		}
 		///@param string path to the directory with the image files.
 		///Creates an instance of the gl_texture object with a path to the data.
-		gl_texture(std::string file_path)
-		{
-			path = file_path;
-			image_stack<T>::load_images(path.append("/*.jpg"));
+		gl_texture(std::string file_mask){
+			image_stack<T>::load_images(file_mask);
 			setTextureType();
 		}
 		///returns the dimentions of the data in the x, y, z directions. 
-		vec<int>
-		getSize()
-		{
+		vec<int> getSize(){
 			stim::vec<int> size(R[1], R[2], R[3]);
 			return size;
 		}
+		void getSize(size_t& x, size_t& y, size_t& z) {
+			x = R[0]; y = R[1]; z = R[2];
+		}
+
 		///@param GLint interp     --GL_LINEAR, GL_NEAREST...
 		///@param GLint twrap      --GL_REPEAR, GL_CLAMP_TO_EDGE...
 		///@param GLenum dataType  --GL_UNSIGNED_BYTE, GL_FLOAT16...
 		///@param GLenum dataFormat--GL_LUMINANCE, GL_RGB...
 		///	Texture paramenters.
-		void
-		setTexParam(GLint interp = GL_LINEAR,
-			    GLint twrap = GL_CLAMP_TO_EDGE,
-			    GLenum dataType = GL_UNSIGNED_BYTE,
-			    GLenum dataFormat = GL_LUMINANCE)
-		{
+		void setTexParam(GLint interp = GL_LINEAR,
+					GLint twrap = GL_CLAMP_TO_EDGE,
+					GLenum dataType = GL_UNSIGNED_BYTE,
+					GLenum dataFormat = GL_LUMINANCE){
 			interpType = interp;
 			texWrap    = twrap;
 			type	   = dataType;
@@ -104,45 +91,34 @@ class gl_texture : public virtual image_stack&lt;T&gt;
 		///@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;
+		void setSpacing(float sx, float sy, float sz){
+			S[1] = sx;
+			S[2] = sy;
+			S[3] = sz;
 		}
 		///Returns a stim::vec that contains the x, y, z sizes of the voxel.
-		vec<float>
-		getDims()
-		{
+		vec<float> getDims(){
 			vec<float> dims(S[1], S[2], S[3]);
 			return dims;
 		}	
-		///@param file_Path location of the directory with the files
+		///@param file_mask specifies the file(s) to be loaded
 		///	Sets the path and calls the loader on that path.
-		void
-		setPath(std::string file_path)
-		{
-			path = file_path;
-			image_stack<T>::load_images(path.append("/*.jpg"));
+		void load(std::string file_mask){
+			image_stack<T>::load_images(file_mask);
 			setTextureType();
 		}
 		///	Returns an std::string path associated with an instance of the gl_texture class.
-		std::string
-		getPath()
-		{
-			return path;
-		}
+		//std::string getPath()
+		//{
+		//	return path;
+		//}
 		///	Returns the GLuint id of the texture created by/associated with the 
-		///	instance of the gl_texture class.
-				
-		GLuint
-		getTexture()
-		{
+		///	instance of the gl_texture class.				
+		GLuint getTexture(){
 			return texID;
 		}
@@ -152,61 +128,24 @@ class gl_texture : public virtual image_stack&lt;T&gt;
 	        //TO DO:::add methods for handling the cases of T
 		// and convert them to GL equivalent.
 		// i.e. an overloaded function that handles paramenter conversion.	
