added a new ENVI interface

David Mayerich
1 parent 6aa04ba2
Showing 6 changed files with 226 additions and 536 deletions Show diff stats
envi/bil.h
envi/binary.h
envi/bip.h
envi/bsq.h
envi/envi.h
envi/envi_header.h
 #ifndef STIM_BIL_H
 #define STIM_BIL_H
-#include "../envi/envi.h"
+#include "../envi/envi_header.h"
 #include "../envi/binary.h"
 #include <cstring>
 #include <utility>
@@ -14,7 +14,7 @@ class bil: public binary&lt;T&gt; {
 protected:
-	envi header;
+	envi_header header;
 public:
@@ -353,7 +353,7 @@ public:
 				target.write(reinterpret_cast<const char*>(p), S);   //write a band data into target file	
 		}
-		header.interleave = rts::envi::BSQ;  //change the type of file in header file
+		header.interleave = rts::envi_header::BSQ;  //change the type of file in header file
 		header.save(headername);
 		free(p);
@@ -387,7 +387,7 @@ public:
 			target.write(reinterpret_cast<const char*>(q), S);   //write a band data into target file	
 		}
-		header.interleave = rts::envi::BIP;  //change the type of file in header file
+		header.interleave = rts::envi_header::BIP;  //change the type of file in header file
 		header.save(headername);
 		free(p);
@@ -3,7 +3,7 @@
 #ifndef RTS_BINARY_H
 #define RTS_BINARY_H
-#include "../envi/envi.h"
+#include "../envi/envi_header.h"
 #include "../math/vector.h"
 #include <fstream>
 #include <sys/stat.h>
-#include "../envi/envi.h"
+#ifndef STIM_BIP_H
+#define STIM_BIP_H
+
+#include "../envi/envi_header.h"
 #include "../envi/bil.h"
 #include "../envi/binary.h"
 #include <cstring>
@@ -12,7 +15,7 @@ class bip: public binary&lt;T&gt; {
 protected:
-	envi header;
+	envi_header header;
 public:
@@ -463,7 +466,7 @@ public:
 			target.write(reinterpret_cast<const char*>(q), S);   //write a band data into target file	
 		}
-		header.interleave = rts::envi::BIL;  //change the type of file in header file
+		header.interleave = rts::envi_header::BIL;  //change the type of file in header file
 		header.save(headername);
 		free(p);
@@ -480,3 +483,5 @@ public:
 	};
 }
+
+#endif
-#include "../envi/envi.h"
+#ifndef STIM_BSQ_H
+#define STIM_BSQ_H
+
+#include "../envi/envi_header.h"
 #include "../envi/binary.h"
+#include "../envi/bil.h"
 #include <cstring>
 #include <utility>
+#include <vector>
 namespace rts{
@@ -11,31 +16,38 @@ class bsq: public binary&lt;T&gt; {
 protected:
-	envi header;
+	//envi_header header;
+
+	std::vector<double> w;	//band wavelengths
 public:
 	using binary<T>::open;
 	using binary<T>::file;
 	using binary<T>::getSlice;
+	using binary<T>::R;
 	//open a file, given the file and its header's names
-	bool open(std::string filename, std::string headername){
+	bool open(std::string filename, unsigned int X, unsigned int Y, unsigned int B, unsigned int header_offset, std::vector<double> wavelengths){
-		if (header.load(headername)==false){
+		/*if (header.load(headername)==false){
 			std::cout<<"ERROR: unable to load header file: "<<headername<<std::endl;
 			return false;
-		}
+		}*/
-		open(filename, vec<unsigned int>(header.samples, header.lines, header.bands), header.header_offset);
-		return true;
+		//copy the wavelengths to the BSQ file structure
+		w = wavelengths;
+
+		return open(filename, vec<unsigned int>(X, Y, B), header_offset);
+
+		return false;
 	}
 	//save one band of the file into the memory, and return the pointer
 	bool band_index( T * p, unsigned int page){
-		if (page >= header.bands){										//make sure the bank number is right
+		if (page >= R[2]){										//make sure the bank number is right
 			std::cout<<"ERROR: page out of range"<<std::endl;
 			return false;
 		}
@@ -46,7 +58,7 @@ public:
