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stim/envi/bip.h 78.6 KB
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  #ifndef STIM_BIP_H
  #define STIM_BIP_H
  
  #include "../envi/envi_header.h"
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  #include "../envi/bil.h"
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  #include "../envi/hsi.h"
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  #include <cstring>
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  #include <complex>
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  #include <utility>
  
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  //CUDA
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  //#ifdef CUDA_FOUND
  #include <stim/cuda/cudatools/error.h>
  #include <cuda_runtime.h>
  #include "cublas_v2.h"
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  #include "cufft.h"
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  //#endif
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  namespace stim{
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  /**
  	The BIP class represents a 3-dimensional binary file stored using band interleaved by pixel (BIP) image encoding. The binary file is stored
  	such that Z-X "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 Z, X, 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.
  */
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  template <typename T>
  
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  class bip: public hsi<T> {
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  protected:
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  	//std::vector<double> w; //band wavelength
  	unsigned long long offset;		//header offset
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  	using hsi<T>::w;				//use the wavelength array in stim::hsi
  	using hsi<T>::nnz;
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  	using binary<T>::progress;
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  	using hsi<T>::X;
  	using hsi<T>::Y;
  	using hsi<T>::Z;
  
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  public:
  
  	using binary<T>::open;
  	using binary<T>::file;
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  	using binary<T>::R;
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  	using binary<T>::read_line_0;
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  	bip(){ hsi<T>::init_bip(); }
  
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  	/// 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
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  	bool open(std::string filename,
  			  unsigned long long X,
  			  unsigned long long Y,
  			  unsigned long long B,
  			  unsigned long long header_offset,
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  			  std::vector<double> wavelengths){
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  		//copy the wavelengths to the BSQ file structure
  		w = wavelengths;
  		//copy the offset to the structure
  		offset = header_offset;
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  		return open(filename, vec<unsigned long long>(B, X, Y), header_offset);
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  	}
  
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  	/// 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.
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  	bool band_index( T * p, unsigned long long page, bool PROGRESS = false){
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  		return binary<T>::read_plane_0(p, page, PROGRESS);
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  	}
  
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  	/// 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.
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  	bool band( T * p, double wavelength, bool PROGRESS = false){
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  		//if there are no wavelengths in the BSQ file
  		if(w.size() == 0)
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  			return band_index(p, (unsigned long long)wavelength, PROGRESS);
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  		unsigned long long XY = X() * Y();	//calculate the number of pixels in a band
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  		unsigned page=0;                      //bands around the wavelength
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  		//get the bands numbers around the wavelength
  
  		//if wavelength is smaller than the first one in header file
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  		if ( w[page] > wavelength ){
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  			band_index(p, page, PROGRESS);
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  			return true;
  		}
  
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  		while( w[page] < wavelength )
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  		{
  			page++;
  			//if wavelength is larger than the last wavelength in header file
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  			if (page == Z()) {
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  				band_index(p, Z()-1, PROGRESS);
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  				return true;
  			}
  		}
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  		if ( wavelength < w[page] )
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  		{
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  			T * p1;
  			T * p2;
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  			p1=(T*)malloc( XY * sizeof(T));                     //memory allocation
  			p2=(T*)malloc( XY * sizeof(T));
  			band_index(p1, page - 1);
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  			band_index(p2, page, PROGRESS);
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  			for(unsigned long long i=0; i < XY; i++){
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  				double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
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  				p[i] = (T)(((double)p2[i] - (double)p1[i]) * r + (double)p1[i]);
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  			}
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  			free(p1);
  			free(p2);
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  		}
  		else                           //if the wavelength is equal to a wavelength in header file
  		{
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  			band_index(p, page, PROGRESS);
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  		}
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  		return true;
  	}
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  	/// 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.
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  	bool spectrum(T * p, unsigned long long x, unsigned long long y, bool PROGRESS = false){
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  		return read_line_0(p, x, y, PROGRESS);				//read a line in the binary YZ plane (dimension order for BIP is ZXY)
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  	}
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  	bool spectrum(T* p, size_t n, bool PROGRESS = false){
  		size_t y = n / X();
  		size_t x = n - y * X();
  		return read_line_0(p, x, y, PROGRESS);				//read a line in the binary YZ plane (dimension order for BIP is ZXY)
  	}
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  	/// Retrieves a band of x values from a given xz plane.
  
  	/// @param p is a pointer to pre-allocated memory at least X * sizeof(T) in size
  	/// @param c is a pointer to an existing XZ plane (size X*Z*sizeof(T))
  	/// @param wavelength is the wavelength of X values to retrieve
  	bool read_x_from_xz(T* p, T* c, double wavelength)
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  	{
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  		unsigned long long B = Z();
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  		unsigned long long page=0;                      //samples around the wavelength
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  		//get the bands numbers around the wavelength
  
  		//if wavelength is smaller than the first one in header file
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  		if ( w[page] > wavelength ){
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  			for(unsigned long long j = 0; j < X(); j++)
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  			{
  				p[j] = c[j * B];
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  			}
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  			return true;
  		}
  
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  		while( w[page] < wavelength )
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  		{
  			page++;
  			//if wavelength is larger than the last wavelength in header file
  			if (page == B) {
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  				for(unsigned long long j = 0; j < X(); j++)
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  				{
  					p[j] = c[(j + 1) * B - 1];
  				}
  				return true;
  			}
  		}
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  		if ( wavelength < w[page] )
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  		{
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  			T * p1;
  			T * p2;
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  			p1=(T*)malloc( X() * sizeof(T));                     //memory allocation
  			p2=(T*)malloc( X() * sizeof(T));
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  			//band_index(p1, page - 1);
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  			for(unsigned long long j = 0; j < X(); j++)
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  			{
  				p1[j] = c[j * B + page - 1];
  			}
  			//band_index(p2, page );
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  			for(unsigned long long j = 0; j < X(); j++)
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  			{
  				p2[j] = c[j * B + page];
  			}
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  			for(unsigned long long i=0; i < X(); i++){
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  				double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
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  				p[i] = (p2[i] - p1[i]) * r + p1[i];
  			}
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  			free(p1);
  			free(p2);
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  		}
  		else                           //if the wavelength is equal to a wavelength in header file
  		{
  			//band_index(p, page);
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  			for(unsigned long long j = 0; j < X(); j++)
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  			{
  				p[j] = c[j * B + page];
  			}
  		}
  
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  		return true;
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  	}
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  	/// Retrieve a single pixel and store it in a pre-allocated double array.
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  	bool pixeld(double* p, unsigned long long n){
  		unsigned long long bandnum = X() * Y();		//calculate numbers in one band
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  		if ( n >= bandnum){							//make sure the pixel number is right
  			std::cout<<"ERROR: sample or line out of range"<<std::endl;
  			return false;
  		}
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  		unsigned long long B = Z();
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  		T* temp = (T*) malloc(B * sizeof(T));						//allocate space for the raw pixel data
  		file.seekg(n * B * sizeof(T), std::ios::beg);				//point to the certain pixel
  		file.read((char *)temp, sizeof(T) * B);					//read the spectrum from disk to the temp pointer
  
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  		for(unsigned long long i = 0; i < B; i++)						//for each element of the spectrum
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  			p[i] = (double) temp[i];							//cast each element to a double value
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  		free(temp);												//free temporary memory
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  		return true;
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  	}
  
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  	/// 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.
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  	bool pixel(T * p, unsigned long long n){
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  		unsigned long long N = X() * Y();					//calculate numbers in one band
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  		if ( n >= N){							//make sure the pixel number is right
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  			std::cout<<"ERROR: sample or line out of range"<<std::endl;
  			return false;
  		}
  
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  		file.seekg(n * Z() * sizeof(T), std::ios::beg);           //point to the certain pixel
  		file.read((char *)p, sizeof(T) * Z());
  		return true;
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  	}
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  	//given a Y ,return a ZX slice
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  	bool read_plane_y(T * p, size_t y){
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  		return binary<T>::read_plane_2(p, y);
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  	}
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  	/// 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.
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  	/// @param wls is the list of baseline points based on band labels.
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  	bool baseline(std::string outname, std::vector<double> base_pts, unsigned char* mask = NULL, bool PROGRESS = false){
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  		std::ofstream target(outname.c_str(), std::ios::binary);	//open the target binary file
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  		unsigned long long N = X() * Y();						//calculate the total number of pixels to be processed
  		unsigned long long B = Z();								//get the number of bands
  		T* s = (T*)malloc(sizeof(T) * B);						//allocate memory to store a pixel
  		T* sbc = (T*)malloc(sizeof(T) * B);						//allocate memory to store the baseline corrected spectrum
  
  		std::vector<T> base_vals;								//allocate space for the values at each baseline point
  		double aw, bw;											//surrounding baseline point wavelengths
  		T av, bv;												//surrounding baseline point values
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  		unsigned long long ai, bi;								//surrounding baseline point band indices
  		for(unsigned long long n = 0; n < N; n++){				//for each pixel in the image
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  			if(mask != NULL && !mask[n]){						//if the pixel isn't masked
  				memset(sbc, 0, sizeof(T) * B);					//set the baseline corrected spectrum to zero
  			}
  			else{
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  				pixel(s, n);										//retrieve the spectrum s
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  				base_vals = hsi<T>::interp_spectrum(s, base_pts);			//get the values at each baseline point
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  				ai = bi = 0;
  				aw = w[0];											//initialize the current baseline points (assume the spectrum starts at 0)
  				av = s[0];
  				bw = base_pts[0];
  				for(unsigned long long b = 0; b < B; b++){			//for each band in the spectrum
  					while(bi < base_pts.size() && base_pts[bi] < w[b])	//while the current wavelength is higher than the second baseline point
  						bi++;											//move to the next baseline point
  					if(bi < base_pts.size()){
  						bw = base_pts[bi];							//set the wavelength for the upper bound baseline point
  						bv = base_vals[bi];							//set the value for the upper bound baseline point
  					}
  					if(bi == base_pts.size()){						//if we have passed the last baseline point
  						bw = w[B-1];								//set the outer bound to the last spectral band
  						bv = s[B-1];
  					}
  					if(bi != 0){
  						ai = bi - 1;								//set the lower bound baseline point index
  						aw = base_pts[ai];							//set the wavelength for the lower bound baseline point
  						av = base_vals[ai];							//set the value for the lower bound baseline point
  					}
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  					sbc[b] = s[b] - hsi<T>::lerp(w[b], av, aw, bv, bw);		//perform the baseline correction and save the new value
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  				}
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  			}
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  			if(PROGRESS) progress = (double)(n+1) / N * 100;	//set the current progress
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  			target.write((char*)sbc, sizeof(T) * B);	//write the corrected data into destination
  		}														//end for each pixel
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  		free(s);
  		free(sbc);
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  		target.close();
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  		return true;
  
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  	}
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  	/// 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.
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  	bool ratio(std::string outname, double w, unsigned char* mask = NULL, bool PROGRESS = false)
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  	{
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  		std::ofstream target(outname.c_str(), std::ios::binary);	//open the target binary file
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  		std::string headername = outname + ".hdr";              //the header file name
  
