fixed merge conficts

Pavel Govyadinov
2 parents 6422f96a 8e2fb2b4
Showing 7 changed files with 63 additions and 51 deletions Show diff stats
stim/envi/bil.h
stim/envi/bip.h
stim/envi/bsq.h
stim/envi/envi.h
stim/image/image.h
stim/parser/filename.h
stim/parser/table.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){
+	bool sift(T* matrix, unsigned char* mask = NULL){
 		size_t Lbytes = sizeof(T) * X();
 		T* line = (T*) malloc( Lbytes );					//allocate space for a line
  
@@ -897,7 +897,7 @@ public:
 				pl = 0;										//initialize the pixel offset for the current line to zero (0)
 				file.read( (char*)line, Lbytes );			//read the current line
 				for(size_t x = 0; x < X(); x++){
-					if(mask[y * X() + x]){					//if the current pixel is masked
+					if(mask == NULL || mask[y * X() + x]){					//if the current pixel is masked
 						size_t i = (p + pl) * Z() + b;		//calculate the index in the sifted matrix
 						matrix[i] = line[x];				//store the current value in the line at the correct matrix location
 						pl++;								//increment the pixel pointer
@@ -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){
+	bool sift(T* matrix, unsigned char* mask = NULL){
 		size_t Bbytes = sizeof(T) * Z();
 		size_t XY = X() * Y();
 		T* band = (T*) malloc( Bbytes );					//allocate space for a line
@@ -826,7 +826,7 @@ public:
  
 		size_t p = 0;										//create counter variables
 		for(size_t xy = 0; xy < XY; xy++){					//for each pixel
-			if(mask[xy]){									//if the current pixel is masked
+			if(mask == NULL || mask[xy]){									//if the current pixel is masked
 				file.read( (char*)band, Bbytes );			//read the current line
 				for(size_t b = 0; b < Z(); b++){			//copy each band value to the sifted matrix
 					size_t i = p * Z() + b;					//calculate the index in the sifted matrix
@@ -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){
+	bool sift(T* matrix, unsigned char* mask = NULL){
 		unsigned long long XY = X() * Y(); 					//Number of XY pixels
 		unsigned long long L = XY * sizeof(T); 				//size of XY plane (in bytes)
  
@@ -61,6 +61,11 @@ class envi{
  
 public:
  
+	/// Default constructor
+	envi(){
+		file = NULL;				//set the file pointer to NULL
+	}
+
 	envi_header header;
  
 	void* malloc_spectrum(){
@@ -665,7 +670,7 @@ 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){
+	bool sift(void* matrix, unsigned char* p = NULL){
  
 		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
 			if (header.data_type == envi_header::float32)
@@ -979,12 +984,13 @@ public:
 	}
  
 	/// Closes the ENVI file.
-	bool close(){
+	void close(){
+		if(file == NULL) return;
 		if(header.interleave == envi_header::BSQ){
 			if(header.data_type ==envi_header::float32)
-				return ((bsq<float>*)file)->close();
+				((bsq<float>*)file)->close();
 			else if(header.data_type == envi_header::float64)
-				return ((bsq<double>*)file)->close();
+				((bsq<double>*)file)->close();
 			else{
 				std::cout<<"ERROR: unidentified data type"<<std::endl;
 				exit(1);
@@ -993,9 +999,9 @@ public:
  
 		else if(header.interleave == envi_header::BIL){
 			if(header.data_type ==envi_header::float32)
-				return ((bil<float>*)file)->close();
+				((bil<float>*)file)->close();
 			else if(header.data_type == envi_header::float64)
-				return ((bil<double>*)file)->close();
+				((bil<double>*)file)->close();
 			else{
 				std::cout<<"ERROR: unidentified data type"<<std::endl;
 				exit(1);
@@ -1004,15 +1010,14 @@ public:
  
 		else if(header.interleave == envi_header::BIP){
 			if(header.data_type ==envi_header::float32)
-				return ((bip<float>*)file)->close();
+				((bip<float>*)file)->close();
 			else if(header.data_type == envi_header::float64)
-				return ((bip<double>*)file)->close();
+				((bip<double>*)file)->close();
 			else{
 				std::cout<<"ERROR: unidentified data type"<<std::endl;
 				exit(1);
 			}
 		}
-		return false;
 	}
  
 	/// Retrieve a single pixel and stores it in pre-allocated memory.
@@ -1181,6 +1186,7 @@ public:
 		else if (header.interleave == envi_header::BIP){
 			if (header.data_type == envi_header::float32){
 				((bip<float>*)file)->spectrum((float*)temp, n, PROGRESS);
+				float test = ((float*)temp)[0];
 				cast<T, float>(ptr, (float*)temp, header.bands);
 			}
 			else if (header.data_type == envi_header::float64){
@@ -225,7 +225,7 @@ public:
  
 		for(size_t x = 0; x < X(); x++){
 			for(size_t y = 0; y < Y(); y++){
-				r.img[r.idx(x, y, c)] = img[idx(x, y, c)];
+				r.img[r.idx(x, y, 0)] = img[idx(x, y, c)];
 			}
 		}
  
@@ -110,7 +110,7 @@ public:
 	}
  
  
-
+	/// Outputs the file name (including prefix and extension)
 	std::string get_name(){
 		if(prefix == "" && ext == "")
 			return "";
@@ -118,14 +118,18 @@ public:
 			return prefix + "." + ext;
 	}
  
