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

Tianshu Cheng
2 parents 6d30a707 3033b886
Showing 5 changed files with 143 additions and 50 deletions Show diff stats
stim/envi/bil.h
stim/envi/bip.h
stim/envi/bsq.h
stim/envi/envi.h
stim/parser/arguments.h
@@ -1005,29 +1005,55 @@ public:
 	/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
 	/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
 	/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
-	bool crop(std::string outfile, unsigned x0, unsigned y0, unsigned x1, unsigned y1){
-
-		//calculate the new number of samples and lines
-		unsigned long long sam = x1 - x0;		//samples
-		unsigned long long lin = y1 - y0;		//lines
-		unsigned long long L = sam * Z() * sizeof(T);
-		//get specified band and save
-		T* temp = (T*)malloc(L);
+	bool crop(std::string outfile, unsigned long long x0,
+								   unsigned long long y0,
+								   unsigned long long x1,
+								   unsigned long long y1,
+								   unsigned long long b0,
+								   unsigned long long b1){
+
+		//calculate the new image parameters
+		unsigned long long samples = x1 - x0;
+		unsigned long long lines = y1 - y0;
+		unsigned long long bands = b1 - b0;
+
+		//calculate the size of a line
+		unsigned long long L = samples * sizeof(T);
+
+
+		//allocate space for a line
+		T* temp = (T*)malloc(bands * L);
+
+		//create an output stream to store the cropped file
 		std::ofstream out(outfile.c_str(), std::ios::binary);
-		unsigned long long jumpb = (X() - sam) * sizeof(T);		//jump pointer to the next band
-		//get start
-		file.seekg((y0 * X() * Z() + x0) * sizeof(T), std::ios::beg);
-		for (unsigned i = 0; i < lin; i++)
+
+		//calculate the distance between bands
+		unsigned long long jumpb = (X() - samples) * sizeof(T);
+
+		//distance needed to jump from the previous line of the last band to the next line of the first band
+		unsigned long long longjump = ((Z() - b1) * X() + b0 * X()) * sizeof(T);
+
+		//set the start position for the cropped region
+		file.seekg((y0 * X() * Z() + b0 * X() + x0) * sizeof(T), std::ios::beg);
+
+		for (unsigned x = 0; x < lines; x++)
 		{
-			for (unsigned j = 0; j < Z(); j++)
+			for (unsigned z = b0; z < b1; z++)
 			{
-				file.read((char *)(temp + j * sam), sizeof(T) * sam);
+				file.read((char *)(temp + z * samples), sizeof(T) * samples);
 				file.seekg(jumpb, std::ios::cur);    //go to the next band	
  
-				thread_data = (double)(i * Z() + j) / (lin * Z()) * 100;
+				thread_data = (double)(x * Z() + z) / (lines * Z()) * 100;
 			}
-			out.write(reinterpret_cast<const char*>(temp), L);   //write slice data into target file	
+
+			//write slice data into target file
+			out.write(reinterpret_cast<const char*>(temp), bands * L);
+
+			//seek to the beginning of the next X-Z slice
+			file.seekg(longjump, std::ios::cur);
 		}
+
+		//free the temporary frame
 		free(temp);
  
 		thread_data = 100;
@@ -1061,26 +1061,57 @@ public:
 	/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
 	/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
 	/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
-	bool crop(std::string outfile, unsigned x0, unsigned y0, unsigned x1, unsigned y1){
+	bool crop(std::string outfile, unsigned long long x0,
+								   unsigned long long y0,
+								   unsigned long long x1,
+								   unsigned long long y1,
+								   unsigned long long b0,
+								   unsigned long long b1){
  
-		//calculate the new number of samples and lines
-		unsigned long long sam = x1 - x0;		//samples
-		unsigned long long lin = y1 - y0;		//lines
-		unsigned long long L = Z() * sizeof(T);
-		//get specified band and save
+		//calculate the new number of samples, lines, and bands
+		unsigned long long samples = x1 - x0;
+		unsigned long long lines = y1 - y0;
+		unsigned long long bands = b1 - b0;
+
+		//calculate the length of one cropped spectrum
+		unsigned long long L = bands * sizeof(T);
+
+		//unsigned long long L = Z() * sizeof(T);
+
+		//allocate space for the spectrum
 		T* temp = (T*)malloc(L);
+
+		//open an output file for binary writing
 		std::ofstream out(outfile.c_str(), std::ios::binary);
-		//get start
-		unsigned long long sp = y0 * X() + x0;		//start pixel
-		for (unsigned i = 0; i < lin; i++)
+
+		//seek to the first pixel in the cropped image
+		file.seekg( (y0 * X() * Z() + x0 * Z() + b0) * sizeof(T), std::ios::beg);
+
+		//distance between sample spectra in the same line
+		unsigned long long jump_sample = ( (Z() - b1) + b0 ) * sizeof(T);
+
+		//distance between sample spectra in adjacent lines
+		unsigned long long jump_line = (X() - x1) * Z() * sizeof(T);
+
+
+		//unsigned long long sp = y0 * X() + x0;		//start pixel
+
+		//for each pixel in the image
+		for (unsigned y = 0; y < lines; y++)
 		{
-			for (unsigned j = 0; j < sam; j++)
+			for (unsigned x = 0; x < samples; x++)
 			{
-				pixel(temp, sp + j + i * X());
+				//read the cropped spectral region
+				file.read( (char*) temp, L );
+				//pixel(temp, sp + x + y * X());
 				out.write(reinterpret_cast<const char*>(temp), L);   //write slice data into target file	
  
