bil.h 34.8 KB
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082
#ifndef STIM_BIL_H
#define STIM_BIL_H

#include "../envi/envi_header.h"
#include "../envi/hsi.h"
#include <cstring>
#include <utility>

namespace stim{

/**
	The BIL class represents a 3-dimensional binary file stored using band interleaved by line (BIL) image encoding. The binary file is stored
	such that X-Z "frames" are stored sequentially to form an image stack along the y-axis. When accessing the data sequentially on disk,
	the dimensions read, from fastest to slowest, are X, Z, Y.

	This class is optimized for data streaming, and therefore supports extremely large (terabyte-scale) files. Data is loaded from disk
	on request. Functions used to access data are written to support efficient reading.
*/

template <typename T>

class bil: public hsi<T> {

protected:
	
	//std::vector<double> w;		//band wavelengths

	/*unsigned long long X(){
		return R[0];
	}
	unsigned long long Y(){
		return R[2];
	}
	unsigned long long Z(){
		return R[1];
	}*/
	using hsi<T>::w;				//use the wavelength array in stim::hsi
	using hsi<T>::nnz;
	using binary<T>::progress;

	/// Call the binary nnz() function for the BIL orientation
	//unsigned long long nnz(unsigned char* mask){
	//	return binary<T>::nnz(mask, X()*Y());
	//}

public:

	using binary<T>::open;
	using binary<T>::file;
	using binary<T>::R;

	bil(){ hsi<T>::init_bil(); }

	/// Open a data file for reading using the class interface.

	/// @param filename is the name of the binary file on disk
	/// @param X is the number of samples along dimension 1
	/// @param Y is the number of samples (lines) along dimension 2
	/// @param B is the number of samples (bands) along dimension 3
	/// @param header_offset is the number of bytes (if any) in the binary header
	/// @param wavelengths is an optional STL vector of size B specifying a numerical label for each band
	bool open(std::string filename, 
			  unsigned long long X, 
			  unsigned long long Y, 
			  unsigned long long B, 
			  unsigned long long header_offset, 
			  std::vector<double> wavelengths){

		w = wavelengths;

		return open(filename, vec<unsigned long long>(X, B, Y), header_offset);

	}

	/// 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.
	bool band_index( T * p, unsigned long long page, bool PROGRESS = false){
		//return binary<T>::read_plane_1(p, page);

		if(PROGRESS) progress = 0;
		unsigned long long L = X() * sizeof(T);		//caculate the number of bytes in a sample line
		unsigned long long jump = X() * (Z() - 1) * sizeof(T);

		if (page >= Z()){										//make sure the bank number is right
			std::cout<<"ERROR: page out of range"<<std::endl;
			return false;
		}

		file.seekg(X() * page * sizeof(T), std::ios::beg);
		for (unsigned long long i = 0; i < Y(); i++)
		{
			file.read((char *)(p + i * X()), L);
			file.seekg( jump, std::ios::cur);
			if(PROGRESS) progress = (double)(i+1) / Y() * 100;
		}

		return true;
	}

	/// 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.
	bool band( T * p, double wavelength, bool PROGRESS = false){

		//if there are no wavelengths in the BSQ file
		if(w.size() == 0)
			return band_index(p, (unsigned long long)wavelength);

		unsigned long long XY = X() * Y();	//calculate the number of pixels in a band
		unsigned long long S = XY * sizeof(T);		//calculate the number of bytes of a band

		unsigned long long page=0;                      //bands around the wavelength
		

		//get the bands numbers around the wavelength

		//if wavelength is smaller than the first one in header file
		if ( w[page] > wavelength ){
			band_index(p, page, PROGRESS);
			return true;
		}

		while( w[page] < wavelength )
		{
			page++;
			//if wavelength is larger than the last wavelength in header file
			if (page == Z()) {
				band_index(p, Z()-1);
				return true;
			}
		}
		if ( wavelength < w[page] )
		{
			T * p1;
			T * p2;
			p1=(T*)malloc(S);                     //memory allocation
			p2=(T*)malloc(S);
			band_index(p1, page - 1);
			band_index(p2, page, PROGRESS);
			for(unsigned long long i=0; i < XY; i++){
				double r = (wavelength - w[page-1]) / (w[page] - w[page-1]);
				p[i] = (T)(((double)p2[i] - (double)p1[i]) * r + (double)p1[i]);
			}
			free(p1);
			free(p2);
		}
		else                           //if the wavelength is equal to a wavelength in header file
		{
			band_index(p, page, PROGRESS);
		}

		return true;
	}

	/// Retrieves a band of x values from a given xz plane.

