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stim/envi/envi.h 80.3 KB
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  #ifndef STIM_ENVI_H
  #define STIM_ENVI_H
  
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  #include <stim/envi/envi_header.h>
  #include <stim/envi/bsq.h>
  #include <stim/envi/bip.h>
  #include <stim/envi/bil.h>
  #include <stim/math/fd_coefficients.h>
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  #include <stim/parser/filename.h>
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  #include <stim/util/filesize.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) : envi(){
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  		header.load(headername);
  
  		fname = filename;					//save the filename
  
  		allocate();
  	}
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  	//used to test if the current ENVI file is valid
  	operator bool(){
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  		if (header.interleave == envi_header::BSQ) {		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
  				return ((bsq<float>*)file)->is_open();
  			else if (header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->is_open();
  			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)->is_open();
  			else if (header.data_type == envi_header::float64)
  				return ((bil<double>*)file)->is_open();
  			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)->is_open();
  			else if (header.data_type == envi_header::float64)
  				return ((bip<double>*)file)->is_open();
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  		else {
  			std::cout << "ERROR: unidentified file type" << std::endl;
  			exit(1);
  		}
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  		return false;
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  	}
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  	//test to determine if the specified file is an ENVI file
  	static bool is_envi(std::string fname, std::string hname = ""){
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  		stim::filename data_file(fname);
  		stim::filename header_file;
  		if(hname == ""){								//if the header isn't provided
  			header_file = data_file;					//assume that it's the same name as the data file, with a .hdr extension
  			header_file = header_file.extension("hdr");
  		}
  		else header_file = hname;						//otherwise load the passed header
  
  		stim::envi_header H;
  		if(H.load(header_file) == false)				//load the header file, if it doesn't load return false
  			return false;
  		size_t targetBytes = H.data_bytes();			//get the number of bytes that SHOULD be in the data file
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  		size_t bytes = stim::file_size(fname);
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  		if (bytes != targetBytes) {
  			std::cout << "ERROR: File size mismatch. Based on the header, a " << targetBytes << " byte file was expected. The data file contains " << bytes << " bytes." << std::endl;
  			return false;			//if the data doesn't match the header, return false
  		}
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  		return true;									//otherwise everything looks fine
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  	}
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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
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  	bool open(stim::iotype io = stim::io_in){
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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);
6708cc25   heziqi   Ziqi added envi c...
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  			}
  			else if(header.data_type == envi_header::float64) {
8057237a   David Mayerich   added an envi::op...
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  				return ((bsq<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
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  			}
  			else
9ef9bdfa   David Mayerich   generated an erro...
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  			{
  				std::cout << "ERROR: The specified data format (" << header.data_type << ") is not supported" << std::endl;
6708cc25   heziqi   Ziqi added envi c...
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  				return false;
9ef9bdfa   David Mayerich   generated an erro...
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  			}
6708cc25   heziqi   Ziqi added envi c...
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  		}
e8eb202f   David Mayerich   added a new ENVI ...
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6708cc25   heziqi   Ziqi added envi c...
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  		else if(header.interleave == envi_header::BIL) {		//if the infile is bil file
  			if(header.data_type == envi_header::float32) {
8057237a   David Mayerich   added an envi::op...
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  				return ((bil<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
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  			}
  			else if(header.data_type == envi_header::float64) {
8057237a   David Mayerich   added an envi::op...
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  				return ((bil<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
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  			}
9ef9bdfa   David Mayerich   generated an erro...
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  			{
  				std::cout << "ERROR: The specified data format (" << header.data_type << ") is not supported" << std::endl;
6708cc25   heziqi   Ziqi added envi c...
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  				return false;
9ef9bdfa   David Mayerich   generated an erro...
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  			}
6708cc25   heziqi   Ziqi added envi c...
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  		}
f92397d2   David Mayerich   fixed a Win32 bug...
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6708cc25   heziqi   Ziqi added envi c...
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  		else if(header.interleave == envi_header::BIP) {		//if the infile is bip file
  			if(header.data_type == envi_header::float32) {
8057237a   David Mayerich   added an envi::op...
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  				return ((bip<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
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  			}
  			else if(header.data_type == envi_header::float64) {
8057237a   David Mayerich   added an envi::op...
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  				return ((bip<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
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  			}
9ef9bdfa   David Mayerich   generated an erro...
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  			{
  				std::cout << "ERROR: The specified data format (" << header.data_type << ") is not supported" << std::endl;
f92397d2   David Mayerich   fixed a Win32 bug...
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  				return false;
9ef9bdfa   David Mayerich   generated an erro...
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  			}
6708cc25   heziqi   Ziqi added envi c...
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  		}
  
f92397d2   David Mayerich   fixed a Win32 bug...
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  		return true;
  
8057237a   David Mayerich   added an envi::op...
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  	}
  
48f356fa   David Mayerich   bug fixes for FFT...
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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
618dce30   David Mayerich   removed warnings ...
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  		size_t nread = fread(&b, sizeof(short), 1, f);					//read the number of bands
  		if(nread != 1){
  			std::cout<<"Error reading band number from Agilent file."<<std::endl;
  			exit(1);
  		}
48f356fa   David Mayerich   bug fixes for FFT...
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  		fseek(f, 13, SEEK_CUR);											//skip the the x and y dimensions
  		short x, y;
618dce30   David Mayerich   removed warnings ...
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  		nread = fread(&x, sizeof(short), 1, f);									//read the image x and y size
  		if(nread != 1){
  			std::cout<<"Error reading X dimension from Agilent file."<<std::endl;
  			exit(1);
  		}
  		nread = fread(&y, sizeof(short), 1, f);
  		if(nread != 1){
  			std::cout<<"Error reading Y dimension from Agilent file."<<std::endl;
  			exit(1);
  		}
48f356fa   David Mayerich   bug fixes for FFT...
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  		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
bb457896   David Mayerich   improved error me...
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  	bool open(std::string filename, stim::envi_header h, stim::iotype io = stim::io_in){
9d3ba0b1   David Mayerich   added stim::hsi a...
465
  		