-		void
-		createTexture()
-		{
-			glPixelStorei(GL_UNPACK_ALIGNMENT,1);
+		void createTexture(){
+			glPixelStorei(GL_UNPACK_ALIGNMENT, 1);
 			glGenTextures(1, &texID);
 			glBindTexture(texture_type, texID);
-			glTexParameteri(texture_type,
-				 GL_TEXTURE_MIN_FILTER,
-				 interpType);
-			glTexParameteri(texture_type,
-				 GL_TEXTURE_MAG_FILTER,
-				 interpType);
-			switch(texture_type)
-			{
+			glTexParameteri(texture_type, GL_TEXTURE_MIN_FILTER, interpType);
+			glTexParameteri(texture_type, GL_TEXTURE_MAG_FILTER, interpType);
+			switch(texture_type){
 				case GL_TEXTURE_3D:
-					glTexParameteri(texture_type,
-						 GL_TEXTURE_WRAP_S,texWrap);
-			// GL_REPEAT);
-			// GL_CLAMP_TO_EDGE);
-					glTexParameteri(texture_type,
-						 GL_TEXTURE_WRAP_T,texWrap);
-			// GL_REPEAT);
-			// GL_CLAMP_TO_EDGE);
-					glTexParameteri(texture_type,
-						 GL_TEXTURE_WRAP_R,texWrap);
-			// GL_REPEAT);
-			// GL_CLAMP_TO_EDGE);
-					glTexImage3D(texture_type,
-						0,
-					//	GL_RGB16,
-						1,
-						R[1],
-						R[2],
-						R[3],
-						0,
-						format,
-						type, 
-						ptr);
-					//GL_UNSIGNED_BYTE can be TYPES, convert to GL equivalents
+					glTexParameteri(texture_type, GL_TEXTURE_WRAP_S, texWrap);
+					glTexParameteri(texture_type, GL_TEXTURE_WRAP_T, texWrap);
+					glTexParameteri(texture_type, GL_TEXTURE_WRAP_R, texWrap);
+					glTexImage3D(texture_type, 0, 1, R[1], R[2], R[3], 0, format, type, ptr);
 					glPixelStorei(GL_PACK_ALIGNMENT,1);
 					break;
 				case GL_TEXTURE_2D:
-					glTexParameteri(texture_type,
-						 GL_TEXTURE_WRAP_S, texWrap);
-					glTexParameteri(texture_type,
-						 GL_TEXTURE_WRAP_T, texWrap);
-					glTexImage2D(texture_type,
-						0,
-						1,
-						R[1],
-						R[2],
-						0,
-						format,
-						type, 
-						ptr);
+					glTexParameteri(texture_type, GL_TEXTURE_WRAP_S, texWrap);
+					glTexParameteri(texture_type, GL_TEXTURE_WRAP_T, texWrap);
+					glTexImage2D(texture_type, 0, 1, R[1], R[2], 0, format, type, ptr);
 					break;
 			}
 		}
@@ -15,78 +15,80 @@ namespace stim{
 	Functions are provided for saving and loading binary data.
 **/
-template<typename T, unsigned int D = 1>
+template<typename T, unsigned int D = 1, typename F = float>
 class grid{
 protected:
-	stim::vec<unsigned long> R;		//elements in each dimension
-	stim::vec<float> S;
+	size_t R[D];							//elements in each dimension
+	F S[D];									//spacing between element samples
 	T* ptr;									//pointer to the data (on the GPU or CPU)
 	///Return the total number of values in the binary file
-	unsigned long samples(){
-
-		unsigned long s = 1;
-		for(unsigned int d = 0; d < D; d++)
+	size_t samples(){
+		size_t s = 1;
+		for(size_t d = 0; d < D; d++)
 			s *= R[d];
-
 		return s;
 	}
 	///Initializes a grid by allocating the necessary memory and setting all values to zero
-	void init(){
-
-		//calculate the total number of values
-		unsigned long S = samples();
-
-		//allocate memory to store the grid
-		ptr = (T*)malloc(sizeof(T) * S);
-
-		//initialize the memory to zero
-		memset(ptr, 0, sizeof(T) * S);
-
+	void init(){		
+		size_t N = samples();						//calculate the total number of values		
+		ptr = (T*)calloc(sizeof(T) * N);			//allocate memory to store the grid		
 	}
 public:
 	///Default constructor doesn't do anything
 	grid(){
-		ptr = NULL;			//set the pointer to NULL so that we know nothing is allocated
+		memset(R, 0, sizeof(size_t) * D);			//initialize the grid dimensions to zero
+		memset(S, 0, sizeof(F) * D);				//initialize the grid size to zero
+		ptr = NULL;									//set the data pointer to NULL
 	}
 	///Constructor used to specify the grid size as a vector
 	/// @param _R is a vector describing the grid resolution
-	grid( stim::vec<unsigned long> _R){
-		
-		//set the grid resolution
-		R = _R;
-
+	grid( stim::vec<size_t> _R){
+		for (size_t d = 0; d < D; d++)
+			R[d] = _R[d];
 		init();		
 	}
 	void
-	setDim(stim::vec<float> s)
-	{
-		S = s;
+	setDim(stim::vec<float> s){
+		for(size_t d = 0; d < D; d++)
+			S[d] = s[d];
 	}
 	///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
-	grid( unsigned long X0, ...){
-
-		R[0] = X0;
-
-		va_list ap;
-		va_start(ap, X0);
-		for(unsigned int d = 1; d<D; d++)
-			R[d] = va_arg(ap, unsigned long);
+	grid( size_t X0, ...){
+		R[0] = X0;									//set the grid size of the first dimension
+		va_list ap;									//get a variable list
+		va_start(ap, X0);							//start the variable list at the first element
+		for(size_t d = 1; d<D; d++)					//for each additional element
+			R[d] = va_arg(ap, size_t);				//read the value from the variable list as a size_t
