fixed problems with memory allocation in stim::image

David Mayerich
1 parent 0288346a
Showing 5 changed files with 50 additions and 105 deletions Show diff stats
stim/envi/bil.h
stim/envi/bip.h
stim/envi/bsq.h
stim/envi/envi.h
stim/image/image.h
@@ -884,7 +884,7 @@ public:
 	///		using the following indexing: i = p*B + b
 	/// @param matrix is the destination for the pixel data
 	/// @param mask is the mask
-	bool sift(T* matrix, unsigned char* mask = NULL){
+	bool sift(T* matrix, unsigned char* mask = NULL, bool PROGRESS = false){
 		size_t Lbytes = sizeof(T) * X();
 		T* line = (T*) malloc( Lbytes );					//allocate space for a line
@@ -903,6 +903,7 @@ public:
 						pl++;								//increment the pixel pointer
 					}
 				}
+				if(PROGRESS) progress = (double)( (y+1)*Z() + 1) / (double)(Y() * Z()) * 100;
 			}
 			p += pl;										//add the line increment to the running pixel index
 		}
@@ -817,7 +817,7 @@ public:
 	///		using the following indexing: i = p*B + b
 	/// @param matrix is the destination for the pixel data
 	/// @param mask is the mask
-	bool sift(T* matrix, unsigned char* mask = NULL){
+	bool sift(T* matrix, unsigned char* mask = NULL, bool PROGRESS = false){
 		size_t Bbytes = sizeof(T) * Z();
 		size_t XY = X() * Y();
 		T* band = (T*) malloc( Bbytes );					//allocate space for a line
@@ -836,6 +836,7 @@ public:
 			}
 			else
 				file.seekg(Bbytes, std::ios::cur);			//otherwise skip this band
+			if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
 		}
 		return true;
 	}
@@ -809,7 +809,7 @@ public:
 	///		using the following indexing: i = p*B + b
 	/// @param matrix is the destination for the pixel data
 	/// @param mask is the mask
-	bool sift(T* matrix, unsigned char* mask = NULL){
+	bool sift(T* matrix, unsigned char* mask = NULL, bool PROGRESS = false){
 		unsigned long long XY = X() * Y(); 					//Number of XY pixels
 		unsigned long long L = XY * sizeof(T); 				//size of XY plane (in bytes)
@@ -827,9 +827,8 @@ public:
 				if(mask == NULL || mask[xy] != 0){				//if the pixel is valid
 					matrix[i*Z() + b] = band_image[xy];			//copy it to the appropriate point in the values[] array
 					i++;
-					//std::cout<<i<<std::endl;
 				}
-
+				if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
 			}
 		}
@@ -670,13 +670,13 @@ public:
 	///		using the following indexing: i = b*P + p
 	/// @param matrix is the destination for the pixel data
 	/// @param p is the mask
-	bool sift(void* matrix, unsigned char* p = NULL){
+	bool sift(void* matrix, unsigned char* p = NULL, bool PROGRESS = false){
 		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
 			if (header.data_type == envi_header::float32)
-				return ((bsq<float>*)file)->sift((float*)matrix, p);
+				return ((bsq<float>*)file)->sift((float*)matrix, p, PROGRESS);
 			else if (header.data_type == envi_header::float64)
-				return ((bsq<double>*)file)->sift((double*)matrix, p);
+				return ((bsq<double>*)file)->sift((double*)matrix, p, PROGRESS);
 			else{
 				std::cout << "ERROR: unidentified data type" << std::endl;
 				exit(1);
@@ -685,9 +685,9 @@ public:
 		if (header.interleave == envi_header::BIP){
 			if (header.data_type == envi_header::float32)
-				return ((bip<float>*)file)->sift((float*)matrix, p);
+				return ((bip<float>*)file)->sift((float*)matrix, p, PROGRESS);
 			else if (header.data_type == envi_header::float64)
-				return ((bip<double>*)file)->sift((double*)matrix, p);
+				return ((bip<double>*)file)->sift((double*)matrix, p, PROGRESS);
 			else{
 				std::cout << "ERROR: unidentified data type" << std::endl;
 				exit(1);
@@ -695,9 +695,9 @@ public:
 		}
 		if (header.interleave == envi_header::BIL){
 			if (header.data_type == envi_header::float32)
-				return ((bil<float>*)file)->sift((float*)matrix, p);
+				return ((bil<float>*)file)->sift((float*)matrix, p, PROGRESS);
 			else if (header.data_type == envi_header::float64)
-				return ((bil<double>*)file)->sift((double*)matrix, p);
+				return ((bil<double>*)file)->sift((double*)matrix, p, PROGRESS);
 			else{
 				std::cout << "ERROR: unidentified data type" << std::endl;
 				exit(1);
@@ -6,7 +6,6 @@
 #include <vector>
 #include <iostream>
 #include <limits>
-#include <typeinfo>
 namespace stim{
 /// This static class provides the STIM interface for loading, saving, and storing 2D images.