	/// @param p is a pointer to pre-allocated memory at least Z * sizeof(T) in size
	/// @param c is a pointer to an existing XZ plane (size X*Z*sizeof(T))
	/// @param wavelength is the wavelength to retrieve
	bool read_x_from_xz(T* p, T* c, double wavelength)
	{
		unsigned long long B = Z();
		unsigned long long L = X() * sizeof(T);

		unsigned long long page=0;                      //samples around the wavelength
		T * p1;
		T * p2;

		//get the bands numbers around the wavelength

		//if wavelength is smaller than the first one in header file
		if ( w[page] > wavelength ){
			memcpy(p, c, L);	
			return true;
		}

		while( w[page] < wavelength )
		{
			page++;
			//if wavelength is larger than the last wavelength in header file
			if (page == B) {
				memcpy(p, c + (B - 1) * X(), L);
				return true;
			}
		}
		if ( wavelength < w[page] )
		{
			p1=(T*)malloc( L );                     //memory allocation
			p2=(T*)malloc( L );

			memcpy(p1, c + (page - 1) * X(), L);
			memcpy(p2, c + page * X(), L);
			
			for(unsigned long long i=0; i < X(); i++){
				double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
				p[i] = (T)(((double)p2[i] - (double)p1[i]) * r + (double)p1[i]);
			}
		}
		else                           //if the wavelength is equal to a wavelength in header file		
			memcpy(p, c + page * X(), L);
		
		return true;		
	}

	/// Retrieve a single spectrum (B-axis line) at a given (x, y) location and stores it in pre-allocated memory.

	/// @param p is a pointer to pre-allocated memory at least B * sizeof(T) in size.
	/// @param x is the x-coordinate (dimension 1) of the spectrum.
	/// @param y is the y-coordinate (dimension 2) of the spectrum.
	bool spectrum(T * p, unsigned long long x, unsigned long long y, bool PROGRESS = false){
		return binary<T>::read_line_1(p, x, y, PROGRESS);
	}

	/// 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.
	bool pixel(T * p, unsigned long long n){

		//calculate the corresponding x, y
		unsigned long long x = n % X();
		unsigned long long y = n / X();

		//get the pixel
		return spectrum(p, x, y);
	}
	
	//given a Y ,return a XZ slice
	bool read_plane_y(T * p, unsigned long long y){
		return binary<T>::read_plane_2(p, y);
	}

		
	/// Perform baseline correction given a list of baseline points and stores the result in a new BSQ file.

	/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
	/// @param wls is the list of baseline points based on band labels.
	bool baseline(std::string outname, std::vector<double> wls, unsigned char* mask = NULL, bool PROGRESS = false){
	
		unsigned long long N = wls.size();			//get the number of baseline points
		
		std::ofstream target(outname.c_str(), std::ios::binary);	//open the target binary file
		std::string headername = outname + ".hdr";              //the header file name		
		
		//simplify image resolution
		unsigned long long ZX = Z() * X();		//calculate the number of points in a Y slice
		unsigned long long L = ZX * sizeof(T);			//calculate the number of bytes of a Y slice
		unsigned long long B = Z();

		T* c;			//pointer to the current Y slice
		c = (T*)malloc(L);  //memory allocation
		