 		va_end(ap);
+		init();										//initialize the grid
+	}
-		init();
+	///Set the spacing between grid sample points
+	/// @param X0... is a list of values describing the grid sample spacing
+	void spacing(F X0, ...) {
+		S[0] = X0;											//set the grid size of the first dimension
+		va_list ap;											//get a variable list
+		va_start(ap, X0);									//start the variable list at the first element
+		for (size_t d = 1; d<D; d++)						//for each additional element
+			S[d] = va_arg(ap, size_t);						//read the value from the variable list as a size_t
+		va_end(ap);
+		init();												//initialize the grid
+	}
+	/// Get the sample spacing for the given dimension
+	F get_spacing(size_t d) {
+		return S[d];
 	}
 	///Writes the binary data to disk
@@ -94,13 +96,9 @@ public:
 	/// @param filename is the name of the binary file to be written
 	void write(std::string filename){
-		std::fstream file;
-
-		//open the file as binary for reading
-		file.open(filename.c_str(), std::ios::out | std::ios::binary);
-
-		//write file to disk
-		file.write((char *)ptr, samples() * sizeof(T));
+		std::fstream file;		
+		file.open(filename.c_str(), std::ios::out | std::ios::binary);		//open the file as binary for reading		
+		file.write((char *)ptr, samples() * sizeof(T));						//write file to disk
 	}
 	///Loads a binary file from disk
@@ -108,44 +106,33 @@ public:
 	/// @param filename is the name of the file containing the binary data
 	/// @param S is the size of the binary file along each dimension
 	/// @param header is the size of the header in bytes
-	void read(std::string filename, stim::vec<unsigned long> S, unsigned long header = 0){
-
-		R = S;	//set the sample resolution
-
-		//allocate space for the data
-		init();
-
-		std::fstream file;
-
-		//open the file as binary for writing
-		file.open(filename.c_str(), std::ios::in | std::ios::binary);
-
-		//seek past the header
-		file.seekg(header, std::ios::beg);
-
-
-		//read the data
-		file.read((char *)ptr, samples() * sizeof(T));
+	void read(std::string filename, stim::vec<size_t> X, unsigned long header = 0){
+		for(size_t d = 0; d < D; d++)
+			R[d] = X[d];																//set the sample resolution		
+		init();																//allocate space for the data
+		std::fstream file;		
+		file.open(filename.c_str(), std::ios::in | std::ios::binary);		//open the file as binary for writing		
+		file.seekg(header, std::ios::beg);									//seek past the header		
+		file.read((char *)ptr, samples() * sizeof(T));						//read the data
 	}
 	///Gets a single value from the grid given a set of coordinates
-
 	/// @param x0... is a list of coordinates specifying the desired value
 	T get(unsigned long x0, ...){
-		va_list ap;
+		va_list ap;									//create a variable list
-		unsigned long F = 1;
-		unsigned long p = x0;
+		unsigned long F = 1;						//initialize the dimension size to 1
+		unsigned long idx = x0;
-		va_start(ap, x0);
-		for(unsigned int d = 1; d<D; d++){
-			F *= R[d-1];
-			p += va_arg(ap, unsigned int) * F;
+		va_start(ap, x0);							//start a variable list
+		for(unsigned int d = 1; d<D; d++){			//for each dimension
+			F *= R[d-1];							//get the size of the first dimension
+			idx += va_arg(ap, unsigned int) * F;	//increment the index
 		}
 		va_end(ap);
-		return ptr[p];
+		return ptr[idx];							//access the appropriate element and return the value
 	}
 	///Sets a value in the grid
@@ -153,20 +140,17 @@ public:
 	/// @param value is the grid point value
 	/// @x0... is the coordinate of the value to be set
 	void set(T value, unsigned long x0, ...){
-
-		va_list ap;
-		
-		unsigned long F = 1;
-		unsigned long p = x0;
-
-		va_start(ap, x0);
-		for(unsigned int d = 1; d<D; d++){
-			F *= R[d-1];
-			p += va_arg(ap, unsigned int) * F;
+		va_list ap;									//create a variable list		
+		unsigned long F = 1;						//initialize the dimension counter to 1
+		unsigned long idx = x0;						//initialize the index to the first variable
+
+		va_start(ap, x0);							//start the variable list
+		for(unsigned int d = 1; d<D; d++){			//for each dimension
+			F *= R[d - 1];
+			idx += va_arg(ap, unsigned int) * F;	//update the index
 		}
 		va_end(ap);
-
-		ptr[p] = value;
+		ptr[idx] = value;							//set the value at the indexed location
 	}
@@ -179,9 +163,7 @@ public:
 		for(unsigned int d = 0; d<D; d++){
 			if(d!=0) result<<", ";
 			result<<R[d];
-
 		}
-
 		result<<"]"<<std::endl;
 		//calculate the number of values to output
@@ -8,9 +8,8 @@
 namespace stim{
-/**This class is used to load 3D grid data from stacks of images
-	The class uses a 4D grid object, where the first dimension is a color value.
