Merge branch 'master' of git.stim.ee.uh.edu:codebase/stimlib

David Mayerich
2 parents 904614c3 fba6e7e3
Showing 3 changed files with 92 additions and 21 deletions Show diff stats
stim/gl/gl_spider.h
stim/grids/image_stack.h
stim/image/image.h
@@ -140,7 +140,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			setMatrix();			//create the transformation matrix.
 			glCallList(dList+1);		//move the templates to p, d, m.
 			int best = getCost(ptexbufferID, numSamplesPos);		//find min cost.
-			std::cerr << best << std::endl;
+//			std::cerr << best << std::endl;
 			stim::vec<float> next(		//find next position.
  				pV[best][0],
 				pV[best][1],
 #ifndef STIM_IMAGE_STACK_H
 #define STIM_IMAGE_STACK_H
-#include "../parser/wildcards.h"
-#include "../parser/filename.h"
-#include "../grids/grid.h"
-#include "../image/image.h"
+#include <stim/parser/wildcards.h>
+#include <stim/parser/filename.h>
+#include <stim/grids/grid.h>
+#include <stim/image/image.h>
 namespace stim{
@@ -48,7 +48,7 @@ public:
 		}
 		//load the first image and set all of the image_stack properties
-		std::cout<<"File to Load: "<<file_list[0].str()<<std::endl;
+//		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
@@ -63,7 +63,7 @@ public:
 		//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;
+//			std::cout<<"File to Load: "<<file_list[i].str()<<std::endl;
 			//load the image
 			stim::image<T> I(file_list[i].str());
@@ -73,8 +73,15 @@ public:
 		}
 	}
-	///Saves a single page to an image file
+	///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)
+	{
+		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){
@@ -83,10 +90,11 @@ public:
 		stim::image<T> I;
 		//retrieve the interlaced data from the image - store it in the grid
-		I.set_interleaved(&ptr[ i * R[0] * R[1] * R[2] ], R[1], R[2], R[0]);
+		I.set_interleaved_rgb(&ptr[ i * R[0] * R[1] * R[2] ], R[1], R[2], R[0]);
 		I.save(file_name);
 	}
+
 	///Sets the dimensions of the image in each direction
 	///Voxel-size.
 	/// @param x size in the x direction
@@ -100,8 +108,24 @@ public:
 		S[2] = y;
 		S[3] = z;
 	}
-	///Saves the entire stack to a set of images
+	///set dimensions of the grid.
+	/// @param channels, number of channels in each image.
+	/// @param width,  number of pixels in width each image.
+	/// @param height, number of pixels in height.
+	/// @param depth,  number of pixels in depth.
+	void init(int channels, int width, int height, int depth)
+	{
+		R.resize(4);
+		R[0] = channels;
+		R[1] = width;
+		R[2] = height;
+		R[3] = depth;
+
+		ptr = (T*)malloc(sizeof(T) * samples());
+	}
+
+	///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)
 	void save_images(std::string file_mask){
@@ -24,6 +24,8 @@ class image{
 	size_t Y() const { return R[2]; }
 	size_t C() const { return R[0]; }
+	size_t bytes(){ return size() * sizeof(T); }
+
 	void init(){								//initializes all variables, assumes no memory is allocated
 		memset(R, 0, sizeof(size_t) * 3);		//set the resolution and number of channels to zero
 		img = NULL;
@@ -31,6 +33,8 @@ class image{
 	void unalloc(){								//frees any resources associated with the image
 		if(img)	free(img);						//if memory has been allocated, free it
+		img=NULL;
+		
 	}
@@ -40,15 +44,17 @@ class image{
 	}
 	void allocate(){
-		img = (T*) malloc( sizeof(T) * R[0] * R[1] * R[2] );	//allocate memory
+		unalloc();
+		img = (T*) malloc( bytes() );	//allocate memory
+		memset(img, 0, bytes());
 	}
 	void allocate(size_t x, size_t y, size_t c){	//allocate memory based on the resolution
+		unalloc();
 		R[0] = c; R[1] = x; R[2] = y;				//set the resolution
 		allocate();									//allocate memory
 	}
-	size_t bytes(){ return size() * sizeof(T); }
 	size_t idx(size_t x, size_t y, size_t c = 0){
 		return y * C() * X() + x * C() + c;
@@ -90,24 +96,27 @@ public:
 	/// Constructor with a filename - loads the specified file
 	image(std::string filename){				//constructor initialize the image with an image file
+		init();
 		load(filename);
 	}
 	/// Create a new image from scratch given a number of samples and channels
 	image(size_t x, size_t y = 1, size_t c = 1){
+		init();
 		allocate(x, y, c);
 	}
 	/// Create a new image with the data given in 'data'
 	image(T* data, size_t x, size_t y, size_t c = 1){
+		init();
 		allocate(x, y, c);
 		memcpy(img, data, bytes());
 	}
 	/// Copy constructor - duplicates an image object
 	image(const stim::image<T>& I){
+		init();
 		allocate(I.X(), I.Y(), I.C());
-		//allocate(I.R[1], I.R[2], I.R[0]);
 		memcpy(img, I.img, bytes());
 	}
@@ -133,11 +142,18 @@ public:
 			exit(1);
 		}
 		allocate(cvImage.cols, cvImage.rows, cvImage.channels());			//allocate space for the image
-		T* cv_ptr = (T*)cvImage.data;
-		if(C() == 1)														//if this is a single-color image, just copy the data
-			memcpy(img, cv_ptr, bytes());
-		if(C() == 3)														//if this is a 3-color image, OpenCV uses BGR interleaving
+		T* cv_ptr = (T*) cvImage.data;
+		if(C() == 1)
+		{
+	//if this is a single-color image, just copy the data
+			memcpy(img, cv_ptr, bytes());     
+		}
+		if(C() == 3)
+		{														//if this is a 3-color image, OpenCV uses BGR interleaving
 			set_interleaved_bgr(cv_ptr, X(), Y());
+		}
+
+		cvImage.release();	
 	}
 	//save a file
@@ -151,16 +167,18 @@ public:
 			get_interleaved_bgr(buffer);
 		cv::Mat cvImage((int)Y(), (int)X(), cv_type(), buffer);
 		cv::imwrite(filename, cvImage);
+		cvImage.release();
+		free(buffer);
 	}
 	//create an image from an interleaved buffer
-	void set_interleaved_rgb(T* buffer, size_t width, size_t height){
-		allocate(width, height, 3);
+	void set_interleaved_rgb(T* buffer, size_t width, size_t height, size_t channels = 3){
+		allocate(width, height, channels);
 		memcpy(img, buffer, bytes());
 	}
-	void set_interleaved_bgr(T* buffer, size_t width, size_t height){
-		allocate(width, height, 3);
+	void set_interleaved_bgr(T* buffer, size_t width, size_t height, size_t channels = 3){
+		allocate(width, height, channels);
 		for(size_t c = 0; c < C(); c++){								//copy directly
 			for(size_t y = 0; y < Y(); y++){
 				for(size_t x = 0; x < X(); x++){
@@ -340,6 +358,34 @@ public:
 		return r;								//return the inverted image
 	}
+	
+	/// Invert an image by calculating I1 = alpha - I0, where alpha is the maximum image value
+	image<T> invert(){
+		size_t N = size();						//calculate the total number of values in the image
+		image<T> r(X(), Y(), C());				//allocate space for the resulting image
+		T white_val = maxv();
+		for(size_t n = 0; n < N; n++)
+			r.img[n] = white_val - img[n];		//perform the inversion
+
+		return r;								//return the inverted image
+	}
+
+	///crops the image from x1 to x0 and y1 to y0 and returns a new (smaller) image.
+	image<T> crop(int x0, int x1, int y0, int y1)
+	{
+		
+		image<T> ret(x1-x0, y1-y0, C());
+		int newWidth = x1-x0;
+		int destidx, srcidx;
+		///for each row, cut what amount of data from the original and put it into the new copy.
+		for(int i = 0; i < (y1-y0); i++)
+		{
+			destidx = i*newWidth*C(); ///destination index one per each row
+			srcidx = ((i+(y0))*X()+x0)*C(); ///source index, one per each row.
+			memcpy(&ret.img[destidx], &img[srcidx], sizeof(T)*newWidth*C());
+		}		
+		return ret;
+	}
 	image<T> srgb2lab(){
 		std::cout<<"ERROR stim::image::srgb2lab - function has been broken, re-implement."<<std::endl;
@@ -358,6 +404,7 @@ public:
 		exit(1);
 	}
+
 	// leila's code for non_interleaving data in 3D
 	//create an data set from an interleaved buffer
 	void set_interleaved3(T* buffer, size_t width, size_t height, size_t depth, size_t channels = 3){