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  		unsigned long long N = X() * Y();						//calculate the total number of pixels to be processed
  		unsigned long long B = Z();								//get the number of bands
  		T* s = (T*)malloc(sizeof(T) * B);						//allocate memory to store a pixel
  		T nv;													//stores the value of the normalized band
  		for(unsigned long long n = 0; n < N; n++){				//for each pixel in the image
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  			if(mask != NULL && !mask[n])						//if the normalization band is below threshold
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  				memset(s, 0, sizeof(T) * B);					//set the output to zero
  			else{
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  				pixel(s, n);										//retrieve the spectrum s
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  				nv = hsi<T>::interp_spectrum(s, w);							//find the value of the normalization band
  
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  				for(unsigned long long b = 0; b < B; b++)			//for each band in the spectrum
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  					s[b] /= nv;										//divide by the normalization value
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  			}
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  			if(PROGRESS) progress = (double)(n+1) / N * 100;	//set the current progress
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  			target.write((char*)s, sizeof(T) * B);	//write the corrected data into destination
  		}														//end for each pixel
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  		free(s);
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  		target.close();
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  		return true;
  	}
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  	void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){
  
  		std::ofstream target(outfile.c_str(), std::ios::binary);	//open the target binary file
  		file.seekg(0, std::ios::beg);								//move the pointer to the current file to the beginning
  
  		size_t B = Z();												//number of spectral components
  		size_t XY = X() * Y();										//calculate the number of pixels
  		size_t Bb = B * sizeof(T);									//number of bytes in a spectrum
  
  		T* spec = (T*) malloc(Bb);									//allocate space for the spectrum
  		T len;
  		for(size_t xy = 0; xy < XY; xy++){							//for each pixel
  			memset(spec, 0, Bb);									//set the spectrum to zero
  			if(mask == NULL || mask[xy]){							//if the pixel is masked
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  				len = 0;											//initialize the
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  				file.read((char*)spec, Bb);							//read a spectrum
  				for(size_t b = 0; b < B; b++)						//for each band
  					len += spec[b]*spec[b];							//add the square of the spectral band
  				len = sqrt(len);									//calculate the square of the sum of squared components
  				for(size_t b = 0; b < B; b++)						//for each band
  					spec[b] /= len;									//divide by the length
  			}
  			else
  				file.seekg(Bb, std::ios::cur);						//otherwise skip a spectrum
  			target.write((char*)spec, Bb);							//output the normalized spectrum
  			if(PROGRESS) progress = (double)(xy + 1) / (double)XY * 100;		//update the progress
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  		}
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  	}
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  	/// Convert the current BIP 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.
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  	bool bil(std::string outname, bool PROGRESS = false)
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  	{
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  		unsigned long long S = X() * Z() * sizeof(T);		//calculate the number of bytes in a ZX slice
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  		std::ofstream target(outname.c_str(), std::ios::binary);
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  		//std::string headername = outname + ".hdr";
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  		T * p;			//pointer to the current ZX slice for bip file
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  		p = (T*)malloc(S);
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  		T * q;			//pointer to the current XZ slice for bil file
  		q = (T*)malloc(S);
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  		for ( unsigned long long i = 0; i < Y(); i++)
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  		{
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  			read_plane_y(p, i);
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  			for ( unsigned long long k = 0; k < Z(); k++)
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  			{
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  				unsigned long long ks = k * X();
  				for ( unsigned long long j = 0; j < X(); j++)
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  					q[ks + j] = p[k + j * Z()];
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  				if(PROGRESS) progress = (double)(i * Z() + k+1) / (Y() * Z()) * 100;
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  			}
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  			target.write(reinterpret_cast<const char*>(q), S);   //write a band data into target file
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  		}
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  		free(p);
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  		free(q);
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  		target.close();
  		return true;
  	}
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  	/// 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.
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  	bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
  
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  		unsigned long long XY = X() * Y();
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  		band(result, wavelength);		//get band
  
  		//perform the baseline correction
  		double r = (double) (wavelength - lb) / (double) (rb - lb);
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  		for(unsigned long long i=0; i < XY; i++){
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  			result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
  		}
  		return true;
  	}
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  	/// 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.
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  	bool height(double lb, double rb, double bandwavelength, T* result){
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  		T* lp;
  		T* rp;
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  		unsigned long long XY = X() * Y();
  		unsigned long long S = XY * sizeof(T);
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  		lp = (T*) malloc(S);			//memory allocation
  		rp = (T*) malloc(S);
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  		band(lp, lb);
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  		band(rp, rb);
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  		baseline_band(lb, rb, lp, rp, bandwavelength, result);
  
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  		free(lp);
  		free(rp);
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  		return true;
  	}
  
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  	/// 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
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  	bool area(double lb, double rb, double lab, double rab, T* result){
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  		T* lp;	//left band pointer
  		T* rp;	//right band pointer
  		T* cur;		//current band 1
  		T* cur2;	//current band 2
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  		unsigned long long XY = X() * Y();
  		unsigned long long S = XY * sizeof(T);
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  		lp = (T*) malloc(S);			//memory allocation
  		rp = (T*) malloc(S);
  		cur = (T*) malloc(S);
  		cur2 = (T*) malloc(S);
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  		memset(result, (char)0, S);
  
  		//find the wavelenght position in the whole band
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  		unsigned long long n = w.size();
  		unsigned long long ai = 0;		//left bound position
  		unsigned long long bi = n - 1;		//right bound position
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  		//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
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  		while (lab >= w[ai]){
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  			ai++;
  		}
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  		while (rab <= w[bi]){
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  			bi--;
  		}
  
  		band(lp, lb);
  		band(rp, rb);
  
  		//calculate the beginning and the ending part
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  		baseline_band(lb, rb, lp, rp, rab, cur2);		//ending part
  		baseline_band(lb, rb, lp, rp, w[bi], cur);
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  		for(unsigned long long j = 0; j < XY; j++){
  			result[j] += (T)((rab - w[bi]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
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  		}
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  		baseline_band(lb, rb, lp, rp, lab, cur2);		//beginnning part
  		baseline_band(lb, rb, lp, rp, w[ai], cur);
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  		for(unsigned long long j = 0; j < XY; j++){
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  			result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
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  		}
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  		//calculate the area
  		ai++;
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  		for(unsigned long long i = ai; i <= bi ;i++)
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  		{
  			baseline_band(lb, rb, lp, rp, w[ai], cur2);
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  			for(unsigned long long j = 0; j < XY; j++)
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  			{
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  				result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
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  			}
  			std::swap(cur,cur2);		//swap the band pointers
  		}
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  		free(lp);
  		free(rp);
  		free(cur);
  		free(cur2);
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  		return true;
  	}
  
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  	/// 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
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  	bool ph_to_ph(T* result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask = NULL){
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  		T* p1 = (T*)malloc(X() * Y() * sizeof(T));
  		T* p2 = (T*)malloc(X() * Y() * sizeof(T));
  
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  		//get the two peak band
  		height(lb1, rb1, pos1, p1);
  		height(lb2, rb2, pos2, p2);
  		//calculate the ratio in result
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  		for(unsigned long long i = 0; i < X() * Y(); i++){
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  			if(p1[i] == 0 && p2[i] ==0)
  				result[i] = 1;
  			else
  				result[i] = p1[i] / p2[i];
  		}
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  		free(p1);
  		free(p2);
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  		return true;
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  	}
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  	/// 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
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  	bool pa_to_ph(T* result, double lb1, double rb1, double lab1, double rab1,
  					double lb2, double rb2, double pos, unsigned char* mask = NULL){
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  		T* p1 = (T*)malloc(X() * Y() * sizeof(T));
  		T* p2 = (T*)malloc(X() * Y() * sizeof(T));
  
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  		//get the area and the peak band
  		area(lb1, rb1, lab1, rab1, p1);
  		height(lb2, rb2, pos, p2);
  		//calculate the ratio in result
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  		for(unsigned long long i = 0; i < X() * Y(); i++){
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  			if(p1[i] == 0 && p2[i] ==0)
  				result[i] = 1;
  			else
  				result[i] = p1[i] / p2[i];
  		}
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  		free(p1);
  		free(p2);
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  		return true;
  	}
  
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  	/// 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)
1a224b6a   David Mayerich   fixed linux compa...
631
  	/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
a23c4132   David Mayerich   Doxygen comments ...
632
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
ba51ae6a   David Mayerich   fixed metric calc...
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  	bool pa_to_pa(T* result, double lb1, double rb1, double lab1, double rab1,
  					double lb2, double rb2, double lab2, double rab2, unsigned char* mask = NULL){
1a224b6a   David Mayerich   fixed linux compa...
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637
638
  
  		T* p1 = (T*)malloc(X() * Y() * sizeof(T));
  		T* p2 = (T*)malloc(X() * Y() * sizeof(T));
  
70407ea9   heziqi   Ziqi completed he...
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  		//get the area and the peak band
  		area(lb1, rb1, lab1, rab1, p1);
  		area(lb2, rb2, lab2, rab2, p2);
  		//calculate the ratio in result
9d3ba0b1   David Mayerich   added stim::hsi a...
643
  		for(unsigned long long i = 0; i < X() * Y(); i++){
70407ea9   heziqi   Ziqi completed he...
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  			if(p1[i] == 0 && p2[i] ==0)
  				result[i] = 1;
  			else
  				result[i] = p1[i] / p2[i];
  		}
517876d6   heziqi   metrics finished ...
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  		free(p1);
  		free(p2);
1a224b6a   David Mayerich   fixed linux compa...
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  		return true;
  	}
517876d6   heziqi   metrics finished ...
654
  
a23c4132   David Mayerich   Doxygen comments ...
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  	/// 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
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  	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
  
9d3ba0b1   David Mayerich   added stim::hsi a...
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  		unsigned long long XY = X() * Y();
  		unsigned long long S = XY * sizeof(T);
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  		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
9d3ba0b1   David Mayerich   added stim::hsi a...
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  		unsigned long long n = w.size();
  		unsigned long long ai = 0;		//left bound position
  		unsigned long long bi = n - 1;		//right bound position
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  		//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);
9d3ba0b1   David Mayerich   added stim::hsi a...
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  		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);
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  		}
  		baseline_band(lb, rb, lp, rp, lab, cur2);		//beginnning part
  		baseline_band(lb, rb, lp, rp, w[ai], cur);
1a224b6a   David Mayerich   fixed linux compa...
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  		for(unsigned long long j = 0; j < XY; j++){
9d3ba0b1   David Mayerich   added stim::hsi a...
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  			result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
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  		}
  
  		//calculate f(x) times x
  		ai++;
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  		for(unsigned long long i = ai; i <= bi ;i++)
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  		{
  			baseline_band(lb, rb, lp, rp, w[ai], cur2);
9d3ba0b1   David Mayerich   added stim::hsi a...
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  			for(unsigned long long j = 0; j < XY; j++)
517876d6   heziqi   metrics finished ...
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  			{
1a224b6a   David Mayerich   fixed linux compa...
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  				result[j] += (T)((w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
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  			}
  			std::swap(cur,cur2);		//swap the band pointers
  		}
  
  		free(lp);
  		free(rp);
  		free(cur);
  		free(cur2);
  		return true;
  	}
  
a23c4132   David Mayerich   Doxygen comments ...
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  	/// 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...
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  	bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
1a224b6a   David Mayerich   fixed linux compa...
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  		T* p1 = (T*)malloc(X() * Y() * sizeof(T));
  		T* p2 = (T*)malloc(X() * Y() * sizeof(T));
  
