codebase / stimlib

  #ifndef STIM_BSQ_H
  #define STIM_BSQ_H
  
  #include "../envi/envi_header.h"

  #include "../envi/binary.h"

  #include "../envi/bil.h"

  #include <cstring>
  #include <utility>

  #include <vector>

  namespace stim{

  /**
  	The BIP class represents a 3-dimensional binary file stored using band sequential (BSQ) image encoding. The binary file is stored
  	such that X-Y "frames" are stored sequentially to form an image stack along the z-axis. When accessing the data sequentially on disk,
  	the dimensions read, from fastest to slowest, are X, Y, Z.
  
  	This class is optimized for data streaming, and therefore supports extremely large (terabyte-scale) files. Data is loaded from disk
  	on request. Functions used to access data are written to support efficient reading.
  */

  template <typename T>
  
  class bsq: public binary<T> {
  

  protected:
  	

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

  	unsigned int offset;

  public:
  

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

  	//using binary<T>::getSlice;

  	using binary<T>::R;

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

  
  	/// @param filename is the name of the binary file on disk
  	/// @param X is the number of samples along dimension 1
  	/// @param Y is the number of samples (lines) along dimension 2
  	/// @param B is the number of samples (bands) along dimension 3
  	/// @param header_offset is the number of bytes (if any) in the binary header
  	/// @param wavelengths is an optional STL vector of size B specifying a numerical label for each band

  	bool open(std::string filename, unsigned int X, unsigned int Y, unsigned int B, unsigned int header_offset, std::vector<double> wavelengths){

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

  		//copy the wavelengths to the structure
  		offset = header_offset;

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

  		
  	}
  

  	/// Retrieve a single band (based on index) and stores it in pre-allocated memory.

  
  	/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
  	/// @param page <= B is the integer number of the band to be copied.

  	bool band_index( T * p, unsigned int page){

  		if (page >= R[2]){										//make sure the bank number is right

  			std::cout<<"ERROR: page out of range"<<std::endl;
  			return false;
  		}

  		//move the file pointer to the start of the page on disk

  		file.seekg(R[0] * R[1] * page * sizeof(T));

  		//read the page from disk

  		file.read((char *)p, sizeof(T) * R[0] * R[1]);
  

  		return true;
  	}
  

  	/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.

  
  	/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
  	/// @param wavelength is a floating point value (usually a wavelength in spectral data) used as a label for the band to be copied.

  	bool band( T * p, double wavelength){

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

  		unsigned int XY = R[0] * R[1];	//calculate the number of pixels in a band

  		unsigned page = 0;                

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

  
  		//if wavelength is smaller than the first one in header file

  		if ( w[page] > wavelength ){

  			band_index(p, page);
  			return true;
  		}
  

  		while( w[page] < wavelength )

  		{
  			page++;

  			//if wavelength is larger than the last wavelength in the header file
  			//	(the wavelength is out of bounds)

  			if (page == R[2]) {

  				band_index(p, R[2]-1);		//return the last band

  				return true;
  			}
  		}

  		//when the page counter points to the first band above 'wavelength'
  		if ( wavelength < w[page] ){

  			//do the interpolation

  			T * p1;
  			T * p2;

  			p1=(T*)malloc( XY * sizeof(T));                     //memory allocation
  			p2=(T*)malloc( XY * sizeof(T));
  			band_index(p1, page - 1);
  			band_index(p2, page );
  			for(unsigned i=0; i < XY; i++){

  				double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);

  				p[i] = (p2[i] - p1[i]) * r + p1[i];
  			}

  			free(p1);
  			free(p2);

  		}

  		//if the wavelength is equal to a wavelength in header file
  		else{
  			band_index(p, page);		//return the band

  		}
  

  		return true;
  	}
  

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

  
  	/// @param p is a pointer to pre-allocated memory at least B * sizeof(T) in size.
  	/// @param x is the x-coordinate (dimension 1) of the spectrum.
  	/// @param y is the y-coordinate (dimension 2) of the spectrum.

  	bool spectrum(T * p, unsigned x, unsigned y){

  
  		unsigned int i;
  

  		if ( x >= R[0] || y >= R[1]){							//make sure the sample and line number is right

  			std::cout<<"ERROR: sample or line out of range"<<std::endl;
  			return false;
  		}
  

  		file.seekg((x + y * R[0]) * sizeof(T), std::ios::beg);           //point to the certain sample and line

  		for (i = 0; i < R[2]; i++)

  		{
  			file.read((char *)(p + i), sizeof(T));

  			file.seekg((R[1] * R[0] - 1) * sizeof(T), std::ios::cur);    //go to the next band

  		}
  

  		return true;	
  	}

  	/// Retrieve a single pixel and stores it in pre-allocated memory.