-				thread_data = (double)(i * sam + j) / (lin * sam) * 100;
+				file.seekg(jump_sample, std::ios::cur);
+
+				thread_data = (double)(y * samples + x) / (lines * samples) * 100;
 			}
+
+			file.seekg(jump_line, std::ios::cur);
 		}
 		free(temp);
  
@@ -968,27 +968,45 @@ public:
 	/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
 	/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
 	/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
-	bool crop(std::string outfile, unsigned x0, unsigned y0, unsigned x1, unsigned y1){
-
-		//calculate the new number of samples and lines
-		unsigned long long sam = x1 - x0;		//samples
-		unsigned long long lin = y1 - y0;		//lines
-		unsigned long long L = sam * lin * sizeof(T);
-		//get specified band and save
+	bool crop(std::string outfile, unsigned long long x0,
+								   unsigned long long y0,
+								   unsigned long long x1,
+								   unsigned long long y1,
+								   unsigned long long b0,
+								   unsigned long long b1){
+
+		//calculate the new number of samples, lines, and bands
+		unsigned long long samples = x1 - x0;
+		unsigned long long lines = y1 - y0;
+		unsigned long long bands = b1 - b0;
+
+		//calculate the size of a single band
+		unsigned long long L = samples * lines * sizeof(T);
+
+		//allocate space for a single band
 		T* temp = (T*)malloc(L);
+
+		//create an output stream to store the output file
 		std::ofstream out(outfile.c_str(), std::ios::binary);
-		unsigned long long jumpb = X() * (Y() - lin) * sizeof(T);		//jump pointer to the next band
-		unsigned long long jumpl = (X() - sam) * sizeof(T);	                           	//jump pointer to the next line
-		//get start
-		file.seekg((y0 * X() + x0) * sizeof(T), std::ios::beg);
-		for (unsigned z = 0; z < Z(); z++)
+
+		//calculate the distance required to jump from the end of one band to the beginning of another
+		unsigned long long jumpb = X() * (Y() - lines) * sizeof(T);
+
+		//calculate the distance required to jump from the end of one line to the beginning of another
+		unsigned long long jumpl = (X() - samples) * sizeof(T);
+
+		//seek to the start of the cropped region in the input file
+		file.seekg( (b0 * X() * Y() + y0 * X() + x0) * sizeof(T), std::ios::beg);
+
+		//for each band
+		for (unsigned long long z = b0; z < b1; z++)
 		{
-			for (unsigned j = 0; j < lin; j++)
+			for (unsigned y = 0; y < lines; y++)
 			{
-				file.read((char *)(temp + j * sam), sizeof(T) * sam);
+				file.read((char *)(temp + y * samples), sizeof(T) * samples);
 				file.seekg(jumpl, std::ios::cur);    //go to the next band	
  
-				thread_data = (double)(z * lin + j) / (Z() * lin) * 100;
+				thread_data = (double)(z * lines + y) / (Z() * lines) * 100;
 			}
 			out.write(reinterpret_cast<const char*>(temp), L);   //write slice data into target file	
 			file.seekg(jumpb, std::ios::cur);
@@ -1022,13 +1022,23 @@ public:
 	/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
 	/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
 	/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
-	bool crop(std::string outfile,unsigned x0, unsigned y0, unsigned x1, unsigned y1){
+	bool crop(std::string outfile,unsigned x0, unsigned y0, unsigned x1, unsigned y1, unsigned b0, unsigned b1){
+
+		//save the header for the cropped file
+		stim::envi_header new_header = header;
+		new_header.samples = x1 - x0;
+		new_header.lines = y1 - y0;
+		new_header.bands = b1 - b0;
+		std::vector<double>::const_iterator first = new_header.wavelength.begin() + b0;
+		std::vector<double>::const_iterator last = new_header.wavelength.begin() + b1;
+		new_header.wavelength = std::vector<double>(first, last);
+		new_header.save(outfile + ".hdr");
  
 		if (header.interleave == envi_header::BSQ){
 			if (header.data_type == envi_header::float32)
-				return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1);
+				return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1);
 			else if (header.data_type == envi_header::float64)
-				return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1);
+				return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1);
 			else{
 				std::cout << "ERROR: unidentified data type" << std::endl;
 				exit(1);
@@ -1036,9 +1046,9 @@ public:
 		}
 		else if (header.interleave == envi_header::BIL){
 			if (header.data_type == envi_header::float32)
-				return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1);
+				return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1);
 			else if (header.data_type == envi_header::float64)
-				return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1);
+				return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1);
 			else{
 				std::cout << "ERROR: unidentified data type" << std::endl;
 				exit(1);
@@ -1046,9 +1056,9 @@ public:
 		}
 		else if (header.interleave == envi_header::BIP){
 			if (header.data_type == envi_header::float32)
-				return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1);
+				return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1);
 			else if (header.data_type == envi_header::float64)
-				return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1);
+				return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1);
 			else{
 				std::cout << "ERROR: unidentified data type" << std::endl;
 				exit(1);
@@ -479,6 +479,14 @@ namespace stim{
         	return args.size();
         }
  
+        /// Returns the number of options that are set
+        unsigned int nopts(){
+        	unsigned int n = 0;									//initialize the counter for the number of options
+        	for(unsigned int i = 0; i < opts.size(); i++)		//go through each option
+        		if(opts[i].is_set()) n++;						//if a value is specified, increment the counter
+        	return n;
+        }
+
         ///Returns the name of an argument, given its index
  
         /// @param a is the index of the requested argument