From 904614c3987dfd1ad775ca77ee2d023e803a8e88 Mon Sep 17 00:00:00 2001
From: David <mayerich@uh.edu>
Date: Mon, 23 May 2016 09:43:13 -0500
Subject: [PATCH] added normalization for BIP files, and added get_noninterleaved to stim::image

---
 stim/envi/bil.h         | 35 ++++++++++++++++++++++++++++++++++-
 stim/envi/bip.h         | 29 ++++++++++++++++++++++++++++-
 stim/image/image.h      | 12 ++++++++++++
 stim/parser/arguments.h | 34 +++++++++++++++++++++++++++++++++-
 4 files changed, 107 insertions(+), 3 deletions(-)

diff --git a/stim/envi/bil.h b/stim/envi/bil.h
index 6890885..f576d4b 100644
--- a/stim/envi/bil.h
+++ b/stim/envi/bil.h
@@ -386,7 +386,40 @@ public:
 		return true;
 	}
 
-	void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){}
+	void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){
+		std::cout<<"ERROR: algorithm not implemented"<<std::endl;
+		exit(1);
+		//This code is almost done but has to be debugged
+		/*std::ofstream target(outfile.c_str(), std::ios::binary);	//open the target binary file		
+
+		size_t B = Z();									//calculate the number of bands
+		size_t L = X();									//get the number of items in a line
+		size_t Lb = L * sizeof(T);						//calculate the number of bytes in a line
+		size_t XY = X() * Y();							//calculate the number of pixels in an image
+
+		T* line = (T*) malloc(Lb);						//allocate space for a line
+		T* len = (T*) malloc(Lb);						//allocate space for the lengths in a line
+
+		for(size_t y = 0; y < Y(); y++){						//for each line in the image
+			file.seekg(y * Lb, std::ios::beg);			//move the pointer to the current file to the beginning
+			for(size_t b = 0; b < B; b++){				//for each band in this line
+				file.read((char*)line, Lb);				//read a line of pixels
+				for(size_t l = 0; l < L; l++)			//for each element in the line for this band
+					len[l] += line[l] * line[l];		//add the square of the spectral component
+			}
+			for(size_t l = 0; l < L; l++)				//for each length element in the line
+				len[l] = sqrt(len[l]);					//calculate the square root of the sum of squares
+			
+			file.seekg(y * Lb, std::ios::beg);			//move the pointer to the current file to the beginning
+			for(size_t b = 0; b < B; b++){				//for each band in this line
+				file.read((char*)line, Lb);				//read a line of pixels
+				for(size_t l = 0; l < L; l++)			//for each element in the line for this band
+					line[l] /= len[l];					//divide each element by the length
+			}
+			target.write((char*)line, Lb);				//write the normalized line to the target file
+			if(PROGRESS) progress = (double)(y+1) / (double)Y();
+		}*/
+	}
 
 	/// Convert the current BIL file to a BSQ file with the specified file name.
 
diff --git a/stim/envi/bip.h b/stim/envi/bip.h
index 908caa4..5e4061d 100644
--- a/stim/envi/bip.h
+++ b/stim/envi/bip.h
@@ -353,7 +353,34 @@ public:
 		return true;
 	}
 
-	void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){}
+	void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){
+
+		std::ofstream target(outfile.c_str(), std::ios::binary);	//open the target binary file
+		file.seekg(0, std::ios::beg);								//move the pointer to the current file to the beginning
+
+		size_t B = Z();												//number of spectral components
+		size_t XY = X() * Y();										//calculate the number of pixels
+		size_t Bb = B * sizeof(T);									//number of bytes in a spectrum
+
+		T* spec = (T*) malloc(Bb);									//allocate space for the spectrum
+		T len;
+		for(size_t xy = 0; xy < XY; xy++){							//for each pixel
+			memset(spec, 0, Bb);									//set the spectrum to zero
+			if(mask == NULL || mask[xy]){							//if the pixel is masked
+				len = 0;											//initialize the 
+				file.read((char*)spec, Bb);							//read a spectrum
+				for(size_t b = 0; b < B; b++)						//for each band
+					len += spec[b]*spec[b];							//add the square of the spectral band
+				len = sqrt(len);									//calculate the square of the sum of squared components
+				for(size_t b = 0; b < B; b++)						//for each band
+					spec[b] /= len;									//divide by the length
+			}
+			else
+				file.seekg(Bb, std::ios::cur);						//otherwise skip a spectrum
+			target.write((char*)spec, Bb);							//output the normalized spectrum
+			if(PROGRESS) progress = (double)(xy + 1) / (double)XY * 100;		//update the progress
+		}		
+	}
 
 
 	/// Convert the current BIP file to a BIL file with the specified file name.
diff --git a/stim/image/image.h b/stim/image/image.h
index d101ec4..6d193dc 100644
--- a/stim/image/image.h
+++ b/stim/image/image.h
@@ -186,6 +186,18 @@ public:
 		memcpy(data, img, bytes());
 	}
 
+	//copies data in the given channel order as a non-interleaved image
+	void get_noninterleaved(T* data){
+		//for each channel
+		for(size_t y = 0; y < Y(); y++){
+			for(size_t x = 0; x < X(); x++){
+				for(size_t c = 0; c < C(); c++){
+					data[c * Y() * X() + y * X() + x] = img[idx(x, y, c)];
+				}
+			}
+		}
+	}
+
 
 	image<T> channel(size_t c){
 
diff --git a/stim/parser/arguments.h b/stim/parser/arguments.h
index 41231f6..3ca819e 100644
--- a/stim/parser/arguments.h
+++ b/stim/parser/arguments.h
@@ -23,18 +23,50 @@ namespace stim{
 		//argument name
 		std::string name;
 
-		//description of the argument
+		//description of the option
 		std::vector<std::string> desc;
 
 		//argument values
 		std::vector<std::string> vals;
 
+		//integral and numerical flags for each argument
+		std::vector<bool> integral;
+		std::vector<bool> numerical;
+
 		//range or example
 		std::string range;
 
 		//flag is true when the argument is user-specified
 		bool flag;
 
+		bool char_numerical(char c){
+			if( (c >= '0' && c <= '9') || c == '-' || c == '.')
+				return true;
+		}
+
+		bool char_integral(char c){
+			if( (c >= '0' && c <= '9') || c == '-')
+				return true;
+		}
+
+		/// Test if a given string contains a numerical (real) value
+		bool test_numerical(std::string v){
+			for(size_t i = 0; i < v.length(); i++){			//for each character in the string
+				if(!char_numerical(v[i]))
+					return false;
+			}
+			return true;
+		}
+
+		/// Test if a given string contains an integer value
+		bool test_integral(std::string v){
+			for(size_t i = 0; i < v.length(); i++){			//for each character in the string
+				if(!char_integral(v[i]))
+					return false;
+			}
+			return true;
+		}
+
 		void parse_val(const std::string &s){
 
 			vals.clear();
--
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