#ifndef STIM_BSQ_H
#define STIM_BSQ_H

#include "../envi/envi_header.h"
#include "../envi/binary.h"
#include "../envi/bil.h"
#include <cstring>
#include <utility>
#include <vector>



namespace stim{

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

	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 bsq: public binary<T> {


protected:

	std::vector<double> w;	//band wavelengths
	unsigned int offset;

	using binary<T>::R;

	unsigned long X(){
		return R[0];
	}
	unsigned long Y(){
		return R[1];
	}
	unsigned long Z(){
		return R[2];
	}

	using binary<T>::nnz;
	using binary<T>::progress;

public:

	using binary<T>::open;
	using binary<T>::file;
	using binary<T>::read_line_2;
	using binary<T>::read_plane_2;
	//using binary<T>::getSlice;


	/// 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 STL vector of size B specifying a numerical label for each band
	bool open(std::string filename, unsigned int X, unsigned int Y, unsigned int B, unsigned int header_offset, std::vector<double> wavelengths){

		//copy the wavelengths to the BSQ file structure
		w = wavelengths;
		//copy the wavelengths to the structure
		offset = header_offset;

		return open(filename, vec<unsigned int>(X, Y, B), 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 int page){
		return read_plane_2(p, page);		//call the binary read_plane function (don't let it update the progress)
	}

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

		unsigned int XY = X() * Y();	//calculate the number of pixels in a band
		unsigned page = 0;


		//get the two neighboring bands (above and below 'wavelength')

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

		while( w[page] < wavelength )
		{
			page++;
			//if wavelength is larger than the last wavelength in the header file
			//	(the wavelength is out of bounds)
			if (page == Z()) {
				band_index(p, Z()-1);		//return the last band
				return true;
			}
		}
		//when the page counter points to the first band above 'wavelength'
		if ( wavelength < w[page] ){

			//do the interpolation
			T * p1;
			T * p2;
			p1=(T*)malloc( XY * sizeof(T));                     //memory allocation
			p2=(T*)malloc( XY * sizeof(T));
			band_index(p1, page - 1);
			band_index(p2, page );
			for(unsigned i=0; i < XY; i++){
				double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
				p[i] = (p2[i] - p1[i]) * r + p1[i];
			}
			free(p1);
			free(p2);
		}
		//if the wavelength is equal to a wavelength in header file
		else{
			band_index(p, page);		//return the band
		}
		if(PROGRESS) progress = 100;
		return true;
	}

	/// Retrieve a single spectrum (Z-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 x, unsigned y, bool PROGRESS = false){
		return read_line_2(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 n){

		unsigned bandnum = X() * Y();		//calculate numbers in one band
		if ( n >= bandnum){							//make sure the pixel number is right
			std::cout<<"ERROR: sample or line out of range"<<std::endl;
			return false;
		}

		file.seekg(n * sizeof(T) + binary<T>::header, std::ios::beg);           //point to the certain pixel
		for (unsigned i = 0; i < Z(); i++)
		{
			file.read((char *)(p + i), sizeof(T));
			file.seekg((bandnum - 1) * sizeof(T), std::ios::cur);    //go to the next band
		}

		return true;
	}

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

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

		unsigned control=0;

		T * a;					//pointers to the high and low band images
		T * b;
		T * c;				//pointer to the current image

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

		if (a == NULL || b == NULL || c == NULL){
			std::cout<<"ERROR: error allocating memory";
			exit(1);
		}


		//initialize lownum, highnum, low, high
		ai=w[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, S);
		}
		//else get the low band
		else{
			control += 1;
			band(a, ai);
			bi = wls[control];
		}
		//get the high band
		band(b, bi);

		//correct every band
		for(unsigned 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];
					band(b, 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, S);	//clear the high band

					ai = bi;
					bi = w[B - 1];
				}
			}

			//get the current band
			band_index(c, cii);
			ci = w[cii];

			//perform the baseline correction
			for(unsigned i=0; i < XY; i++){
				if(mask != NULL && !mask[i])								//if the pixel is excluded by a mask
					c[i] = 0;												//set the value to zero
				else{
					double r = (double) (ci - ai) / (double) (bi - ai);
					c[i] =(T) ( c[i] - (b[i] - a[i]) * r - a[i] );
				}
			}

			target.write(reinterpret_cast<const char*>(c), S);   //write the corrected data into destination

			if(PROGRESS)progress = (double)(cii+1) / B * 100;

		}

		//header.save(headername);         //save the new header file

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

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

		T * b;					//pointers to the certain wavelength band
		T * c;				//pointer to the current image