		T* a;			//pointer to the two YZ lines surrounding the current YZ line
		T* b;
		
		a = (T*)malloc(X() * sizeof(T));
		b = (T*)malloc(X() * sizeof(T));


		double ai, bi;	//stores the two baseline points wavelength surrounding the current band
		double ci;		//stores the current band's wavelength
		unsigned long long control;

		if (a == NULL || b == NULL || c == NULL){
			std::cout<<"ERROR: error allocating memory";
			exit(1);
		}
	//	loop start	correct every y slice
		
		for (unsigned long long k =0; k < Y(); k++)
		{
			//get the current y slice
			read_plane_y(c, k);
		
			//initialize lownum, highnum, low, high		
			ai = w[0];
			control=0;
			//if no baseline point is specified at band 0,
			//set the baseline point at band 0 to 0
			if(wls[0] != w[0]){
				bi = wls[control];			
				memset(a, (char)0, X() * sizeof(T) );
			}
			//else get the low band
			else{
				control++;
				read_x_from_xz(a, c, ai);
				bi = wls[control];
			}
			//get the high band
			read_x_from_xz(b, c, bi);
		
			//correct every YZ line
			
			for(unsigned long long cii = 0; cii < B; cii++){

				//update baseline points, if necessary
				if( w[cii] >= bi && cii != B - 1) {
					//if the high band is now on the last BL point
					if (control != N-1) {
	
						control++;		//increment the index
	
						std::swap(a, b);	//swap the baseline band pointers
	
						ai = bi;
						bi = wls[control];
						read_x_from_xz(b, c, bi);
	
					}
					//if the last BL point on the last band of the file?
					else if ( wls[control] < w[B - 1]) {
	
						std::swap(a, b);	//swap the baseline band pointers
	
						memset(b, (char)0, X() * sizeof(T) );	//clear the high band
	
						ai = bi;
						bi = w[B - 1];
					}
				}
			
				ci = w[cii];
				
				unsigned long long jump = cii * X();
				//perform the baseline correction
				for(unsigned i=0; i < X(); i++)
				{
					double r = (double) (ci - ai) / (double) (bi - ai);
					c[i + jump] =(T) ( c[i + jump] - (b[i] - a[i]) * r - a[i] );
				}
				
			}//loop for YZ line end  
			target.write(reinterpret_cast<const char*>(c), L);   //write the corrected data into destination	

			if(PROGRESS) progress = (double)(k+1) / Y() * 100;
		}//loop for Y slice end		
		
		free(a);
		free(b);
		free(c);
		target.close();

		return true;	
		
	}
		
	/// Normalize all spectra based on the value of a single band, storing the result in a new BSQ file.

	/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
	///	@param w is the label specifying the band that the hyperspectral image will be normalized to.
	///	@param t is a threshold specified such that a spectrum with a value at w less than t is set to zero. Setting this threshold allows the user to limit division by extremely small numbers.
	bool normalize(std::string outname, double w, unsigned char* mask = NULL, bool PROGRESS = false)
	{
		unsigned long long B = Z();		//calculate the number of bands
		unsigned long long ZX = Z() * X();
		unsigned long long XY = X() * Y();	//calculate the number of pixels in a band
		unsigned long long S = XY * sizeof(T);		//calculate the number of bytes in a band		
		unsigned long long L = ZX * sizeof(T);

		std::ofstream target(outname.c_str(), std::ios::binary);	//open the target binary file
		std::string headername = outname + ".hdr";              //the header file name

		T * c;				//pointer to the current ZX slice
		T * b;				//pointer to the standard band

		b = (T*)malloc( S );     //memory allocation
		c = (T*)malloc( L ); 

		band(b, w);             //get the certain band into memory

		for(unsigned long long j = 0; j < Y(); j++)
		{
			read_plane_y(c, j);
			for(unsigned long long i = 0; i < B; i++)
			{
				for(unsigned long long m = 0; m < X(); m++)
				{
					if( mask != NULL && !mask[m + j * X()] )
						c[m + i * X()] = (T)0.0;
					else
						c[m + i * X()] = c[m + i * X()] / b[m + j * X()];
				}								
			}
			target.write(reinterpret_cast<const char*>(c), L);   //write normalized data into destination

			if(PROGRESS) progress = (double)(j+1) / Y() * 100;
		}
		
		free(b);
		free(c);
		target.close();
		return true;
	}
	
	/// Convert the current BIL file to a BSQ file with the specified file name.

