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

David Mayerich
2 parents 96e8ab1f 618dce30
Showing 7 changed files with 104 additions and 18 deletions Show diff stats
matlab/images2ENVI.m
stim/envi/binary.h
stim/envi/envi.h
stim/image/image.h
stim/math/filters/conv2.h
stim/math/filters/gauss2.h
stim/math/filters/sepconv2.h
+function images2ENVI( image_struct, filename )
+%HSIWRITE : This function generates a hyperspectral binary image and header
+% based on multi-dimention image
+%
+%
+% This function accepts a srutcture which contains several channels.
+% It creates a 'bsq' interleaved image and a ENVI header filer correspoing
+% to the information of the image
+
+fields = fieldnames(image_struct);
+
+% check all images to have the same size
+for i = 1 : size (fields, 1)
+    for j = 1 : size (fields, 1)
+        if size(image_struct.(fields{i}))~= size(image_struct.(fields{i}))
+            fprintf ('Dimension of input images do not Match !');
+            exit;
+        end
+    end
+end
+
+
+
+
+
+% Extracting the needed information
+base_image = image_struct.(fields{1});
+
+rows = size(base_image, 1);
+columns = size(base_image, 2);
+bands = size(fields,1);
+multiDimImage = base_image';                                                % Matlab stores column major, transposing make it row major to be saved on memory
+
+% Create multi-dimentional image
+for j = 1 : size(fields,1)
+    multiDimImage(:,:,j) = (image_struct.(fields{j})');                     % Matlab stores column major, transposing make it row major to be saved on memory
+end
+
+% create the binary image
+HSImage = reshape (multiDimImage, [rows*columns*bands, 1]);
+if (~isfloat(HSImage))
+    HSImage_float = single(HSImage);                                         % casting to float
+end
+multibandwrite(HSImage_float,filename,'bsq');
+
+
+% create the header file
+info.samples = columns;
+info.lines = rows;
+info.bands = bands;
+info.header_offset = 0;
+info.file_type = 'ENVI Standard';
+info.data_type = 4;
+info.interleave = 'bsq';
+
+
+
+
+fid = fopen(strcat(filename, '.hdr'),'w');                                  % open a file to write the header file
+fprintf(fid,'%s\n','ENVI');                                                 % first line of the header file showing it is an ENVI file
+
+info_fields=fieldnames(info);
+for i = 1:length(info_fields)
+    parameter = info_fields{i};                                             % get the parameter of each line
+    value = info.(info_fields{i});                                          % get the corresponding value of the parameter
+    parameter(strfind(parameter,'_')) = ' ';                                % change '_' to ' '
+    line=[parameter,' = ',num2str(value)];                                  % create the line of the hdr file
+    fprintf(fid,'%s\n',line);                                               % write it to the hdr file
+end
+
+fclose(fid);                                                                % clode the header file
+
+end
+
@@ -15,7 +15,7 @@
 #include <unistd.h>
 #endif
  
-#ifdef CUDA_FOUND
+#ifdef USE_CUDA
 //CUDA externs
 void gpu_permute(char* dest, char* src, size_t sx, size_t sy, size_t sz, size_t d0, size_t d1, size_t d2, size_t typesize);
 #include <stim/cuda/cudatools/error.h>
@@ -647,7 +647,7 @@ public:
 		std::chrono::high_resolution_clock::time_point t0, t1;
 		t0 = std::chrono::high_resolution_clock::now();
  
-#ifdef CUDA_FOUND
+#ifdef USE_CUDA
 		T* gpu_src;
 		HANDLE_ERROR( cudaMalloc(&gpu_src, sx*sy*sz*sizeof(T)) );
 		HANDLE_ERROR( cudaMemcpy(gpu_src, src, sx*sy*sz*sizeof(T), cudaMemcpyHostToDevice) );
@@ -359,11 +359,23 @@ public:
  
 		fseek(f, 9, SEEK_SET);											//seek to the number of bands
 		short b;														//allocate space for the number of bands
-		fread(&b, sizeof(short), 1, f);									//read the number of bands
+		size_t nread = fread(&b, sizeof(short), 1, f);					//read the number of bands
+		if(nread != 1){
+			std::cout<<"Error reading band number from Agilent file."<<std::endl;
+			exit(1);
+		}
 		fseek(f, 13, SEEK_CUR);											//skip the the x and y dimensions
 		short x, y;
-		fread(&x, sizeof(short), 1, f);									//read the image x and y size
-		fread(&y, sizeof(short), 1, f);
+		nread = fread(&x, sizeof(short), 1, f);									//read the image x and y size
+		if(nread != 1){
+			std::cout<<"Error reading X dimension from Agilent file."<<std::endl;
+			exit(1);
+		}
+		nread = fread(&y, sizeof(short), 1, f);
+		if(nread != 1){
+			std::cout<<"Error reading Y dimension from Agilent file."<<std::endl;
+			exit(1);
+		}
 		fclose(f);														//close the file
  
 		//store the information from the Agilent header in the ENVI header
@@ -141,7 +141,7 @@ public:
  
 	//save a Netpbm file
 	void load_netpbm(std::string filename) {
-		std::ifstream infile(filename, std::ios::in | std::ios::binary);		//open an output file
+		std::ifstream infile(filename.c_str(), std::ios::in | std::ios::binary);		//open an output file
 		if (!infile) {
 			std::cout << "Error opening input file in image::load_netpbm()" << std::endl;
 			exit(1);
@@ -244,7 +244,7 @@ public:
  