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

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

		for(unsigned j = 0; j < B; j++)
		{
			band_index(c, j);                     //get the current band into memory
			for(unsigned i = 0; i < XY; i++)
			{
				if(mask != NULL && !mask[i])
					c[i] = (T)0.0;
				else
					c[i] = c[i] / b[i];
			}
			target.write(reinterpret_cast<const char*>(c), S);   //write normalized data into destination

			if(PROGRESS) progress = (double)(j+1) / B * 100;
		}



		//header.save(headername);         //save the new header file

		free(b);
		free(c);
		target.close();
		return true;
	}

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

	/// @param outname is the name of the output BIL file to be saved to disk.
	bool bil(std::string outname, bool PROGRESS = false)
	{
		//simplify image resolution
		//unsigned int L = X() * Z() * sizeof(T);		//calculate the number of bytes of a ZX slice
		unsigned int jump = (Y() - 1) * X() * sizeof(T);

		std::ofstream target(outname.c_str(), std::ios::binary);
		std::string headername = outname + ".hdr";

		unsigned int L = X();
		T* line = (T*)malloc(sizeof(T) * L);

		for ( unsigned y = 0; y < Y(); y++)									//for each y position
		{
			file.seekg(y * X() * sizeof(T), std::ios::beg);					//seek to the beginning of the xz slice
			for ( unsigned z = 0; z < Z(); z++ )							//for each band
			{
				file.read((char *)line, sizeof(T) * X());					//read a line
				target.write((char*)line, sizeof(T) * X());					//write the line to the output file
				file.seekg(jump, std::ios::cur);							//seek to the next band
				if(PROGRESS) progress = (double)((y+1) * Z() + z + 1) / (Z() * Y()) * 100;	//update the progress counter
			}
			//std::cout<<progress<<": "<<y<<std::endl;
		}

		free(line);
		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 XY = X() * Y();
		band(result, wavelength);		//get band

		//perform the baseline correction
		double r = (double) (wavelength - lb) / (double) (rb - lb);
		for(unsigned 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 XY = X() * Y();
		unsigned 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 XY = X() * Y();
		unsigned 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 int n = w.size();
		unsigned int ai = 0;		//left bound position
		unsigned int 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 j = 0; j < XY; j++){
			result[j] += (rab - w[bi]) * (cur[j] + 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 j = 0; j < XY; j++){
			result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;
		}

		//calculate the area
		ai++;
		for(unsigned i = ai; i <= bi ;i++)
		{
			baseline_band(lb, rb, lp, rp, w[ai], cur2);
			for(unsigned j = 0; j < XY; j++)
			{
				result[j] += (w[ai] - w[ai-1]) * (cur[j] + 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 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 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 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 XY = X() * Y();
		unsigned 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 int n = w.size();
		unsigned int ai = 0;		//left bound position
		unsigned int 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 j = 0; j < XY; j++){
			result[j] += (rab - w[bi]) * (rab + w[bi]) * (cur[j] + 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 j = 0; j < XY; j++){
			result[j] += (w[ai] - lab) * (w[ai] + lab) * (cur[j] + cur2[j]) / 4.0;
		}

		//calculate f(x) times x
		ai++;
		for(unsigned i = ai; i <= bi ;i++)
		{
			baseline_band(lb, rb, lp, rp, w[ai], cur2);
			for(unsigned j = 0; j < XY; j++)
			{
				result[j] += (w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * (cur[j] + 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 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 = NULL, bool PROGRESS = false){

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

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

			if(PROGRESS) progress = (double) (i+1) / (X() * Y());
		}

		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);

		unsigned XY = X() * Y();		//calculate number of a band
		unsigned L = XY * sizeof(T);

		T * temp = (T*)malloc(L);

		for (unsigned i = 0; i < Z(); i++)			//for each spectral bin
		{
			band_index(temp, i);					//get the specified band (by index)
			for ( unsigned j = 0; j < XY; j++)		// for each pixel
			{
				if(p[j] == 0){						//if the mask is 0 at that pixel
					temp[j] = 0;					//set temp to zero
				}
				else{
					continue;
				}
			}
			target.write(reinterpret_cast<const char*>(temp), L);   //write the XY slice at that band to disk
		}
		target.close();
		free(temp);
		return true;
	}

	/// Copies all spectra corresponding to nonzero values of a mask into a pre-allocated matrix of size (B x P)
	///		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 = p*B + b
	/// @param matrix is the destination for the pixel data
	/// @param mask is the mask
	bool sift(T* matrix, unsigned char* mask){
		unsigned long long XY = X() * Y(); 					//Number of XY pixels
		unsigned long long L = XY * sizeof(T); 				//size of XY plane (in bytes)