 	bool getBand( T * p, double wavelength){
-		unsigned int XY = header.samples * header.lines;	//calculate the number of pixels in a band
+		unsigned int XY = R[0] * R[1];	//calculate the number of pixels in a band
 		unsigned page=0;                      //bands around the wavelength
 		T * p1;
@@ -55,28 +67,28 @@ public:
 		//get the bands numbers around the wavelength
 		//if wavelength is smaller than the first one in header file
-		if ( header.wavelength[page] > wavelength ){
+		if ( w[page] > wavelength ){
 			band_index(p, page);
 			return true;
 		}
-		while( header.wavelength[page] < wavelength )
+		while( w[page] < wavelength )
 		{
 			page++;
 			//if wavelength is larger than the last wavelength in header file
-			if (page == header.bands) {
-				getSlice(p, 2, header.bands-1);
+			if (page == R[2]) {
+				getSlice(p, 2, R[2]-1);
 				return true;
 			}
 		}
-		if ( wavelength < header.wavelength[page] )
+		if ( wavelength < w[page] )
 		{
 			p1=(T*)malloc( XY * sizeof(T));                     //memory allocation
 			p2=(T*)malloc( XY * sizeof(T));
 			band_index(p1, page - 1);
 			band_index(p2, page );
 			for(unsigned i=0; i < XY; i++){
-				double r = (double) (wavelength - header.wavelength[page-1]) / (double) (header.wavelength[page] - header.wavelength[page-1]);
+				double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
 				p[i] = (p2[i] - p1[i]) * r + p1[i];
 			}
 		}
@@ -93,16 +105,16 @@ public:
 		unsigned int i;
-		if ( x >= header.samples || y >= header.lines){							//make sure the sample and line number is right
+		if ( x >= R[0] || y >= R[1]){							//make sure the sample and line number is right
 			std::cout<<"ERROR: sample or line out of range"<<std::endl;
 			return false;
 		}
-		file.seekg((x + y * header.samples) * sizeof(T), std::ios::beg);           //point to the certain sample and line
-		for (i = 0; i < header.bands; i++)
+		file.seekg((x + y * R[0]) * sizeof(T), std::ios::beg);           //point to the certain sample and line
+		for (i = 0; i < R[3]; i++)
 		{
 			file.read((char *)(p + i), sizeof(T));
-			file.seekg((header.lines * header.samples - 1) * sizeof(T), std::ios::cur);    //go to the next band
+			file.seekg((R[1] * R[0] - 1) * sizeof(T), std::ios::cur);    //go to the next band
 		}
 		return true;	
@@ -118,8 +130,8 @@ public:
 		std::string headername = outname + ".hdr";              //the header file name
 		//simplify image resolution
-		unsigned int B = header.bands;		//calculate the number of bands
-		unsigned int XY = header.samples * header.lines;	//calculate the number of pixels in a band
+		unsigned int B = R[2];		//calculate the number of bands
+		unsigned int XY = R[0] * R[1];	//calculate the number of pixels in a band
 		unsigned int S = XY * sizeof(T);		//calculate the number of bytes in a band
 		double ai, bi;	//stores the two baseline points wavelength surrounding the current band
@@ -142,11 +154,11 @@ public:
 		//initialize lownum, highnum, low, high		
-		ai=header.wavelength[0];
+		ai=w[0];
 		//if no baseline point is specified at band 0,
 			//set the baseline point at band 0 to 0
-		if(wls[0] != header.wavelength[0]){
+		if(wls[0] != w[0]){
 			bi = wls[control];			
 			memset(a, (char)0, S);
 		}
@@ -163,7 +175,7 @@ public:
 		for(unsigned cii = 0; cii < B; cii++){
 			//update baseline points, if necessary
-			if( header.wavelength[cii] >= bi && cii != B - 1) {
+			if( w[cii] >= bi && cii != B - 1) {
 				//if the high band is now on the last BL point?
 				if (control != N-1) {
@@ -177,20 +189,20 @@ public:
 				}
 				//if the last BL point on the last band of the file?