  
  	/// @param p is a pointer to pre-allocated memory at least sizeof(T) in size.
  	/// @param n is an integer index to the pixel using linear array indexing.

  	bool pixel(T * p, unsigned n){
  
  		unsigned bandnum = R[0] * R[1];		//calculate numbers in one band
  		if ( n >= bandnum){							//make sure the pixel number is right
  			std::cout<<"ERROR: sample or line out of range"<<std::endl;
  			return false;
  		}
  
  		file.seekg(n * sizeof(T), std::ios::beg);           //point to the certain pixel
  		for (unsigned i = 0; i < R[2]; i++)
  		{
  			file.read((char *)(p + i), sizeof(T));
  			file.seekg((bandnum - 1) * sizeof(T), std::ios::cur);    //go to the next band
  		}
  
  		return true;	
  	}
  

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

  
  	/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
  	/// @param wls is the list of baseline points based on band labels.	

  	bool baseline(std::string outname, std::vector<double> wls )
  	{
  		unsigned N = wls.size();			//get the number of baseline points

  		std::ofstream target(outname.c_str(), std::ios::binary);	//open the target binary file

  		std::string headername = outname + ".hdr";              //the header file name

  
  		//simplify image resolution

  		unsigned int B = R[2];		//calculate the number of bands
  		unsigned int XY = R[0] * R[1];	//calculate the number of pixels in a band

  		unsigned int S = XY * sizeof(T);		//calculate the number of bytes in a band
  
  		double ai, bi;	//stores the two baseline points wavelength surrounding the current band
  		double ci;		//stores the current band's wavelength

  		unsigned control=0;
  
  		T * a;					//pointers to the high and low band images
  		T * b;
  		T * c;				//pointer to the current image
  
  		a = (T*)malloc( S );     //memory allocation
  		b = (T*)malloc( S ); 
  		c = (T*)malloc( S ); 
  
  		if (a == NULL || b == NULL || c == NULL){
  			std::cout<<"ERROR: error allocating memory";
  			exit(1);
  		}
  
  
  		//initialize lownum, highnum, low, high		

  		ai=w[0];

  
  		//if no baseline point is specified at band 0,
  			//set the baseline point at band 0 to 0

  		if(wls[0] != w[0]){

  			bi = wls[control];			
  			memset(a, (char)0, S);
  		}
  		//else get the low band
  		else{
  			control += 1;

  			band(a, ai);

  			bi = wls[control];
  		}
  		//get the high band

  		band(b, bi);

  
  		//correct every band 
  		for(unsigned cii = 0; cii < B; cii++){
  
  			//update baseline points, if necessary

  			if( w[cii] >= bi && cii != B - 1) {

  				//if the high band is now on the last BL point?
  				if (control != N-1) {
  
  					control++;		//increment the index
  
  					std::swap(a, b);	//swap the baseline band pointers
  
  					ai = bi;
  					bi = wls[control];

  					band(b, bi);

  
  				}
  				//if the last BL point on the last band of the file?

  				else if ( wls[control] < w[B - 1]) {

  
  					std::swap(a, b);	//swap the baseline band pointers
  
  					memset(b, (char)0, S);	//clear the high band
  
  					ai = bi;

  					bi = w[B - 1];

  				}
  			}
  
  			//get the current band
  			band_index(c, cii);

  			ci = w[cii];

  			
  			//perform the baseline correction
  			for(unsigned i=0; i < XY; i++){
  				double r = (double) (ci - ai) / (double) (bi - ai);

  				c[i] =(T) ( c[i] - (b[i] - a[i]) * r - a[i] );

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

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

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

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

  
  	/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
  	///	@param w is the label specifying the band that the hyperspectral image will be normalized to.
  	///	@param t is a threshold specified such that a spectrum with a value at w less than t is set to zero. Setting this threshold allows the user to limit division by extremely small numbers.

  	bool normalize(std::string outname, double w, double t = 0.0)

  	{

  		unsigned int B = R[2];		//calculate the number of bands
  		unsigned int XY = R[0] * R[1];	//calculate the number of pixels in a band

  		unsigned int S = XY * sizeof(T);		//calculate the number of bytes in a band
  
  		std::ofstream target(outname.c_str(), std::ios::binary);	//open the target binary file
  		std::string headername = outname + ".hdr";              //the header file name
  
  		T * b;					//pointers to the certain wavelength band
  		T * c;				//pointer to the current image
  
  		b = (T*)malloc( S );     //memory allocation
  		c = (T*)malloc( S ); 
  

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

  
  		for(unsigned j = 0; j < B; j++)
  		{
  			band_index(c, j);                     //get the current band into memory
  			for(unsigned i = 0; i < XY; i++)
  			{

  				if(b[i] < t)
  					c[i] = (T)0.0;
  				else
  					c[i] = c[i] / b[i];

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

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

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

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

  
  	/// @param outname is the name of the output BIP file to be saved to disk.