8057237a   David Mayerich   added an envi::op...
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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();
  
bb457896   David Mayerich   improved error me...
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  		return open(io);						//open the ENVI file;
8057237a   David Mayerich   added an envi::op...
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f92397d2   David Mayerich   fixed a Win32 bug...
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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
bb457896   David Mayerich   improved error me...
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  	bool open(std::string filename, std::string headername, stim::iotype io = stim::io_in){
f92397d2   David Mayerich   fixed a Win32 bug...
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  		//allocate memory
  		//allocate();
  
  		stim::envi_header h;
bb457896   David Mayerich   improved error me...
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  		if (!h.load(headername)) {
  			std::cout << "Error loading header file: " << headername << std::endl;
  			return false;
  		}
f92397d2   David Mayerich   fixed a Win32 bug...
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  		//load the header
  		//header.load(headername);
  
bb457896   David Mayerich   improved error me...
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  		return open(filename, h, io);
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...
504
  		header.save(outfile + ".hdr");
6708cc25   heziqi   Ziqi added envi c...
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  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
e8eb202f   David Mayerich   added a new ENVI ...
506
  			if(header.data_type ==envi_header::float32)
c30dd3e6   David Mayerich   added vector norm...
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  				return ((bsq<float>*)file)->ratio(outfile, band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
508
  			else if(header.data_type == envi_header::float64)
c30dd3e6   David Mayerich   added vector norm...
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  				return ((bsq<double>*)file)->ratio(outfile,band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
e8eb202f   David Mayerich   added a new ENVI ...
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6708cc25   heziqi   Ziqi added envi c...
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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...
516
  				return ((bil<float>*)file)->ratio(outfile, band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
517
  			else if(header.data_type == envi_header::float64)
c30dd3e6   David Mayerich   added vector norm...
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  				return ((bil<double>*)file)->ratio(outfile,band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
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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)
c30dd3e6   David Mayerich   added vector norm...
525
  				return ((bip<float>*)file)->ratio(outfile, band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
526
  			else if(header.data_type == envi_header::float64)
c30dd3e6   David Mayerich   added vector norm...
527
  				return ((bip<double>*)file)->ratio(outfile,band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
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  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
e933c14e   David Mayerich   cleaned up the code
536
  		return false;
6708cc25   heziqi   Ziqi added envi c...
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  	}
  
c30dd3e6   David Mayerich   added vector norm...
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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);
  		}
  	}
  
b31c02eb   David Mayerich   added a --select ...
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  	bool select(std::string outfile, std::vector<double> bandlist, unsigned char* MASK = NULL, bool PROGRESS = false) {
  		stim::envi_header new_header = header;					//copy all of the data from the current header file to the new one
  		new_header.bands = bandlist.size();						//the number of bands in the new file is equal to the number of bands provided by the user
  		new_header.wavelength = bandlist;						//the wavelength values in the output file are the same as those specified by the user
  		new_header.band_names.empty();							//no band names will be provided in the output file
  		new_header.save(outfile + ".hdr");						//save the output header file
  
  		if (header.interleave == envi_header::BSQ) {		//if the infile is bip file
  			if (header.data_type == envi_header::float32)
  				return ((bsq<float>*)file)->select(outfile, bandlist, MASK, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->select(outfile, bandlist, MASK, PROGRESS);
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  		else if (header.interleave == envi_header::BIL) {		//if the infile is bip file
  			if (header.data_type == envi_header::float32)
  				return ((bil<float>*)file)->select(outfile, bandlist, MASK, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bil<double>*)file)->select(outfile, bandlist, 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)
  				return ((bip<float>*)file)->select(outfile, bandlist, MASK, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bip<double>*)file)->select(outfile, bandlist, MASK, PROGRESS);
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
610
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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...
614
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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...
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  		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...
618
  				return ((bsq<float>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
619
  			else if(header.data_type == envi_header::float64)
798cea97   David Mayerich   added progress ba...
620
  				return ((bsq<double>*)file)->baseline(outfile,w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
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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...
629
  				return ((bil<float>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
630
  			else if(header.data_type == envi_header::float64)
798cea97   David Mayerich   added progress ba...
631
  				return ((bil<double>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
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  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
f92397d2   David Mayerich   fixed a Win32 bug...
638
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
6708cc25   heziqi   Ziqi added envi c...
639
  			if(header.data_type ==envi_header::float32)
798cea97   David Mayerich   added progress ba...
640
  				return ((bip<float>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
641
  			else if(header.data_type == envi_header::float64)
798cea97   David Mayerich   added progress ba...
642
  				return ((bip<double>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
643
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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);
  		}
  	}
  
dd5aab2f   David Mayerich   fixed errors in s...
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  	/// Project an array of coefficients onto a basis matrix
  
  	void project(std::string outfile, double* center, double* basis, size_t M, std::vector<double> bands, unsigned char* mask, int cuda_device = 0, bool PROGRESS = false) {
63fc1df8   David Mayerich   added an inverse ...
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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)
dd5aab2f   David Mayerich   fixed errors in s...
670
  				((bip<float>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
63fc1df8   David Mayerich   added an inverse ...
671
  			else if(header.data_type == envi_header::float64)
dd5aab2f   David Mayerich   fixed errors in s...
672
  				((bip<double>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
63fc1df8   David Mayerich   added an inverse ...
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  			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
dd5aab2f   David Mayerich   fixed errors in s...
681
  		out_hdr.wavelength = bands;
9d3ba0b1   David Mayerich   added stim::hsi a...
682
  		out_hdr.band_names.clear();
63fc1df8   David Mayerich   added an inverse ...
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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 ...
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716
  	/// 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...
717
  	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...
718
  		