	/// @param outname is the name of the output BSQ file to be saved to disk.
	bool bsq(std::string outname, bool PROGRESS = false)
	{
		unsigned long long S = X() * Y() * sizeof(T);		//calculate the number of bytes in a band
		
		std::ofstream target(outname.c_str(), std::ios::binary);
		std::string headername = outname + ".hdr";
		
		T * p;			//pointer to the current band
		p = (T*)malloc(S);
		
		for ( unsigned long long i = 0; i < Z(); i++)
		{			
				band_index(p, i);
				target.write(reinterpret_cast<const char*>(p), S);   //write a band data into target file

				if(PROGRESS) progress = (double)(i+1) / Z() * 100;	//store the progress for the current operation	
		}

		free(p);
		target.close();
		return true;
	}

	/// Convert the current BIL file to a BIP file with the specified file name.

	/// @param outname is the name of the output BIP file to be saved to disk.
	bool bip(std::string outname, bool PROGRESS = false)
	{
		unsigned long long S = X() * Z() * sizeof(T);		//calculate the number of bytes in a ZX slice
		
		std::ofstream target(outname.c_str(), std::ios::binary);
		std::string headername = outname + ".hdr";
		
		T * p;			//pointer to the current XZ slice for bil file
		p = (T*)malloc(S);
		T * q;			//pointer to the current ZX slice for bip file
		q = (T*)malloc(S);
		
		for ( unsigned long long i = 0; i < Y(); i++)
		{			
			read_plane_y(p, i);
			for ( unsigned long long k = 0; k < Z(); k++)
			{
				unsigned long long ks = k * X();
				for ( unsigned long long j = 0; j < X(); j++)
					q[k + j * Z()] = p[ks + j];

				if(PROGRESS) progress = (double)((i+1) * Z() + k+1) / (Z() * Y()) * 100;	//store the progress for the current operation	
			}
			
			target.write(reinterpret_cast<const char*>(q), S);   //write a band data into target file	
		}

		free(p);
		free(q);
		target.close();
		return true;
	}


	/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.

	/// @param lb is the label value for the left baseline point
	/// @param rb is the label value for the right baseline point
	/// @param lp is a pointer to an array holding the band image for the left baseline point
	/// @param rp is a pointer to an array holding the band image for the right baseline point
	/// @param wavelength is the label value for the requested baseline-corrected band
	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
	bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){

		unsigned long long XY = X() * Y();
		band(result, wavelength);		//get band

		//perform the baseline correction
		double r = (double) (wavelength - lb) / (double) (rb - lb);
		for(unsigned long long i=0; i < XY; i++){
			result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
		}
		return true;
	}

	/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.

	/// @param lb is the label value for the left baseline point
	/// @param rb is the label value for the right baseline point
	/// @param bandwavelength is the label value for the desired baseline-corrected band
	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
	bool height(double lb, double rb, double bandwavelength, T* result){

		T* lp;
		T* rp;
		unsigned long long XY = X() * Y();
		unsigned long long S = XY * sizeof(T);
		lp = (T*) malloc(S);			//memory allocation
		rp = (T*) malloc(S);

		band(lp, lb);
		band(rp, rb);		

		baseline_band(lb, rb, lp, rp, bandwavelength, result);

		free(lp);
		free(rp);
		return true;
	}



	/// Calculate the area under the spectrum between two specified points and stores the result in a pre-allocated array.