  	bool bip(std::string outname)
  	{

  		std::string temp = outname + "_temp";
  		std::string headtemp = temp + ".hdr";
  		//first creat a temporary bil file and convert bsq file to bil file
  		bil(temp);
  

  		stim::bil<T> n;

  		if(n.open(temp, R[0], R[1], R[2], offset, w)==false){        //open infile

  			std::cout<<"ERROR: unable to open input file"<<std::endl;
  			exit(1);

  		}

  		//then convert bil file to bip file
  		n.bip(outname);
  		n.close();
  		remove(temp.c_str());
  		remove(headtemp.c_str());

  		return true;
  	}

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

  
  	/// @param outname is the name of the output BIL file to be saved to disk.

  	bool bil(std::string outname)
  	{
  		//simplify image resolution

  		unsigned int L = R[0] * R[2] * sizeof(T);		//calculate the number of bytes of a ZX slice

  		unsigned int jump = (R[1] - 1) * R[0] * sizeof(T);

  		
  		std::ofstream target(outname.c_str(), std::ios::binary);
  		std::string headername = outname + ".hdr";
  		
  		T * p;			//pointer to the current spectrum
  		p = (T*)malloc(L);
  		

  		for ( unsigned i = 0; i < R[1]; i++)

  		{

  			file.seekg(R[0] * i * sizeof(T), std::ios::beg);
  			for ( unsigned j = 0; j < R[2]; j++ )

  			{

  				file.read((char *)(p + j * R[0]), sizeof(T) * R[0]);

  				file.seekg(jump, std::ios::cur);    //go to the next band	
  			}					
  			target.write(reinterpret_cast<const char*>(p), L);   //write XZ slice data into target file	
  		}

  		//header.interleave = rts::envi_header::BIL;  //change the type of file in header file
  		//header.save(headername);

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

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

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

  	bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
  
  		unsigned XY = R[0] * R[1];
  		band(result, wavelength);		//get band
  
  		//perform the baseline correction
  		double r = (double) (wavelength - lb) / (double) (rb - lb);
  		for(unsigned i=0; i < XY; i++){
  			result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
  		}
  		return true;
  	}

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

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

  	bool height(double lb, double rb, double bandwavelength, T* result){

  
  		T* lp;
  		T* rp;

  		unsigned XY = R[0] * R[1];
  		unsigned S = XY * sizeof(T);
  		lp = (T*) malloc(S);			//memory allocation
  		rp = (T*) malloc(S);

  		band(lp, lb);

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

  		free(lp);
  		free(rp);

  		return true;
  	}
  

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

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

  	bool area(double lb, double rb, double lab, double rab, T* result){

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

  
  		unsigned XY = R[0] * R[1];
  		unsigned S = XY * sizeof(T);
  
  		lp = (T*) malloc(S);			//memory allocation
  		rp = (T*) malloc(S);
  		cur = (T*) malloc(S);
  		cur2 = (T*) malloc(S);

  
  		memset(result, (char)0, S);
  
  		//find the wavelenght position in the whole band
  		unsigned int n = w.size();
  		unsigned int ai = 0;		//left bound position
  		unsigned int bi = n - 1;		//right bound position
  
  
  
  		//to make sure the left and the right bound are in the bandwidth
  		if (lb < w[0] || rb < w[0] || lb > w[n-1] || rb >w[n-1]){
  			std::cout<<"ERROR: left bound or right bound out of bandwidth"<<std::endl;
  			exit(1);
  		}
  		//to make sure rigth bound is bigger than left bound
  		else if(lb > rb){
  			std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
  			exit(1);
  		}
  
  		//get the position of lb and rb

  		while (lab >= w[ai]){

  			ai++;
  		}

  		while (rab <= w[bi]){

  			bi--;
  		}
  
  		band(lp, lb);
  		band(rp, rb);
  
  		//calculate the beginning and the ending part

  		baseline_band(lb, rb, lp, rp, rab, cur2);		//ending part
  		baseline_band(lb, rb, lp, rp, w[bi], cur);

  		for(unsigned j = 0; j < XY; j++){

  			result[j] += (rab - w[bi]) * (cur[j] + cur2[j]) / 2.0;

  		}

  		baseline_band(lb, rb, lp, rp, lab, cur2);		//beginnning part
  		baseline_band(lb, rb, lp, rp, w[ai], cur);

  		for(unsigned j = 0; j < XY; j++){	

  			result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;

  		}

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

  		free(lp);
  		free(rp);
  		free(cur);
  		free(cur2);

  		return true;
  	}
  

  	/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.

  
  	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
  	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
  	/// @param pos1 is the label value for the first peak (numerator) position
  	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
  	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
  	/// @param pos2 is the label value for the second peak (denominator) position
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size

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

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

  
  		free(p1);
  		free(p2);

  		return true;	
  	}
  	

  	/// Compute the ratio between a peak area and peak height.

  
  	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
  	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
  	/// @param pos1 is the label value for the first peak (numerator) position
  	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
  	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
  	/// @param pos2 is the label value for the second peak (denominator) position
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size

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