6708cc25   heziqi   Ziqi added envi c...
719
720
  		if(header.interleave == envi_header::BSQ){			//if the infile is bsq file
  
a2bf1d08   David Mayerich   general bug fixes...
721
  			if(header.data_type ==envi_header::float32){		//ERROR
6708cc25   heziqi   Ziqi added envi c...
722
723
724
725
  				if(interleave == envi_header::BSQ){
  					std::cout<<"ERROR:  is already BSQ file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
726
  				else if(interleave == envi_header::BIL)			//convert BSQ -> BIL
c6251f8b   David Mayerich   allows user to de...
727
  					((bsq<float>*)file)->bil(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
a2bf1d08   David Mayerich   general bug fixes...
728
  				else if(interleave == envi_header::BIP){			//ERROR
cf5b4c92   David Mayerich   simplified asynch...
729
  					//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
474c351a   David Mayerich   output timing dat...
730
  					((bsq<float>*)file)->bip(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
cf5b4c92   David Mayerich   simplified asynch...
731
  					//exit(1);
63fc1df8   David Mayerich   added an inverse ...
732
  				}
6708cc25   heziqi   Ziqi added envi c...
733
734
735
  			}
  
  			else if(header.data_type == envi_header::float64){		//if the data type is float
a2bf1d08   David Mayerich   general bug fixes...
736
  				if(interleave == envi_header::BSQ){							//ERROR
6708cc25   heziqi   Ziqi added envi c...
737
738
739
  					std::cout<<"ERROR:  is already BSQ file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
740
  				else if(interleave == envi_header::BIL)					//convert BSQ -> BIL
c6251f8b   David Mayerich   allows user to de...
741
  					((bsq<double>*)file)->bil(outfile, PROGRESS, OPTIMIZATION);
a2bf1d08   David Mayerich   general bug fixes...
742
  				else if(interleave == envi_header::BIP){					//ERROR
cf5b4c92   David Mayerich   simplified asynch...
743
  					//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
f7cf19e4   David Mayerich   fixed warnings, t...
744
  					((bsq<double>*)file)->bip(outfile, PROGRESS, OPTIMIZATION);
cf5b4c92   David Mayerich   simplified asynch...
745
  					//exit(1);
63fc1df8   David Mayerich   added an inverse ...
746
  				}
6708cc25   heziqi   Ziqi added envi c...
747
  			}
f92397d2   David Mayerich   fixed a Win32 bug...
748
  
6708cc25   heziqi   Ziqi added envi c...
749
750
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
f92397d2   David Mayerich   fixed a Win32 bug...
751
  				exit(1);
6708cc25   heziqi   Ziqi added envi c...
752
753
754
755
756
  			}
  		}
  
  		else if(header.interleave == envi_header::BIL){
  
a2bf1d08   David Mayerich   general bug fixes...
757
  			if(header.data_type ==envi_header::float32){						//ERROR
6708cc25   heziqi   Ziqi added envi c...
758
759
760
761
  				if(interleave == envi_header::BIL){
  					std::cout<<"ERROR:  is already BIL file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
762
763
764
765
  				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...
766
767
  			}
  
a2bf1d08   David Mayerich   general bug fixes...
768
769
  			else if(header.data_type == envi_header::float64){
  				if(interleave == envi_header::BIL){								//ERROR
6708cc25   heziqi   Ziqi added envi c...
770
771
772
  					std::cout<<"ERROR:  is already BIL file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
773
774
775
776
  				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...
777
  			}
f92397d2   David Mayerich   fixed a Win32 bug...
778
  
6708cc25   heziqi   Ziqi added envi c...
779
780
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
f92397d2   David Mayerich   fixed a Win32 bug...
781
  				exit(1);
6708cc25   heziqi   Ziqi added envi c...
782
783
784
785
  			}
  		}
  
  		else if(header.interleave == envi_header::BIP){
f92397d2   David Mayerich   fixed a Win32 bug...
786
  
a2bf1d08   David Mayerich   general bug fixes...
787
788
  			if(header.data_type ==envi_header::float32){
  				if(interleave == envi_header::BIP){								//ERROR
6708cc25   heziqi   Ziqi added envi c...
789
790
791
  					std::cout<<"ERROR:  is already BIP file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
792
793
794
  				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 ...
795
796
797
798
  					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...
799
800
  			}
  
a2bf1d08   David Mayerich   general bug fixes...
801
802
  			else if(header.data_type == envi_header::float64){
  				if(interleave == envi_header::BIP){								//ERROR
6708cc25   heziqi   Ziqi added envi c...
803
804
805
  					std::cout<<"ERROR:  is already BIP file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
806
807
808
  				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 ...
809
810
811
812
  					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...
813
  			}
f92397d2   David Mayerich   fixed a Win32 bug...
814
  
6708cc25   heziqi   Ziqi added envi c...
815
816
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
f92397d2   David Mayerich   fixed a Win32 bug...
817
  				exit(1);
6708cc25   heziqi   Ziqi added envi c...
818
819
  			}
  		}
f92397d2   David Mayerich   fixed a Win32 bug...
820
  