517876d6   heziqi   metrics finished ...
747
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  		//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
9d3ba0b1   David Mayerich   added stim::hsi a...
751
  		for(unsigned long long i = 0; i < X() * Y(); i++){
ba51ae6a   David Mayerich   fixed metric calc...
752
  			if(mask == NULL || mask[i])
517876d6   heziqi   metrics finished ...
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  				result[i] = p1[i] / p2[i];
  		}
  
  		free(p1);
  		free(p2);
1a224b6a   David Mayerich   fixed linux compa...
758
  		return true;
517876d6   heziqi   metrics finished ...
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  	}
  
a23c4132   David Mayerich   Doxygen comments ...
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  	/// 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
e37ce7bf   David Mayerich   added the ability...
768
  	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
769
  
724ec347   David Mayerich   simplified the EN...
770
  		T* temp = (T*)malloc(X() * Y() * sizeof(T));		//allocate memory for the certain band
798cea97   David Mayerich   added progress ba...
771
  		band(temp, mask_band, PROGRESS);
4a6f666c   heziqi   Added mask method
772
  
9d3ba0b1   David Mayerich   added stim::hsi a...
773
  		for (unsigned long long i = 0; i < X() * Y();i++) {
e37ce7bf   David Mayerich   added the ability...
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  			if(mask == NULL || mask[i] != 0){
  				if(temp[i] > lower && temp[i] < upper){
  					out_mask[i] = 255;
  				}
  				else
  					out_mask[i] = 0;
  			}
4a6f666c   heziqi   Added mask method
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  		}
  
517876d6   heziqi   metrics finished ...
783
  		free(temp);
4a6f666c   heziqi   Added mask method
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  		return true;
  
  	}
  
a23c4132   David Mayerich   Doxygen comments ...
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  	/// 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.
6a46c8ff   David Mayerich   fixed bugs in app...
792
  	bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
740f8cd2   heziqi   added apply_mask
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795
  
  		std::ofstream target(outfile.c_str(), std::ios::binary);
  
9d3ba0b1   David Mayerich   added stim::hsi a...
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  		unsigned long long ZX = Z() * X();		//calculate the number of values in a page (XZ in BIP)
  		unsigned long long L = ZX * sizeof(T);	//calculate the number of bytes in a page
740f8cd2   heziqi   added apply_mask
798
  
1a55a328   David Mayerich   Added comments fo...
799
  		T * temp = (T*)malloc(L);		//allocate space for that page
740f8cd2   heziqi   added apply_mask
800
  
9d3ba0b1   David Mayerich   added stim::hsi a...
801
  		for (unsigned long long i = 0; i < Y(); i++)			//for each page (Y in BIP)
740f8cd2   heziqi   added apply_mask
802
  		{
724ec347   David Mayerich   simplified the EN...
803
  			read_plane_y(temp, i);							//load that page (it's pointed to by temp)
9d3ba0b1   David Mayerich   added stim::hsi a...
804
  			for ( unsigned long long j = 0; j < X(); j++)	//for each X value
740f8cd2   heziqi   added apply_mask
805
  			{
9d3ba0b1   David Mayerich   added stim::hsi a...
806
  				for (unsigned long long k = 0; k < Z(); k++)	//for each B value (band)
740f8cd2   heziqi   added apply_mask
807
  				{
724ec347   David Mayerich   simplified the EN...
808
809
  					if (p[i * X() + j] == 0)	//if the mask value is zero
  					temp[j * Z() + k] = 0;			//set the pixel value to zero
1a55a328   David Mayerich   Added comments fo...
810
  				else								//otherwise just continue
740f8cd2   heziqi   added apply_mask
811
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  					continue;
  				}
  			}
1a55a328   David Mayerich   Added comments fo...
814
  			target.write(reinterpret_cast<const char*>(temp), L);   //write the edited band data into target file
6a46c8ff   David Mayerich   fixed bugs in app...
815
  			if(PROGRESS) progress = (double)(i+1) / (double)Y() * 100;
740f8cd2   heziqi   added apply_mask
816
  		}
1a55a328   David Mayerich   Added comments fo...
817
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819
  		target.close();						//close the target file
  		free(temp);							//free allocated memory
  		return true;						//return true
740f8cd2   heziqi   added apply_mask
820
821
  	}
  
ba51ae6a   David Mayerich   fixed metric calc...
822
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  	/// 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
814eb271   David Mayerich   fixed problems wi...
827
  	bool sift(T* matrix, unsigned char* mask = NULL, bool PROGRESS = false){
ba51ae6a   David Mayerich   fixed metric calc...
828
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  		size_t Bbytes = sizeof(T) * Z();
  		size_t XY = X() * Y();
  		T* band = (T*) malloc( Bbytes );					//allocate space for a line
  
  		file.seekg(0, std::ios::beg);	//seek to the beginning of the file
1a224b6a   David Mayerich   fixed linux compa...
833
  
ba51ae6a   David Mayerich   fixed metric calc...
834
835
  		size_t p = 0;										//create counter variables
  		for(size_t xy = 0; xy < XY; xy++){					//for each pixel
d4aa4cf7   David Mayerich   fixed the in-memo...
836
  			if(mask == NULL || mask[xy]){									//if the current pixel is masked
ba51ae6a   David Mayerich   fixed metric calc...
837
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  				file.read( (char*)band, Bbytes );			//read the current line
  				for(size_t b = 0; b < Z(); b++){			//copy each band value to the sifted matrix
  					size_t i = p * Z() + b;					//calculate the index in the sifted matrix
  					matrix[i] = band[b];					//store the current value in the line at the correct matrix location
  				}
  				p++;									//increment the pixel pointer
  			}
  			else
1a224b6a   David Mayerich   fixed linux compa...
845
  				file.seekg(Bbytes, std::ios::cur);			//otherwise skip this band
814eb271   David Mayerich   fixed problems wi...
846
  			if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
ba51ae6a   David Mayerich   fixed metric calc...
847
848
849
  		}
  		return true;
  	}
e843658b   Brad Deutsch   Previous push did...
850
  
2fcab4f0   David Mayerich   added unsifting f...
851
  	/// Saves to disk only those spectra corresponding to mask values != 0
c1078e19   David Mayerich   HSIproc bug fixes...
852
  	bool sift(std::string outfile, unsigned char* mask, bool PROGRESS = false){
8550e94f   David Mayerich   added sifting and...
853
854
  
  		//reset the file pointer to the beginning of the file
1a224b6a   David Mayerich   fixed linux compa...
855
  		file.seekg(0, std::ios::beg);
8550e94f   David Mayerich   added sifting and...
856
857
  
  		// open an output stream
e843658b   Brad Deutsch   Previous push did...
858
859
  		std::ofstream target(outfile.c_str(), std::ios::binary);
  
8550e94f   David Mayerich   added sifting and...
860
  		//allocate space for a single spectrum
9d3ba0b1   David Mayerich   added stim::hsi a...
861
  		unsigned long long B = Z();
8550e94f   David Mayerich   added sifting and...
862
  		T* spectrum = (T*) malloc(B * sizeof(T));
e843658b   Brad Deutsch   Previous push did...
863
  
8550e94f   David Mayerich   added sifting and...
864
  		//calculate the number of pixels in a band
9d3ba0b1   David Mayerich   added stim::hsi a...
865
  		unsigned long long XY = X() * Y();
e843658b   Brad Deutsch   Previous push did...
866
  
8550e94f   David Mayerich   added sifting and...
867
  		//for each pixel
9d3ba0b1   David Mayerich   added stim::hsi a...
868
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  		unsigned long long skip = 0;					//number of spectra to skip
  		for(unsigned long long x = 0; x < XY; x++){
8550e94f   David Mayerich   added sifting and...
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  			//if the current pixel isn't masked
  			if( mask[x] == 0){
  				//increment the number of skipped pixels
  				skip++;
e843658b   Brad Deutsch   Previous push did...
875
  			}
8550e94f   David Mayerich   added sifting and...
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  			//if the current pixel is masked
  			else{
  
  				//skip the intermediate pixels
  				file.seekg(skip * B * sizeof(T), std::ios::cur);
  
  				//set the skip value to zero
  				skip = 0;
  
  				//read this pixel into memory
  				file.read((char *)spectrum, B * sizeof(T));
  
  				//write this pixel out
  				target.write((char *)spectrum, B * sizeof(T));
8550e94f   David Mayerich   added sifting and...
890
  			}
9d3ba0b1   David Mayerich   added stim::hsi a...
891
  			if(PROGRESS) progress = (double) (x+1) / XY * 100;
8550e94f   David Mayerich   added sifting and...
892
  
e843658b   Brad Deutsch   Previous push did...
893
  		}
8550e94f   David Mayerich   added sifting and...
894
895
  
  		//close the output file
e843658b   Brad Deutsch   Previous push did...
896
  		target.close();
8550e94f   David Mayerich   added sifting and...
897
  		free(spectrum);
cbce396e   David Mayerich   added support for...
898
  
cbce396e   David Mayerich   added support for...
899
  		return true;
8550e94f   David Mayerich   added sifting and...
900
901
  	}
  
a2bf1d08   David Mayerich   general bug fixes...
902
  	bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
8550e94f   David Mayerich   added sifting and...
903
904
905
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  		// open an output stream
  		std::ofstream target(outfile.c_str(), std::ios::binary);
  
  		//reset the file pointer to the beginning of the file
1a224b6a   David Mayerich   fixed linux compa...
908
  		file.seekg(0, std::ios::beg);
8550e94f   David Mayerich   added sifting and...
909
910
  
  		//allocate space for a single spectrum
9d3ba0b1   David Mayerich   added stim::hsi a...
911
  		unsigned long long B = Z();
8550e94f   David Mayerich   added sifting and...
912
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918
  		T* spectrum = (T*) malloc(B * sizeof(T));
  
  		//allocate space for a spectrum of zeros
  		T* zeros = (T*) malloc(B * sizeof(T));
  		memset(zeros, 0, B * sizeof(T));
  
  		//calculate the number of pixels in a band
9d3ba0b1   David Mayerich   added stim::hsi a...
919
  		unsigned long long XY = samples * lines;
8550e94f   David Mayerich   added sifting and...
920
921
  
  		//for each pixel
9d3ba0b1   David Mayerich   added stim::hsi a...
922
923
  		unsigned long long skip = 0;					//number of spectra to skip
  		for(unsigned long long x = 0; x < XY; x++){
8550e94f   David Mayerich   added sifting and...
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  			//if the current pixel isn't masked
  			if( mask[x] == 0){
  
  				//write a bunch of zeros
  				target.write((char *)zeros, B * sizeof(T));
  			}
  			//if the current pixel is masked
  			else{
  
  				//read a pixel into memory
  				file.read((char *)spectrum, B * sizeof(T));
  
  				//write this pixel out
  				target.write((char *)spectrum, B * sizeof(T));
  			}
  
a2bf1d08   David Mayerich   general bug fixes...
941
  			if(PROGRESS) progress = (double)(x + 1) / XY * 100;
3150c537   David Mayerich   added further pro...
942
  
8550e94f   David Mayerich   added sifting and...
943
944
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946
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948
  		}
  
