bip.h
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#ifndef STIM_BIP_H
#define STIM_BIP_H
#include "../envi/envi_header.h"
#include "../envi/bil.h"
#include "../envi/hsi.h"
#include <cstring>
#include <utility>
//CUDA
#include <cuda_runtime.h>
#include "cublas_v2.h"
namespace stim{
/**
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.
*/
template <typename T>
class bip: public hsi<T> {
protected:
//std::vector<double> w; //band wavelength
unsigned long long offset; //header offset
/*unsigned long long X(){
return R[1];
}
unsigned long long Y(){
return R[2];
}
unsigned long long Z(){
return R[0];
}*/
using hsi<T>::w; //use the wavelength array in stim::hsi
using hsi<T>::nnz;
using binary<T>::progress;
/// Call the binary nnz() function for the BIP orientation
//unsigned long long nnz(unsigned char* mask){
// return binary<T>::nnz(mask, X()*Y());
//}
/// Linear interpolation of a spectral value given the bounding spectral samples
/*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 (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;
}*/
public:
using binary<T>::open;
using binary<T>::file;
using binary<T>::R;
using binary<T>::read_line_0;
bip(){ hsi<T>::init_bip(); }
/// Open a data file for reading using the class interface.
/// @param filename is the name of the binary file on disk
/// @param X is the number of samples along dimension 1
/// @param Y is the number of samples (lines) along dimension 2
/// @param B is the number of samples (bands) along dimension 3
/// @param header_offset is the number of bytes (if any) in the binary header
/// @param wavelengths is an optional STL vector of size B specifying a numerical label for each band
bool open(std::string filename,
unsigned long long X,
unsigned long long Y,
unsigned long long B,
unsigned long long header_offset,
std::vector<double> wavelengths){
//copy the wavelengths to the BSQ file structure
w = wavelengths;
//copy the offset to the structure
offset = header_offset;
return open(filename, vec<unsigned long long>(B, X, Y), header_offset);
}
/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
/// @param page <= B is the integer number of the band to be copied.
bool band_index( T * p, unsigned long long page, bool PROGRESS = false){
return binary<T>::read_plane_0(p, page, PROGRESS);
}
/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
/// @param wavelength is a floating point value (usually a wavelength in spectral data) used as a label for the band to be copied.
bool band( T * p, double wavelength, bool PROGRESS = false){
//if there are no wavelengths in the BSQ file
if(w.size() == 0)
return band_index(p, (unsigned long long)wavelength, PROGRESS);
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned page=0; //bands around the wavelength
//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
if ( w[page] > wavelength ){
band_index(p, page, PROGRESS);
return true;
}
while( w[page] < wavelength )
{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == Z()) {
band_index(p, Z()-1, PROGRESS);
return true;
}
}
if ( wavelength < w[page] )
{
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, PROGRESS);
for(unsigned long long i=0; i < XY; i++){
double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
p[i] = (T)(((double)p2[i] - (double)p1[i]) * r + (double)p1[i]);
}
free(p1);
free(p2);
}
else //if the wavelength is equal to a wavelength in header file
{
band_index(p, page, PROGRESS);
}
return true;
}
/// Retrieve a single spectrum (Z-axis line) at a given (x, y) location and stores it in pre-allocated memory.
/// @param p is a pointer to pre-allocated memory at least B * sizeof(T) in size.
/// @param x is the x-coordinate (dimension 1) of the spectrum.