6708cc25   heziqi   Ziqi added envi c...
821
822
823
824
  		else{
  			std::cout<<"ERROR: unidentified interleave type"<<std::endl;
  			exit(1);
  		}
a2bf1d08   David Mayerich   general bug fixes...
825
826
827
828
829
  		stim::envi_header h = header;
  		h.interleave = interleave;
  		h.save(outfile + ".hdr");
  
  		return true;
f92397d2   David Mayerich   fixed a Win32 bug...
830
  
6708cc25   heziqi   Ziqi added envi c...
831
832
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
833
834
835
836
837
  	/// 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...
838
  	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
839
840
841
  
  		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...
842
  				return ((bsq<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
843
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
844
  				return ((bsq<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
845
846
847
848
849
850
  			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...
851
  				return ((bil<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
852
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
853
  				return ((bil<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
854
855
856
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
cacc3cdc   heziqi   attempt to fix CImg
857
  
4a6f666c   heziqi   Added mask method
858
859
  		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...
860
  				return ((bip<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
861
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
862
  				return ((bip<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
863
864
865
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
bba4f4d9   David Mayerich   minor warning fixes
866
867
  
  		return false;
740f8cd2   heziqi   added apply_mask
868
869
  	}
  
ba51ae6a   David Mayerich   fixed metric calc...
870
  	/// Creates a mask with a true value for all pixels that contain finite values
e37ce7bf   David Mayerich   added the ability...
871
  	void mask_finite(unsigned char* out_mask, unsigned char* mask = NULL, bool PROGRESS = false){
ba51ae6a   David Mayerich   fixed metric calc...
872
873
  		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...
874
  				((bsq<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
875
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
876
  				((bsq<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
877
878
879
880
881
882
  			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...
883
  				((bil<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
884
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
885
  				((bil<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
886
887
888
889
890
891
  			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...
892
  				((bip<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
893
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
894
  				((bip<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
895
896
897
898
899
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
900
901
902
903
  	/// 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...
904
  	void apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false)
740f8cd2   heziqi   added apply_mask
905
  	{
e843658b   Brad Deutsch   Previous push did...
906
907
  		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...
908
  				((bsq<float>*)file)->apply_mask(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
909
  			else if (header.data_type == envi_header::float64)
6a46c8ff   David Mayerich   fixed bugs in app...
910
  				((bsq<double>*)file)->apply_mask(outfile, p, PROGRESS);
740f8cd2   heziqi   added apply_mask
911
  			else
e843658b   Brad Deutsch   Previous push did...
912
  				std::cout << "ERROR: unidentified data type" << std::endl;
740f8cd2   heziqi   added apply_mask
913
914
  		}
  
e843658b   Brad Deutsch   Previous push did...
915
916
  		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...
917
  				((bil<float>*)file)->apply_mask(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
918
  			else if (header.data_type == envi_header::float64)
6a46c8ff   David Mayerich   fixed bugs in app...
919
  				((bil<double>*)file)->apply_mask(outfile, p, PROGRESS);
740f8cd2   heziqi   added apply_mask
920
  			else
e843658b   Brad Deutsch   Previous push did...
921
  				std::cout << "ERROR: unidentified data type" << std::endl;
740f8cd2   heziqi   added apply_mask
922
923
  		}
  
e843658b   Brad Deutsch   Previous push did...
924
925
  		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...
926
  				((bip<float>*)file)->apply_mask(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
927
  			else if (header.data_type == envi_header::float64)
6a46c8ff   David Mayerich   fixed bugs in app...
928
  				((bip<double>*)file)->apply_mask(outfile, p, PROGRESS);
740f8cd2   heziqi   added apply_mask
929
  			else
e843658b   Brad Deutsch   Previous push did...
930
  				std::cout << "ERROR: unidentified data type" << std::endl;
740f8cd2   heziqi   added apply_mask
931
  		}
4a6f666c   heziqi   Added mask method
932
933
  
  		else{
e843658b   Brad Deutsch   Previous push did...
934
935
936
  			std::cout << "ERROR: unidentified file type" << std::endl;
  			exit(1);
  		}
6a46c8ff   David Mayerich   fixed bugs in app...
937
  		header.save(outfile + ".hdr");
e843658b   Brad Deutsch   Previous push did...
938
939
  	}
  
3d0b6243   David Mayerich   fixed hsiproc bug...
940
941
942
  	/// 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...
943
944
  	/// @param matrix is the destination for the pixel data
  	/// @param p is the mask
814eb271   David Mayerich   fixed problems wi...
945
  	bool sift(void* matrix, unsigned char* p = NULL, bool PROGRESS = false){
43dec788   David Mayerich   added code for si...
946
947
948
  
  		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...
949
  				return ((bsq<float>*)file)->sift((float*)matrix, p, PROGRESS);
43dec788   David Mayerich   added code for si...
950
  			else if (header.data_type == envi_header::float64)
814eb271   David Mayerich   fixed problems wi...
951
  				return ((bsq<double>*)file)->sift((double*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
952
  			else{
43dec788   David Mayerich   added code for si...
953
  				std::cout << "ERROR: unidentified data type" << std::endl;
ba51ae6a   David Mayerich   fixed metric calc...
954
955
  				exit(1);
  			}
43dec788   David Mayerich   added code for si...
956
  		}
3d0b6243   David Mayerich   fixed hsiproc bug...
957
958
  