	/// @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 value for the left bound (start of the integration)
	/// @param rab is the label value for the right bound (end of the integration)
	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
	bool area(double lb, double rb, double lab, double rab, T* result){

		T* lp;	//left band pointer
		T* rp;	//right band pointer
		T* cur;		//current band 1
		T* cur2;	//current band 2

		unsigned long long XY = X() * Y();
		unsigned long long S = XY * sizeof(T);

		lp = (T*) malloc(S);			//memory allocation
		rp = (T*) malloc(S);
		cur = (T*) malloc(S);
		cur2 = (T*) malloc(S);

		memset(result, (char)0, S);

		//find the wavelenght position in the whole band
		unsigned long long n = w.size();
		unsigned long long ai = 0;		//left bound position
		unsigned long long bi = n - 1;		//right bound position



		//to make sure the left and the right bound are in the bandwidth
		if (lb < w[0] || rb < w[0] || lb > w[n-1] || rb >w[n-1]){
			std::cout<<"ERROR: left bound or right bound out of bandwidth"<<std::endl;
			exit(1);
		}
		//to make sure rigth bound is bigger than left bound
		else if(lb > rb){
			std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
			exit(1);
		}

		//get the position of lb and rb
		while (lab >= w[ai]){
			ai++;
		}
		while (rab <= w[bi]){
			bi--;
		}

		band(lp, lb);
		band(rp, rb);

		//calculate the beginning and the ending part
		baseline_band(lb, rb, lp, rp, rab, cur2);		//ending part
		baseline_band(lb, rb, lp, rp, w[bi], cur);
		for(unsigned long long j = 0; j < XY; j++){
			result[j] += (T)((rab - w[bi]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
		}
		baseline_band(lb, rb, lp, rp, lab, cur2);		//beginnning part
		baseline_band(lb, rb, lp, rp, w[ai], cur);
		for(unsigned long long j = 0; j < XY; j++){	
			result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
		}

		//calculate the area
		ai++;
		for(unsigned long long i = ai; i <= bi ;i++)
		{
			baseline_band(lb, rb, lp, rp, w[ai], cur2);
			for(unsigned long long j = 0; j < XY; j++)
			{
				result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0); 
			}
			std::swap(cur,cur2);		//swap the band pointers
		}

		free(lp);
		free(rp);
		free(cur);
		free(cur2);
		return true;
	}

	/// 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
	bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){

		T* p1 = (T*)malloc(X() * Y() * sizeof(T));
		T* p2 = (T*)malloc(X() * Y() * sizeof(T));
		
		//get the two peak band
		height(lb1, rb1, pos1, p1);
		height(lb2, rb2, pos2, p2);
		//calculate the ratio in result
		for(unsigned long long i = 0; i < X() * Y(); i++){
			if(p1[i] == 0 && p2[i] ==0)
				result[i] = 1;
			else
				result[i] = p1[i] / p2[i];
		}

		free(p1);
		free(p2);
		return true;	
	}
	
	/// 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
	bool pa_to_ph(double lb1, double rb1, double lab1, double rab1,
					double lb2, double rb2, double pos, T* result){
		
		T* p1 = (T*)malloc(X() * Y() * sizeof(T));
		T* p2 = (T*)malloc(X() * Y() * sizeof(T));
		
		//get the area and the peak band
		area(lb1, rb1, lab1, rab1, p1);
		height(lb2, rb2, pos, p2);
		//calculate the ratio in result
		for(unsigned long long i = 0; i < X() * Y(); i++){
			if(p1[i] == 0 && p2[i] ==0)
				result[i] = 1;
			else
				result[i] = p1[i] / p2[i];
		}

		free(p1);
		free(p2);
		return true;	
	}		
	
	/// 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)
	/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)	
	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
	bool pa_to_pa(double lb1, double rb1, double lab1, double rab1,
					double lb2, double rb2, double lab2, double rab2, T* result){
		
		T* p1 = (T*)malloc(X() * Y() * sizeof(T));
		T* p2 = (T*)malloc(X() * Y() * sizeof(T));
		