  		//close the output file
  		target.close();
  		free(spectrum);
  
a2bf1d08   David Mayerich   general bug fixes...
949
  		//progress = 100;
3150c537   David Mayerich   added further pro...
950
  
e843658b   Brad Deutsch   Previous push did...
951
  		return true;
8550e94f   David Mayerich   added sifting and...
952
953
  
  
e843658b   Brad Deutsch   Previous push did...
954
955
  	}
  
a23c4132   David Mayerich   Doxygen comments ...
956
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959
  	/// 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
dd5aab2f   David Mayerich   fixed errors in s...
960
  	bool mean_spectrum(double* m, double* std = NULL, unsigned char* mask = NULL, bool PROGRESS = false){
9d3ba0b1   David Mayerich   added stim::hsi a...
961
962
  		unsigned long long XY = X() * Y();							//calculate the total number of pixels in the HSI
  		T* temp = (T*)malloc(sizeof(T) * Z());						//allocate space for the current spectrum to be read
35a7195f   David Mayerich   added median spec...
963
964
965
  		memset(m, 0, Z() * sizeof(double));							//set the mean spectrum to zero
  		double* e_x2 = (double*)malloc(Z() * sizeof(double));		//allocate space for E[x^2]
  		memset(e_x2, 0, Z() * sizeof(double));						//set all values for E[x^2] to zero
9d3ba0b1   David Mayerich   added stim::hsi a...
966
967
  
  		unsigned long long count = nnz(mask);									//calculate the number of masked pixels
35a7195f   David Mayerich   added median spec...
968
  		double x;
9d3ba0b1   David Mayerich   added stim::hsi a...
969
970
971
972
  		for (unsigned long long i = 0; i < XY; i++){							//for each pixel in the HSI
  			if (mask == NULL || mask[i] != 0){						//if the pixel is masked
  				pixel(temp, i);										//get the spectrum
  				for (unsigned long long j = 0; j < Z(); j++){					//for each spectral component
35a7195f   David Mayerich   added median spec...
973
974
975
  					x = temp[j];
  					m[j] += x / (double)count;		//add the weighted value to the average
  					e_x2[j] += x*x / (double)count;
a43c4fe1   heziqi   Added crop in env...
976
977
  				}
  			}
9d3ba0b1   David Mayerich   added stim::hsi a...
978
  			if(PROGRESS) progress = (double)(i+1) / XY * 100;		//increment the progress
a43c4fe1   heziqi   Added crop in env...
979
  		}
2aa68315   David Mayerich   major bug fixes f...
980
  
35a7195f   David Mayerich   added median spec...
981
  		//calculate the standard deviation
dd5aab2f   David Mayerich   fixed errors in s...
982
983
984
985
  		if (std != NULL) {
  			for (size_t i = 0; i < Z(); i++)
  				std[i] = sqrt(e_x2[i] - m[i] * m[i]);
  		}
35a7195f   David Mayerich   added median spec...
986
  
a43c4fe1   heziqi   Added crop in env...
987
  		free(temp);
a43c4fe1   heziqi   Added crop in env...
988
989
  		return true;
  	}
2781a48c   David Mayerich   fixed cuBLAS func...
990
  //#ifdef CUDA_FOUND
c6f526c2   David Mayerich   added cuBLAS supp...
991
  	/// Calculate the covariance matrix for masked pixels using cuBLAS
9d3ba0b1   David Mayerich   added stim::hsi a...
992
  	/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
2781a48c   David Mayerich   fixed cuBLAS func...
993
  	int co_matrix_cublas(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
c6f526c2   David Mayerich   added cuBLAS supp...
994
  
1a224b6a   David Mayerich   fixed linux compa...
995
  		cudaError_t cudaStat;
c6f526c2   David Mayerich   added cuBLAS supp...
996
997
  		cublasStatus_t stat;
  		cublasHandle_t handle;
1a224b6a   David Mayerich   fixed linux compa...
998
  
c6f526c2   David Mayerich   added cuBLAS supp...
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
  		unsigned long long XY = X() * Y();									//calculate the number of elements in a band image
  		unsigned long long B = Z();											//calculate the number of spectral elements
  
  		double* s = (double*)malloc(sizeof(double) * B);					//allocate space for the spectrum that will be pulled from the file
  		double* s_dev;														//declare a device pointer that will store the spectrum on the GPU
  		double* A_dev;														//declare a device pointer that will store the covariance matrix on the GPU
  		double* avg_dev;													//declare a device pointer that will store the average spectrum
  		cudaStat = cudaMalloc(&s_dev, B * sizeof(double));					//allocate space on the CUDA device for the spectrum
  		cudaStat = cudaMalloc(&A_dev, B * B * sizeof(double));				//allocate space on the CUDA device for the covariance matrix
  		cudaStat = cudaMemset(A_dev, 0, B * B * sizeof(double));			//initialize the covariance matrix to zero (0)
  		cudaStat = cudaMalloc(&avg_dev, B * sizeof(double));				//allocate space on the CUDA device for the average spectrum
9d3ba0b1   David Mayerich   added stim::hsi a...
1010
  		stat = cublasSetVector((int)B, sizeof(double), avg, 1, avg_dev, 1);		//copy the average spectrum to the CUDA device
1a224b6a   David Mayerich   fixed linux compa...
1011
  
c6f526c2   David Mayerich   added cuBLAS supp...
1012
1013
1014
1015
  		double ger_alpha = 1.0/(double)XY;									//scale the outer product by the inverse of the number of samples (mean outer product)
  		double axpy_alpha = -1;												//multiplication factor for the average spectrum (in order to perform a subtraction)
  
  		stat = cublasCreate(&handle);										//create a cuBLAS instance
2781a48c   David Mayerich   fixed cuBLAS func...
1016
1017
  		if (stat != CUBLAS_STATUS_SUCCESS) return 1;						//test the cuBLAS instance to make sure it is valid
  
1c92dffe   David Mayerich   simplified CUDA i...
1018
  		//else std::cout<<"Using cuBLAS to calculate the mean covariance matrix..."<<std::endl;
c6f526c2   David Mayerich   added cuBLAS supp...
1019
  		for (unsigned long long xy = 0; xy < XY; xy++){										//for each pixel
5a5359da   David Mayerich   fixed - allows th...
1020
1021
  			if (mask == NULL || mask[xy] != 0){
  				pixeld(s, xy);																	//retreive the spectrum at the current xy pixel location
9d3ba0b1   David Mayerich   added stim::hsi a...
1022
1023
1024
  				stat = cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1);						//copy the spectrum from the host to the device
  				stat = cublasDaxpy(handle, (int)B, &axpy_alpha, avg_dev, 1, s_dev, 1);				//subtract the average spectrum
  				stat = cublasDsyr(handle, CUBLAS_FILL_MODE_UPPER, (int)B, &ger_alpha, s_dev, 1, A_dev, (int)B);	//calculate the covariance matrix (symmetric outer product)
5a5359da   David Mayerich   fixed - allows th...
1025
  			}
63fc1df8   David Mayerich   added an inverse ...
1026
  			if(PROGRESS) progress = (double)(xy+1) / XY * 100;													//record the current progress
5a5359da   David Mayerich   fixed - allows th...
1027
  
c6f526c2   David Mayerich   added cuBLAS supp...
1028
1029
  		}
  
9d3ba0b1   David Mayerich   added stim::hsi a...
1030
  		cublasGetMatrix((int)B, (int)B, sizeof(double), A_dev, (int)B, co, (int)B);					//copy the result from the GPU to the CPU
c6f526c2   David Mayerich   added cuBLAS supp...
1031
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  		cudaFree(A_dev);														//clean up allocated device memory
  		cudaFree(s_dev);
  		cudaFree(avg_dev);
  
9d3ba0b1   David Mayerich   added stim::hsi a...
1036
1037
  		for(unsigned long long i = 0; i < B; i++){										//copy the upper triangular portion to the lower triangular portion
  			for(unsigned long long j = i+1; j < B; j++){
c6f526c2   David Mayerich   added cuBLAS supp...
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  				co[B * i + j] = co[B * j + i];
  			}
  		}
  
2781a48c   David Mayerich   fixed cuBLAS func...
1042
  		return 0;
c6f526c2   David Mayerich   added cuBLAS supp...
1043
  	}
2781a48c   David Mayerich   fixed cuBLAS func...
1044
  //#endif
1a224b6a   David Mayerich   fixed linux compa...
1045
  
2aa68315   David Mayerich   major bug fixes f...
1046
  	/// Calculate the covariance matrix for all masked pixels in the image with 64-bit floating point precision.
a23c4132   David Mayerich   Doxygen comments ...
1047
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  	/// @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...
1051
  	bool co_matrix(double* co, double* avg, unsigned char *mask, int cuda_device = 0, bool PROGRESS = false){
2781a48c   David Mayerich   fixed cuBLAS func...
1052
  		progress = 0;
c6f526c2   David Mayerich   added cuBLAS supp...
1053
  
dd5aab2f   David Mayerich   fixed errors in s...
1054
  		if(cuda_device >= 0){													//if a CUDA device is specified
dc99699e   David Mayerich   implemented a no-...
1055
1056
  			int dev_count;
  			HANDLE_ERROR(cudaGetDeviceCount(&dev_count));						//get the number of CUDA devices
dd5aab2f   David Mayerich   fixed errors in s...
1057
  			if(dev_count > 0 && dev_count > cuda_device){							//if the first device is not an emulator
1c92dffe   David Mayerich   simplified CUDA i...
1058
  				cudaDeviceProp prop;
dd5aab2f   David Mayerich   fixed errors in s...
1059
1060
  				cudaGetDeviceProperties(&prop, cuda_device);									//get the property of the requested CUDA device
  				if (prop.major != 9999) {
1c92dffe   David Mayerich   simplified CUDA i...
1061
  					std::cout << "Using CUDA device [" << cuda_device << "] to calculate the mean covariance matrix..."<<std::endl;
dd5aab2f   David Mayerich   fixed errors in s...
1062
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1065
  					HANDLE_ERROR(cudaSetDevice(cuda_device));
  					int status = co_matrix_cublas(co, avg, mask, PROGRESS);			//use cuBLAS to calculate the covariance matrix
  					if (status == 0) return true;									//if the cuBLAS function returned correctly, we're done
  				}
1c92dffe   David Mayerich   simplified CUDA i...
1066
1067
  			}																	//otherwise continue using the CPU		
  			std::cout<<"WARNING: cuBLAS failed, using CPU"<<std::endl;
dc99699e   David Mayerich   implemented a no-...
1068
  		}
a43c4fe1   heziqi   Added crop in env...
1069
  		//memory allocation
2aa68315   David Mayerich   major bug fixes f...
1070
1071
  		unsigned long long XY = X() * Y();
  		unsigned long long B = Z();
a43c4fe1   heziqi   Added crop in env...
1072
  		T* temp = (T*)malloc(sizeof(T) * B);
9d3ba0b1   David Mayerich   added stim::hsi a...
1073
1074
  
  		unsigned long long count = nnz(mask);								//count the number of masked pixels
63fc1df8   David Mayerich   added an inverse ...
1075
  
2aa68315   David Mayerich   major bug fixes f...
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  		//initialize covariance matrix
  		memset(co, 0, B * B * sizeof(double));
  