-				else if ( wls[control] < header.wavelength[B - 1]) {
+				else if ( wls[control] < w[B - 1]) {
 					std::swap(a, b);	//swap the baseline band pointers
 					memset(b, (char)0, S);	//clear the high band
 					ai = bi;
-					bi = header.wavelength[B - 1];
+					bi = w[B - 1];
 				}
 			}
 			//get the current band
 			band_index(c, cii);
-			ci = header.wavelength[cii];
+			ci = w[cii];
 			//perform the baseline correction
 			for(unsigned i=0; i < XY; i++){
@@ -202,7 +214,7 @@ public:
 		}	
-		header.save(headername);         //save the new header file
+		//header.save(headername);         //save the new header file
 		free(a);
 		free(b);
@@ -214,8 +226,9 @@ public:
 	// normalize the BSQ file
 	bool normalize(std::string outname, double band)
 	{
-		unsigned int B = header.bands;		//calculate the number of bands
-		unsigned int XY = header.samples * header.lines;	//calculate the number of pixels in a band
+		std::cout<<"NORMALIZE A BSQ FILE"<<std::endl;
+		unsigned int B = R[2];		//calculate the number of bands
+		unsigned int XY = R[0] * R[1];	//calculate the number of pixels in a band
 		unsigned int S = XY * sizeof(T);		//calculate the number of bytes in a band
 		std::ofstream target(outname.c_str(), std::ios::binary);	//open the target binary file
@@ -239,7 +252,7 @@ public:
 			target.write(reinterpret_cast<const char*>(c), S);   //write normalized data into destination
 		}
-		header.save(headername);         //save the new header file
+		//header.save(headername);         //save the new header file
 		free(b);
 		free(c);
@@ -272,8 +285,8 @@ public:
 	bool bil(std::string outname)
 	{
 		//simplify image resolution
-		unsigned int L = header.samples * header.bands * sizeof(T);		//calculate the number of bytes of a ZX slice
-		unsigned int jump = (header.lines - 1) * header.samples * sizeof(T);  
+		unsigned int L = R[0] * R[1] * sizeof(T);		//calculate the number of bytes of a ZX slice
+		unsigned int jump = (R[1] - 1) * R[0] * sizeof(T);
 		std::ofstream target(outname.c_str(), std::ios::binary);
 		std::string headername = outname + ".hdr";
@@ -281,18 +294,18 @@ public:
 		T * p;			//pointer to the current spectrum
 		p = (T*)malloc(L);
-		for ( unsigned i = 0; i < header.lines; i++)
+		for ( unsigned i = 0; i < R[1]; i++)
 		{
-			file.seekg(header.samples * i * sizeof(T), std::ios::beg);
-			for ( unsigned j = 0; j < header.bands; j++ )
+			file.seekg(R[0] * i * sizeof(T), std::ios::beg);
+			for ( unsigned j = 0; j < R[2]; j++ )
 			{
-				file.read((char *)(p + j * header.samples), sizeof(T) * header.samples);
+				file.read((char *)(p + j * R[0]), sizeof(T) * R[0]);
 				file.seekg(jump, std::ios::cur);    //go to the next band	
 			}					
 			target.write(reinterpret_cast<const char*>(p), L);   //write XZ slice data into target file	
 		}
-		header.interleave = rts::envi::BIL;  //change the type of file in header file
-		header.save(headername);
+		//header.interleave = rts::envi_header::BIL;  //change the type of file in header file
+		//header.save(headername);
 		free(p);
 		target.close();
@@ -308,4 +321,6 @@ public:
 	};
 }
+#endif
+
-#ifndef ENVI_HEADER_H
-#define ENVI_HEADER_H
-
-#include <string>
-#include <iostream>
-#include <fstream>
-#include <sstream>
-#include <vector>
-#include <stdlib.h>
-
-//information from an ENVI header file
-//A good resource can be found here: http://www.exelisvis.com/docs/enviheaderfiles.html
-
-namespace rts{
-
-struct envi
-{
-	enum dataType {dummy0, int8, int16, int32, float32, float64, complex32, dummy7, dummy8, complex64, dummy10, dummy11, uint16, uint32, int64, uint64};
-	enum interleaveType {BIP, BIL, BSQ};	//bip = Z,X,Y; bil = X,Z,Y; bsq = X,Y,Z
-	enum endianType {endianLittle, endianBig};
-
-	std::string name;
-
-	std::string description;
-
-	unsigned int samples;	//x-axis
-	unsigned int lines;		//y-axis
-	unsigned int bands;		//spectral axis
-	unsigned int header_offset;		//header offset for binary file (in bytes)
-	std::string file_type;			//should be "ENVI Standard"
-
