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stim/envi/envi.h 67 KB
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  #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"
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  #include "../math/fd_coefficients.h"
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  #include <iostream>
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  #include <fstream>
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  //#include "../image/image.h"
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  namespace stim{
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  /** This class implements reading of ENVI hyperspectral files. These files can be stored in multiple orientations
  	(including BSQ, BIP, and BIL) in order to optimize streaming speed depending on applications. Basic ENVI
  	files are stored on disk as a large binary file with a corresponding header. Code for reading and processing
  	ENVI header files is in the envi_header class.
  */
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  class envi{
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  	void* file;		//void pointer to the relevant file reader (bip, bsq, or bil - with appropriate data type)
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  	std::string fname;					//file name used for repeated opening and closing
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  	//allocate sufficient space for a spectrum based on the data type and number of bands
  	void* alloc_array(size_t len){
  		switch(header.data_type){
  		case envi_header::int8:
  			return malloc(len);
  		case envi_header::int16:
  		case envi_header::uint16:
  			return malloc(2 * len);
  		case envi_header::int32:
  		case envi_header::uint32:
  		case envi_header::float32:
  			return malloc(4 * len);
  		case envi_header::int64:
  		case envi_header::uint64:
  		case envi_header::float64:
  		case envi_header::complex32:
  			return malloc(8 * len);
  		case envi_header::complex64:
  			return malloc(16 * len);
  		default:
  			std::cout<<"ERROR stim::envi data type not recognized for spectral allocation"<<std::endl;
  			exit(1);
  		}
  	}
  
  	//cast a value to DEST type from SRC type
  	template<typename DST, typename SRC>
  	inline void cast(DST* dst, SRC* src){
  		(*dst) = (DST)(*src);
  	}
  
  	//cast an array from type SRC to type DEST
  	template<typename DST, typename SRC>
  	inline void cast(DST* dst, SRC* src, size_t len){
  		for(size_t i = 0; i < len; i++)
  			cast(&dst[i], &src[i]);
  	}
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  public:
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  	envi_header header;
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  	/// Default constructor
  	envi(){
  		file = NULL;				//set the file pointer to NULL
  	}
  
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  	envi(std::string filename, std::string headername){
  		header.load(headername);
  
  		fname = filename;					//save the filename
  
  		allocate();
  	}
  
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  	void* malloc_spectrum(){
  		return alloc_array(header.bands);
  	}
  
  	void* malloc_band(){
  		return alloc_array(header.samples * header.lines);
  	}
  
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  	void set_buffer_frac(double memfrac = 0.5){
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  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
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  				((bsq<float>*)file)->set_buffer_frac(memfrac);
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  			else if(header.data_type == envi_header::float64)
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  				((bsq<double>*)file)->set_buffer_frac(memfrac);
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
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  				((bil<float>*)file)->set_buffer_frac(memfrac);
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  			else if(header.data_type == envi_header::float64)
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  				((bil<double>*)file)->set_buffer_frac(memfrac);
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
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  				((bip<float>*)file)->set_buffer_frac(memfrac);
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  			else if(header.data_type == envi_header::float64)
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  				((bip<double>*)file)->set_buffer_frac(memfrac);
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  	}
  
  	void set_buffer_raw(size_t bytes){
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
  				((bsq<float>*)file)->set_buffer_raw(bytes);
  			else if(header.data_type == envi_header::float64)
  				((bsq<double>*)file)->set_buffer_raw(bytes);
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
  				((bil<float>*)file)->set_buffer_raw(bytes);
  			else if(header.data_type == envi_header::float64)
  				((bil<double>*)file)->set_buffer_raw(bytes);
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
  				((bip<float>*)file)->set_buffer_raw(bytes);
  			else if(header.data_type == envi_header::float64)
  				((bip<double>*)file)->set_buffer_raw(bytes);
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  	}
  
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  	/// Returns the size of the data type in bytes
  	unsigned int type_size(){
  		if(header.data_type == envi_header::float32) return 4;
  		if(header.data_type == envi_header::float64) return 8;
  
  		exit(1);
  	}
  
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  	size_t X(){ return header.samples; }
  	size_t Y(){ return header.lines; }
  	size_t Z(){ return header.bands; }
  	size_t B(){ return Z();	}
  
  	/// Return the size of the data set in bytes
  	size_t bytes(){
  		return X() * Y() * Z() * type_size();
  	}
  
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  	/// Returns the progress of the current processing operation as a percentage
  	void reset_progress(){
  
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
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  				((bsq<float>*)file)->reset_progress();
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  			else if(header.data_type == envi_header::float64)
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  				((bsq<double>*)file)->reset_progress();
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
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  				((bil<float>*)file)->reset_progress();
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  			else if(header.data_type == envi_header::float64)
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  				((bil<double>*)file)->reset_progress();
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
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  				((bip<float>*)file)->reset_progress();
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  			else if(header.data_type == envi_header::float64)
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  				((bip<double>*)file)->reset_progress();
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  	}
  
  	/// Returns the progress of the current processing operation as a percentage
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  	double progress(){
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  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
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  				return ((bsq<float>*)file)->get_progress();
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  			else if(header.data_type == envi_header::float64)
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  				return ((bsq<double>*)file)->get_progress();
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
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  				return ((bil<float>*)file)->get_progress();
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  			else if(header.data_type == envi_header::float64)
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  				return ((bil<double>*)file)->get_progress();
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
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  				return ((bip<float>*)file)->get_progress();
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  			else if(header.data_type == envi_header::float64)
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  				return ((bip<double>*)file)->get_progress();
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  		}
  		return 0;
  	}
  
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  	/// Returns the progress of the current processing operation as a percentage
  	size_t data_rate(){
  
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
  				return ((bsq<float>*)file)->get_data_rate();
  			else if(header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->get_data_rate();
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
  				return ((bil<float>*)file)->get_data_rate();
  			else if(header.data_type == envi_header::float64)
  				return ((bil<double>*)file)->get_data_rate();
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
  				return ((bip<float>*)file)->get_data_rate();
  			else if(header.data_type == envi_header::float64)
  				return ((bip<double>*)file)->get_data_rate();
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  		}
  		return 0;
  	}
  
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  	/// Allocate memory for a new ENVI file based on the current interleave format (BIP, BIL, BSQ) and data type.
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  	void allocate(){
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  		file = NULL;	//set file to a NULL pointer
  
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  		if(header.interleave == envi_header::BSQ){
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  			if(header.data_type ==envi_header::float32)
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  				file = new bsq<float>();
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  			else if(header.data_type == envi_header::float64)
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  				file = new bsq<double>();
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  		}
  		else if(header.interleave == envi_header::BIP){
  			if(header.data_type ==envi_header::float32)
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  				file = new bip<float>();
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  			else if(header.data_type == envi_header::float64)
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  				file = new bip<double>();
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  		}
  		else if(header.interleave == envi_header::BIL){
  			if(header.data_type ==envi_header::float32)
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  				file = new bil<float>();
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  			else if(header.data_type == envi_header::float64)
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  				file = new bil<double>();
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  		}
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  	}
  