  		//calculate covariance matrix
2aa68315   David Mayerich   major bug fixes f...
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  		double* co_half = (double*) malloc(B * B * sizeof(double));			//allocate space for a higher-precision intermediate matrix
  		double* temp_precise = (double*) malloc(B * sizeof(double));
  		memset(co_half, 0, B * B * sizeof(double));							//initialize the high-precision matrix with zeros
  		unsigned long long idx;													//stores i*B to speed indexing
  		for (unsigned long long xy = 0; xy < XY; xy++){
  			if (mask == NULL || mask[xy] != 0){
  				pixel(temp, xy);												//retreive the spectrum at the current xy pixel location
  				for(unsigned long long b = 0; b < B; b++)									//subtract the mean from this spectrum and increase the precision
  					temp_precise[b] = (double)temp[b] - (double)avg[b];
  				idx = 0;
  				for (unsigned long long b0 = 0; b0 < B; b0++){								//for each band
  					for (unsigned long long b1 = b0; b1 < B; b1++)
  						co_half[idx++] += temp_precise[b0] * temp_precise[b1];
a43c4fe1   heziqi   Added crop in env...
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  				}
  			}
63fc1df8   David Mayerich   added an inverse ...
1095
  			if(PROGRESS) progress = (double)(xy+1) / XY * 100;
a43c4fe1   heziqi   Added crop in env...
1096
  		}
2aa68315   David Mayerich   major bug fixes f...
1097
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  		idx = 0;
  		for (unsigned long long i = 0; i < B; i++){										//copy the precision matrix to both halves of the output matrix
  			for (unsigned long long j = i; j < B; j++){
  				co[j * B + i] = co[i * B + j] = co_half[idx++] / (double) count;
a43c4fe1   heziqi   Added crop in env...
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  			}
  		}
  
a43c4fe1   heziqi   Added crop in env...
1104
  		free(temp);
2aa68315   David Mayerich   major bug fixes f...
1105
  		free(temp_precise);
a43c4fe1   heziqi   Added crop in env...
1106
1107
1108
  		return true;
  	}
  
334547d8   sam   changes for mnf: ...
1109
  
1ee79b84   David Mayerich   more accurate noi...
1110
  	int coNoise_matrix_cublas(double* coN, double* avg, unsigned char *mask, bool PROGRESS = false) {
334547d8   sam   changes for mnf: ...
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  		cudaError_t cudaStat;
  		cublasStatus_t stat;
  		cublasHandle_t handle;
  
  		progress = 0;													    //initialize the progress to zero (0)
  		unsigned long long XY = X() * Y();									//calculate the number of elements in a band image
  		unsigned long long B = Z();											//calculate the number of spectral elements
  
  		double* s = (double*)malloc(sizeof(double) * B);					//allocate space for the spectrum that will be pulled from the file
  		double* s_dev;														//declare a device pointer that will store the spectrum on the GPU
  
1ee79b84   David Mayerich   more accurate noi...
1123
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  		double* s2 = (double*)malloc(sizeof(double) * B);					//allocate space for the spectrum of second pixel that will be pulled from the file
  		double* s2_dev;														//  device pointer on the GPU
  		cudaStat = cudaMalloc(&s2_dev, B * sizeof(double));					//  allocate space on the CUDA device
  		cudaStat = cudaMemset(s2_dev, 0, B * sizeof(double));               //  initialize s2_dev to zero (0)
334547d8   sam   changes for mnf: ...
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  		double* A_dev;														//declare a device pointer that will store the covariance matrix on the GPU
  		double* avg_dev;													//declare a device pointer that will store the average spectrum
  		cudaStat = cudaMalloc(&s_dev, B * sizeof(double));					//allocate space on the CUDA device for the spectrum
  		cudaStat = cudaMalloc(&A_dev, B * B * sizeof(double));				//allocate space on the CUDA device for the covariance matrix
  		cudaStat = cudaMemset(A_dev, 0, B * B * sizeof(double));			//initialize the covariance matrix to zero (0)
  		cudaStat = cudaMalloc(&avg_dev, B * sizeof(double));				//allocate space on the CUDA device for the average spectrum
  		stat = cublasSetVector((int)B, sizeof(double), avg, 1, avg_dev, 1);		//copy the average spectrum to the CUDA device
  
1ee79b84   David Mayerich   more accurate noi...
1136
  		double ger_alpha = 1.0 / (double)XY;									//scale the outer product by the inverse of the number of samples (mean outer product)
334547d8   sam   changes for mnf: ...
1137
1138
  		double axpy_alpha = -1;												//multiplication factor for the average spectrum (in order to perform a subtraction)
  
2781a48c   David Mayerich   fixed cuBLAS func...
1139
1140
1141
  		CUBLAS_HANDLE_ERROR(cublasCreate(&handle));							//create a cuBLAS instance
  		if (stat != CUBLAS_STATUS_SUCCESS) return 1;						//test the cuBLAS instance to make sure it is valid
  
1ee79b84   David Mayerich   more accurate noi...
1142
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  		for (unsigned long long xy = 0; xy < XY; xy++) {										//for each pixel
  			if (mask == NULL || mask[xy] != 0) {
  				pixeld(s, xy);                                        //retreive the spectrum at the current xy pixel location
  				if (xy < XY - X()) {
  					pixeld(s2, xy + X());                              //retreive the spectrum at the current xy+X pixel location, which is adjacent (bellow) to the pixel at xy location (in y direction)
  				}
  				else {
  					pixeld(s2, xy - X());                               //for the last row we consider the the adjacent pixel which is located above pixel xy
  				}
  				stat = cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1);						//copy the spectrum of first pixel from the host to the device
334547d8   sam   changes for mnf: ...
1152
1153
  				stat = cublasDaxpy(handle, (int)B, &axpy_alpha, avg_dev, 1, s_dev, 1);				//subtract the average spectrum
  
1ee79b84   David Mayerich   more accurate noi...
1154
1155
  				stat = cublasSetVector((int)B, sizeof(double), s2, 1, s2_dev, 1);					//copy the spectrum of second pixel from the host to the device
  				stat = cublasDaxpy(handle, (int)B, &axpy_alpha, avg_dev, 1, s2_dev, 1);				//subtract the average spectrum
334547d8   sam   changes for mnf: ...
1156
  
1ee79b84   David Mayerich   more accurate noi...
1157
  				stat = cublasDaxpy(handle, (int)B, &axpy_alpha, s2_dev, 1, s_dev, 1);	   //Minimum/Maximum Autocorrelation Factors (MAF) method : subtranct each pixel from adjacent pixel (in y direction)
334547d8   sam   changes for mnf: ...
1158
1159
1160
  
  				stat = cublasDsyr(handle, CUBLAS_FILL_MODE_UPPER, (int)B, &ger_alpha, s_dev, 1, A_dev, (int)B);	//calculate the covariance matrix (symmetric outer product)
  			}
1ee79b84   David Mayerich   more accurate noi...
1161
  			if (PROGRESS) progress = (double)(xy + 1) / XY * 100;													//record the current progress
334547d8   sam   changes for mnf: ...
1162
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  		}
  
  		cublasGetMatrix((int)B, (int)B, sizeof(double), A_dev, (int)B, coN, (int)B);					//copy the result from the GPU to the CPU
  
  		cudaFree(A_dev);														//clean up allocated device memory
  		cudaFree(s_dev);
  		cudaFree(s2_dev);
  		cudaFree(avg_dev);
  
1ee79b84   David Mayerich   more accurate noi...
1172
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  		for (unsigned long long i = 0; i < B; i++) {										//copy the upper triangular portion to the lower triangular portion
  			for (unsigned long long j = i + 1; j < B; j++) {
334547d8   sam   changes for mnf: ...
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  				coN[B * i + j] = coN[B * j + i];
  			}
  		}
  
dc99699e   David Mayerich   implemented a no-...
1178
  		return 0;
334547d8   sam   changes for mnf: ...
1179
  	}
1ee79b84   David Mayerich   more accurate noi...
1180
  	//#endif
334547d8   sam   changes for mnf: ...
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  	/// Calculate the covariance of noise matrix for all masked pixels in the image with 64-bit floating point precision.
  
  	/// @param coN 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
1ee79b84   David Mayerich   more accurate noi...
1187
  	bool coNoise_matrix(double* coN, double* avg, unsigned char *mask, int cuda_device = 0, bool PROGRESS = false) {
dc99699e   David Mayerich   implemented a no-...
1188
  
1c92dffe   David Mayerich   simplified CUDA i...
1189
  		if (cuda_device >= 0) {													//if a CUDA device is specified
dc99699e   David Mayerich   implemented a no-...
1190
1191
  			int dev_count;
  			HANDLE_ERROR(cudaGetDeviceCount(&dev_count));						//get the number of CUDA devices
1c92dffe   David Mayerich   simplified CUDA i...
1192
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  			if (dev_count > 0 && dev_count > cuda_device) {							//if the first device is not an emulator
  				cudaDeviceProp prop;
  				cudaGetDeviceProperties(&prop, cuda_device);									//get the property of the requested CUDA device
  				if (prop.major != 9999) {
  					std::cout << "Using CUDA device [" << cuda_device << "] to calculate the noise covariance matrix..." << std::endl;
  					HANDLE_ERROR(cudaSetDevice(cuda_device));
  					int status = coNoise_matrix_cublas(coN, avg, mask, PROGRESS);			//use cuBLAS to calculate the covariance matrix
  					if (status == 0) return true;									//if the cuBLAS function returned correctly, we're done
  				}
1ee79b84   David Mayerich   more accurate noi...
1201
  			}																	//otherwise continue using the CPU
1c92dffe   David Mayerich   simplified CUDA i...
1202
  			std::cout << "WARNING: cuBLAS failed, using CPU" << std::endl;
dc99699e   David Mayerich   implemented a no-...
1203
  		}
334547d8   sam   changes for mnf: ...
1204
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  		progress = 0;
  		//memory allocation
  		unsigned long long XY = X() * Y();
  		unsigned long long B = Z();
  		T* temp = (T*)malloc(sizeof(T) * B);
1ee79b84   David Mayerich   more accurate noi...
1210
  		T* temp2 = (T*)malloc(sizeof(T) * B);
334547d8   sam   changes for mnf: ...
1211
1212
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  		unsigned long long count = nnz(mask);								//count the number of masked pixels
  
1ee79b84   David Mayerich   more accurate noi...
1214
  																			//initialize covariance matrix of noise
334547d8   sam   changes for mnf: ...
1215
1216
1217
  		memset(coN, 0, B * B * sizeof(double));
  
  		//calculate covariance matrix
1ee79b84   David Mayerich   more accurate noi...
1218
1219
1220
  		double* coN_half = (double*)malloc(B * B * sizeof(double));			//allocate space for a higher-precision intermediate matrix
  		double* temp_precise = (double*)malloc(B * sizeof(double));
  		double* temp_precise2 = (double*)malloc(B * sizeof(double));
334547d8   sam   changes for mnf: ...
1221
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  		memset(coN_half, 0, B * B * sizeof(double));							//initialize the high-precision matrix with zeros
  		unsigned long long idx;													//stores i*B to speed indexing
1ee79b84   David Mayerich   more accurate noi...
1223
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  		for (unsigned long long xy = 0; xy < XY; xy++) {
  			if (mask == NULL || mask[xy] != 0) {
  				pixel(temp, xy);                                        //retreive the spectrum at the current xy pixel location
  				if (xy < XY - X()) {
  					pixel(temp2, xy + X());                              //retreive the spectrum at the current xy+X pixel location, which is adjacent (bellow) to the pixel at xy location (in y direction)
  				}
  				else {
  					pixel(temp2, xy - X());                               //for the last row we consider the the adjacent pixel which is located above pixel xy
  				}
  				for (unsigned long long b = 0; b < B; b++) {									//subtract the mean from this spectrum and increase the precision
334547d8   sam   changes for mnf: ...
1233
  					temp_precise[b] = (double)temp[b] - (double)avg[b];
1ee79b84   David Mayerich   more accurate noi...
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  					temp_precise2[b] = (double)temp2[b] - (double)avg[b];
  				}
334547d8   sam   changes for mnf: ...
1236
  