		//get the area and the peak band
		area(lb1, rb1, lab1, rab1, p1);
		area(lb2, rb2, lab2, rab2, p2);
		//calculate the ratio in result
		for(unsigned long long i = 0; i < X() * Y(); i++){
			if(p1[i] == 0 && p2[i] ==0)
				result[i] = 1;
			else
				result[i] = p1[i] / p2[i];
		}

		free(p1);
		free(p2);
		return true;	
	}		

	/// Compute the definite integral 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 definite integral
	/// @param rab is the label for the end of the definite integral
	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
	bool x_area(double lb, double rb, double lab, double rab, T* result){
		T* lp;	//left band pointer
		T* rp;	//right band pointer
		T* cur;		//current band 1
		T* cur2;	//current band 2

		unsigned long long XY = X() * Y();
		unsigned long long S = XY * sizeof(T);

		lp = (T*) malloc(S);			//memory allocation
		rp = (T*) malloc(S);
		cur = (T*) malloc(S);
		cur2 = (T*) malloc(S);

		memset(result, (char)0, S);

		//find the wavelenght position in the whole band
		unsigned long long n = w.size();
		unsigned long long ai = 0;		//left bound position
		unsigned long long bi = n - 1;		//right bound position

		//to make sure the left and the right bound are in the bandwidth
		if (lb < w[0] || rb < w[0] || lb > w[n-1] || rb >w[n-1]){
			std::cout<<"ERROR: left bound or right bound out of bandwidth"<<std::endl;
			exit(1);
		}
		//to make sure rigth bound is bigger than left bound
		else if(lb > rb){
			std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
			exit(1);
		}

		//get the position of lb and rb
		while (lab >= w[ai]){
			ai++;
		}
		while (rab <= w[bi]){
			bi--;
		}

		band(lp, lb);
		band(rp, rb);

		//calculate the beginning and the ending part
		baseline_band(lb, rb, lp, rp, rab, cur2);		//ending part
		baseline_band(lb, rb, lp, rp, w[bi], cur);
		for(unsigned long long j = 0; j < XY; j++){
			result[j] += (T)((rab - w[bi]) * (rab + w[bi]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
		}
		baseline_band(lb, rb, lp, rp, lab, cur2);		//beginnning part
		baseline_band(lb, rb, lp, rp, w[ai], cur);
		for(unsigned long long j = 0; j < XY; j++){	
			result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
		}

		//calculate f(x) times x
		ai++;
		for(unsigned long long i = ai; i <= bi ;i++)
		{
			baseline_band(lb, rb, lp, rp, w[ai], cur2);
			for(unsigned long long j = 0; j < XY; j++)
			{
				result[j] += (T)((w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 4.0); 
			}
			std::swap(cur,cur2);		//swap the band pointers
		}

		free(lp);
		free(rp);
		free(cur);
		free(cur2);
		return true;
	}

	/// 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
	bool cpoint(double lb, double rb, double lab, double rab, T* result){
		T* p1 = (T*)malloc(X() * Y() * sizeof(T));
		T* p2 = (T*)malloc(X() * Y() * sizeof(T));
		
		//get the area and the peak band
		x_area(lb, rb, lab, rab, p1);
		area(lb, rb, lab, rab, p2);
		//calculate the ratio in result
		for(unsigned long long i = 0; i < X() * Y(); i++){
			if(p1[i] == 0 && p2[i] ==0)
				result[i] = 1;
			else
				result[i] = p1[i] / p2[i];
		}

		free(p1);
		free(p2);
		return true;	
	}

	/// Create a mask based on a given band and threshold value.

	/// All pixels in the
	/// specified band greater than the threshold are true and all pixels less than the threshold are false.
	/// @param mask_band is the band used to specify the mask
	/// @param threshold is the threshold used to determine if the mask value is true or false
	/// @param p is a pointer to a pre-allocated array at least X * Y in size
	bool build_mask(double mask_band, double threshold, unsigned char* p, bool PROGRESS = false){

		T* temp = (T*)malloc(X() * Y() * sizeof(T));		//allocate memory for the certain band
		band(temp, mask_band, PROGRESS);

		for (unsigned long long i = 0; i < X() * Y(); i++) {
			if (temp[i] < threshold)
				p[i] = 0;
			else
				p[i] = 255;
		}

		free(temp);
		return true;
	}

	/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.