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  	/// Open a previously opened ENVI file
  	bool open(){
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  		//load the file
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  		if(header.interleave == envi_header::BSQ) {		//if the infile is bsq file
  			if(header.data_type == envi_header::float32) {
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  				return ((bsq<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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  			}
  			else if(header.data_type == envi_header::float64) {
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  				return ((bsq<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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  			}
  			else
  				return false;
  		}
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  		else if(header.interleave == envi_header::BIL) {		//if the infile is bil file
  			if(header.data_type == envi_header::float32) {
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  				return ((bil<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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  			}
  			else if(header.data_type == envi_header::float64) {
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  				return ((bil<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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  			}
  			else
  				return false;
  		}
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  		else if(header.interleave == envi_header::BIP) {		//if the infile is bip file
  			if(header.data_type == envi_header::float32) {
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  				return ((bip<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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  			}
  			else if(header.data_type == envi_header::float64) {
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  				return ((bip<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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  			}
  			else
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  				return false;
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  		}
  
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  		return true;
  
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  	}
  
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  	/// Open an Agilent binary file as an ENVI stream
  	bool open_agilent(std::string filename){
  		fname = filename;												//store the file name
  
  		//Open the file temporarily to get the header information
  		FILE* f = fopen(filename.c_str(), "r");							//open the binary file for reading
  		if(f == NULL) return false;										//return false if no file is opened
  
  		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
  		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);
  		fclose(f);														//close the file
  
  		//store the information from the Agilent header in the ENVI header
  		header.bands = b;
  		header.samples = x;
  		header.lines = y;
  		header.data_type = envi_header::float32;						//all values are 32-bit floats
  		header.header_offset = 1020;									//number of bytes in an Agilent binary header
  		header.interleave = envi_header::BSQ;							//all Agilent binary files are BSQ
  
  		allocate();														//allocate the streaming file object
  		open();															//open the file for streaming
  
  		return true;
  	}
  
8057237a   David Mayerich   added an envi::op...
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  	/// Open an existing ENVI file given the filename and a header structure
  
  	/// @param filename is the name of the ENVI binary file
  	/// @param header is an ENVI header structure
  	bool open(std::string filename, stim::envi_header h){
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8057237a   David Mayerich   added an envi::op...
389
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  		header = h;							//store the header
  		fname = filename;					//save the filename
  
9d3ba0b1   David Mayerich   added stim::hsi a...
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  		allocate();
  
8057237a   David Mayerich   added an envi::op...
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  		return open();						//open the ENVI file;
  		
  
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  	}
  
  	/// Open an existing ENVI file given the file and header names.
  
  	/// @param filename is the name of the ENVI binary file
  	/// @param headername is the name of the ENVI header file
  	bool open(std::string filename, std::string headername){
  
  		//allocate memory
  		//allocate();
  
  		stim::envi_header h;
  		h.load(headername);
  
  		//load the header
  		//header.load(headername);
  
  		return open(filename, h);
e8eb202f   David Mayerich   added a new ENVI ...
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  	}
  
cb455f98   David Mayerich   removed old ENVI ...
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  	/// Normalize a hyperspectral ENVI file given a band number and threshold.
  
  	/// @param outfile is the name of the normalized file to be output
  	/// @param band is the band label to be output
  	/// @param threshold is a threshold value specified such that normalization will only be done to values in the band > threshold (preventing division by small numbers)
c30dd3e6   David Mayerich   added vector norm...
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  	bool ratio(std::string outfile, double band, unsigned char* mask = NULL, bool PROGRESS = false){
a2bf1d08   David Mayerich   general bug fixes...
424
  		header.save(outfile + ".hdr");
6708cc25   heziqi   Ziqi added envi c...
425
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
e8eb202f   David Mayerich   added a new ENVI ...
426
  			if(header.data_type ==envi_header::float32)
c30dd3e6   David Mayerich   added vector norm...
427
  				return ((bsq<float>*)file)->ratio(outfile, band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
428
  			else if(header.data_type == envi_header::float64)
c30dd3e6   David Mayerich   added vector norm...
429
  				return ((bsq<double>*)file)->ratio(outfile,band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
430
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
e8eb202f   David Mayerich   added a new ENVI ...
433
  
6708cc25   heziqi   Ziqi added envi c...
434
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  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
c30dd3e6   David Mayerich   added vector norm...
436
  				return ((bil<float>*)file)->ratio(outfile, band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
437
  			else if(header.data_type == envi_header::float64)
c30dd3e6   David Mayerich   added vector norm...
438
  				return ((bil<double>*)file)->ratio(outfile,band, mask, PROGRESS);
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
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445
  				return ((bip<float>*)file)->ratio(outfile, band, mask, PROGRESS);
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446
  			else if(header.data_type == envi_header::float64)
c30dd3e6   David Mayerich   added vector norm...
447
  				return ((bip<double>*)file)->ratio(outfile,band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
448
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
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456
  		return false;
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457
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  	}
  
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  	/// Perform vector normalization on the ENVI image
  	void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){
  		header.save(outfile + ".hdr");
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
  				((bsq<float>*)file)->normalize(outfile, mask, PROGRESS);
  			else if(header.data_type == envi_header::float64)
  				((bsq<double>*)file)->normalize(outfile, mask, PROGRESS);
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
  				((bil<float>*)file)->normalize(outfile, mask, PROGRESS);
  			else if(header.data_type == envi_header::float64)
  				((bil<double>*)file)->normalize(outfile, mask, PROGRESS);
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
  				((bip<float>*)file)->normalize(outfile, mask, PROGRESS);
  			else if(header.data_type == envi_header::float64)
  				((bip<double>*)file)->normalize(outfile, mask, PROGRESS);
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
495
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  	/// Performs piecewise linear baseline correction of a hyperspectral file/
  
  	/// @param outfile is the file name for the baseline corrected output
  	/// @param w is a list of band labels to serve as baseline points (zero values)
798cea97   David Mayerich   added progress ba...
499
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  	bool baseline(std::string outfile, std::vector<double> w, unsigned char* mask = NULL, bool PROGRESS = false){
  		header.save(outfile + ".hdr");
6708cc25   heziqi   Ziqi added envi c...
501
502
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
798cea97   David Mayerich   added progress ba...
503
  				return ((bsq<float>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
504
  			else if(header.data_type == envi_header::float64)
798cea97   David Mayerich   added progress ba...
505
  				return ((bsq<double>*)file)->baseline(outfile,w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
506
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  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
798cea97   David Mayerich   added progress ba...
514
  				return ((bil<float>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
515
  			else if(header.data_type == envi_header::float64)
798cea97   David Mayerich   added progress ba...
516
  				return ((bil<double>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
517
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  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
f92397d2   David Mayerich   fixed a Win32 bug...
523
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
6708cc25   heziqi   Ziqi added envi c...
524
  			if(header.data_type ==envi_header::float32)
798cea97   David Mayerich   added progress ba...
525
  				return ((bip<float>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
526
  			else if(header.data_type == envi_header::float64)
798cea97   David Mayerich   added progress ba...
527
  				return ((bip<double>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
528
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  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  	}
  