-	envi::dataType data_type;			//data representation; common value is 4 (32-bit float)
-
-
-	envi::interleaveType interleave;
-
-	std::string sensor_type;		//not really used
-
-	envi::endianType byte_order;			//little = least significant bit first (most systems)
-
-	double x_start, y_start;		//coordinates of the upper-left corner of the image
-	std::string wavelength_units;	//stored wavelength units
-	std::string z_plot_titles[2];
-
-	double pixel_size[2];			//pixel size along X and Y
-
-	std::vector<std::string> band_names;	//name for each band in the image
-	std::vector<double> wavelength;		//wavelength for each band
-
-	void init(){
-        name = "";
-
-		//specify default values for a new or empty ENVI file
-		samples = 0;
-		lines = 0;
-		bands = 0;
-		header_offset = 0;
-		data_type = float32;
-		interleave = BSQ;
-		byte_order = endianLittle;
-		x_start = y_start = 0;
-		pixel_size[0] = pixel_size[1] = 1;
-
-		//strings
-		file_type = "ENVI Standard";
-		sensor_type = "Unknown";
-		wavelength_units = "Unknown";
-		z_plot_titles[0] = z_plot_titles[1] = "Unknown";
-	}
-
-	envi(){
-		init();
-	}
-	envi(std::string name){
-		init();
-		load(name);
-	}
-
-	std::string trim(std::string line){
-		//trims whitespace from the beginning and end of line
-		unsigned int start_i, end_i;
-		for(start_i=0; start_i < line.length(); start_i++)
-			if(line[start_i] != 32)
-			{
-				break;
-			}
-
-		for(end_i = line.length()-1; end_i >= start_i; end_i--)
-			if(line[end_i] != ' ')
-			{
-				break;
-			}
-
-		return line.substr(start_i, end_i - start_i+1);
-	}
-
-
-	std::string get_token(std::string line){
-		//returns a variable name; in this case we look for the '=' sign
-		size_t i = line.find_first_of('=');
-
-		std::string result;
-		if(i != std::string::npos)
-			result = trim(line.substr(0, i-1));
-
-		return result;
-	}
-
-	std::string get_data_str(std::string line){
-		size_t i = line.find_first_of('=');
-
-		std::string result;
-		if(i != std::string::npos)
-			result = trim(line.substr(i+1));
-		else
-		{
-			std::cout<<"ENVI Header error - data not found for token: "<<get_token(line)<<std::endl;
-			exit(1);
-		}
-		return result;
-	}
-
-	std::string get_brace_str(std::string token, std::string line, std::ifstream &file)
-	{
-		//this function assembles all of the characters between curly braces
-		//this is how strings are defined within an ENVI file
-
-		std::string result;
-
-		//first, find the starting brace
-		size_t i;
-		do
-		{
-			i = line.find_first_of('{');
-			if(i != std::string::npos)
-				break;
-		}while(file);
-
-		//if i is still npos, we have reached the end of the file without a brace...something is wrong
-		if(i == std::string::npos)
-		{
-			std::cout<<"ENVI Header error - string token declared without being defined: "<<token<<std::endl;
-			exit(1);
-		}
-		line = line.substr(i+1);
-
-		//copy character data into the result string until we find a closing brace
-		while(file)
-		{
-			i = line.find_first_of('}');
-
-
-			if(i != std::string::npos)
-			{
-				result += line.substr(0, i);
-				break;
-			}
-			else
-				result += line;
-
-			getline(file, line);
-		}
-
-		if(i == std::string::npos)
-		{
-			std::cout<<"ENVI Header error - string token declared without a terminating '}': "<<token<<std::endl;
-			exit(1);
-		}
-
-		return trim(result);
-	}
-
-	std::vector<std::string> get_string_seq(std::string token, std::string sequence)
-	{
-		//this function returns a sequence of comma-delimited strings
-		std::vector<std::string> result;
-
-		std::string entry;
-		size_t i;
-		do
-		{
-			i = sequence.find_first_of(',');
-			entry = sequence.substr(0, i);
-			sequence = sequence.substr(i+1);
-			result.push_back(trim(entry));
-		}while(i != std::string::npos);
-
-		return result;
-	}
-
-	std::vector<double> get_double_seq(std::string token, std::string sequence)
-	{
-		//this function returns a sequence of comma-delimited strings
-		std::vector<double> result;
-		std::string entry;
-		size_t i;
-		do
-		{
-			i = sequence.find_first_of(',');
-			entry = sequence.substr(0, i);