	/// @param outfile is the name of the masked output file
	/// @param p is a pointer to memory of size X * Y, where p(i) = 0 for pixels that will be set to zero.
	bool apply_mask(std::string outfile, unsigned char* p){

		std::ofstream target(outfile.c_str(), std::ios::binary);

		//I THINK THIS IS WRONG
		unsigned long long XZ = X() * Z();		//calculate the number of values in a page on disk
		unsigned long long L = XZ * sizeof(T);	//calculate the size of the page (in bytes)

		T * temp = (T*)malloc(L);		//allocate memory for a temporary page

		for (unsigned long long i = 0; i < Y(); i++)			//for each value in Y() (BIP should be X)
		{
			read_plane_y(temp, i);							//retrieve an ZX slice, stored in temp
			for ( unsigned long long j = 0; j < Z(); j++)	//for each Z() (Y)
			{
				for (unsigned long long k = 0; k < X(); k++) //for each band
				{
				if(p[i * X() + k] == 0)
					temp[j * X() + k] = 0;
				else
					continue;
				}
			}
			target.write(reinterpret_cast<const char*>(temp), L);   //write a band data into target file	
		}
		target.close();
		free(temp);
		return true;
	}

	/// Saves to disk only those spectra corresponding to mask values != 0
	/// Unlike the BIP and BSQ versions of this function, this version saves a different format: the BIL file is saved as a BIP
	bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false){
		// Assume X() = X, Y() = Y, Z() = Z.
		std::ofstream target(outfile.c_str(), std::ios::binary);

		//for loading pages:
		unsigned long long XZ = X() * Z();		//calculate the number of values in an XZ page on disk
		unsigned long long B = Z();			//calculate the number of bands
		unsigned long long L = XZ * sizeof(T);	//calculate the size of the page (in bytes)

		//allocate temporary memory for a XZ slice
		T* slice = (T*) malloc(L);

		//allocate temporary memory for a spectrum
		T* spec = (T*) malloc(B * sizeof(T));

		//for each slice along the y axis
		for (unsigned long long y = 0; y < Y(); y++)			//Select a page by choosing Y coordinate, Y()
		{
			read_plane_y(slice, y);							//retrieve an ZX page, store in "slice"

			//for each sample along X			
			for (unsigned long long x = 0; x < X(); x++)		//Select a pixel by choosing X coordinate in the page, X()
			{
				//if the mask != 0 at that xy pixel
				if (p[y * X() + x] != 0)					//if the mask != 0 at that XY pixel
				{
					//for each band at that pixel
					for (unsigned long long b = 0; b < B; b++)		//Select a voxel by choosing Z coordinate at the pixel
					{
						spec[b] = slice[b*X() + x];		//Pass the correct spectral value from XZ page into the spectrum to be saved.
					}
					target.write((char*)spec, B * sizeof(T));		//write that spectrum to disk. Size is L2.
				}

				if(PROGRESS) progress = (double) ((y+1) * X() + x+1) / (Y() * X()) * 100;
			}
		}
		target.close();
		free(slice);
		free(spec);

		return true;
	}

	/// Calculate the mean band value (average along B) at each pixel location.

	/// @param p is a pointer to memory of size X * Y * sizeof(T) that will store the band averages.
	bool band_avg(T* p){
		unsigned long long XZ = X() * Z();
		T* temp = (T*)malloc(sizeof(T) * XZ);
		T* line = (T*)malloc(sizeof(T) * X());

		for (unsigned long long i = 0; i < Y(); i++){
			getY(temp, i);
			//initialize x-line
			for (unsigned long long j = 0; j < X(); j++){
				line[j] = 0;
			}
			unsigned long long c = 0;
			for (unsigned long long j = 0; j < Z(); j++){
				for (unsigned long long k = 0; k < X(); k++){
					line[k] += temp[c] / (T)Z();
					c++;
				}
			}
			for (unsigned long long j = 0; j < X(); j++){
				p[j + i * X()] = line[j];
			}
		}
		free(temp);
		return true;
	}