9d3ba0b1   David Mayerich   added stim::hsi a...
540
  	void project(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask, bool PROGRESS = false){
63fc1df8   David Mayerich   added an inverse ...
541
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  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			std::cout<<"ERROR: BSQ projection not supported"<<std::endl;
  			exit(1);
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			std::cout<<"ERROR: BIL projection not supported"<<std::endl;
  			exit(1);
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
9d3ba0b1   David Mayerich   added stim::hsi a...
553
  				((bip<float>*)file)->project(outfile, center, basis, M, mask, PROGRESS);
63fc1df8   David Mayerich   added an inverse ...
554
  			else if(header.data_type == envi_header::float64)
9d3ba0b1   David Mayerich   added stim::hsi a...
555
  				((bip<double>*)file)->project(outfile, center, basis, M, mask, PROGRESS);
63fc1df8   David Mayerich   added an inverse ...
556
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563
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		stim::envi_header out_hdr = header;							
  		out_hdr.bands = M;											//set the number of bands in the output header
9d3ba0b1   David Mayerich   added stim::hsi a...
564
565
  		out_hdr.wavelength.clear();
  		out_hdr.band_names.clear();
63fc1df8   David Mayerich   added an inverse ...
566
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  		out_hdr.save(outfile + ".hdr");								//save the output header
  	}
  
  	void inverse(std::string outfile, double* center, double* basis, unsigned long long B, unsigned long long C = 0, bool PROGRESS = false){
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			std::cout<<"ERROR: BSQ projection not supported"<<std::endl;
  			exit(1);
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			std::cout<<"ERROR: BIL projection not supported"<<std::endl;
  			exit(1);
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
  				((bip<float>*)file)->inverse(outfile, center, basis, B, C, PROGRESS);
  			else if(header.data_type == envi_header::float64)
  				((bip<double>*)file)->inverse(outfile, center, basis, B, C, PROGRESS);
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		stim::envi_header out_hdr = header;							
  		out_hdr.bands = B;											//set the number of bands in the output header
  		out_hdr.save(outfile + ".hdr");								//save the output header
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
596
597
598
599
  	/// Converts ENVI files between interleave types (BSQ, BIL, and BIP)
  
  	/// @param outfile is the file name for the converted output
  	/// @param interleave is the interleave format for the destination file
c6251f8b   David Mayerich   allows user to de...
600
  	bool convert(std::string outfile, stim::envi_header::interleaveType interleave, bool PROGRESS = false, bool VERBOSE = false, bool OPTIMIZATION = true){
a2bf1d08   David Mayerich   general bug fixes...
601
  		
6708cc25   heziqi   Ziqi added envi c...
602
603
  		if(header.interleave == envi_header::BSQ){			//if the infile is bsq file
  
a2bf1d08   David Mayerich   general bug fixes...
604
  			if(header.data_type ==envi_header::float32){		//ERROR
6708cc25   heziqi   Ziqi added envi c...
605
606
607
608
  				if(interleave == envi_header::BSQ){
  					std::cout<<"ERROR:  is already BSQ file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
609
  				else if(interleave == envi_header::BIL)			//convert BSQ -> BIL
c6251f8b   David Mayerich   allows user to de...
610
  					((bsq<float>*)file)->bil(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
a2bf1d08   David Mayerich   general bug fixes...
611
  				else if(interleave == envi_header::BIP){			//ERROR
cf5b4c92   David Mayerich   simplified asynch...
612
  					//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
474c351a   David Mayerich   output timing dat...
613
  					((bsq<float>*)file)->bip(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
cf5b4c92   David Mayerich   simplified asynch...
614
  					//exit(1);
63fc1df8   David Mayerich   added an inverse ...
615
  				}
6708cc25   heziqi   Ziqi added envi c...
616
617
618
  			}
  
  			else if(header.data_type == envi_header::float64){		//if the data type is float
a2bf1d08   David Mayerich   general bug fixes...
619
  				if(interleave == envi_header::BSQ){							//ERROR
6708cc25   heziqi   Ziqi added envi c...
620
621
622
  					std::cout<<"ERROR:  is already BSQ file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
623
  				else if(interleave == envi_header::BIL)					//convert BSQ -> BIL
c6251f8b   David Mayerich   allows user to de...
624
  					((bsq<double>*)file)->bil(outfile, PROGRESS, OPTIMIZATION);
a2bf1d08   David Mayerich   general bug fixes...
625
  				else if(interleave == envi_header::BIP){					//ERROR
cf5b4c92   David Mayerich   simplified asynch...
626
  					//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
c6251f8b   David Mayerich   allows user to de...
627
  					((bsq<float>*)file)->bip(outfile, PROGRESS, OPTIMIZATION);
cf5b4c92   David Mayerich   simplified asynch...
628
  					//exit(1);
63fc1df8   David Mayerich   added an inverse ...
629
  				}
6708cc25   heziqi   Ziqi added envi c...
630
  			}
f92397d2   David Mayerich   fixed a Win32 bug...
631
  
6708cc25   heziqi   Ziqi added envi c...
632
633
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
f92397d2   David Mayerich   fixed a Win32 bug...
634
  				exit(1);
6708cc25   heziqi   Ziqi added envi c...
635
636
637
638
639
  			}
  		}
  
  		else if(header.interleave == envi_header::BIL){
  
a2bf1d08   David Mayerich   general bug fixes...
640
  			if(header.data_type ==envi_header::float32){						//ERROR
6708cc25   heziqi   Ziqi added envi c...
641
642
643
644
  				if(interleave == envi_header::BIL){
  					std::cout<<"ERROR:  is already BIL file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
645
646
647
648
  				else if(interleave == envi_header::BSQ)							//BIL -> BSQ
  					((bil<float>*)file)->bsq(outfile, PROGRESS);
  				else if(interleave == envi_header::BIP)							//BIL -> BIP
  					((bil<float>*)file)->bip(outfile, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
649
650
  			}
  
a2bf1d08   David Mayerich   general bug fixes...
651
652
  			else if(header.data_type == envi_header::float64){
  				if(interleave == envi_header::BIL){								//ERROR
6708cc25   heziqi   Ziqi added envi c...
653
654
655
  					std::cout<<"ERROR:  is already BIL file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
656
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659
  				else if(interleave == envi_header::BSQ)							//BIL -> BSQ
  					((bil<double>*)file)->bsq(outfile, PROGRESS);
  				else if(interleave == envi_header::BIP)							//BIL -> BIP
  					((bil<double>*)file)->bip(outfile, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
660
  			}
f92397d2   David Mayerich   fixed a Win32 bug...
661
  