@@ -25,8 +24,6 @@ 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;
@@ -34,7 +31,6 @@ class image{
 	void unalloc(){								//frees any resources associated with the image
 		if(img)	free(img);						//if memory has been allocated, free it
-		img=NULL;		
 	}
@@ -45,16 +41,15 @@ class image{
 	void allocate(){
 		unalloc();
-		img = (T*) malloc( bytes() );	//allocate memory
-		memset(img, 0, bytes());
+		img = (T*) malloc( sizeof(T) * R[0] * R[1] * R[2] );	//allocate memory
 	}
 	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;
@@ -62,23 +57,13 @@ class image{
 	int cv_type(){
-		// The following is C++ 11 code, but causes problems on some compilers (ex. nvcc). Below is my best approximation to a solution
-
-		//if(std::is_same<T, unsigned char>::value)	return CV_MAKETYPE(CV_8U, (int)C());
-		//if(std::is_same<T, char>::value)			return CV_MAKETYPE(CV_8S, (int)C());
-		//if(std::is_same<T, unsigned short>::value)	return CV_MAKETYPE(CV_16U, (int)C());
-		//if(std::is_same<T, short>::value)			return CV_MAKETYPE(CV_16S, (int)C());
-		//if(std::is_same<T, int>::value)				return CV_MAKETYPE(CV_32S, (int)C());
-		//if(std::is_same<T, float>::value)			return CV_MAKETYPE(CV_32F, (int)C());
-		//if(std::is_same<T, double>::value)			return CV_MAKETYPE(CV_64F, (int)C());
-
-		if(typeid(T) == typeid(unsigned char))		return CV_MAKETYPE(CV_8U, (int)C());
-		if(typeid(T) == typeid(char))				return CV_MAKETYPE(CV_8S, (int)C());
-		if(typeid(T) == typeid(unsigned short))		return CV_MAKETYPE(CV_16U, (int)C());
-		if(typeid(T) == typeid(short))				return CV_MAKETYPE(CV_16S, (int)C());
-		if(typeid(T) == typeid(int))				return CV_MAKETYPE(CV_32S, (int)C());
-		if(typeid(T) == typeid(float))				return CV_MAKETYPE(CV_32F, (int)C());
-		if(typeid(T) == typeid(double))				return CV_MAKETYPE(CV_64F, (int)C());
+		if(std::is_same<T, unsigned char>::value)	return CV_MAKETYPE(CV_8U, (int)C());
+		if(std::is_same<T, char>::value)			return CV_MAKETYPE(CV_8S, (int)C());
+		if(std::is_same<T, unsigned short>::value)	return CV_MAKETYPE(CV_16U, (int)C());
+		if(std::is_same<T, short>::value)			return CV_MAKETYPE(CV_16S, (int)C());
+		if(std::is_same<T, int>::value)				return CV_MAKETYPE(CV_32S, (int)C());
+		if(std::is_same<T, float>::value)			return CV_MAKETYPE(CV_32F, (int)C());
+		if(std::is_same<T, double>::value)			return CV_MAKETYPE(CV_64F, (int)C());
 		std::cout<<"ERROR in stim::image::cv_type - no valid data type found"<<std::endl;
 		exit(1);
@@ -86,35 +71,23 @@ class image{
 	/// Returns the value for "white" based on the dynamic range (assumes white is 1.0 for floating point images)
 	T white(){
-		// The following is C++ 11 code, but causes problems on some compilers (ex. nvcc). Below is my best approximation to a solution
-
-		//if(std::is_same<T, unsigned char>::value)		return UCHAR_MAX;
-		//if(std::is_same<T, unsigned short>::value)		return SHRT_MAX;
-		//if(std::is_same<T, unsigned>::value)			return UINT_MAX;
-		//if(std::is_same<T, unsigned long>::value)		return ULONG_MAX;
-		//if(std::is_same<T, unsigned long long>::value)	return ULLONG_MAX;
-		//if(std::is_same<T, float>::value)				return 1.0f;
-		//if(std::is_same<T, double>::value)				return 1.0;