  		if (header.interleave == envi_header::BIP){
ba51ae6a   David Mayerich   fixed metric calc...
959
  			if (header.data_type == envi_header::float32)
814eb271   David Mayerich   fixed problems wi...
960
  				return ((bip<float>*)file)->sift((float*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
961
  			else if (header.data_type == envi_header::float64)
814eb271   David Mayerich   fixed problems wi...
962
  				return ((bip<double>*)file)->sift((double*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
963
964
965
966
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
3d0b6243   David Mayerich   fixed hsiproc bug...
967
968
  		}
  		if (header.interleave == envi_header::BIL){
ba51ae6a   David Mayerich   fixed metric calc...
969
  			if (header.data_type == envi_header::float32)
814eb271   David Mayerich   fixed problems wi...
970
  				return ((bil<float>*)file)->sift((float*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
971
  			else if (header.data_type == envi_header::float64)
814eb271   David Mayerich   fixed problems wi...
972
  				return ((bil<double>*)file)->sift((double*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
973
974
975
976
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
3d0b6243   David Mayerich   fixed hsiproc bug...
977
  		}
43dec788   David Mayerich   added code for si...
978
979
980
981
  		return false;
  
  	}
  
3d0b6243   David Mayerich   fixed hsiproc bug...
982
  	/// Saves in an array only those spectra corresponding to nonzero values of the mask.
43dec788   David Mayerich   added code for si...
983
984
  	/// @param outfile is the name of the sifted output file
  	/// @param p is the mask
c1078e19   David Mayerich   HSIproc bug fixes...
985
  	bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
e843658b   Brad Deutsch   Previous push did...
986
987
  	{
  
2fcab4f0   David Mayerich   added unsifting f...
988
  		//calculate the number of non-zero values in the mask
9d3ba0b1   David Mayerich   added stim::hsi a...
989
990
991
  		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...
992
993
994
995
996
  			if( p[i] > 0 ) nnz++;
  
  		//create a new header
  		envi_header new_header = header;
  
f7e99517   David Mayerich   added sifting for...
997
998
  		//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...
999
  			new_header.interleave = envi_header::BIP;
f7e99517   David Mayerich   added sifting for...
1000
  
2fcab4f0   David Mayerich   added unsifting f...
1001
1002
1003
1004
1005
  		//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...
1006
1007
  		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...
1008
  				return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
1009
  			else if (header.data_type == envi_header::float64)
c1078e19   David Mayerich   HSIproc bug fixes...
1010
  				return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
1011
1012
1013
1014
1015
1016
  			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...
1017
  				return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
1018
  			else if (header.data_type == envi_header::float64)
c1078e19   David Mayerich   HSIproc bug fixes...
1019
  				return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
1020
1021
1022
1023
1024
1025
  			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...
1026
  				return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
1027
  			else if (header.data_type == envi_header::float64)
c1078e19   David Mayerich   HSIproc bug fixes...
1028
  				return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
1029
1030
1031
1032
1033
1034
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  
  		else{
  			std::cout << "ERROR: unidentified file type" << std::endl;
4a6f666c   heziqi   Added mask method
1035
1036
  			exit(1);
  		}
4a6f666c   heziqi   Added mask method
1037
  		return false;
cacc3cdc   heziqi   attempt to fix CImg
1038
1039
  	}
  
a2bf1d08   David Mayerich   general bug fixes...
1040
  	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...
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
  
  		//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...
1053
  				return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
2fcab4f0   David Mayerich   added unsifting f...
1054
  			else if (header.data_type == envi_header::float64)
a2bf1d08   David Mayerich   general bug fixes...
1055
  				return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
2fcab4f0   David Mayerich   added unsifting f...
1056
1057
1058
1059
1060
  			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...
1061
  
2fcab4f0   David Mayerich   added unsifting f...
1062
1063
1064
1065
  				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...
1066
  
8550e94f   David Mayerich   added sifting and...
1067
  			if (header.data_type == envi_header::float32)
a2bf1d08   David Mayerich   general bug fixes...
1068
  				return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
8550e94f   David Mayerich   added sifting and...
1069
  			else if (header.data_type == envi_header::float64)
a2bf1d08   David Mayerich   general bug fixes...
1070
  				return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
8550e94f   David Mayerich   added sifting and...
1071
1072
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
2fcab4f0   David Mayerich   added unsifting f...
1073
1074
1075
1076
  		}
  
  		else{
  			std::cout << "ERROR: unidentified file type" << std::endl;
2fcab4f0   David Mayerich   added unsifting f...
1077
  		}
cbce396e   David Mayerich   added support for...
1078
  		return 0;
2fcab4f0   David Mayerich   added unsifting f...
1079
1080
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1081
1082
1083
1084
1085
1086
1087
1088
1089
  	/// 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...
1090
  	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...
1091
1092
  		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...
1093
  				return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
1094
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1095
  				return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
1096
  			else
11ff9d7e   David Mayerich   improved user out...
1097
  				std::cout<<"envi::ph_to_ph ERROR - unidentified data type"<<std::endl;
20c212c0   heziqi   Ziqi added functi...
1098
1099
1100
1101
  		}
  
  		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...
1102
  				return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
1103
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1104
  				return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
1105
  			else
11ff9d7e   David Mayerich   improved user out...
1106
  				std::cout<<"envi::ph_to_ph ERROR - unidentified data type"<<std::endl;
20c212c0   heziqi   Ziqi added functi...
1107
1108
1109
1110
  		}
  