-			sequence = sequence.substr(i+1);
-			result.push_back(atof(entry.c_str()));
-			//std::cout<<entry<<"   ";
-		}while(i != std::string::npos);
-
-		return result;
-	}
-
-	bool load(std::string filename)
-	{
-		//open the header file
-		std::ifstream file(filename.c_str());
-
-		if(!file)
-		{
-            return false;
-		}
-
-		//the first line should just be "ENVI"
-		std::string line;
-		file>>line;
-		if(line != "ENVI")
-		{
-			std::cout<<"ENVI Header Error: The header doesn't appear to be an ENVI file. The first line should be 'ENVI'."<<std::endl;
-			exit(1);
-		}
-
-		//for each line in the file, get the token
-		std::string token;
-
-        //get a line
-        getline(file, line);
-		while(file)
-		{
-
-
-
-			//get the token
-			token = get_token(line);
-
-			if(token == "description")
-				description = get_brace_str(token, line, file);
-			else if(token == "band names")
-			{
-				std::string string_sequence = get_brace_str(token, line, file);
-				band_names = get_string_seq(token, string_sequence);
-			}
-			else if(token == "wavelength")
-			{
-				std::string string_sequence = get_brace_str(token, line, file);
-				wavelength = get_double_seq(token, string_sequence);
-			}
-			else if(token == "pixel size")
-			{
-				std::string string_sequence = get_brace_str(token, line, file);
-				std::vector<double> pxsize = get_double_seq(token, string_sequence);
-				pixel_size[0] = pxsize[0];
-				pixel_size[1] = pxsize[1];
-			}
-			else if(token == "z plot titles")
-			{
-				std::string string_sequence = get_brace_str(token, line, file);
-				std::vector<std::string> titles = get_string_seq(token, string_sequence);
-				z_plot_titles[0] = titles[0];
-				z_plot_titles[1] = titles[1];
-			}
-
-			else if(token == "samples")
-				samples = atoi(get_data_str(line).c_str());
-			else if(token == "lines")
-				lines = atoi(get_data_str(line).c_str());
-			else if(token == "bands")
-				bands = atoi(get_data_str(line).c_str());
-			else if(token == "header offset")
-				header_offset = atoi(get_data_str(line).c_str());
-			else if(token == "file type")
-				file_type = get_data_str(line);
-			else if(token == "data type")
-				data_type = (dataType)atoi(get_data_str(line).c_str());
-			else if(token == "interleave")
-			{
-				std::string interleave_str = get_data_str(line);
-				if(interleave_str == "bip")
-					interleave = BIP;
-				else if(interleave_str == "bil")
-					interleave = BIL;
-				else if(interleave_str == "bsq")
-					interleave = BSQ;
-			}
-			else if(token == "sensor type")
-				sensor_type = get_data_str(line);
-			else if(token == "byte order")
-				byte_order = (endianType)atoi(get_data_str(line).c_str());
-			else if(token == "x start")
-				x_start = atof(get_data_str(line).c_str());
-			else if(token == "y start")
-				y_start = atof(get_data_str(line).c_str());
-			else if(token == "wavelength units")
-				wavelength_units = get_data_str(line);
-
-            //get the next line
-            getline(file, line);
-		}
-
-		//make sure the number of bands matches the number of wavelengths
-		unsigned int wavelengths = wavelength.size();
-		if(bands != wavelengths)
-		{
-            std::cout<<"ENVI Header Error -- Number of wavelengths doesn't match the number of bands.  Bands = "<<bands<<", Wavelengths = "<<wavelength.size()<<std::endl;
-            exit(1);
-        }
-
-		//close the file
-		file.close();
-
-		//set the file name
-		name = filename;
-
-		return true;
-	}
-
-	void save(std::string filename)
-	{
-		//open a file
-		std::ofstream outfile(filename.c_str());
-
-		//write the ENVI type identifier
-		outfile<<"ENVI"<<std::endl;
-
-		//output all of the data
-		outfile<<"description = {"<<std::endl;
-		outfile<<"  "<<description<<"}"<<std::endl;
-
-		outfile<<"samples = "<<samples<<std::endl;
-		outfile<<"lines = "<<lines<<std::endl;
-		outfile<<"bands = "<<bands<<std::endl;
-		outfile<<"header offset = "<<header_offset<<std::endl;
-		outfile<<"file type = "<<file_type<<std::endl;
-		outfile<<"data type = "<<data_type<<std::endl;
-		outfile<<"interleave = ";