6708cc25   heziqi   Ziqi added envi c...
662
663
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
f92397d2   David Mayerich   fixed a Win32 bug...
664
  				exit(1);
6708cc25   heziqi   Ziqi added envi c...
665
666
667
668
  			}
  		}
  
  		else if(header.interleave == envi_header::BIP){
f92397d2   David Mayerich   fixed a Win32 bug...
669
  
a2bf1d08   David Mayerich   general bug fixes...
670
671
  			if(header.data_type ==envi_header::float32){
  				if(interleave == envi_header::BIP){								//ERROR
6708cc25   heziqi   Ziqi added envi c...
672
673
674
  					std::cout<<"ERROR:  is already BIP file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
675
676
677
  				else if(interleave == envi_header::BIL)							//BIP -> BIL
  					((bip<float>*)file)->bil(outfile, PROGRESS);
  				else if(interleave == envi_header::BSQ){						//ERROR
63fc1df8   David Mayerich   added an inverse ...
678
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681
  					std::cout<<"ERROR: conversion from BIP to BSQ isn't practical; use BIP->BIL->BSQ instead"<<std::endl;
  					//return ((bsq<float>*)file)->bip(outfile, PROGRESS);
  					exit(1);
  				}
6708cc25   heziqi   Ziqi added envi c...
682
683
  			}
  
a2bf1d08   David Mayerich   general bug fixes...
684
685
  			else if(header.data_type == envi_header::float64){
  				if(interleave == envi_header::BIP){								//ERROR
6708cc25   heziqi   Ziqi added envi c...
686
687
688
  					std::cout<<"ERROR:  is already BIP file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
689
690
691
  				else if(interleave == envi_header::BIL)							//BIP -> BIL
  					((bip<double>*)file)->bil(outfile, PROGRESS);
  				else if(interleave == envi_header::BSQ){						//ERROR
63fc1df8   David Mayerich   added an inverse ...
692
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695
  					std::cout<<"ERROR: conversion from BIP to BSQ isn't practical; use BIP->BIL->BSQ instead"<<std::endl;
  					//return ((bsq<float>*)file)->bip(outfile, PROGRESS);
  					exit(1);
  				}
6708cc25   heziqi   Ziqi added envi c...
696
  			}
f92397d2   David Mayerich   fixed a Win32 bug...
697
  
6708cc25   heziqi   Ziqi added envi c...
698
699
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
f92397d2   David Mayerich   fixed a Win32 bug...
700
  				exit(1);
6708cc25   heziqi   Ziqi added envi c...
701
702
  			}
  		}
f92397d2   David Mayerich   fixed a Win32 bug...
703
  
6708cc25   heziqi   Ziqi added envi c...
704
705
706
707
  		else{
  			std::cout<<"ERROR: unidentified interleave type"<<std::endl;
  			exit(1);
  		}
a2bf1d08   David Mayerich   general bug fixes...
708
709
710
711
712
  		stim::envi_header h = header;
  		h.interleave = interleave;
  		h.save(outfile + ".hdr");
  
  		return true;
f92397d2   David Mayerich   fixed a Win32 bug...
713
  
6708cc25   heziqi   Ziqi added envi c...
714
715
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
716
717
718
719
720
  	/// Builds a mask from a band image and threshold value
  
  	/// @param mask_band is the label for the band that will be used to build the mask
  	/// @param threshold is a value selected such that all band values greater than threshold will have a mask value of 'true'
  	/// @param p is memory of size X*Y that will store the resulting mask
e37ce7bf   David Mayerich   added the ability...
721
  	bool build_mask(unsigned char* out_mask, double mask_band, double lower, double upper, unsigned char* mask = NULL, bool PROGRESS = false)	{
4a6f666c   heziqi   Added mask method
722
723
724
  
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
725
  				return ((bsq<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
726
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
727
  				return ((bsq<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
728
729
730
731
732
733
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
734
  				return ((bil<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
735
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
736
  				return ((bil<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
737
738
739
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
cacc3cdc   heziqi   attempt to fix CImg
740
  
4a6f666c   heziqi   Added mask method
741
742
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
743
  				return ((bip<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
744
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
745
  				return ((bip<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
746
747
748
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
bba4f4d9   David Mayerich   minor warning fixes
749
750
  
  		return false;
740f8cd2   heziqi   added apply_mask
751
752
  	}
  
ba51ae6a   David Mayerich   fixed metric calc...
753
  	/// Creates a mask with a true value for all pixels that contain finite values
e37ce7bf   David Mayerich   added the ability...
754
  	void mask_finite(unsigned char* out_mask, unsigned char* mask = NULL, bool PROGRESS = false){
ba51ae6a   David Mayerich   fixed metric calc...
755
756
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
757
  				((bsq<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
758
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
759
  				((bsq<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
760
761
762
763
764
765
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
766
  				((bil<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
767
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
768
  				((bil<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
769
770
771
772
773
774
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
775
  				((bip<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
776
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
777
  				((bip<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
778
779
780
781
782
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
783
784
785
786
  	/// Applies a mask to the ENVI file.
  
  	/// @param outfile is the name of the resulting masked output file
  	/// @param p is memory of size X*Y containing the mask (0 = false, all other values are true)
6a46c8ff   David Mayerich   fixed bugs in app...
787
  	void apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false)
740f8cd2   heziqi   added apply_mask
788
  	{
e843658b   Brad Deutsch   Previous push did...
789
790
  		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
6a46c8ff   David Mayerich   fixed bugs in app...
791
  				((bsq<float>*)file)->apply_mask(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
792
  			else if (header.data_type == envi_header::float64)
6a46c8ff   David Mayerich   fixed bugs in app...
793
  				((bsq<double>*)file)->apply_mask(outfile, p, PROGRESS);
740f8cd2   heziqi   added apply_mask
794
  			else
e843658b   Brad Deutsch   Previous push did...
795
  				std::cout << "ERROR: unidentified data type" << std::endl;
740f8cd2   heziqi   added apply_mask
796
797
  		}
  
e843658b   Brad Deutsch   Previous push did...
798
799
  		else if (header.interleave == envi_header::BIL){		//if the infile is bil file
  			if (header.data_type == envi_header::float32)
6a46c8ff   David Mayerich   fixed bugs in app...
800
  				((bil<float>*)file)->apply_mask(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
801
  			else if (header.data_type == envi_header::float64)
6a46c8ff   David Mayerich   fixed bugs in app...
802
  				((bil<double>*)file)->apply_mask(outfile, p, PROGRESS);
740f8cd2   heziqi   added apply_mask
803
  			else
e843658b   Brad Deutsch   Previous push did...
804
  				std::cout << "ERROR: unidentified data type" << std::endl;
740f8cd2   heziqi   added apply_mask
805
806
  		}
  
e843658b   Brad Deutsch   Previous push did...
807
808
  		else if (header.interleave == envi_header::BIP){		//if the infile is bip file
  			if (header.data_type == envi_header::float32)
6a46c8ff   David Mayerich   fixed bugs in app...
809
  				((bip<float>*)file)->apply_mask(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
810
  			else if (header.data_type == envi_header::float64)
6a46c8ff   David Mayerich   fixed bugs in app...
811
  				((bip<double>*)file)->apply_mask(outfile, p, PROGRESS);
740f8cd2   heziqi   added apply_mask
812
  			else
e843658b   Brad Deutsch   Previous push did...
813
  				std::cout << "ERROR: unidentified data type" << std::endl;
740f8cd2   heziqi   added apply_mask
814
  		}
4a6f666c   heziqi   Added mask method
815
816
  
  		else{
e843658b   Brad Deutsch   Previous push did...
817
818
819
  			std::cout << "ERROR: unidentified file type" << std::endl;
  			exit(1);
  		}
6a46c8ff   David Mayerich   fixed bugs in app...
820
  		header.save(outfile + ".hdr");
e843658b   Brad Deutsch   Previous push did...
821
822
  	}
  