		//calculate the number of pixels in the mask
		unsigned long long P = 0;
		if(mask == NULL) P = XY;
		else{
			for(unsigned long long xy = 0; xy < XY; xy++){
				if(mask[xy] != 0) P++;
			}
		}

		T* band_image = (T*) malloc( XY * sizeof(T));		//allocate space for a single band

		unsigned long long i;								//pixel index into the sifted array
		for(unsigned long long b = 0; b < Z(); b++){		//for each band in the data set
			band_index(band_image, b);						//retrieve an image of that band

			i = 0;
			for(unsigned long long xy = 0; xy < XY; xy++){
				if(mask == NULL || mask[xy] != 0){				//if the pixel is valid
					matrix[i*Z() + b] = band_image[xy];			//copy it to the appropriate point in the values[] array
					i++;
				}
			}
		}

		return true;
	}

	/// Saves only those spectra corresponding to mask value != 0 to pre-allocated memory
	/// @param matrix is the destination for the sifted pixels
	/// @param p is the mask file used for sifting
	/*bool sift(T* matrix, unsigned char* p){

		// open a band (XY plane)
		unsigned long XY = X() * Y(); 					//Number of XY pixels
		unsigned long L = XY * sizeof(T); 				//size of XY pixels

		//count the number of masked pixels
		unsigned long P = 0;												//allocate space for the number of pixels
		for(unsigned long xy = 0; xy < XY; xy++){ 	//count the number of pixels
			if(p[xy] != 0) P++;
		}

		T* bandvals = (T*) malloc(sizeof(T) * P);			//allocate a temporary array to store the pixels for a single band
		memset(matrix, 0, sizeof(T) * P * Z());
		for (unsigned long z = 0; z < Z(); z++){		//for each band

			if(!sift_band(bandvals, z, p)){
				std::cout<<"ERROR sifting band index "<<z<<std::endl;
				exit(1);
			}

			for(unsigned long p = 0; p < P; p++)		//for each pixel in the array representing a single band
				matrix[p * Z() + z] = bandvals[p];			//copy it to the appropriate location in the matrix
		}

		free(bandvals);				//clean up temporary memory
		return true;
	}*/

	/// Saves to disk only those spectra corresponding to mask values != 0
	/// @param outfile is the name of the sifted ENVI file to be written to disk
	/// @param unsigned char* p is the mask file used for sifting
	bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false){
		std::ofstream target(outfile.c_str(), std::ios::binary);
		// open a band (XY plane)
		unsigned long XY = X() * Y(); //Number of XY pixels
		unsigned long L = XY * sizeof(T); //size of XY pixels
		unsigned long long B = Z();

		T * temp = (T*)malloc(L); //allocate memory for a band
		T * temp_vox = (T*)malloc(sizeof(T)); //allocate memory for one voxel

		for (unsigned long i = 0; i < B; i++)			//for each spectral bin
		{
			band_index(temp, i);					//get the specified band (XY sheet by index)
			for (unsigned long j = 0; j < XY; j++)		// for each pixel
			{
				if (p[j] != 0){						//if the mask is != 0 at that pixel
					temp_vox[0] = temp[j];
					target.write(reinterpret_cast<const char*>(temp_vox), sizeof(T));   //write the XY slice at that band to disk
				}
				else{
					continue;
				}

				
			}
			if(PROGRESS) progress = (double)(i+1)/ B * 100;
		}
		target.close();
		free(temp);

		progress = 100;

		return true;
	}

	/// Generates a spectral image from a matrix of spectral values in lexicographic order and a mask
	bool unsift(std::string outfile, unsigned char* p, unsigned int samples, unsigned int lines){

		//create a binary output stream
		std::ofstream target(outfile.c_str(), std::ios::binary);

		//make sure that there's only one line
		if(Y() != 1){
			std::cout<<"ERROR in stim::bsq::sift() - number of lines does not equal 1"<<std::endl;
			return false;
		}

		std::cout<<"started sifting"<<std::endl;

		//get the number of pixels and bands in the input image
		unsigned long P = X(); 					//Number of pixels
		unsigned long B = Z();					//number of bands
		unsigned long XY = samples * lines;		//total number of pixels in an unsifted image

		// allocate memory for a sifted band
		T * sifted = (T*)malloc(P * sizeof(T)); //allocate memory for a band

		//allocate memory for an unsifted band image
		T* unsifted = (T*) malloc(XY * sizeof(T));