  		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...
1111
  				return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
1112
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1113
  				return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
70407ea9   heziqi   Ziqi completed he...
1114
  			else
11ff9d7e   David Mayerich   improved user out...
1115
  				std::cout<<"envi::ph_to_ph ERROR - unidentified data type"<<std::endl;
70407ea9   heziqi   Ziqi completed he...
1116
1117
1118
  		}
  
  		else{
11ff9d7e   David Mayerich   improved user out...
1119
  			std::cout<<"envi::ph_to_ph ERROR - unidentified file type"<<std::endl;
70407ea9   heziqi   Ziqi completed he...
1120
1121
1122
1123
1124
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1125
1126
1127
1128
1129
1130
1131
1132
1133
  	/// 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...
1134
  	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...
1135
1136
  		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...
1137
  				return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1138
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1139
  				return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1140
1141
1142
1143
1144
1145
  			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...
1146
  				return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1147
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1148
  				return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1149
1150
1151
1152
1153
1154
  			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...
1155
  				return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1156
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1157
  				return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
  			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 ...
1169
1170
1171
1172
1173
1174
1175
1176
1177
  	/// 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...
1178
  	/// @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 ...
1179
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
ba51ae6a   David Mayerich   fixed metric calc...
1180
1181
  	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...
1182
1183
  		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...
1184
  				return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1185
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1186
  				return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1187
1188
1189
1190
1191
1192
  			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...
1193
  				return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1194
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1195
  				return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1196
1197
1198
1199
1200
1201
  			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...
1202
  				return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1203
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1204
  				return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
20c212c0   heziqi   Ziqi added functi...
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
  			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 ...
1216
1217
1218
1219
1220
1221
1222
  	/// 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...
1223
  	bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
517876d6   heziqi   metrics finished ...
1224
1225
  		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...
1226
  				return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1227
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1228
  				return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1229
1230
1231
1232
1233
1234
  			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...
1235
  				return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1236
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1237
  				return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1238
1239
1240
1241
1242
1243
  			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...
1244
  				return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1245
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1246
  				return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
  			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 ...
1258
  	/// Closes the ENVI file.
edb975b0   David Mayerich   created a stim::e...
1259
1260
  	void close(){
  		if(file == NULL) return;
6708cc25   heziqi   Ziqi added envi c...
1261
1262
  		if(header.interleave == envi_header::BSQ){
  			if(header.data_type ==envi_header::float32)
edb975b0   David Mayerich   created a stim::e...
1263
  				((bsq<float>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1264
  			else if(header.data_type == envi_header::float64)
edb975b0   David Mayerich   created a stim::e...
1265
  				((bsq<double>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1266
1267
1268
1269
1270
1271
1272
1273
  			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...
1274
  				((bil<float>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1275
  			else if(header.data_type == envi_header::float64)
edb975b0   David Mayerich   created a stim::e...
1276
  				((bil<double>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1277
1278
1279
1280
1281
1282
1283
1284
  			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...
1285
  				((bip<float>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1286
  			else if(header.data_type == envi_header::float64)
edb975b0   David Mayerich   created a stim::e...
1287
  				((bip<double>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1288
1289
1290
1291
1292
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
e8eb202f   David Mayerich   added a new ENVI ...
1293
  	}
cb455f98   David Mayerich   removed old ENVI ...
1294
1295
1296
1297
1298
  
  	/// 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...
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
  	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 ...
1332
  
cb455f98   David Mayerich   removed old ENVI ...
1333
  	/// Saves a header file describing the current ENVI file parameters.
e8eb202f   David Mayerich   added a new ENVI ...
1334
1335
1336
1337
1338
1339
1340
1341
  	bool save_header(std::string filename){
  
  		//save the header file here
  		header.save(filename);
  
  		return true;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1342
1343
1344
1345
  	/// 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 ...
1346
  	bool band(void* ptr, double wavelength, bool PROGRESS = false){
d1d8ef91   David Mayerich   added band readin...
1347
1348
1349
  
  		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 ...
1350
  				return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1351
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1352
  				return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1353
1354
1355
1356
1357
1358
1359
  			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 ...
1360
  				return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1361
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1362
  				return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1363
1364
1365
1366
1367
1368
1369
  			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 ...
1370
  				return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1371
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1372
  				return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1373
1374
1375
1376
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
d1d8ef91   David Mayerich   added band readin...
1377
  		}
ee4dea28   David Mayerich   fixed errors in c...
1378
  		return false;
1582ce07   David Mayerich   added band_index(...
1379
1380
  	}
  
f4069d3f   David Mayerich   fixed the crop fu...
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
  	void band_bounds(double wavelength, size_t& low, size_t& high) {
  		if (header.interleave == envi_header::BSQ) {		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->band_bounds(wavelength, low, high);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->band_bounds(wavelength, low, high);
  			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)->band_bounds(wavelength, low, high);
  			else if (header.data_type == envi_header::float64)
  				((bil<double>*)file)->band_bounds(wavelength, low, high);
  			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)->band_bounds(wavelength, low, high);
  			else if (header.data_type == envi_header::float64)
  				((bip<double>*)file)->band_bounds(wavelength, low, high);
  			else {
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  	}
  
735a2a24   David Mayerich   started testing o...
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
  	// 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...
1454
  				float test = ((float*)temp)[0];
735a2a24   David Mayerich   started testing o...
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
  				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);
  			}
  		}
889c89dd   David Mayerich   fixed memory leak...
1466
  		free(temp);
735a2a24   David Mayerich   started testing o...
1467
1468
1469
1470
1471
1472
1473
1474
  	}
  