3d0b6243   David Mayerich   fixed hsiproc bug...
823
824
825
  	/// Copies all spectra corresponding to nonzero values of a mask into a pre-allocated matrix of size (P x B)
  	///		where P is the number of masked pixels and B is the number of bands. The allocated memory can be accessed
  	///		using the following indexing: i = b*P + p
43dec788   David Mayerich   added code for si...
826
827
  	/// @param matrix is the destination for the pixel data
  	/// @param p is the mask
814eb271   David Mayerich   fixed problems wi...
828
  	bool sift(void* matrix, unsigned char* p = NULL, bool PROGRESS = false){
43dec788   David Mayerich   added code for si...
829
830
831
  
  		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
814eb271   David Mayerich   fixed problems wi...
832
  				return ((bsq<float>*)file)->sift((float*)matrix, p, PROGRESS);
43dec788   David Mayerich   added code for si...
833
  			else if (header.data_type == envi_header::float64)
814eb271   David Mayerich   fixed problems wi...
834
  				return ((bsq<double>*)file)->sift((double*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
835
  			else{
43dec788   David Mayerich   added code for si...
836
  				std::cout << "ERROR: unidentified data type" << std::endl;
ba51ae6a   David Mayerich   fixed metric calc...
837
838
  				exit(1);
  			}
43dec788   David Mayerich   added code for si...
839
  		}
3d0b6243   David Mayerich   fixed hsiproc bug...
840
841
  
  		if (header.interleave == envi_header::BIP){
ba51ae6a   David Mayerich   fixed metric calc...
842
  			if (header.data_type == envi_header::float32)
814eb271   David Mayerich   fixed problems wi...
843
  				return ((bip<float>*)file)->sift((float*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
844
  			else if (header.data_type == envi_header::float64)
814eb271   David Mayerich   fixed problems wi...
845
  				return ((bip<double>*)file)->sift((double*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
846
847
848
849
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
3d0b6243   David Mayerich   fixed hsiproc bug...
850
851
  		}
  		if (header.interleave == envi_header::BIL){
ba51ae6a   David Mayerich   fixed metric calc...
852
  			if (header.data_type == envi_header::float32)
814eb271   David Mayerich   fixed problems wi...
853
  				return ((bil<float>*)file)->sift((float*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
854
  			else if (header.data_type == envi_header::float64)
814eb271   David Mayerich   fixed problems wi...
855
  				return ((bil<double>*)file)->sift((double*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
856
857
858
859
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
3d0b6243   David Mayerich   fixed hsiproc bug...
860
  		}
43dec788   David Mayerich   added code for si...
861
862
863
864
  		return false;
  
  	}
  
3d0b6243   David Mayerich   fixed hsiproc bug...
865
  	/// Saves in an array only those spectra corresponding to nonzero values of the mask.
43dec788   David Mayerich   added code for si...
866
867
  	/// @param outfile is the name of the sifted output file
  	/// @param p is the mask
c1078e19   David Mayerich   HSIproc bug fixes...
868
  	bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
e843658b   Brad Deutsch   Previous push did...
869
870
  	{
  
2fcab4f0   David Mayerich   added unsifting f...
871
  		//calculate the number of non-zero values in the mask
9d3ba0b1   David Mayerich   added stim::hsi a...
872
873
874
  		unsigned long long nnz = 0;
  		unsigned long long npixels = header.lines * header.samples;
  		for(unsigned long long i = 0; i < npixels; i++)
2fcab4f0   David Mayerich   added unsifting f...
875
876
877
878
879
  			if( p[i] > 0 ) nnz++;
  
  		//create a new header
  		envi_header new_header = header;
  
f7e99517   David Mayerich   added sifting for...
880
881
  		//if a BIL file is sifted, it's saved as a BIP
  		if(header.interleave == envi_header::BIL)
f92397d2   David Mayerich   fixed a Win32 bug...
882
  			new_header.interleave = envi_header::BIP;
f7e99517   David Mayerich   added sifting for...
883
  
2fcab4f0   David Mayerich   added unsifting f...
884
885
886
887
888
  		//set the number of lines to 1 (this is a matrix with 1 line and N samples)
  		new_header.lines = 1;
  		new_header.samples = nnz;
  		new_header.save(outfile + ".hdr");
  
e843658b   Brad Deutsch   Previous push did...
889
890
  		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
c1078e19   David Mayerich   HSIproc bug fixes...
891
  				return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
892
  			else if (header.data_type == envi_header::float64)
c1078e19   David Mayerich   HSIproc bug fixes...
893
  				return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
894
895
896
897
898
899
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  
  		else if (header.interleave == envi_header::BIL){		//if the infile is bil file
  			if (header.data_type == envi_header::float32)
c1078e19   David Mayerich   HSIproc bug fixes...
900
  				return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
901
  			else if (header.data_type == envi_header::float64)
c1078e19   David Mayerich   HSIproc bug fixes...
902
  				return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
903
904
905
906
907
908
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  
  		else if (header.interleave == envi_header::BIP){		//if the infile is bip file
  			if (header.data_type == envi_header::float32)
c1078e19   David Mayerich   HSIproc bug fixes...
909
  				return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
910
  			else if (header.data_type == envi_header::float64)
c1078e19   David Mayerich   HSIproc bug fixes...
911
  				return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
912
913
914
915
916
917
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  
  		else{
  			std::cout << "ERROR: unidentified file type" << std::endl;
4a6f666c   heziqi   Added mask method
918
919
  			exit(1);
  		}
4a6f666c   heziqi   Added mask method
920
  		return false;
cacc3cdc   heziqi   attempt to fix CImg
921
922
  	}
  
a2bf1d08   David Mayerich   general bug fixes...
923
  	bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
2fcab4f0   David Mayerich   added unsifting f...
924
925
926
927
928
929
930
931
932
933
934
935
  
  		//create a new header
  		envi_header new_header = header;
  
  		//set the number of lines and samples in the output file (that's all that changes)
  		new_header.lines = lines;
  		new_header.samples = samples;
  		new_header.save(outfile + ".hdr");
  
  
  		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
a2bf1d08   David Mayerich   general bug fixes...
936
  				return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
2fcab4f0   David Mayerich   added unsifting f...
937
  			else if (header.data_type == envi_header::float64)
a2bf1d08   David Mayerich   general bug fixes...
938
  				return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
2fcab4f0   David Mayerich   added unsifting f...
939
940
941
942
943
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  
  		else if (header.interleave == envi_header::BIL){		//if the infile is bil file
f92397d2   David Mayerich   fixed a Win32 bug...
944
  
2fcab4f0   David Mayerich   added unsifting f...
945
946
947
948
  				std::cout << "ERROR in stim::envi::unsift - BIL files aren't supported yet" << std::endl;
  		}
  
  		else if (header.interleave == envi_header::BIP){		//if the infile is bip file
f92397d2   David Mayerich   fixed a Win32 bug...
949
  
8550e94f   David Mayerich   added sifting and...
950
  			if (header.data_type == envi_header::float32)
a2bf1d08   David Mayerich   general bug fixes...
951
  				return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
8550e94f   David Mayerich   added sifting and...
952
  			else if (header.data_type == envi_header::float64)
a2bf1d08   David Mayerich   general bug fixes...
953
  				return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
8550e94f   David Mayerich   added sifting and...
954
955
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
2fcab4f0   David Mayerich   added unsifting f...
956
957
958
959
  		}
  
  		else{
  			std::cout << "ERROR: unidentified file type" << std::endl;
2fcab4f0   David Mayerich   added unsifting f...
960
  		}
cbce396e   David Mayerich   added support for...
961
  		return 0;
2fcab4f0   David Mayerich   added unsifting f...
962
963
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
964
965
966
967
968
969
970
971
972
  	/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
  