-**/
+///This class is used to load 3D grid data from stacks of images
+//	The class uses a 4D grid object, where the first dimension is a color value.
 template<typename T>
 class image_stack : public virtual stim::grid<T, 4>{
@@ -24,20 +23,17 @@ protected:
 	using stim::grid<T, 4>::read;
 public:
+	//default constructor
+	image_stack() : grid<T, 4>() {
-	///Load an image stack based on a file mask. Images are loaded in alphanumeric order.
+	}
+	///Load an image stack based on a file mask. Images are loaded in alphanumeric order
 	/// @param file_mask is the mask describing images to be loaded
 	void load_images(std::string file_mask){
 		stim::filename file_path(file_mask);
-		//if the file path is relative, update it with the current working directory
-//		if(file_path.is_relative()){
-//			stim::filename wd = stim::filename::cwd();
-//			file_path = wd.get_relative(file_mask);
-//		}
-
 		//get the list of files
 		std::vector<stim::filename> file_list = file_path.get_list();
@@ -50,7 +46,6 @@ public:
 			std::cout << file_list[i].str() << std::endl;
 		//load the first image and set all of the image_stack properties
-//		std::cout<<"File to Load: "<<file_list[0].str()<<std::endl;
 		stim::image<T> I(file_list[0].str());
 		//set the image resolution and number of channels
@@ -63,37 +58,25 @@ public:
 		ptr = (T*)malloc(sizeof(T) * samples());
 		//load and copy each image into the grid
-		for(unsigned int i = 0; i<R[3]; i++){
-
-//			std::cout<<"File to Load: "<<file_list[i].str()<<std::endl;
-			//load the image
-			stim::image<T> I(file_list[i].str());
-
-			//retrieve the interlaced data from the image - store it in the grid
-			I.get_interleaved_rgb(&ptr[ i * R[0] * R[1] * R[2] ]);
-			
+		for(unsigned int i = 0; i<R[3]; i++){			
+			stim::image<T> I(file_list[i].str());					//load the image			
+			I.get_interleaved_rgb(&ptr[ i * R[0] * R[1] * R[2] ]);	//retrieve the interlaced data from the image - store it in the grid			
 		}
 	}
 	///Inserts image I into slot i.
 	/// @param stim::image<T> I; image to insert.
 	/// @int I, where to place the image.
-	void insert_image(stim::image<T> I, int i)
-	{
+	void insert_image(stim::image<T> I, int i){
 		I.get_interleaved_rgb(&ptr[i *R[0] *R[1] *R[2] ]);
 	}
 	///Saves a single page to an image file
 	/// @param file_name is the name of the image file to be created
 	/// @param i is the page to be saved
-	void save_image(std::string file_name, unsigned int i){
-
-		//create an image
-		stim::image<T> I;
-
-		//retrieve the interlaced data from the image - store it in the grid
-		I.set_interleaved_rgb(&ptr[ i * R[0] * R[1] * R[2] ], R[1], R[2], R[0]);
-
+	void save_image(std::string file_name, unsigned int i){		
+		stim::image<T> I;											//create an image		
+		I.set_interleaved_rgb(&ptr[ i * R[0] * R[1] * R[2] ], R[1], R[2], R[0]);	//retrieve the interlaced data from the image - store it in the grid
 		I.save(file_name);
 	}
@@ -133,12 +116,6 @@ public:
 		stim::filename file_path(file_mask);
-		//if the file path is relative, update it with the current working directory
-//		if(file_path.is_relative()){
-//			stim::filename wd = stim::filename::cwd();
-//			file_path = wd.get_relative(file_mask);
-//		}
-
 		//create a list of file names
 		std::vector<std::string> file_list = stim::wildcards::increment(file_path.str(), 0, R[3]-1, 1);
@@ -186,6 +186,7 @@ public:
 		d = vec3<float>(0, 0, 1);
 		up = vec3<float>(0, 1, 0);
 		focus = 1;
+		fov = 60;
 	}