stim/envi/hsi.h

#ifndef STIM_HSI_H
#define STIM_HSI_H
#include "../envi/envi_header.h"
#include "../envi/binary.h"
#include <cstring>
#include <utility>
#ifdef _WIN32
	#include <float.h>
#else
	#include<cmath>
#endif
namespace stim{
/**
	The BIL class represents a 3-dimensional binary file stored using band interleaved by line (BIL) image encoding. The binary file is stored
	such that X-Z "frames" are stored sequentially to form an image stack along the y-axis. When accessing the data sequentially on disk,
	the dimensions read, from fastest to slowest, are X, Z, Y.
	This class is optimized for data streaming, and therefore supports extremely large (terabyte-scale) files. Data is loaded from disk
	on request. Functions used to access data are written to support efficient reading.
*/
template <typename T>
class hsi: public binary<T> {
protected:
	unsigned char O[3];					//order of dimensions (orientation on disk)
										//[X Y B]: [0 1 2] = bsq, [0 2 1] = bil, [1 2 0] = bip
	std::vector<double> w;		//band wavelengths
	unsigned long long X(){ return R[O[0]]; }
	unsigned long long Y(){ return R[O[1]]; }
	unsigned long long Z(){ return R[O[2]]; }
	/// Initialize axis orders based on common interleave formats
	void init_bsq(){ O[0] = 0; O[1] = 1; O[2] = 2; }
	void init_bil(){ O[0] = 0; O[1] = 2; O[2] = 1; }
	void init_bip(){ O[0] = 1; O[1] = 2; O[2] = 0; }
	/// Calculate the number of masked pixels in a given mask
	unsigned long long nnz(unsigned char* mask){
		unsigned long long XY = X() * Y();							//calculate the total number of pixels in the HSI
		if(mask == NULL) return XY;									//if the mask is null, assume that all of the pixels are masked
		unsigned long long n = 0;									//initialize the number of masked pixels to zero (0)
		for(unsigned long long xy = 0; xy < XY; xy++)				//for each pixel in the HSI
			if(mask[xy]) n++;										//if the mask value is nonzero, increment the number of masked pixels
		return n;													//return the number of masked pixels
	}
	T lerp(double w, T low_v, double low_w, T high_v, double high_w){
		if(low_w == high_w) return low_v;										//if the interval is of zero length, just return one of the bounds
		double alpha = (w - low_w) / (high_w - low_w);							//calculate the interpolation factor
		return (T)((1.0 - alpha) * low_v + alpha * high_v);							//interpolate
	}
	/// Gets the two band indices surrounding a given wavelength
	void band_bounds(double wavelength, unsigned long long& low, unsigned long long& high){
		unsigned long long B = Z();
		for(high = 0; high < B; high++){
			if(w[high] > wavelength) break;
		}
		low = 0;
		if(high > 0)
			low = high-1;
	}
	/// Get the list of band numbers that bound a list of wavelengths
	void band_bounds(std::vector<double> wavelengths, 
					 std::vector<unsigned long long>& low_bands, 
					 std::vector<unsigned long long>& high_bands){
		unsigned long long W = w.size();									//get the number of wavelengths in the list
		low_bands.resize(W);												//pre-allocate space for the band lists
		high_bands.resize(W);
		for(unsigned long long wl = 0; wl < W; wl++){						//for each wavelength
			band_bounds(wavelengths[wl], low_bands[wl], high_bands[wl]);	//find the low and high bands
		}
	}
	/// Returns the interpolated in the given spectrum based on the given wavelength
	/// @param s is the spectrum in main memory of length Z()
	/// @param wavelength is the wavelength value to interpolate out
	T interp_spectrum(T* s, double wavelength){
		unsigned long long low, high;								//indices for the bands surrounding wavelength
		band_bounds(wavelength, low, high);							//get the surrounding band indices
		if(high == w.size()) return s[w.size()-1];					//if the high band is above the wavelength range, return the highest wavelength value
		