  	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
  	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
  	/// @param pos1 is the label value for the first peak (numerator) position
  	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
  	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
  	/// @param pos2 is the label value for the second peak (denominator) position
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
ba51ae6a   David Mayerich   fixed metric calc...
973
  	bool ph_to_ph(void * result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask){
20c212c0   heziqi   Ziqi added functi...
974
975
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
976
  				return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
977
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
978
  				return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
979
980
981
982
983
984
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
985
  				return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
986
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
987
  				return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
988
989
990
991
992
993
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
994
  				return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
995
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
996
  				return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
70407ea9   heziqi   Ziqi completed he...
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1008
1009
1010
1011
1012
1013
1014
1015
1016
  	/// Compute the ratio between a peak area and peak height.
  
  	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
  	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
  	/// @param pos1 is the label value for the first peak (numerator) position
  	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
  	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
  	/// @param pos2 is the label value for the second peak (denominator) position
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
ba51ae6a   David Mayerich   fixed metric calc...
1017
  	bool pa_to_ph(void* result, double lb1, double rb1, double lab1, double rab1, double lb2, double rb2, double pos, unsigned char* mask = NULL){
70407ea9   heziqi   Ziqi completed he...
1018
1019
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1020
  				return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1021
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1022
  				return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1023
1024
1025
1026
1027
1028
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1029
  				return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1030
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1031
  				return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1032
1033
1034
1035
1036
1037
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1038
  				return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1039
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1040
  				return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1052
1053
1054
1055
1056
1057
1058
1059
1060
  	/// Compute the ratio between two peak areas.
  
  	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
  	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
  	/// @param lab1 is the label value for the left bound (start of the integration) of the first peak (numerator)
  	/// @param rab1 is the label value for the right bound (end of the integration) of the first peak (numerator)
  	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
  	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
  	/// @param lab2 is the label value for the left bound (start of the integration) of the second peak (denominator)
f92397d2   David Mayerich   fixed a Win32 bug...
1061
  	/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
cb455f98   David Mayerich   removed old ENVI ...
1062
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
ba51ae6a   David Mayerich   fixed metric calc...
1063
1064
  	bool pa_to_pa(void* result, double lb1, double rb1, double lab1, double rab1,
  					double lb2, double rb2, double lab2, double rab2, unsigned char* mask = NULL){
70407ea9   heziqi   Ziqi completed he...
1065
1066
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1067
  				return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1068
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1069
  				return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1070
1071
1072
1073
1074
1075
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1076
  				return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1077
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1078
  				return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1079
1080
1081
1082
1083
1084
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1085
  				return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1086
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1087
  				return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
20c212c0   heziqi   Ziqi added functi...
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1099
1100
1101
1102
1103
1104
1105
  	/// Compute the centroid of a baseline corrected peak.
  
  	/// @param lb is the label value for the left baseline point
  	/// @param rb is the label value for the right baseline point
  	/// @param lab is the label for the start of the peak
  	/// @param rab is the label for the end of the peak
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
ba51ae6a   David Mayerich   fixed metric calc...
1106
  	bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
517876d6   heziqi   metrics finished ...
1107
1108
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1109
  				return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1110
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1111
  				return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1112
1113
1114
1115
1116
1117
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1118
  				return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1119
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1120
  				return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1121
1122
1123
1124
1125
1126
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1127
  				return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1128
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1129
  				return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1141
  	/// Closes the ENVI file.
edb975b0   David Mayerich   created a stim::e...
1142
1143
  	void close(){
  		if(file == NULL) return;
6708cc25   heziqi   Ziqi added envi c...
1144
1145
  		if(header.interleave == envi_header::BSQ){
  			if(header.data_type ==envi_header::float32)
edb975b0   David Mayerich   created a stim::e...
1146
  				((bsq<float>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1147
  			else if(header.data_type == envi_header::float64)
edb975b0   David Mayerich   created a stim::e...
1148
  				((bsq<double>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1149
1150
1151
1152
1153
1154
1155
1156
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		else if(header.interleave == envi_header::BIL){
  			if(header.data_type ==envi_header::float32)
edb975b0   David Mayerich   created a stim::e...
1157
  				((bil<float>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1158
  			else if(header.data_type == envi_header::float64)
edb975b0   David Mayerich   created a stim::e...
1159
  				((bil<double>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1160
1161
1162
1163
1164
1165
1166
1167
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		else if(header.interleave == envi_header::BIP){
  			if(header.data_type ==envi_header::float32)
edb975b0   David Mayerich   created a stim::e...
1168
  				((bip<float>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1169
  			else if(header.data_type == envi_header::float64)
edb975b0   David Mayerich   created a stim::e...
1170
  				((bip<double>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1171
1172
1173
1174
1175
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
e8eb202f   David Mayerich   added a new ENVI ...
1176
  	}
cb455f98   David Mayerich   removed old ENVI ...
1177
1178
1179
1180
1181
  
  	/// Retrieve a single pixel and stores it in pre-allocated memory.
  
  	/// @param p is a pointer to pre-allocated memory at least sizeof(T) in size.
  	/// @param n is an integer index to the pixel using linear array indexing.
bfe9c6db   heziqi   added feature_mat...
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
  	bool pixel(void * p, unsigned n){
  		if(header.interleave == envi_header::BSQ){
  			if(header.data_type ==envi_header::float32)
  				return ((bsq<float>*)file)->pixel((float*)p, n);
  			else if(header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->pixel((double*)p, n);
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  		else if(header.interleave == envi_header::BIL){
  			if(header.data_type ==envi_header::float32)
  				return ((bil<float>*)file)->pixel((float*)p, n);
  			else if(header.data_type == envi_header::float64)
  				return ((bil<double>*)file)->pixel((double*)p, n);
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  		else if(header.interleave == envi_header::BIP){
  			if(header.data_type ==envi_header::float32)
  				return ((bip<float>*)file)->pixel((float*)p, n);
  			else if(header.data_type == envi_header::float64)
  				return ((bip<double>*)file)->pixel((double*)p, n);
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
e8eb202f   David Mayerich   added a new ENVI ...
1215
  
cb455f98   David Mayerich   removed old ENVI ...
1216
  	/// Saves a header file describing the current ENVI file parameters.
e8eb202f   David Mayerich   added a new ENVI ...
1217
1218
1219
1220
1221
1222
1223
1224
  	bool save_header(std::string filename){
  
  		//save the header file here
  		header.save(filename);
  
  		return true;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1225
1226
1227
1228
  	/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
  
  	/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
  	/// @param wavelength is a floating point value (usually a wavelength in spectral data) used as a label for the band to be copied.
63fc1df8   David Mayerich   added an inverse ...
1229
  	bool band(void* ptr, double wavelength, bool PROGRESS = false){
d1d8ef91   David Mayerich   added band readin...
1230
1231
1232
  