1ee79b84   David Mayerich   more accurate noi...
1237
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  				for (unsigned long long b2 = 0; b2 < B; b2++)	    //Minimum/Maximum Autocorrelation Factors (MAF) method : subtranct each pixel from adjacent pixel (in y direction)
  					temp_precise[b2] -= temp_precise2[b2];
334547d8   sam   changes for mnf: ...
1239
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  				idx = 0;
1ee79b84   David Mayerich   more accurate noi...
1241
  				for (unsigned long long b0 = 0; b0 < B; b0++) {								//for each band
334547d8   sam   changes for mnf: ...
1242
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  					for (unsigned long long b1 = b0; b1 < B; b1++)
  						coN_half[idx++] += temp_precise[b0] * temp_precise[b1];
  				}
  			}
1ee79b84   David Mayerich   more accurate noi...
1246
  			if (PROGRESS) progress = (double)(xy + 1) / XY * 100;
334547d8   sam   changes for mnf: ...
1247
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  		}
  		idx = 0;
1ee79b84   David Mayerich   more accurate noi...
1249
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  		for (unsigned long long i = 0; i < B; i++) {										//copy the precision matrix to both halves of the output matrix
  			for (unsigned long long j = i; j < B; j++) {
  				coN[j * B + i] = coN[i * B + j] = coN_half[idx++] / (double)count;
334547d8   sam   changes for mnf: ...
1252
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  			}
  		}
  
  		free(temp);
1ee79b84   David Mayerich   more accurate noi...
1256
  		free(temp2);
334547d8   sam   changes for mnf: ...
1257
  		free(temp_precise);
1ee79b84   David Mayerich   more accurate noi...
1258
  		free(temp_precise2);
334547d8   sam   changes for mnf: ...
1259
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  		return true;
  	}
  
334547d8   sam   changes for mnf: ...
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      /// Project the spectra onto a set of basis functions
  	/// @param outfile is the name of the new binary output file that will be created
  	/// @param center is a spectrum about which the data set will be rotated (ex. when performing mean centering)
  	/// @param basis a set of basis vectors that the data set will be projected onto (after centering)
  	/// @param M is the number of basis vectors
  	/// @param mask is a character mask used to limit processing to valid pixels
  	bool project_cublas(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask = NULL, bool PROGRESS = false){
  
1c92dffe   David Mayerich   simplified CUDA i...
1270
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  		//cudaError_t cudaStat;
  		//cublasStatus_t stat;
334547d8   sam   changes for mnf: ...
1272
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  		cublasHandle_t handle;
  
  		std::ofstream target(outfile.c_str(), std::ios::binary);	//open the target binary file
334547d8   sam   changes for mnf: ...
1275
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  		progress = 0;													    //initialize the progress to zero (0)
  		unsigned long long XY = X() * Y();									//calculate the number of elements in a band image
  		unsigned long long B = Z();											//calculate the number of spectral elements
  
  		double* s = (double*)malloc(sizeof(double) * B);					//allocate space for the spectrum that will be pulled from the file
  		double* s_dev;														//declare a device pointer that will store the spectrum on the GPU
1c92dffe   David Mayerich   simplified CUDA i...
1282
  		HANDLE_ERROR(cudaMalloc(&s_dev, B * sizeof(double)));				//allocate space on the CUDA device for the spectrum
334547d8   sam   changes for mnf: ...
1283
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          double* basis_dev;														//  device pointer on the GPU
1c92dffe   David Mayerich   simplified CUDA i...
1286
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          HANDLE_ERROR(cudaMalloc(&basis_dev, M * B * sizeof(double)));					//  allocate space on the CUDA device
          HANDLE_ERROR(cudaMemset(basis_dev, 0, M * B * sizeof(double)));               //  initialize basis_dev to zero (0)
334547d8   sam   changes for mnf: ...
1288
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          /// transposing basis matrix (because cuBLAS is column-major)
          double *basis_Transposed = (double*)malloc(M * B * sizeof(double));
          memset(basis_Transposed, 0, M * B * sizeof(double));
          for (int i = 0; i<M; i++)
              for (int j = 0; j<B; j++)
              basis_Transposed[i+j*M] = basis[i*B+j];
1c92dffe   David Mayerich   simplified CUDA i...
1296
1297
  		//copy the basis_Transposed matrix to the CUDA device (both matrices are stored in column-major format)
  		CUBLAS_HANDLE_ERROR(cublasSetMatrix((int)M, (int)B, sizeof(double),basis_Transposed, (int)M, basis_dev, (int)M));
334547d8   sam   changes for mnf: ...
1298
  
1c92dffe   David Mayerich   simplified CUDA i...
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  		double* center_dev;																						//declare a device pointer that will store the center (average)
  		HANDLE_ERROR(cudaMalloc(&center_dev, B * sizeof(double)));									//allocate space on the CUDA device for the center (average)
  		CUBLAS_HANDLE_ERROR(cublasSetVector((int)B, sizeof(double), center, 1, center_dev, 1));			//copy the center vector (average) to the CUDA device (from host to device)
334547d8   sam   changes for mnf: ...
1302
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1c92dffe   David Mayerich   simplified CUDA i...
1304
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          double* A = (double*)malloc(sizeof(double) * M);								//allocate space for the projected pixel on the host
          double* A_dev;																	//declare a device pointer that will store the projected pixel on the GPU
  		HANDLE_ERROR(cudaMalloc(&A_dev,M * sizeof(double)));				    //allocate space on the CUDA device for the projected pixel
  		HANDLE_ERROR(cudaMemset(A_dev, 0,M * sizeof(double)));		        //initialize the projected pixel to zero (0)
334547d8   sam   changes for mnf: ...
1308
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  		double axpy_alpha = -1;												//multiplication factor for the center (in order to perform a subtraction)
  		double axpy_alpha2 = 1;												//multiplication factor for the matrix-vector multiplication
          double axpy_beta = 0;												//multiplication factor for the matrix-vector multiplication (there is no second scalor)
  
1c92dffe   David Mayerich   simplified CUDA i...
1313
  		CUBLAS_HANDLE_ERROR(cublasCreate(&handle));					//create a cuBLAS instance
334547d8   sam   changes for mnf: ...
1314
  
08d1c3b9   David Mayerich   fixed casting war...
1315
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          T* temp = (T*)malloc(sizeof(T) * M);													//allocate space for the projected pixel to be written on the disc
  		size_t i;
  		for (unsigned long long xy = 0; xy < XY; xy++){											//for each pixel
334547d8   sam   changes for mnf: ...
1318
  			if (mask == NULL || mask[xy] != 0){
08d1c3b9   David Mayerich   fixed casting war...
1319
  				pixeld(s, xy);																	//retreive the spectrum at the current xy pixel location
334547d8   sam   changes for mnf: ...
1320
  
1c92dffe   David Mayerich   simplified CUDA i...
1321
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  				CUBLAS_HANDLE_ERROR(cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1));						    //copy the spectrum from the host to the device
                  CUBLAS_HANDLE_ERROR(cublasDaxpy(handle, (int)B, &axpy_alpha, center_dev, 1, s_dev, 1));					//subtract the center (average)
                  CUBLAS_HANDLE_ERROR(cublasDgemv(handle,CUBLAS_OP_N,(int)M,(int)B,&axpy_alpha2,basis_dev,(int)M,s_dev,1,&axpy_beta,A_dev,1));         //performs the matrix-vector multiplication
                  CUBLAS_HANDLE_ERROR(cublasGetVector((int)M, sizeof(double), A_dev, 1, A, 1));							//copy the projected pixel to the host (from GPU to CPU)
  						
08d1c3b9   David Mayerich   fixed casting war...
1326
  				for(i = 0; i < M; i++)	temp[i] = (T)A[i];										//casting projected pixel from double to whatever T is
334547d8   sam   changes for mnf: ...
1327
  			}
3a880d1c   David Mayerich   fixed PCA and BIP...
1328
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  			else
  				memset(temp, 0, sizeof(T) * M);
334547d8   sam   changes for mnf: ...
1330
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  			target.write(reinterpret_cast<const char*>(temp), sizeof(T) * M);					  //write the projected vector
  			if(PROGRESS) progress = (double)(xy+1) / XY * 100;									    //record the current progress
  
  		}
  
          //clean up allocated device memory
1c92dffe   David Mayerich   simplified CUDA i...
1337
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  		HANDLE_ERROR(cudaFree(A_dev));
  		HANDLE_ERROR(cudaFree(s_dev));
  		HANDLE_ERROR(cudaFree(basis_dev));
  		HANDLE_ERROR(cudaFree(center_dev));
  		CUBLAS_HANDLE_ERROR(cublasDestroy(handle));
334547d8   sam   changes for mnf: ...
1342
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  		free(A);
  		free(s);
  		free(temp);
  		target.close();												//close the output file
08d1c3b9   David Mayerich   fixed casting war...
1346
  		
334547d8   sam   changes for mnf: ...
1347
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  		return true;
  	}
334547d8   sam   changes for mnf: ...
1349
  
812a2741   David Mayerich   added documentati...
1350
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  	/// Project the spectra onto a set of basis functions
  	/// @param outfile is the name of the new binary output file that will be created
  	/// @param center is a spectrum about which the data set will be rotated (ex. when performing mean centering)
  	/// @param basis a set of basis vectors that the data set will be projected onto (after centering)
  	/// @param M is the number of basis vectors
  	/// @param mask is a character mask used to limit processing to valid pixels
dd5aab2f   David Mayerich   fixed errors in s...
1356
  	bool project(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask = NULL, int cuda_device = 0, bool PROGRESS = false){
dd5aab2f   David Mayerich   fixed errors in s...
1357
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  		if (cuda_device >= 0) {													//if a CUDA device is specified
  			int dev_count;
  			HANDLE_ERROR(cudaGetDeviceCount(&dev_count));						//get the number of CUDA devices
dd5aab2f   David Mayerich   fixed errors in s...
1360
  			if (dev_count > 0 && dev_count > cuda_device) {							//if the first device is not an emulator
1c92dffe   David Mayerich   simplified CUDA i...
1361
  				cudaDeviceProp prop;
dd5aab2f   David Mayerich   fixed errors in s...
1362
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  				cudaGetDeviceProperties(&prop, cuda_device);									//get the property of the requested CUDA device
  				if (prop.major != 9999) {
1c92dffe   David Mayerich   simplified CUDA i...
1364
  					std::cout << "Using CUDA device [" << cuda_device << "] to perform a basis projection..." << std::endl;
dd5aab2f   David Mayerich   fixed errors in s...
1365
  					HANDLE_ERROR(cudaSetDevice(cuda_device));
1c92dffe   David Mayerich   simplified CUDA i...
1366
  					return project_cublas(outfile, center, basis, M, mask, PROGRESS);
dd5aab2f   David Mayerich   fixed errors in s...
1367
  				}
1c92dffe   David Mayerich   simplified CUDA i...
1368
1369
  			}																	//otherwise continue using the CPU		
  			std::cout << "WARNING: cuBLAS failed, using CPU" << std::endl;
dd5aab2f   David Mayerich   fixed errors in s...
1370
1371
  		}
  		