 	//save a Netpbm file
 	void save_netpbm(std::string filename) {
-		std::ofstream outfile(filename, std::ios::out | std::ios::binary);		//open an output file
+		std::ofstream outfile(filename.c_str(), std::ios::out | std::ios::binary);		//open an output file
 		if(!outfile) {
 			std::cout << "Error generating output file in image::save_netpbm()" << std::endl;
 			exit(1);
@@ -356,8 +356,8 @@ public:
 	}
  
 	/// Returns an std::vector containing each channel as a separate image
-	std::vector<image<T>> split() const {
-		std::vector<image<T>> r;			//create an image array
+	std::vector< image<T> > split() const {
+		std::vector< image<T> > r;			//create an image array
 		r.resize(C());						//create images for each channel
  
 		for (size_t c = 0; c < C(); c++) {	//for each channel
@@ -367,7 +367,7 @@ public:
 	}
  
 	/// Merge a series of single-channel images into a multi-channel image
-	void merge(std::vector<image<T>>& list) {
+	void merge(std::vector< image<T> >& list) {
 		size_t x = list[0].width();				//calculate the size of the image
 		size_t y = list[0].height();
 		allocate(x, y, list.size());			//re-allocate the image
@@ -10,7 +10,7 @@
 namespace stim {
 #ifdef __CUDACC__
 	//Kernel function that performs the 2D convolution.
-	template<typename T, typename K = T>
+	template<typename T, typename K>
 	__global__ void kernel_conv2(T* out, T* in, K* kernel, size_t sx, size_t sy, size_t kx, size_t ky) {
 		extern __shared__ T s[];								//declare a shared memory array
 		size_t xi = blockIdx.x * blockDim.x + threadIdx.x;	//threads correspond to indices into the output image
@@ -52,7 +52,7 @@ namespace stim {
 	//@param sy is the size of the input image along Y
 	//@param kx is the size of the kernel along X
 	//@param ky is the size of the kernel along Y
-	template<typename T, typename K = T>
+	template<typename T, typename K>
 	void gpu_conv2(T* out, T* in, K* kernel, size_t sx, size_t sy, size_t kx, size_t ky) {
 		cudaDeviceProp p;
 		HANDLE_ERROR(cudaGetDeviceProperties(&p, 0));
@@ -77,7 +77,7 @@ namespace stim {
 	//@param sy is the size of the input image along Y
 	//@param kx is the size of the kernel along X
 	//@param ky is the size of the kernel along Y
-	template<typename T, typename K = T>
+	template<typename T, typename K>
 	void cpu_conv2(T* out, T* in, K* kernel, size_t sx, size_t sy, size_t kx, size_t ky) {
 		size_t X = sx - kx + 1;					//x size of the output image
 		size_t Y = sy - ky + 1;					//y size of the output image
@@ -16,7 +16,7 @@ namespace stim {
 	///@param stdx is the standard deviation (in pixels) along the x axis
 	///@param stdy is the standard deviation (in pixels) along the y axis
 	///@param nstds specifies the number of standard deviations of the Gaussian that will be kept in the kernel
-	template<typename T, typename K = T>
+	template<typename T, typename K>
 	stim::image<T> cpu_gauss2(const stim::image<T>& in, K stdx, K stdy, size_t nstds = 3) {
 		size_t kx = stdx * nstds * 2;					//calculate the kernel sizes
 		size_t ky = stdy * nstds * 2;
@@ -33,8 +33,8 @@ namespace stim {
 		for (size_t yi = 0; yi < ky; yi++)
 			gy[yi] = gauss1d((K)yi, muy, stdy);
  
-		std::vector<stim::image<T>> IN = in.split();	//split the input image into channels
-		std::vector<stim::image<T>> R = r.split();		//split the output image into channels
+		std::vector< stim::image<T> > IN = in.split();	//split the input image into channels
+		std::vector< stim::image<T> > R = r.split();		//split the output image into channels
 		for (size_t c = 0; c < in.channels(); c++)		//for each channel
 			cpu_sepconv2(R[c].data(), IN[c].data(), gx, gy, IN[c].width(), IN[c].height(), kx, ky);
  
@@ -15,7 +15,7 @@ namespace stim {
 	//@param sy is the size of the input image along Y
 	//@param kx is the size of the kernel along X
 	//@param ky is the size of the kernel along Y
-	template<typename T, typename K = T>
+	template<typename T, typename K>
 	void gpu_sepconv2(T* out, T* in, K* k0, K* k1, size_t sx, size_t sy, size_t kx, size_t ky) {
 		cudaDeviceProp p;
 		HANDLE_ERROR(cudaGetDeviceProperties(&p, 0));
@@ -54,7 +54,7 @@ namespace stim {
 	//@param sy is the size of the input image along Y
 	//@param kx is the size of the kernel along X
 	//@param ky is the size of the kernel along Y
-	template<typename T, typename K = T>
+	template<typename T, typename K>
 	void cpu_sepconv2(T* out, T* in, K* k0, K* k1, size_t sx, size_t sy, size_t kx, size_t ky) {
 		size_t X = sx - kx + 1;					//x size of the output image
 		size_t Y = sy - ky + 1;