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1233
  				return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1234
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1235
  				return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1236
1237
1238
1239
1240
1241
1242
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1243
  				return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1244
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1245
  				return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1246
1247
1248
1249
1250
1251
1252
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1253
  				return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1254
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1255
  				return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1256
1257
1258
1259
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
d1d8ef91   David Mayerich   added band readin...
1260
  		}
ee4dea28   David Mayerich   fixed errors in c...
1261
  		return false;
1582ce07   David Mayerich   added band_index(...
1262
1263
  	}
  
735a2a24   David Mayerich   started testing o...
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
  	// Retrieve a spectrum at the specified 1D location
  
  	/// @param ptr is a pointer to pre-allocated memory of size B*sizeof(T)
  	/// @param x is the 1D coordinate of the spectrum
  	template<typename T>
  	void spectrum(T* ptr, size_t n, bool PROGRESS = false){
  
  		void* temp = alloc_array(header.bands);		//allocate space for the output array
  
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32){
  				((bsq<float>*)file)->spectrum((float*)temp, n, PROGRESS);
  				cast<T, float>(ptr, (float*)temp, header.bands);
  			}
  			else if (header.data_type == envi_header::float64){
  				((bsq<double>*)file)->spectrum((double*)temp, n, PROGRESS);
  				cast<T, double>(ptr, (double*)temp, header.bands);
  			}
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32){
  				((bil<float>*)file)->spectrum((float*)temp, n, PROGRESS);
  				cast<T, float>(ptr, (float*)temp, header.bands);
  			}
  			else if (header.data_type == envi_header::float64){
  				((bil<double>*)file)->spectrum((double*)temp, n, PROGRESS);
  				cast<T, double>(ptr, (double*)temp, header.bands);
  			}
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32){
  				((bip<float>*)file)->spectrum((float*)temp, n, PROGRESS);
d4aa4cf7   David Mayerich   fixed the in-memo...
1304
  				float test = ((float*)temp)[0];
735a2a24   David Mayerich   started testing o...
1305
1306
1307
1308
1309
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  				cast<T, float>(ptr, (float*)temp, header.bands);
  			}
  			else if (header.data_type == envi_header::float64){
  				((bip<double>*)file)->spectrum((double*)temp, n, PROGRESS);
  				cast<T, double>(ptr, (double*)temp, header.bands);
  			}
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  	}
  
  	/// Retrieve a spectrum from the specified (x, y) location
  
  	/// @param ptr is a pointer to pre-allocated memory of size B*sizeof(T)
  	/// @param x is the x-coordinate of the spectrum
  	/// @param y is the y-coordinate of the spectrum
  	template<typename T>
d0ef98e3   David Mayerich   fixed a Linux com...
1324
  	void spectrum(T* ptr, size_t x, size_t y, bool PROGRESS = false){
735a2a24   David Mayerich   started testing o...
1325
  
c4dd399a   David Mayerich   fixed a Linux com...
1326
  		spectrum<T>(ptr, y * header.samples + x, PROGRESS);
724ec347   David Mayerich   simplified the EN...
1327
1328
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1329
1330
1331
1332
  	/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
  
  	/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
  	/// @param page <= B is the integer number of the band to be copied.
9d3ba0b1   David Mayerich   added stim::hsi a...
1333
  	bool band_index(void* ptr, unsigned long long b){
081f2c9f   heziqi   made bip bil file...
1334
1335
  		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
1582ce07   David Mayerich   added band_index(...
1336
  				return ((bsq<float>*)file)->band_index((float*)ptr, b);
081f2c9f   heziqi   made bip bil file...
1337
1338
1339
1340
1341
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  			else if (header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->band_index((double*)ptr, b);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
  				return ((bil<float>*)file)->band_index((float*)ptr, b);
  			else if (header.data_type == envi_header::float64)
  				return ((bil<double>*)file)->band_index((double*)ptr, b);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				return ((bip<float>*)file)->band_index((float*)ptr, b);
  			else if (header.data_type == envi_header::float64)
  				return ((bip<double>*)file)->band_index((double*)ptr, b);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
1582ce07   David Mayerich   added band_index(...
1363
1364
  		}
  		return false;
d1d8ef91   David Mayerich   added band readin...
1365
  	}
f92397d2   David Mayerich   fixed a Win32 bug...
1366
  
cb455f98   David Mayerich   removed old ENVI ...
1367
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1369
1370
  	/// Calculate the mean value for all masked (or valid) pixels in a band and returns the average spectrum
  
  	/// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
  	/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
63fc1df8   David Mayerich   added an inverse ...
1371
  	bool avg_band(double * p, unsigned char* mask, bool PROGRESS = false){
a43c4fe1   heziqi   Added crop in env...
1372
1373
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1374
  				return ((bsq<float>*)file)->avg_band(p, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1375
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1376
  				return ((bsq<double>*)file)->avg_band(p,  mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1377
1378
1379
1380
1381
1382
1383
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1384
  				return ((bil<float>*)file)->avg_band(p,  mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1385
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1386
  				return ((bil<double>*)file)->avg_band(p,  mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1387
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1391
1392
1393
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1394
  				return ((bip<float>*)file)->avg_band(p, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1395
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1396
  				return ((bip<double>*)file)->avg_band(p, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1397
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  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
e8eb202f   David Mayerich   added a new ENVI ...
1404
  
cb455f98   David Mayerich   removed old ENVI ...
1405
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  	/// Calculate the covariance matrix for all masked pixels in the image.
  
  	/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
  	/// @param avg is a pointer to memory of size B that stores the average spectrum
  	/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
63fc1df8   David Mayerich   added an inverse ...
1410
  	bool co_matrix(double* co, double* avg, unsigned char* mask, bool PROGRESS = false){
a43c4fe1   heziqi   Added crop in env...
1411
  		if (header.interleave == envi_header::BSQ){
63fc1df8   David Mayerich   added an inverse ...
1412
1413
  			std::cout<<"ERROR: calculating the covariance matrix for a BSQ file is impractical; convert to BIL or BIP first"<<std::endl;
  			exit(1);
a43c4fe1   heziqi   Added crop in env...
1414
1415
1416
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1417
  				return ((bil<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1418
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1419
  				return ((bil<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1420
1421
1422
1423
1424
1425
1426
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1427
  				return ((bip<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1428
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1429
  				return ((bip<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1430
1431
1432
1433
1434
1435
1436
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
0df38ff3   heziqi   fixed head detached
1437
  
334547d8   sam   changes for mnf: ...
1438
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  	/// Calculate the covariance of noise matrix for all masked pixels in the image.
  
  	/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
  	/// @param avg is a pointer to memory of size B that stores the average spectrum
  	/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
  	bool coNoise_matrix(double* coN, double* avg, unsigned char* mask, bool PROGRESS = false){
  		if (header.interleave == envi_header::BSQ){
  			std::cout<<"ERROR: calculating the covariance matrix of noise for a BSQ file is impractical; convert to BIP first"<<std::endl;
  			exit(1);
  		}
  
  
  		else if (header.interleave == envi_header::BIL){
  		        std::cout<<"ERROR: calculating the covariance matrix of noise for a BIL file is impractical; convert to BIP first"<<std::endl;
                  exit(1);
  			 }
  
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				return ((bip<float>*)file)->coNoise_matrix(coN, avg, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bip<double>*)file)->coNoise_matrix(coN, avg, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
e8eb202f   David Mayerich   added a new ENVI ...
1467
  
cb455f98   David Mayerich   removed old ENVI ...
1468
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1471
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1474
  	/// Crop a region of the image and save it to a new file.
  