63fc1df8   David Mayerich   added an inverse ...
1372
  		std::ofstream target(outfile.c_str(), std::ios::binary);	//open the target binary file
9d3ba0b1   David Mayerich   added stim::hsi a...
1373
  		//std::string headername = outfile + ".hdr";					//the header file name
63fc1df8   David Mayerich   added an inverse ...
1374
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  		//memory allocation
  		unsigned long long XY = X() * Y();
  		unsigned long long B = Z();
  
  		T* s = (T*)malloc(sizeof(T) * B);							//allocate space for the spectrum
  		T* rs = (T*)malloc(sizeof(T) * M);							//allocate space for the projected spectrum
  		double* bv;													//pointer to the current projection vector
  		for(unsigned long long xy = 0; xy < XY; xy++){				//for each spectrum in the image
9d3ba0b1   David Mayerich   added stim::hsi a...
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  			memset(rs, 0, sizeof(T) * M);
  			if(mask == NULL || mask[xy]){
  				pixel(s, xy);											//load the spectrum
  				for(unsigned long long m = 0; m < M; m++){				//for each basis vector
  					bv = &basis[m * B];									//assign 'bv' to the beginning of the basis vector
  					for(unsigned long long b = 0; b < B; b++){			//for each band
  						rs[m] += (T)(((double)s[b] - center[b]) * bv[b]);		//center the spectrum and perform the projection
  					}
63fc1df8   David Mayerich   added an inverse ...
1391
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  				}
  			}
1a224b6a   David Mayerich   fixed linux compa...
1393
  
63fc1df8   David Mayerich   added an inverse ...
1394
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  			target.write(reinterpret_cast<const char*>(rs), sizeof(T) * M);					//write the projected vector
  			if(PROGRESS) progress = (double)(xy+1) / XY * 100;
  		}
  
  		free(s);													//free temporary storage arrays
  		free(rs);
  		target.close();												//close the output file
08d1c3b9   David Mayerich   fixed casting war...
1401
  		
63fc1df8   David Mayerich   added an inverse ...
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  		return true;
  	}
  
  	bool inverse(std::string outfile, double* center, double* basis, unsigned long long B, unsigned long long C = 0, bool PROGRESS = false){
  
  		std::ofstream target(outfile.c_str(), std::ios::binary);	//open the target binary file
  		std::string headername = outfile + ".hdr";					//the header file name
  
  		//memory allocation
  		unsigned long long XY = X() * Y();
  		if(C == 0) C = Z();											//if no coefficient number is given, assume all are used
  		C = std::min<unsigned long long>(C, Z());					//set the number of coefficients (the user can specify fewer)
  
  		T* coeff = (T*)malloc(sizeof(T) * Z());						//allocate space for the coefficients
  		T* s = (T*)malloc(sizeof(T) * B);							//allocate space for the spectrum
  		double* bv;													//pointer to the current projection vector
  		for(unsigned long long xy = 0; xy < XY; xy++){				//for each pixel in the image (expressed as a set of coefficients)
  			pixel(coeff, xy);										//load the coefficients
  			memset(s, 0, sizeof(T) * B);							//initialize the spectrum to zero (0)
  			for(unsigned long long c = 0; c < C; c++){				//for each basis vector coefficient
  				bv = &basis[c * B];									//assign 'bv' to the beginning of the basis vector
1a224b6a   David Mayerich   fixed linux compa...
1423
  				for(unsigned long long b = 0; b < B; b++){			//for each component of the basis vector
9d3ba0b1   David Mayerich   added stim::hsi a...
1424
  					s[b] += (T)((double)coeff[c] * bv[b] + center[b]);			//calculate the contribution of each element of the basis vector in the final spectrum
63fc1df8   David Mayerich   added an inverse ...
1425
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  				}
  			}
  
  			target.write(reinterpret_cast<const char*>(s), sizeof(T) * B);					//write the projected vector
  			if(PROGRESS) progress = (double)(xy+1) / XY * 100;
  		}
  
  		free(coeff);												//free temporary storage arrays
  		free(s);
  		target.close();												//close the output file
  
  		return true;
  	}
  
0df38ff3   heziqi   fixed head detached
1439
  
a23c4132   David Mayerich   Doxygen comments ...
1440
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  	/// 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
e9bddc57   David Mayerich   added band croppi...
1447
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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,
63fc1df8   David Mayerich   added an inverse ...
1452
1453
  								   unsigned long long b1,
  								   bool PROGRESS = false){
a43c4fe1   heziqi   Added crop in env...
1454
  
3033b886   David Mayerich   implemented spect...
1455
  		//calculate the new number of samples, lines, and bands
f78ceb64   David Mayerich   fixed BIP croppin...
1456
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  		unsigned long long samples = x1 - x0 + 1;
  		unsigned long long lines = y1 - y0 + 1;
  		unsigned long long bands = b1 - b0 + 1;
3033b886   David Mayerich   implemented spect...
1459
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  		//calculate the length of one cropped spectrum
  		unsigned long long L = bands * sizeof(T);
  
  		//unsigned long long L = Z() * sizeof(T);
  
  		//allocate space for the spectrum
f78ceb64   David Mayerich   fixed BIP croppin...
1466
  		char* temp = (char*)malloc(L);
3033b886   David Mayerich   implemented spect...
1467
1468
  
  		//open an output file for binary writing
a43c4fe1   heziqi   Added crop in env...
1469
  		std::ofstream out(outfile.c_str(), std::ios::binary);
3033b886   David Mayerich   implemented spect...
1470
1471
  
  		//seek to the first pixel in the cropped image
f78ceb64   David Mayerich   fixed BIP croppin...
1472
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1475
  		size_t startx = x0 * Z();
  		size_t starty = y0 * X() * Z();
  		size_t startb = b0;
  		file.seekg( (starty + startx + startb) * sizeof(T), std::ios::beg);
3033b886   David Mayerich   implemented spect...
1476
1477
  
  		//distance between sample spectra in the same line
f78ceb64   David Mayerich   fixed BIP croppin...
1478
1479
  		size_t dist_between_samples = Z() - bands;
  		size_t jump_sample = dist_between_samples * sizeof(T);
3033b886   David Mayerich   implemented spect...
1480
1481
  
  		//distance between sample spectra in adjacent lines
f78ceb64   David Mayerich   fixed BIP croppin...
1482
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  		//unsigned long long jump_line = ( X() - x1 + x0 ) * Z() * sizeof(T);
  		size_t dist_between_lines = X() - samples;
  		size_t jump_line = dist_between_lines * Z() * sizeof(T);
3033b886   David Mayerich   implemented spect...
1485
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  		//unsigned long long sp = y0 * X() + x0;		//start pixel
  
  		//for each pixel in the image
f78ceb64   David Mayerich   fixed BIP croppin...
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1491
  		for (unsigned y = 0; y < lines; y++) {
  			for (unsigned x = 0; x < samples; x++) {
3033b886   David Mayerich   implemented spect...
1492
  				//read the cropped spectral region
f78ceb64   David Mayerich   fixed BIP croppin...
1493
  				file.read(temp, L );
3033b886   David Mayerich   implemented spect...
1494
  				//pixel(temp, sp + x + y * X());
f78ceb64   David Mayerich   fixed BIP croppin...
1495
  				out.write(temp, L);   //write slice data into target file
3150c537   David Mayerich   added further pro...
1496
  
3033b886   David Mayerich   implemented spect...
1497
1498
  				file.seekg(jump_sample, std::ios::cur);
  
dd5aab2f   David Mayerich   fixed errors in s...
1499
  				if(PROGRESS) progress = (double)(y * samples + x + 1) / (lines * samples) * 100;
a43c4fe1   heziqi   Added crop in env...
1500
  			}
3033b886   David Mayerich   implemented spect...
1501
1502
  
  			file.seekg(jump_line, std::ios::cur);
a43c4fe1   heziqi   Added crop in env...
1503
1504
  		}
  		free(temp);
f78ceb64   David Mayerich   fixed BIP croppin...
1505
  		out.close();
3150c537   David Mayerich   added further pro...
1506
  
a43c4fe1   heziqi   Added crop in env...
1507
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  		return true;
  	}
  
dc8eb8aa   David Mayerich   added band trimmi...
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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> band_array, bool PROGRESS = false){
  
  		std::ofstream out(outfile.c_str(), std::ios::binary);	//open the output file for writing
  		file.seekg(0, std::ios::beg);							//move to the beginning of the input file
  
  		size_t B = Z();								//calculate the number of elements in a spectrum
  		size_t Bdst = Z() - band_array.size();		//calculate the number of elements in an output spectrum
  		size_t Bb = B * sizeof(T);					//calculate the number of bytes in a spectrum
  		size_t XY = X() * Y();						//calculate the number of pixels in the image
  		T* src = (T*)malloc(Bb);					//allocate space to store an input spectrum
  		T* dst = (T*)malloc(Bdst * sizeof(T));		//allocate space to store an output spectrum
  
  		size_t i;									//index into the band array
  		size_t bdst;								//index into the output array
  		for(size_t xy = 0; xy < XY; xy++){			//for each pixel
  			i = 0;
  			bdst = 0;
  			file.read((char*)src, Bb);				//read a spectrum
  			for(size_t b = 0; b < B; b++){			//for each band
  				if(b != band_array[i]){				//if the band isn't trimmed
  					dst[bdst] = src[b];				//copy the band value to the output spectrum
  					bdst++;
  				}
  				else i++;							//otherwise increment i
  			}
  			out.write((char*)dst, Bdst * sizeof(T));	//write the output spectrum
  			if(PROGRESS) progress = (double)(xy + 1) / (double) XY * 100;
  		}
  		free(src);
  		free(dst);
  	}
  
2ce6954b   David Mayerich   added the ability...
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  	/// Combine two BIP images along the Y axis
  
  	/// @param outfile is the combined file to be output
  	/// @param infile is the input file stream for the image to combine with this one
  	/// @param Sx is the size of the second image along X
  	/// @param Sy is the size of the second image along Y
  	/// @param offset is a shift (negative or positive) in the combined image to the left or right
  	void combine(std::string outfile, bip<T>* C, long long xp, long long yp, bool PROGRESS = false){
  		std::ofstream out(outfile.c_str(), std::ios::binary);	//open the output file for writing
  		file.seekg(0, std::ios::beg);								//move to the beginning of both files
  		C->file.seekg(0, std::ios::beg);
  
  		size_t S[2];				//size of the output band image
  		size_t p0[2];				//position of the current image in the output
  		size_t p1[2];				//position of the source image in the output
  
  		hsi<T>::calc_combined_size(xp, yp, C->X(), C->Y(), S[0], S[1], p0[0], p0[1], p1[0], p1[1]);	//calculate the image placement parameters
  
  		size_t spec_bytes = Z() * sizeof(T);						//calculate the number of bytes in a spectrum
  		T* spec = (T*)malloc(spec_bytes);							//allocate space for a spectrum
  
  		for(size_t y = 0; y < S[1]; y++){							//for each pixel in the destination image
  			for(size_t x = 0; x < S[0]; x++){
  				if(x >= p0[0] && x < p0[0] + X() && y >= p0[1] && y < p0[1] + Y())	//if this pixel is in the current image
  					file.read((char*)spec, spec_bytes);
  				else if(x >= p1[0] && x < p1[0] + C->X() && y >= p1[1] && y < p1[1] + C->Y())	//if this pixel is in the source image
  					C->file.read((char*)spec, spec_bytes);
  				else
  					memset(spec, 0, spec_bytes);
  				out.write((char*)spec, spec_bytes);					//write to the output file
  			}
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  			if(PROGRESS) progress = (double)( (y+1) * S[0] + 1) / (double) (S[0] * S[1]) * 100;
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  		}
  	}
  
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  	///Append two files together along the band dimension
  	void append(std::string outfile, bip<T>* C, bool PROGRESS = false) {
  		std::ofstream out(outfile.c_str(), std::ios::binary);	//open the output file for writing
  		file.seekg(0, std::ios::beg);							//move to the beginning of both files
  		C->file.seekg(0, std::ios::beg);
  		size_t a_bytes = Z() * sizeof(T);					//calculate the number of bytes in a single plane of this file
  		size_t b_bytes = C->Z() * sizeof(T);			//calculate the number of bytes in a single plane of the appending file
  		T* a = (T*)malloc(a_bytes);								//allocate space for a plane of the current file
  		T* b = (T*)malloc(b_bytes);								//allocate space for a plane of the appended file
  		if (PROGRESS) progress = 0;
  		for (size_t xy = 0; xy < X()*Y(); xy++) {
  			spectrum(a, xy);								//read a plane from the current file
  			out.write((char*)a, a_bytes);								//write the plane to disk
  			C->spectrum(b, xy);								//read a plane from the appending file
  			out.write((char*)b, b_bytes);
  			if (PROGRESS) progress = (double)(xy + 1) / (double)(X() * Y()) * 100;
  		}
  
  		out.close();
  	}
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  	/// Convolve the given band range with a kernel specified by a vector of coefficients.
  