		return lerp(wavelength, s[low], w[low], s[high], w[high]);
	}
	/// Returns the interpolated value corresponding to the given list of wavelengths
	std::vector<T> interp_spectrum(T* s, std::vector<double> wavelengths){
		unsigned long long N = wavelengths.size();						//get the number of wavelength measurements
		std::vector<T> v;												//allocate space for the resulting values
		v.resize(wavelengths.size());
		for(unsigned long long n = 0; n < N; n++){						//for each measurement
			v[n] = interp_spectrum(s, wavelengths[n]);					//interpolate the measurement
		}
		return v;
	}
	/// Returns the 1D on-disk index of a specified pixel location and band
	size_t idx(size_t x, size_t y, size_t b){
		size_t c[3];										//generate a coefficient list
		c[O[0]] = x;										//assign the coordinates based on the coefficient order
		c[O[1]] = y;
		c[O[2]] = b;
		return c[2] * R[0] * R[1] + c[1] * R[0] + c[0];		//calculate and return the index (trust me this works)
	}
	/// Returns the 3D coordinates of a specified index
	void xyb(size_t idx, size_t& x, size_t& y, size_t& b){
		size_t c[3];
		c[2] = idx / (R[0] * R[1]);
		c[1] = (idx - c[2] * R[0] * R[1]) / R[0];
		c[0] = idx - c[2] * R[0] * R[1] - c[1] * R[0];
		x = c[O[0]];
		y = c[O[1]];
		b = c[O[2]];
	}
public:
			/// Get a mask that has all pixels with inf or NaN values masked out (false)
	void mask_finite(unsigned char* mask, bool PROGRESS = false){
		size_t XY = X() * Y();
		memset(mask, 255, XY * sizeof(unsigned char));				//initialize the mask to zero (0)
		T* page = (T*)malloc(R[0] * R[1] * sizeof(T));		//allocate space for a page of data
		
		for(size_t p = 0; p < R[2]; p++){					//for each page
			binary<T>::read_page(page, p);					//read a page
			for(size_t i = 0; i < R[0] * R[1]; i++){		//for each pixel in that page
				
#ifdef _WIN32
				if(!_finite(page[i])){						//if the value at index i is finite
#else
				if(!std::isfinite(page[i])){					//C++11 implementation
#endif
					size_t x, y, b;
					xyb(p * R[0] * R[1] + i, x, y, b);							//find the 3D coordinates of the value
					mask[ y * X() + x ] = 0;				//mask the pixel (it's not bad)
				}
			}
			if(PROGRESS) progress = (double)(p + 1) / (double)R[2] * 100;
		}
	}
	void calc_combined_size(long long xp, long long yp, long long Sx, long long Sy,
							size_t& Sfx, size_t& Sfy){
		long long left = std::min<long long>(0, xp);										//calculate the left edge of the final image
		long long right = std::max<long long>((long long)X(), Sx + xp);						//calculate the right edge of the final image
		long long top = std::min<long long>(0, yp);											//calculate the top edge of the final image
		long long bottom = std::max<long long>((long long)Y(), Sy + yp);					//calculate the bottom edge of the final image
		Sfx = right - left;
		Sfy = bottom - top;													//calculate the size of the final image
	}
	/// Calculates the necessary image size required to combine two images given the specified offset (position) of the second image
	void calc_combined_size(long long xp, long long yp, long long Sx, long long Sy, 
							size_t& Sfx, size_t& Sfy,
							size_t& p0_x, size_t& p0_y,
							size_t& p1_x, size_t& p1_y){
		calc_combined_size(xp, yp, Sx, Sy, Sfx, Sfy);
		p0_x = p0_y = p1_x = p1_y = 0;										//initialize all boundary positions to zero
		
		if(xp < 0) p0_x = -xp;												//set the left positions of the current and source image
		else p1_x = xp;
		if(yp < 0) p0_y = -yp;
		else p1_y = yp;
	}
	/// Inserts an image of a band into a larger image
	void pad_band(T* padded, T* src, size_t x0, size_t x1, size_t y0, size_t y1){
		size_t w = X();										//calculate the number of pixels in a line
		size_t wb = w * sizeof(T);							//calculate the number of bytes in a line
		pw = (X() + x0 + x1);								//calculate the width of the padded image
		pwb = pw * sizeof(T);								//calculate the number of bytes in a line of the padded image
		for(size_t y = 0; y < Y(); y++){								//for each line in the real image
			memcpy( &padded[ (y + y0) * pw + x0 ], &src[y * w], wb );	//use memcpy to copy the line to the appropriate place in the padded image
		}
	}
};
}		//end namespace STIM
#endif