-		if(interleave == BIP)
-			outfile<<"bip";
-		if(interleave == BIL)
-			outfile<<"bil";
-		if(interleave == BSQ)
-			outfile<<"bsq";
-			outfile<<std::endl;
-		outfile<<"sensor type = "<<sensor_type<<std::endl;
-		outfile<<"byte order = "<<byte_order<<std::endl;
-		outfile<<"x start = "<<x_start<<std::endl;
-		outfile<<"y start = "<<y_start<<std::endl;
-		outfile<<"wavelength units = "<<wavelength_units<<std::endl;
-		outfile<<"z plot titles = {";
-			outfile<<z_plot_titles[0]<<", "<<z_plot_titles[1]<<"}"<<std::endl;
-		outfile<<"pixel size = {"<<pixel_size[0]<<", "<<pixel_size[1]<<", units=Meters}"<<std::endl;
-		if(band_names.size() > 0)
-		{
-			outfile<<"band names = {"<<std::endl;
-			for(unsigned int i=0; i<band_names.size(); i++)
-			{
-				outfile<<band_names[i];
-				if(i < band_names.size() - 1)
-					outfile<<", ";
-			}
-			outfile<<"}"<<std::endl;
-		}
-		outfile<<"wavelength = {"<<std::endl;
-			for(unsigned int i=0; i<wavelength.size()-1; i++)
-				outfile<<wavelength[i]<<", ";
-			outfile<<wavelength.back()<<"}"<<std::endl;
-
-		outfile.close();
-	}
-
-	void save()
-	{
-        //std::cout<<"ENVI Header Name: "<<name<<std::endl;
-		save(name);
-	}
-
-	//returns the size of a single value (in bytes)
-	unsigned int valsize()
-	{
-		switch(data_type)
-		{
-		case int8:			//1 = 8-bit byte
-			return 1;
-		case int16:			//16-bit signed integer
-		case uint16:		//16-bit unsigned integer
-			return 2;
-		case int32:			//32-bit signed long integer
-		case float32:		//32-bit floating point
-		case uint32:		//32-bit unsigned long integer
-			return 4;
-		case float64:		//64-bit double-precision floating point
-		case complex32:		//32-bit complex value
-		case int64:		    //64-bit signed long integer
-		case uint64:		//64-bit unsigned long integer
-			return 8;
-		case complex64:		//64-bit complex value
-			return 16;
-		default:
-			return 0;
-		}
-
-	}
-};		//end EnviHeader
-}
-#endif
+#ifndef STIM_ENVI_H
+#define STIM_ENVI_H
+
+#include "../envi/envi_header.h"
+#include "../envi/bsq.h"
+#include "../envi/bip.h"
+#include "../envi/bil.h"
+
+namespace rts{
+
+//container class for an ENVI binary file reader
+class envi{
+
+	envi_header header;
+
+	void* file;		//void pointer to the relevant file reader (bip, bsq, or bil - with appropriate data type)
+
+public:
+
+	bool allocate(){
+
+		file = NULL;	//set file to a NULL pointer
+
+		if(header.interleave == envi_header::BSQ)
+			if(header.data_type ==envi_header::float32)
+				return(file = new bsq<float>());
+
+		exit(1);	//if the function hasn't already returned, we don't handle this state
+
+	}
+
+	bool open(std::string filename, std::string headername){
+
+		//allocate memory
+		allocate();
+
+		//load the header
+		header.load(headername);
+
+		//load the file
+		if(header.interleave == envi_header::BSQ)
+			if(header.data_type ==envi_header::float32)
+				return ((bsq<float>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
+
+		//handle other permutations.....
+
+		exit(1);
+	}
+
+	bool normalize(std::string outfile, double band){
+
+		if(header.interleave == envi_header::BSQ)
+			if(header.data_type ==envi_header::float32)
+				return ((bsq<float>*)file)->normalize(outfile, band);
+
+		exit(1);
+	}
+
+	bool save_header(std::string filename){
+
+		//save the header file here
+		header.save(filename);
+
+		return true;
+	}
+
+
+
+
+
+};
+
+}	//end namespace rts
+
+#endif
-#ifndef ENVI_HEADER_H
-#define ENVI_HEADER_H
-
+#ifndef ENVI_HEADER_H
+#define ENVI_HEADER_H
+
 #include <string>
-#include <iostream>
+#include <iostream>
 #include <fstream>
-#include <sstream>
-#include <vector>
-#include <stdlib.h>
-
+#include <sstream>
+#include <vector>
+#include <stdlib.h>
+
 //information from an ENVI header file
-//A good resource can be found here: http://www.exelisvis.com/docs/enviheaderfiles.html
-
-namespace Envi
-{
-    enum dataType {dummy0, int8, int16, int32, float32, float64, complex32, dummy7, dummy8, complex64, dummy10, dummy11, uint16, uint32, int64, uint64};
-    enum interleaveType {BIP, BIL, BSQ};	//bip = Z,X,Y; bil = X,Z,Y; bsq = X,Y,Z