  	/// 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...
1475
  	void spectrum(T* ptr, size_t x, size_t y, bool PROGRESS = false){
735a2a24   David Mayerich   started testing o...
1476
  
c4dd399a   David Mayerich   fixed a Linux com...
1477
  		spectrum<T>(ptr, y * header.samples + x, PROGRESS);
724ec347   David Mayerich   simplified the EN...
1478
1479
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1480
1481
1482
1483
  	/// 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...
1484
  	bool band_index(void* ptr, unsigned long long b){
081f2c9f   heziqi   made bip bil file...
1485
1486
  		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(...
1487
  				return ((bsq<float>*)file)->band_index((float*)ptr, b);
081f2c9f   heziqi   made bip bil file...
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
  			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(...
1514
1515
  		}
  		return false;
d1d8ef91   David Mayerich   added band readin...
1516
  	}
f92397d2   David Mayerich   fixed a Win32 bug...
1517
  
cb455f98   David Mayerich   removed old ENVI ...
1518
1519
1520
1521
  	/// 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
35a7195f   David Mayerich   added median spec...
1522
  	bool mean_spectrum(double * p, double* std, unsigned char* mask, bool PROGRESS = false){
a43c4fe1   heziqi   Added crop in env...
1523
1524
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
35a7195f   David Mayerich   added median spec...
1525
  				return ((bsq<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1526
  			else if (header.data_type == envi_header::float64)
35a7195f   David Mayerich   added median spec...
1527
  				return ((bsq<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1528
1529
1530
1531
1532
1533
1534
  			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)
35a7195f   David Mayerich   added median spec...
1535
  				return ((bil<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1536
  			else if (header.data_type == envi_header::float64)
35a7195f   David Mayerich   added median spec...
1537
  				return ((bil<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1538
1539
1540
1541
1542
1543
1544
  			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)
35a7195f   David Mayerich   added median spec...
1545
  				return ((bip<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1546
  			else if (header.data_type == envi_header::float64)
35a7195f   David Mayerich   added median spec...
1547
  				return ((bip<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1548
1549
1550
1551
1552
1553
1554
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
e8eb202f   David Mayerich   added a new ENVI ...
1555
  
35a7195f   David Mayerich   added median spec...
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
  	/// 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
  	bool median_spectrum(double* m, unsigned char* mask, bool PROGRESS = false){
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				return ((bsq<float>*)file)->median_spectrum(m, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->median_spectrum(m, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else{
  			std::cout<<"ERROR: median calculation is only supported for BSQ interleave types. Convert to process."<<std::endl;
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1578
1579
1580
1581
1582
  	/// 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
dd5aab2f   David Mayerich   fixed errors in s...
1583
  	bool co_matrix(double* co, double* avg, unsigned char* mask, int cuda_device, bool PROGRESS = false){
a43c4fe1   heziqi   Added crop in env...
1584
  		if (header.interleave == envi_header::BSQ){
63fc1df8   David Mayerich   added an inverse ...
1585
1586
  			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...
1587
1588
1589
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
dd5aab2f   David Mayerich   fixed errors in s...
1590
  				return ((bil<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1591
  			else if (header.data_type == envi_header::float64)
dd5aab2f   David Mayerich   fixed errors in s...
1592
  				return ((bil<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1593
1594
1595
1596
1597
1598
1599
  			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)
dd5aab2f   David Mayerich   fixed errors in s...
1600
  				return ((bip<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1601
  			else if (header.data_type == envi_header::float64)
dd5aab2f   David Mayerich   fixed errors in s...
1602
  				return ((bip<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1603
1604
1605
1606
1607
1608
1609
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
0df38ff3   heziqi   fixed head detached
1610
  
334547d8   sam   changes for mnf: ...
1611
1612
1613
1614
1615
  	/// 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
dd5aab2f   David Mayerich   fixed errors in s...
1616
  	bool coNoise_matrix(double* coN, double* avg, unsigned char* mask, int cuda_device = 0, bool PROGRESS = false){
334547d8   sam   changes for mnf: ...
1617
1618
1619
1620
1621
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  		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)
dd5aab2f   David Mayerich   fixed errors in s...
1630
  				return ((bip<float>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
334547d8   sam   changes for mnf: ...
1631
  			else if (header.data_type == envi_header::float64)
dd5aab2f   David Mayerich   fixed errors in s...
1632
  				return ((bip<double>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
334547d8   sam   changes for mnf: ...
1633
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  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
e8eb202f   David Mayerich   added a new ENVI ...
1640
  
cb455f98   David Mayerich   removed old ENVI ...
1641
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1647
  	/// 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...
1648
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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...
1656
  
177c7863   David Mayerich   updated the ENVI ...
1657
1658
  		//save the header for the cropped file
  		stim::envi_header new_header = header;
f78ceb64   David Mayerich   fixed BIP croppin...
1659
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  		new_header.samples = x1 - x0 + 1;
  		new_header.lines = y1 - y0 + 1;
  		new_header.bands = b1 - b0 + 1;
177c7863   David Mayerich   updated the ENVI ...
1662
  		std::vector<double>::const_iterator first = new_header.wavelength.begin() + b0;
f78ceb64   David Mayerich   fixed BIP croppin...
1663
  		std::vector<double>::const_iterator last = new_header.wavelength.begin() + b1 + 1;
177c7863   David Mayerich   updated the ENVI ...
1664
1665
1666
  		new_header.wavelength = std::vector<double>(first, last);
  		new_header.save(outfile + ".hdr");
  
a43c4fe1   heziqi   Added crop in env...
1667
1668
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1669
  				return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1670
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1671
  				return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1672
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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)
63fc1df8   David Mayerich   added an inverse ...
1679
  				return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1680
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1681
  				return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1682
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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)
63fc1df8   David Mayerich   added an inverse ...
1689
  				return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1690
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1691
  				return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1692
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  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
0df38ff3   heziqi   fixed head detached
1699
  
bb61cb18   David Mayerich   added subimage fu...
1700
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  	void subimages(std::string outfile, size_t nx, size_t ny, unsigned char* mask, bool PROGRESS = false){
  		
  		size_t nnz = 0;													//initialize the number of subimages to zero
  		for(size_t i = 0; i < header.lines * header.samples; i++)		//for each pixel in the mask
  			if(mask[i]) nnz++;											//if the pixel is valid, add a subimage
  