	/// 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 avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
		unsigned long long XZ = X() * Z();
		unsigned long long XY = X() * Y();
		T* temp = (T*)malloc(sizeof(T) * XZ);
		for (unsigned long long j = 0; j < Z(); j++){
			p[j] = 0;
		}
		//calculate vaild number in a band
		unsigned long long count = 0;
		for (unsigned long long j = 0; j < XY; j++){
			if (mask == NULL || mask[j] != 0){
				count++;
			}
		}
		for (unsigned long long k = 0; k < Y(); k++){
			read_plane_y(temp, k);
			unsigned long long kx = k * X();
			for (unsigned long long i = 0; i < X(); i++){
				if (mask == NULL || mask[kx + i] != 0){
					for (unsigned long long j = 0; j < Z(); j++){
						p[j] += temp[j * X() + i] / (double)count;
					}
				}
			}
			if(PROGRESS) progress = (double)(k+1) / Y() * 100;
		}
		free(temp);
		return true;
	}

	/// 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
	bool co_matrix(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
		progress = 0;
		//memory allocation
		unsigned long long xy = X() * Y();
		unsigned long long B = Z();
		T* temp = (T*)malloc(sizeof(T) * B);
		//count vaild pixels in a band
		unsigned long long count = 0;
		for (unsigned long long j = 0; j < xy; j++){
			if (mask == NULL || mask[j] != 0){
				count++;
			}
		}
		//initialize correlation matrix
		for (unsigned long long i = 0; i < B; i++){
			for (unsigned long long k = 0; k < B; k++){
				co[i * B + k] = 0;
			}
		}
		//calculate correlation coefficient matrix
		for (unsigned long long j = 0; j < xy; j++){
			if (mask == NULL || mask[j] != 0){
				pixel(temp, j);
				for (unsigned long long i = 0; i < B; i++){
					for (unsigned long long k = i; k < B; k++){
						co[i * B + k] += ((double)temp[i] - (double)avg[i]) * ((double)temp[k] - (double)avg[k]) / (double)count;
					}
				}
			}
			if(PROGRESS) progress = (double)(j+1) / xy * 100;
		}
		//because correlation matrix is symmetric
		for (unsigned long long i = 0; i < B; i++){
			for (unsigned long long k = i + 1; k < B; k++){
				co[k * B + i] = co[i * B + k];
			}
		}

		free(temp);
		return true;
	}


	/// 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
	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){

		//calculate the new image parameters
		unsigned long long samples = x1 - x0;
		unsigned long long lines = y1 - y0;
		unsigned long long bands = b1 - b0;

		//calculate the size of a line
		unsigned long long L = samples * sizeof(T);


		//allocate space for a line
		T* temp = (T*)malloc(bands * L);

		//create an output stream to store the cropped file
		std::ofstream out(outfile.c_str(), std::ios::binary);

		//calculate the distance between bands
		unsigned long long jumpb = (X() - samples) * sizeof(T);

		//distance needed to jump from the previous line of the last band to the next line of the first band
		unsigned long long longjump = ((Z() - b1) * X() + b0 * X()) * sizeof(T);

		//set the start position for the cropped region
		file.seekg((y0 * X() * Z() + b0 * X() + x0) * sizeof(T), std::ios::beg);

		for (unsigned long long x = 0; x < lines; x++)
		{
			for (unsigned long long z = b0; z < b1; z++)
			{
				file.read((char *)(temp + z * samples), sizeof(T) * samples);
				file.seekg(jumpb, std::ios::cur);    //go to the next band	

				if(PROGRESS) progress = (double)(x * Z() + z+1) / (lines * Z()) * 100;
			}

			//write slice data into target file
			out.write(reinterpret_cast<const char*>(temp), bands * L);

			//seek to the beginning of the next X-Z slice
			file.seekg(longjump, std::ios::cur);
		}

		//free the temporary frame
		free(temp);

		return true;
	}


	/// Close the file.
	bool close(){
		file.close();
		return true;
	}

	};
}

#endif