-    enum endianType {endianLittle, endianBig};
-}
-struct EnviHeader
+//A good resource can be found here: http://www.exelisvis.com/docs/enviheaderfiles.html
+
+namespace rts{
+
+struct envi_header
 {
+	enum dataType {dummy0, int8, int16, int32, float32, float64, complex32, dummy7, dummy8, complex64, dummy10, dummy11, uint16, uint32, int64, uint64};
+	enum interleaveType {BIP, BIL, BSQ};	//bip = Z,X,Y; bil = X,Z,Y; bsq = X,Y,Z
+	enum endianType {endianLittle, endianBig};
+
 	std::string name;
 	std::string description;
@@ -27,16 +27,16 @@ struct EnviHeader
 	unsigned int lines;		//y-axis
 	unsigned int bands;		//spectral axis
 	unsigned int header_offset;		//header offset for binary file (in bytes)
-	std::string file_type;			//should be "ENVI Standard"
-
-	Envi::dataType data_type;			//data representation; common value is 4 (32-bit float)
+	std::string file_type;			//should be "ENVI Standard"
+
+	envi_header::dataType data_type;			//data representation; common value is 4 (32-bit float)
-	Envi::interleaveType interleave;
+	envi_header::interleaveType interleave;
 	std::string sensor_type;		//not really used
-	Envi::endianType byte_order;			//little = least significant bit first (most systems)
+	envi_header::endianType byte_order;			//little = least significant bit first (most systems)
 	double x_start, y_start;		//coordinates of the upper-left corner of the image
 	std::string wavelength_units;	//stored wavelength units
@@ -47,18 +47,17 @@ struct EnviHeader
 	std::vector<std::string> band_names;	//name for each band in the image
 	std::vector<double> wavelength;		//wavelength for each band
-	EnviHeader()
-	{
-        name = "";
+	void init(){
+        name = "";
 		//specify default values for a new or empty ENVI file
 		samples = 0;
 		lines = 0;
 		bands = 0;
 		header_offset = 0;
-		data_type = Envi::float32;
-		interleave = Envi::BSQ;
-		byte_order = Envi::endianLittle;
+		data_type = float32;
+		interleave = BSQ;
+		byte_order = endianLittle;
 		x_start = y_start = 0;
 		pixel_size[0] = pixel_size[1] = 1;
@@ -69,8 +68,15 @@ struct EnviHeader
 		z_plot_titles[0] = z_plot_titles[1] = "Unknown";
 	}
-	std::string trim(std::string line)
-	{
+	envi_header(){
+		init();
+	}
+	envi_header(std::string name){
+		init();
+		load(name);
+	}
+
+	std::string trim(std::string line){
 		//trims whitespace from the beginning and end of line
 		unsigned int start_i, end_i;
 		for(start_i=0; start_i < line.length(); start_i++)
@@ -89,8 +95,7 @@ struct EnviHeader
 	}
-	std::string get_token(std::string line)
-	{
+	std::string get_token(std::string line){
 		//returns a variable name; in this case we look for the '=' sign
 		size_t i = line.find_first_of('=');
@@ -101,8 +106,7 @@ struct EnviHeader
 		return result;
 	}
-	std::string get_data_str(std::string line)
-	{
+	std::string get_data_str(std::string line){
 		size_t i = line.find_first_of('=');
 		std::string result;
@@ -187,15 +191,15 @@ struct EnviHeader
 	std::vector<double> get_double_seq(std::string token, std::string sequence)
 	{
 		//this function returns a sequence of comma-delimited strings
-		std::vector<double> result;
+		std::vector<double> result;
 		std::string entry;
 		size_t i;
 		do
 		{
 			i = sequence.find_first_of(',');
-			entry = sequence.substr(0, i);
+			entry = sequence.substr(0, i);
 			sequence = sequence.substr(i+1);
-			result.push_back(atof(entry.c_str()));
+			result.push_back(atof(entry.c_str()));
 			//std::cout<<entry<<"   ";
 		}while(i != std::string::npos);
@@ -208,7 +212,7 @@ struct EnviHeader
 		std::ifstream file(filename.c_str());
 		if(!file)
-		{
+		{
             return false;
 		}
@@ -219,11 +223,11 @@ struct EnviHeader
 		{
 			std::cout<<"ENVI Header Error: The header doesn't appear to be an ENVI file. The first line should be 'ENVI'."<<std::endl;
 			exit(1);
-		}
+		}
 		//for each line in the file, get the token
-		std::string token;
-
+		std::string token;
+
         //get a line
         getline(file, line);
 		while(file)
@@ -272,46 +276,46 @@ struct EnviHeader