  	/// @param outfile is an already open stream to the output file
  	/// @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...
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  	void convolve(std::string outfile, std::vector<double> C, size_t start, size_t end, unsigned char* mask = NULL, bool PROGRESS = false){
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  		std::ofstream out(outfile.c_str(), std::ios::binary);		//open the output file for writing
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  		size_t N = end - start + 1;									//number of bands in the output spectrum
  		size_t Nb = N * sizeof(T);									//size of the output spectrum in bytes
  		size_t B = Z();												//calculate the number of values in a spectrum
  		size_t Bb = B * sizeof(T);									//calculate the size of a spectrum in bytes
  
  		file.seekg(0, std::ios::beg);								//move to the beginning of the input file
  
  		size_t nC = C.size();										//get the number of bands that the kernel spans
  		T* inspec = (T*)malloc(Bb);									//allocate space for the input spectrum
  		T* outspec = (T*)malloc(Nb);								//allocate space for the output spectrum
  
  		size_t XY = X() * Y();										//number of pixels in the image
  		for(size_t xy = 0; xy < XY; xy++){							//for each pixel
  			file.read((char*)inspec, Bb);							//read an input spectrum
  			memset(outspec, 0, Nb);									//set the output spectrum to zero (0)
9d77bbd9   David Mayerich   updates for HSIvi...
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  			if(mask == NULL || mask[xy]){
  				for(size_t b = 0; b < N; b++){							//for each component of the spectrum
  					for(size_t c = 0; c < nC; c++){						//for each coefficient in the kernel
  						outspec[b] += (T)(inspec[b + start + c] * C[c]);		//perform the sum/multiply part of the convolution
  					}
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  				}
  			}
  			out.write((char*)outspec, Nb);							//output the band
  			if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
  		}
  	}
  
9d77bbd9   David Mayerich   updates for HSIvi...
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  	void deriv(std::string outfile, size_t d, size_t order, const std::vector<double> w, unsigned char* mask = NULL, bool PROGRESS = false){
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  		std::ofstream out(outfile.c_str(), std::ios::binary);		//open the output file for writing
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  		size_t B = Z();												//calculate the number of values in a spectrum
  		size_t Bb = B * sizeof(T);									//calculate the size of a spectrum in bytes
  
  		bool UNIFORM = true;
  		double ds = w[1] - w[0];									//initialize ds
  		for(size_t b = 1; b < B; b++)								//test to see if the spectral spacing is uniform (if it is, convolution is much faster)
  			if(w[b] - w[b-1] != ds) UNIFORM = false;
  
  		size_t nC = order + d;									//approximating a derivative requires order + d samples
  
  		file.seekg(0, std::ios::beg);								//move to the beginning of the input file
  
  		T* inspec = (T*)malloc(Bb);									//allocate space for the input spectrum
  		T* outspec = (T*)malloc(Bb);								//allocate space for the output spectrum
  
  		size_t XY = X() * Y();										//number of pixels in the image
  		size_t mid = (size_t)(nC / 2);							//calculate the mid point of the kernel
  		size_t iw;													//index to the first wavelength used to evaluate the derivative at this band
  		for(size_t xy = 0; xy < XY; xy++){							//for each pixel
  			file.read((char*)inspec, Bb);							//read an input spectrum
  			memset(outspec, 0, Bb);									//set the output spectrum to zero (0)
9d77bbd9   David Mayerich   updates for HSIvi...
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  			if(mask == NULL || mask[xy]){
  				iw = 0;
  				for(size_t b = 0; b < mid; b++){							//for each component of the spectrum
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  					std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC);			//get the wavelengths corresponding to each sample
  					std::vector<double> C = diff_coefficients(w[b], w_pts, d);					//get the optimal sample weights
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  					for(size_t c = 0; c < nC; c++)						//for each coefficient in the kernel
  						outspec[b] += (T)(inspec[iw + c] * C[c]);		//perform the sum/multiply part of the convolution
  				}
  				std::vector<double> w_pts(w.begin(), w.begin() + nC);			//get the wavelengths corresponding to each sample
  				std::vector<double> C = diff_coefficients(w[0], w_pts, d);					//get the optimal sample weights
  				for(size_t b = mid; b <= B - (nC - mid); b++){
  					iw = b - mid;
  					if(!UNIFORM){																//if the spacing is non-uniform, we have to re-calculate these points every iteration
  						std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC);			//get the wavelengths corresponding to each sample
  						std::vector<double> C = diff_coefficients(w[b], w_pts, d);					//get the optimal sample weights
  					}
  					for(size_t c = 0; c < nC; c++)						//for each coefficient in the kernel
  						outspec[b] += (T)(inspec[iw + c] * C[c]);		//perform the sum/multiply part of the convolution
  				}
  				iw = B - nC;
  				for(size_t b = B - (nC - mid) + 1; b < B; b++){
  					std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC);			//get the wavelengths corresponding to each sample
  					std::vector<double> C = diff_coefficients(w[b], w_pts, d);					//get the optimal sample weights
  					for(size_t c = 0; c < nC; c++)						//for each coefficient in the kernel
  						outspec[b] += (T)(inspec[iw + c] * C[c]);		//perform the sum/multiply part of the convolution
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  				}
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  			}
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  			out.write((char*)outspec, Bb);							//output the band
  			if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
  		}
  	}
  
278c622b   David Mayerich   finished Windows ...
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  	bool multiply(std::string outname, double v, unsigned char* mask = NULL, bool PROGRESS = false){
  		std::ofstream target(outname.c_str(), std::ios::binary);		//open the target binary file
  		std::string headername = outname + ".hdr";						//the header file name
  
  		unsigned long long N = X() * Y();								//calculate the total number of pixels to be processed
  		unsigned long long B = Z();										//get the number of bands
  		T* s = (T*)malloc(sizeof(T) * B);								//allocate memory to store a pixel
  		for(unsigned long long n = 0; n < N; n++){						//for each pixel in the image
  			if(mask == NULL || mask[n]){								//if the pixel is masked
  				for(size_t b = 0; b < B; b++)							//for each band in the spectrum
  					s[b] *= (T)v;											//multiply
  			}
  
  			if(PROGRESS) progress = (double)(n+1) / N * 100;			//set the current progress
  
  			target.write((char*)s, sizeof(T) * B);						//write the corrected data into destination
  		}																//end for each pixel
  
  		free(s);														//free the spectrum
  		target.close();													//close the output file
  		return true;
  	}
  
  	bool add(std::string outname, double v, unsigned char* mask = NULL, bool PROGRESS = false){
  		std::ofstream target(outname.c_str(), std::ios::binary);		//open the target binary file
  		std::string headername = outname + ".hdr";						//the header file name
  
  		unsigned long long N = X() * Y();								//calculate the total number of pixels to be processed
  		unsigned long long B = Z();										//get the number of bands
  		T* s = (T*)malloc(sizeof(T) * B);								//allocate memory to store a pixel
  		for(unsigned long long n = 0; n < N; n++){						//for each pixel in the image
  			if(mask == NULL || mask[n]){								//if the pixel is masked
  				for(size_t b = 0; b < B; b++)							//for each band in the spectrum
  					s[b] += (T)v;											//multiply
  			}
  
  			if(PROGRESS) progress = (double)(n+1) / N * 100;			//set the current progress
  
  			target.write((char*)s, sizeof(T) * B);						//write the corrected data into destination
  		}																//end for each pixel
  
  		free(s);														//free the spectrum
  		target.close();													//close the output file
  		return true;
  	}
  
9d34229e   David Mayerich   restructured the ...
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  	int fft(std::string outname, size_t bandmin, size_t bandmax, size_t samples = 0, T* ratio = NULL, size_t rx = 0, size_t ry = 0, bool PROGRESS = false, int device = 0){
  		if(device == -1){
  			std::cout<<"ERROR: GPU required for FFT (uses cuFFT)."<<std::endl;
  			exit(1);
  		}
  		if(samples == 0) samples = Z();								//if samples are specified, use all of them
  		if(samples > Z()){
  			std::cout<<"ERROR: stim::envi doesn't support FFT padding just yet."<<std::endl;
  			exit(1);
  		}
  		int nd;															//stores the number of CUDA devices
  		HANDLE_ERROR(cudaGetDeviceCount(&nd));							//get the number of CUDA devices
  		if(device >= nd){												//test for the existence of the requested device
  			std::cout<<"ERROR: requested CUDA device for stim::envi::fft() doesn't exist"<<std::endl;
  			exit(1);
  		}
  		HANDLE_ERROR(cudaSetDevice(device));							//set the CUDA device
  		cudaDeviceProp prop;
  		HANDLE_ERROR(cudaGetDeviceProperties(&prop, device));			//get the CUDA device properties
  
  		size_t B = Z();
  		size_t S = samples;
  		size_t fft_size = S * sizeof(T);								//number of bytes for each FFT
  		size_t cuda_bytes = prop.totalGlobalMem;						//get the number of bytes of global memory available
  		size_t cuda_use = (size_t)floor(cuda_bytes * 0.2);								//only use 80%
  		size_t nS = cuda_use / fft_size;								//calculate the number of spectra that can be loaded onto the GPU as a single batch
  		size_t batch_bytes = nS * fft_size;								//calculate the size of a batch (in bytes)
  		size_t fft_bytes = nS * (S/2 + 1) * sizeof(cufftComplex);
  		T* batch = (T*) malloc(batch_bytes);							//allocate space in host memory to store a batch
  		memset(batch, 0, batch_bytes);
  		std::complex<T>* batch_fft = (std::complex<T>*) malloc(fft_bytes);
  		T* gpu_batch;													//device pointer to the batch
  		HANDLE_ERROR(cudaMalloc(&gpu_batch, batch_bytes));				//allocate space<