  	/// @param outfile is the file name for the new cropped image
  	/// @param x0 is the lower-left x pixel coordinate to be included in the cropped image
  	/// @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
c8c976a9   David Mayerich   replaced CImg wit...
1475
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  	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, 
  			  bool PROGRESS = false){
a43c4fe1   heziqi   Added crop in env...
1483
  
177c7863   David Mayerich   updated the ENVI ...
1484
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1493
  		//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");
  
a43c4fe1   heziqi   Added crop in env...
1494
1495
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1496
  				return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1497
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1498
  				return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1499
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1501
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1503
1504
1505
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1506
  				return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1507
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1508
  				return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1509
1510
1511
1512
1513
1514
1515
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1516
  				return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1517
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1518
  				return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1519
1520
1521
1522
1523
1524
1525
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
0df38ff3   heziqi   fixed head detached
1526
  
dc8eb8aa   David Mayerich   added band trimmi...
1527
1528
1529
1530
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1584
  	/// Remove a list of bands from the ENVI file
  
  	/// @param outfile is the file name for the output hyperspectral image (with trimmed bands)
  	/// @param b is an array of bands to be eliminated
  	void trim(std::string outfile, std::vector<size_t> trimmed, bool PROGRESS = false){
  		
  		envi_header h = header;
  		h.bands = header.bands - trimmed.size();			//calculate the new number of bands
  		if(header.wavelength.size() != 0)
  			h.wavelength.resize(h.bands);
  		if(header.band_names.size() != 0)
  			h.band_names.resize(h.bands);
  		size_t it = 0;									//allocate an index into the trimmed bands array
  		size_t i = 0;
  		for(size_t b = 0; b < header.bands; b++){		//for each band
  			if(b != trimmed[it]){
  				if(h.wavelength.size()) h.wavelength[i] = header.wavelength[b];
  				if(h.band_names.size()) h.band_names[i] = header.band_names[i];
  				i++;
  			}
  			else it++;
  		}
  		h.save(outfile + ".hdr");
  
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				return ((bsq<float>*)file)->trim(outfile, trimmed, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->trim(outfile, trimmed, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
  				return ((bil<float>*)file)->trim(outfile, trimmed, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bil<double>*)file)->trim(outfile, trimmed, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				return ((bip<float>*)file)->trim(outfile, trimmed, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bip<double>*)file)->trim(outfile, trimmed, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		
  
  	}
  
2ce6954b   David Mayerich   added the ability...
1585
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1632
  	/// Combine two ENVI images along the Y axis
  
  	/// @param outfile is the combined file to be output
  	/// @param C is the ENVI object for the image to be combined
  	void combine(std::string outfile, envi C, long long x, long long y, bool PROGRESS = false){
  		envi_header h = header;
  		
  		long long left = std::min<long long>(0, x);													//calculate the left edge of the final image
  		long long right = std::max<long long>((long long)header.samples, C.header.samples + x);		//calculate the right edge of the final image
  		long long top = std::min<long long>(0, y);													//calculate the top edge of the final image
  		long long bottom = std::max<long long>((long long)header.lines, C.header.lines + y);		//calculate the bottom edge of the final image
  
  		h.samples = right - left;
  		h.lines = bottom - top;
  	
  		h.save(outfile + ".hdr");
  
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->combine(outfile, (bsq<float>*)C.file, x, y, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->combine(outfile, (bsq<double>*)C.file, x, y, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
  				((bil<float>*)file)->combine(outfile, (bil<float>*)C.file, x, y, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bil<double>*)file)->combine(outfile, (bil<double>*)C.file, x, y, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				((bip<float>*)file)->combine(outfile, (bip<float>*)C.file, x, y, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bip<double>*)file)->combine(outfile, (bip<double>*)C.file, x, y, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  	}
9b2a5d71   David Mayerich   implemented finit...
1633
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1638
1639
1640
  
  	/// Convolve the given band range with a kernel specified by a vector of coefficients.
  
  	/// @param outfile is the combined file to be output
  	/// @param c is an array of coefficients
  	/// @param start is the band to start processing (the first coefficient starts here)
  	/// @param nbands is the number of bands to process
  	/// @param center is the index for the center coefficient for the kernel (used to set the wavelengths in the output file)
9d77bbd9   David Mayerich   updates for HSIvi...
1641
  	void convolve(std::string outfile, std::vector<double> C, size_t start, size_t end, size_t center = 0, unsigned char* mask = NULL, bool PROGRESS = false){
9b2a5d71   David Mayerich   implemented finit...
1642
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  		size_t nbands = end - start + 1;
  		envi_header h = header;												//copy the current header
  		h.bands = nbands;													//set the number of new bands
  		if(header.wavelength.size() != 0){
  			h.wavelength.resize(nbands);									//set the number of wavelengths to the number of bands
  			for(size_t b = 0; b < nbands; b++)
  				h.wavelength[b] = header.wavelength[b+center];
  		}
  		if(header.band_names.size() != 0){
  			h.band_names.resize(nbands);
  			for(size_t b = 0; b < nbands; b++)
  				h.band_names[b] = header.band_names[b+center];
  		}
  		h.save(outfile + ".hdr");											//save the new header
  
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1659
  				((bsq<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
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  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1661
  				((bsq<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
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  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1669
  				((bil<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1670
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1671
  				((bil<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
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  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1679
  				((bip<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1680
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1681
  				((bip<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
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  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  	}
  
  	/// Approximates the nth derivative of the spectra to the specified order
  
  	/// @param outfile is the file where the derivative approximation will be saved
  	/// @n is the derivative to be calculated
  	/// @order is the order of the error (must be even)
9d77bbd9   David Mayerich   updates for HSIvi...
1694
  	void deriv(std::string outfile, size_t d, size_t order, unsigned char* mask = NULL, bool PROGRESS = false){
9b2a5d71   David Mayerich   implemented finit...
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  		header.save(outfile + ".hdr");
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1698
  				((bsq<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1699
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1700
  				((bsq<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
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  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1709
  				((bil<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1710
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1711
  				((bil<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1712
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  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1720
  				((bip<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1721
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1722
  				((bip<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1723
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  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		exit(1);
  	}
278c622b   David Mayerich   finished Windows ...
1730
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  	void multiply(std::string outfile, double v, unsigned char* mask = NULL, bool PROGRESS = false){
  		header.save(outfile + ".hdr");
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
  				((bil<float>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bil<double>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				((bip<float>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bip<double>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		exit(1);
  	}
  
  	void add(std::string outfile, double v, unsigned char* mask = NULL, bool PROGRESS = false){
  		header.save(outfile + ".hdr");
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->add(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->add(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
  				((bil<float>*)file)->add(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bil<double>*)file)->add(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				((bip<float>*)file)->add(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bip<double>*)file)->add(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		exit(1);
  	}
  };	//end ENVI
e8eb202f   David Mayerich   added a new ENVI ...
1805
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  }	//end namespace rts
  
  #endif