+	/// Output the file extension only (usually three characters after a '.')
 	std::string get_extension(){
 		return ext;
 	}
  
+	/// Output the file prefix only (name before the extension)
 	std::string get_prefix(){
 		return prefix;
 	}
  
+	/// Output the entire path (not including the filename)
+	///		ex. "c:\this\is\the\directory\"
 	std::string dir(){
 		std::stringstream ss;
  
@@ -154,17 +158,17 @@ public:
 		ext = "";				//file extension
 	}
  
+	/// Output the entire string, including the path and filename
+	///		ex. "c:\this\is\a\directory\file.txt"
 	std::string str(){
-
-		std::stringstream ss;
-
-		ss<<dir()<<get_name();
-
-		return ss.str();
+		std::stringstream ss;					//create a string stream
+		ss<<dir()<<get_name();					//push the directory and filename to that stream
+		return ss.str();						//convert the stream to a string and return it
 	}
  
 	//*****************************************************************************************************************
 	// output is the directory and the prefix and the extension of the files, which are looking for in that directory.
+	/// David: I have no idea what this is doing. It looks identical to dir()
 	std::string dir_fname(){
 		std::stringstream ss;
  
@@ -190,20 +194,17 @@ public:
 	std::string f_name(std::string file_name){
 		std::stringstream ss;
  
-		//if the path is absolute
-		if(absolute){
-			//output the drive letter if in Windows
+		if(absolute){ 								//if the path is absolute
 			#ifdef _WIN32
-				ss<<drive<<":";
+				ss<<drive<<":";						//output the drive letter if in Windows
 			#endif
-			ss<<STIM_FILENAME_DIV;
+			ss<<STIM_FILENAME_DIV;					//output a path divider
 		}
  
-		//output the directory
-		for(unsigned int d = 0; d < path.size(); d++)
-			ss<<path[d]<<STIM_FILENAME_DIV;
+		for(unsigned int d = 0; d < path.size(); d++)	//for each directory in the current path
+			ss<<path[d]<<STIM_FILENAME_DIV;				//add that directory, interspersing path dividers
  
-		stim::filename fn = file_name;
+		stim::filename fn = file_name;					
 			std::string fn_prefix = fn.prefix;
 			std::string fn_ext = fn.ext;
 		ss<<fn_prefix + '.' + fn_ext;
@@ -212,38 +213,41 @@ public:
  
 	}
  
+	/// Returns a list of files using the current filename as a template.
+	/// For example:
+	///			C:\this\is\a\path\file*.txt
+	///		can be used as a template to find a series of files file001.txt, file002.txt, file003.txt, etc.
 	std::vector<stim::filename> get_list(){
-#ifdef _WIN32
-	//get a list of files matching the current template
+		//this is OS dependent, so we're starting with Windows
+		//the Unix version requires Boost
  
+#ifdef _WIN32
+		stim::filename filepath(dir_fname());									//initialize filepath with the mask					
  
-		//stim::filename file_path;
-		stim::filename filepath(dir_fname());
-
-		HANDLE            hFind = INVALID_HANDLE_VALUE;
+		HANDLE            hFind = INVALID_HANDLE_VALUE;							//allocate data structures for looping through files
 		WIN32_FIND_DATAA   FindFileData;
-		std::vector<stim::filename> file_list;
+		std::vector<stim::filename> file_list;									//initialize a list to hold all matching filenames
  
-		hFind = FindFirstFileA((filepath.str().c_str()), &FindFileData);
+		hFind = FindFirstFileA((filepath.str().c_str()), &FindFileData);		//find the first file that matches the specified file path
  
-		if (hFind == INVALID_HANDLE_VALUE) {
-			printf ("Invalid file handle. Error is %u.\n", GetLastError());
+		if (hFind == INVALID_HANDLE_VALUE) { 									//if there are no matching files
+			printf ("Invalid file handle. Error is %u.\n", GetLastError());		//print an error
 		}
 		else {
-			std::string file_name = FindFileData.cFileName;					//get the file name
-			std::string file_path = dir();
-			stim::filename current_file(file_path + file_name);
-			file_list.push_back(current_file);
+			std::string file_name = FindFileData.cFileName;						//save the file name
+			std::string file_path = dir();										//the file is in the specified directory, so save it
+			stim::filename current_file(file_path + file_name);					//create a stim::filename structure representing this file
+			file_list.push_back(current_file);									//push the new stim::filename to the file list
  
 			// List all the other files in the directory.
-			while (FindNextFileA(hFind, &FindFileData) != 0){
-				file_name = FindFileData.cFileName;
-				current_file = (f_name(file_name));
-				file_list.push_back(current_file);
+			while (FindNextFileA(hFind, &FindFileData) != 0){ 					//iterate until there are no more matching files
+				file_name = FindFileData.cFileName;								//save the next file
+				current_file = (f_name(file_name));								//append the directory
+				file_list.push_back(current_file);								//push it to the list
 			}
-			FindClose(hFind);
+			FindClose(hFind);													//close the file data structure
 		}
-		return file_list;
+		return file_list;														//return the list of files
  
 #elif BOOST_PRECOMPILED
  
@@ -34,6 +34,8 @@ namespace stim{
 		template<typename T>
 		T operator<<(T i){
 			std::stringstream ss;
+			if(std::is_fundamental<T>())						//if the data type is numeric
+				ss<<std::setprecision(std::numeric_limits<T>::digits10 + 3);	//set the precision to account for all digits
 			ss<<i;
 			TABLE[y].push_back(ss.str());
 			x++;