/// @param y is the y-coordinate (dimension 2) of the spectrum.
bool spectrum(T * p, unsigned long long x, unsigned long long y, bool PROGRESS = false){
return read_line_0(p, x, y, PROGRESS); //read a line in the binary YZ plane (dimension order for BIP is ZXY)
}
/// 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)
{
unsigned long long B = Z();
unsigned long long page=0; //samples around the wavelength
//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
if ( w[page] > wavelength ){
for(unsigned long long j = 0; j < X(); j++)
{
p[j] = c[j * B];
}
return true;
}
while( w[page] < wavelength )
{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == B) {
for(unsigned long long j = 0; j < X(); j++)
{
p[j] = c[(j + 1) * B - 1];
}
return true;
}
}
if ( wavelength < w[page] )
{
T * p1;
T * p2;
p1=(T*)malloc( X() * sizeof(T)); //memory allocation
p2=(T*)malloc( X() * sizeof(T));
//band_index(p1, page - 1);
for(unsigned long long j = 0; j < X(); j++)
{
p1[j] = c[j * B + page - 1];
}
//band_index(p2, page );
for(unsigned long long j = 0; j < X(); j++)
{
p2[j] = c[j * B + page];
}
for(unsigned long long i=0; i < X(); 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);
}
else //if the wavelength is equal to a wavelength in header file
{
//band_index(p, page);
for(unsigned long long j = 0; j < X(); j++)
{
p[j] = c[j * B + page];
}
}
return true;
}
/// Retrieve a single pixel and store it in a pre-allocated double array.
bool pixeld(double* p, unsigned long long n){
unsigned long long bandnum = X() * Y(); //calculate numbers in one band
if ( n >= bandnum){ //make sure the pixel number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
unsigned long long B = Z();
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
for(unsigned long long i = 0; i < B; i++) //for each element of the spectrum
p[i] = (double) temp[i]; //cast each element to a double value
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 long long n){
unsigned long long N = X() * Y(); //calculate numbers in one band
if ( n >= N){ //make sure the pixel number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
file.seekg(n * Z() * sizeof(T), std::ios::beg); //point to the certain pixel
file.read((char *)p, sizeof(T) * Z());
return true;
}
//given a Y ,return a ZX slice
bool read_plane_y(T * p, unsigned long long y){
return binary<T>::read_plane_2(p, y);
}
/// Perform baseline correction given a list of baseline points and stores the result in a new BSQ file.
/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
/// @param wls is the list of baseline points based on band labels.
bool baseline(std::string outname, std::vector<double> base_pts, unsigned char* mask = NULL, bool PROGRESS = false){
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
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
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
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{
pixel(s, n); //retrieve the spectrum s
base_vals = interp_spectrum(s, base_pts); //get the values at each baseline point
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
}
sbc[b] = s[b] - lerp(w[b], av, aw, bv, bw); //perform the baseline correction and save the new value
}
}
if(PROGRESS) progress = (double)(n+1) / N * 100; //set the current progress
target.write((char*)sbc, sizeof(T) * B); //write the corrected data into destination
} //end for each pixel
free(s);
free(sbc);
target.close();
return true;
}
/// Normalize all spectra based on the value of a single band, storing the result in a new BSQ file.
/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
/// @param w is the label specifying the band that the hyperspectral image will be normalized to.
/// @param t is a threshold specified such that a spectrum with a value at w less than t is set to zero. Setting this threshold allows the user to limit division by extremely small numbers.
bool normalize(std::string outname, double w, unsigned char* mask = NULL, bool PROGRESS = false)
{
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
T nv; //stores the value of the normalized band
for(unsigned long long n = 0; n < N; n++){ //for each pixel in the image
if(mask != NULL && !mask[n]) //if the normalization band is below threshold
memset(s, 0, sizeof(T) * B); //set the output to zero
else{
pixel(s, n); //retrieve the spectrum s
nv = interp_spectrum(s, w); //find the value of the normalization band
for(unsigned long long b = 0; b < B; b++) //for each band in the spectrum
s[b] /= nv; //divide by the normalization value
}
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);
target.close();
return true;
}
/// 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.