		//for each band
		for(unsigned long b = 0; b < B; b++){

			//set the unsifted index value to zero
			unsigned long i = 0;

			//retrieve the sifted band (masked pixels only)
			band_index(sifted, b);

			//for each pixel in the final image (treat it as a 1D image)
			for(unsigned long xi = 0; xi < XY; xi++){
				if( p[xi] == 0 )
					unsifted[xi] = 0;
				else{
					unsifted[xi] = sifted[i];
					i++;
				}
				//std::cout<<xi<<"/"<<XY<<",   "<<b<<"/"<<B<<std::endl;
				progress = (double)(b * XY + xi) / (B * XY) * 100;
			}
			//std::cout<<b*XY<<"/"<<B*XY<<"      "<<B<<"-"<<XY<<std::endl;
			//write the band image to disk
			target.write(reinterpret_cast<const char*>(unsifted), sizeof(T) * XY);
		}

		//std::cout<<"unsifted"<<std::endl;
		progress = 100;

		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 XY = X() * Y();
		T* temp = (T*)malloc(sizeof(T) * XY);
		//initialize p
		band_index(p, 0);
		for (unsigned j = 0; j < XY; j++){
			p[j] /= (T)Z();
		}
		//get every band and add them all
		for (unsigned i = 1; i < Z(); i++){
			band_index(temp, i);
			for (unsigned j = 0; j < XY; j++){
				p[j] += temp[j]/(T)Z();
			}
		}
		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 XY = X() * Y();
		unsigned long long count = 0;						//count will store the number of masked pixels
		T* temp = (T*)malloc(sizeof(T) * XY);
		//calculate this loop counts the number of true pixels in the mask
		for (unsigned j = 0; j < XY; j++){
			if (mask == NULL || mask[j] != 0){
				count++;
			}
		}
		//this loops goes through each band in B (Z())
		//	masked (or valid) pixels from that band are averaged and the average is stored in p
		for (unsigned long long i = 0; i < Z(); i++){
			p[i] = 0;
			band_index(temp, i);				//get the band image and store it in temp
			for (unsigned long long j = 0; j < XY; j++){	//loop through temp, averaging valid pixels
				if (mask == NULL || mask[j] != 0){
					p[i] += (double)temp[j] / (double)count;
				}
			}
			if(PROGRESS) progress = (double)(i+1) / Z() * 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){
		progress = 0;							//initialize thread data for timers and progress bars
		//memory allocation
		unsigned long long xy = X() * Y();
		unsigned long long B = Z();
		T* bandi = (T*)malloc(sizeof(T) * xy);
		T* bandj = (T*)malloc(sizeof(T) * xy);

		//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++;
			}
		}
		//calculate correlation coefficient matrix
		for (unsigned long long i = 0; i < B; i++)
		{
			band_index(bandi, i);
			for (unsigned long long j = i; j < B; j++){
				band_index(bandj, j);
				double numerator = 0;			//to calculate element in correlation coefficient matrix, numerator part
				//calculate the R(i,j) in correlation coeffient matrix
				for (unsigned long long k = 0; k < xy; k++){
					if (mask == NULL || mask[k] != 0){
						numerator += ((double)bandi[k] - (double)avg[i]) * ((double)bandj[k] - (double)avg[j]) / (double)count;
					}
				}
				co[i*B + j] = numerator;
				co[j*B + i] = numerator;		//because correlated matrix is a symmetric matrix
			}
			progress = (double)i / B * 100;
		}
		free(bandi);
		free(bandj);

		progress = 100;							//processing complete

		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 number of samples, lines, and bands
		unsigned long long samples = x1 - x0;
		unsigned long long lines = y1 - y0;
		unsigned long long bands = b1 - b0;

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

		//allocate space for a single band
		T* temp = (T*)malloc(L);

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

		//calculate the distance required to jump from the end of one band to the beginning of another
		unsigned long long jumpb = X() * (Y() - lines) * sizeof(T);

		//calculate the distance required to jump from the end of one line to the beginning of another
		unsigned long long jumpl = (X() - samples) * sizeof(T);

		//seek to the start of the cropped region in the input file
		file.seekg( (b0 * X() * Y() + y0 * X() + x0) * sizeof(T), std::ios::beg);

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

				if(PROGRESS) progress = (double)((z+1) * lines + y + 1) / ((b1 - b0) * lines) * 100;
			}
			out.write(reinterpret_cast<const char*>(temp), L);   //write slice data into target file
			file.seekg(jumpb, std::ios::cur);
		}
		free(temp);

		return true;
	}


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

	};
}

#endif