 			else if(token == "file type")
 				file_type = get_data_str(line);
 			else if(token == "data type")
-				data_type = (Envi::dataType)atoi(get_data_str(line).c_str());
+				data_type = (dataType)atoi(get_data_str(line).c_str());
 			else if(token == "interleave")
 			{
 				std::string interleave_str = get_data_str(line);
 				if(interleave_str == "bip")
-					interleave = Envi::BIP;
+					interleave = BIP;
 				else if(interleave_str == "bil")
-					interleave = Envi::BIL;
+					interleave = BIL;
 				else if(interleave_str == "bsq")
-					interleave = Envi::BSQ;
+					interleave = BSQ;
 			}
 			else if(token == "sensor type")
 				sensor_type = get_data_str(line);
 			else if(token == "byte order")
-				byte_order = (Envi::endianType)atoi(get_data_str(line).c_str());
+				byte_order = (endianType)atoi(get_data_str(line).c_str());
 			else if(token == "x start")
 				x_start = atof(get_data_str(line).c_str());
 			else if(token == "y start")
 				y_start = atof(get_data_str(line).c_str());
 			else if(token == "wavelength units")
-				wavelength_units = get_data_str(line);
-
-            //get the next line
+				wavelength_units = get_data_str(line);
+
+            //get the next line
             getline(file, line);
-		}
-
-		//make sure the number of bands matches the number of wavelengths
-		unsigned int wavelengths = wavelength.size();
-		if(bands != wavelengths)
-		{
-            std::cout<<"ENVI Header Error -- Number of wavelengths doesn't match the number of bands.  Bands = "<<bands<<", Wavelengths = "<<wavelength.size()<<std::endl;
-            exit(1);
+		}
+
+		//make sure the number of bands matches the number of wavelengths
+		unsigned int wavelengths = wavelength.size();
+		if(bands != wavelengths)
+		{
+            std::cout<<"ENVI Header Error -- Number of wavelengths doesn't match the number of bands.  Bands = "<<bands<<", Wavelengths = "<<wavelength.size()<<std::endl;
+            exit(1);
         }
 		//close the file
-		file.close();
-
-		//set the file name
-		name = filename;
-
+		file.close();
+
+		//set the file name
+		name = filename;
+
 		return true;
 	}
@@ -334,11 +338,11 @@ struct EnviHeader
 		outfile<<"file type = "<<file_type<<std::endl;
 		outfile<<"data type = "<<data_type<<std::endl;
 		outfile<<"interleave = ";
-		if(interleave == Envi::BIP)
+		if(interleave == BIP)
 			outfile<<"bip";
-		if(interleave == Envi::BIL)
+		if(interleave == BIL)
 			outfile<<"bil";
-		if(interleave == Envi::BSQ)
+		if(interleave == BSQ)
 			outfile<<"bsq";
 			outfile<<std::endl;
 		outfile<<"sensor type = "<<sensor_type<<std::endl;
@@ -369,7 +373,7 @@ struct EnviHeader
 	}
 	void save()
-	{
+	{
         //std::cout<<"ENVI Header Name: "<<name<<std::endl;
 		save(name);
 	}
@@ -379,27 +383,27 @@ struct EnviHeader
 	{
 		switch(data_type)
 		{
-		case Envi::int8:			//1 = 8-bit byte
+		case int8:			//1 = 8-bit byte
 			return 1;
-		case Envi::int16:			//16-bit signed integer
-		case Envi::uint16:		//16-bit unsigned integer
+		case int16:			//16-bit signed integer
+		case uint16:		//16-bit unsigned integer
 			return 2;
-		case Envi::int32:			//32-bit signed long integer
-		case Envi::float32:		//32-bit floating point
-		case Envi::uint32:		//32-bit unsigned long integer
+		case int32:			//32-bit signed long integer
+		case float32:		//32-bit floating point
+		case uint32:		//32-bit unsigned long integer
 			return 4;
-		case Envi::float64:		//64-bit double-precision floating point
-		case Envi::complex32:		//32-bit complex value
-		case Envi::int64:		    //64-bit signed long integer
-		case Envi::uint64:		//64-bit unsigned long integer
+		case float64:		//64-bit double-precision floating point
+		case complex32:		//32-bit complex value
+		case int64:		    //64-bit signed long integer
+		case uint64:		//64-bit unsigned long integer
 			return 8;
-		case Envi::complex64:		//64-bit complex value
+		case complex64:		//64-bit complex value
 			return 16;
 		default:
 			return 0;
 		}
 	}
-};		//end EnviHeader
-
-#endif
+};		//end EnviHeader
+}
+#endif