  
  		//save the header for the cropped file
  		stim::envi_header new_header = header;
  		new_header.samples = nx;									//calculate the width of the output image (concatenated subimages)
  		new_header.lines = nnz * ny;											//calculate the height of the output image (height of subimages)
  		
  
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->subimages(outfile, nx, ny, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->subimages(outfile, nx, ny, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			std::cout << "ERROR: unidentified data type" << std::endl;
  			exit(1);
  		}
  		else if (header.interleave == envi_header::BIP){
  			std::cout << "ERROR: unidentified data type" << std::endl;
  			exit(1);
  		}
  
  		new_header.save(outfile + ".hdr");									//save the header for the output file
  	}
  
dc8eb8aa   David Mayerich   added band trimmi...
1735
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  	/// 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...
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  	/// 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...
1841
  
82a7c08c   David Mayerich   added an append c...
1842
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  	void append(std::string outfile, envi C, bool PROGRESS = false) {
  		if (C.header.samples != header.samples ||									//verify that the images are the same size
  			C.header.lines != header.lines) {
  			std::cout << "ERROR - appended images must be the same size: input = [" << header.samples << " x " << header.lines << "], output = [" << C.header.samples << " x " << C.header.lines << "]" << std::endl;
  			exit(1);
  		}
  		if (C.header.interleave != header.interleave) {
  			std::cout << "ERROR - appended images must have the same interleave format" << std::endl;
  			exit(1);
  		}
  
  		stim::envi_header new_header = header;												//create a header for the output image
  		new_header.bands = header.bands + C.header.bands;									//calculate the number of bands in the new image
  
  		if (header.wavelength.size() != 0 && C.header.wavelength.size() != 0) {				//if both files contain wavelength information
  			for (size_t b = 0; b < C.header.wavelength.size(); b++)
  				new_header.wavelength.push_back(C.header.wavelength[b]);					//append the wavelength labels to the new header array
  		}
  		else new_header.wavelength.clear();
  
  		if (header.band_names.size() != 0 && C.header.band_names.size() != 0) {				//if both files contain band name information
  			for (size_t b = 0; b < C.header.band_names.size(); b++)
  				new_header.band_names.push_back(C.header.band_names[b]);					//append the wavelength labels to the new header array
  		}
  		else new_header.wavelength.clear();
  
  		new_header.save(outfile + ".hdr");													//save the output
  
  		if (header.interleave == envi_header::BSQ) {
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->append(outfile, (bsq<float>*)C.file, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->append(outfile, (bsq<double>*)C.file, 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)->append(outfile, (bil<float>*)C.file, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bil<double>*)file)->append(outfile, (bil<double>*)C.file, 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)->append(outfile, (bip<float>*)C.file, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bip<double>*)file)->append(outfile, (bip<double>*)C.file, PROGRESS);
  			else {
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  	}
  
9b2a5d71   David Mayerich   implemented finit...
1903
1904
1905
1906
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1909
  	/// 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...
1910
  	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...
1911
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1916
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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...
1928
  				((bsq<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1929
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1930
  				((bsq<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1931
1932
1933
1934
1935
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1937
  			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...
1938
  				((bil<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1939
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1940
  				((bil<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1941
1942
1943
1944
1945
1946
1947
  			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...
1948
  				((bip<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1949
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1950
  				((bip<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1951
1952
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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...
1963
  	void deriv(std::string outfile, size_t d, size_t order, unsigned char* mask = NULL, bool PROGRESS = false){
9b2a5d71   David Mayerich   implemented finit...
1964
1965
1966
  		header.save(outfile + ".hdr");
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1967
  				((bsq<float>*)file)->deriv(outfile, d, order, header.wavelength, 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...
1969
  				((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...
1978
  				((bil<float>*)file)->deriv(outfile, d, order, header.wavelength, 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...
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  				((bil<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::BIP){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1989
  				((bip<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1990
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1991
  				((bip<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);
  			}
  		}
  		exit(1);
  	}
278c622b   David Mayerich   finished Windows ...
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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);
  	}
9d34229e   David Mayerich   restructured the ...
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  	void fft(std::string outfile, double band_min, double band_max, size_t samples = 0, void* ratio = NULL, size_t rx = 0, size_t ry = 0, bool PROGRESS = false, int cuda_device = 0){
6e9cf1ac   David Mayerich   fixed image bug i...
2078
  		if(samples == 0) samples = header.bands;
f1365506   David Mayerich   modifications to ...
2079
  		//double B = (double)header.bands;
9d34229e   David Mayerich   restructured the ...
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  		double delta = header.wavelength[1] - header.wavelength[0];					//calculate spacing in the current domain
  		double span = samples * delta;											//calculate the span in the current domain
  		double fft_delta = 1.0 / span;												//calculate the span in the FFT domain
  		double fft_max = fft_delta * samples/2;										//calculate the maximum range of the FFT
  
  		if(band_max > fft_max) band_max = fft_max;									//the user gave a band outside of the FFT range, reset the band to the maximum available
  		size_t start_i = (size_t)std::ceil(band_min / fft_delta);					//calculate the first band to store
  		size_t size_i = (size_t)std::floor(band_max / fft_delta) - start_i + 1;		//calculate the number of bands to store