-
-		if(typeid(T) == typeid(unsigned char))		return UCHAR_MAX;
-		if(typeid(T) == typeid(unsigned short))		return SHRT_MAX;
-		if(typeid(T) == typeid(unsigned))			return UINT_MAX;
-		if(typeid(T) == typeid(unsigned long))		return ULONG_MAX;
-		if(typeid(T) == typeid(unsigned long long))	return ULLONG_MAX;
-		if(typeid(T) == typeid(float))				return 1.0f;
-		if(typeid(T) == typeid(double))				return 1.0;
+		if(std::is_same<T, unsigned char>::value)		return UCHAR_MAX;
+		if(std::is_same<T, unsigned short>::value)		return SHRT_MAX;
+		if(std::is_same<T, unsigned>::value)			return UINT_MAX;
+		if(std::is_same<T, unsigned long>::value)		return ULONG_MAX;
+		if(std::is_same<T, unsigned long long>::value)	return ULLONG_MAX;
+		if(std::is_same<T, float>::value)				return 1.0f;
+		if(std::is_same<T, double>::value)				return 1.0;
 		std::cout<<"ERROR in stim::image::white - no white value known for this data type"<<std::endl;
-		exit(1);
+
 	}
 public:
 	/// Default constructor - creates an empty image object
-	image(){
-		init();						//initialize all variables to zero, don't allocate any memory
-	}							
+	image(){ init(); }							//initialize all variables to zero, don't allocate any memory
 	/// Constructor with a filename - loads the specified file
 	image(std::string filename){				//constructor initialize the image with an image file
@@ -136,7 +109,7 @@ public:
 	}
 	/// Copy constructor - duplicates an image object
-	image(const stim::image<T> &I){
+	image(const stim::image<T>& I){
 		init();
 		allocate(I.X(), I.Y(), I.C());
 		memcpy(img, I.img, bytes());
@@ -147,7 +120,16 @@ public:
 		free(img);
 	}
+	/*stim::image<T> operator=(const stim::image<T>& I){
+		if(&I == this)									//handle self-assignment
+			return *this;
+		allocate(I.X(), I.Y(), I.C());
+		memcpy(img, I.img, bytes());
+		return *this;
+	}*/
+
 	stim::image<T>& operator=(const stim::image<T>& I){
+		init();
 		if(&I == this)									//handle self-assignment
 			return *this;
 		allocate(I.X(), I.Y(), I.C());
@@ -160,22 +142,15 @@ public:
 		cv::Mat cvImage = cv::imread(filename, CV_LOAD_IMAGE_UNCHANGED);	//use OpenCV to open the image file
 		if(!cvImage.data){
-			std::cout<<"ERROR stim::image::load() - unable to find image "<<filename<<" ["<<__FILE__<<" (line "<<__LINE__<<")]"<<std::endl;
+			std::cout<<"ERROR stim::image::load() - unable to find image "<<filename<<std::endl;
 			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
@@ -189,18 +164,16 @@ 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, size_t channels = 3){
-		allocate(width, height, channels);
+	void set_interleaved_rgb(T* buffer, size_t width, size_t height){
+		allocate(width, height, 3);
 		memcpy(img, buffer, bytes());
 	}
-	void set_interleaved_bgr(T* buffer, size_t width, size_t height, size_t channels = 3){
-		allocate(width, height, channels);
+	void set_interleaved_bgr(T* buffer, size_t width, size_t height){
+		allocate(width, height, 3);
 		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++){
@@ -380,34 +353,6 @@ 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;
@@ -426,7 +371,6 @@ 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){