bool bil(std::string outname, bool PROGRESS = false)
{
unsigned long long S = X() * Z() * sizeof(T); //calculate the number of bytes in a ZX slice
std::ofstream target(outname.c_str(), std::ios::binary);
//std::string headername = outname + ".hdr";
T * p; //pointer to the current ZX slice for bip file
p = (T*)malloc(S);
T * q; //pointer to the current XZ slice for bil file
q = (T*)malloc(S);
for ( unsigned long long i = 0; i < Y(); i++)
{
read_plane_y(p, i);
for ( unsigned long long k = 0; k < Z(); k++)
{
unsigned long long ks = k * X();
for ( unsigned long long j = 0; j < X(); j++)
q[ks + j] = p[k + j * Z()];
if(PROGRESS) progress = (double)(i * Z() + k+1) / (Y() * Z()) * 100;
}
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
}
free(p);
free(q);
target.close();
return true;
}
/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lp is a pointer to an array holding the band image for the left baseline point
/// @param rp is a pointer to an array holding the band image for the right baseline point
/// @param wavelength is the label value for the requested baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
unsigned long long XY = X() * Y();
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
for(unsigned long long i=0; i < XY; i++){
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param bandwavelength is the label value for the desired baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
bool height(double lb, double rb, double bandwavelength, T* result){
T* lp;
T* rp;
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
band(lp, lb);
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
free(lp);
free(rp);
return true;
}
/// Calculate the area under the spectrum between two specified points and stores the result in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label value for the left bound (start of the integration)
/// @param rab is the label value for the right bound (end of the integration)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
bool area(double lb, double rb, double lab, double rab, T* result){
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
memset(result, (char)0, S);
//find the wavelenght position in the whole band
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long bi = n - 1; //right bound position
//to make sure the left and the right bound are in the bandwidth
if (lb < w[0] || rb < w[0] || lb > w[n-1] || rb >w[n-1]){
std::cout<<"ERROR: left bound or right bound out of bandwidth"<<std::endl;
exit(1);
}
//to make sure rigth bound is bigger than left bound
else if(lb > rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
exit(1);
}
//get the position of lb and rb
while (lab >= w[ai]){
ai++;
}
while (rab <= w[bi]){
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((rab - w[bi]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
}
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
}
//calculate the area
ai++;
for(unsigned long long i = ai; i <= bi ;i++)
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
for(unsigned long long j = 0; j < XY; j++)
{
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param pos1 is the label value for the first peak (numerator) position
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param pos2 is the label value for the second peak (denominator) position
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
//get the two peak band
height(lb1, rb1, pos1, p1);
height(lb2, rb2, pos2, p2);
//calculate the ratio in result
for(unsigned long long i = 0; i < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// Compute the ratio between a peak area and peak height.
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param pos1 is the label value for the first peak (numerator) position
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param pos2 is the label value for the second peak (denominator) position
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
bool pa_to_ph(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, T* result){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
height(lb2, rb2, pos, p2);
//calculate the ratio in result
for(unsigned long long i = 0; i < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// Compute the ratio between two peak areas.
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param lab1 is the label value for the left bound (start of the integration) of the first peak (numerator)
/// @param rab1 is the label value for the right bound (end of the integration) of the first peak (numerator)
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param lab2 is the label value for the left bound (start of the integration) of the second peak (denominator)
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
bool pa_to_pa(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, T* result){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
area(lb2, rb2, lab2, rab2, p2);
//calculate the ratio in result
for(unsigned long long i = 0; i < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// Compute the definite integral of a baseline corrected peak.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label for the start of the definite integral
/// @param rab is the label for the end of the definite integral
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
bool x_area(double lb, double rb, double lab, double rab, T* result){
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
memset(result, (char)0, S);
//find the wavelenght position in the whole band
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long bi = n - 1; //right bound position
//to make sure the left and the right bound are in the bandwidth
if (lb < w[0] || rb < w[0] || lb > w[n-1] || rb >w[n-1]){
std::cout<<"ERROR: left bound or right bound out of bandwidth"<<std::endl;
exit(1);
}
//to make sure rigth bound is bigger than left bound
else if(lb > rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
exit(1);
}
//get the position of lb and rb
while (lab >= w[ai]){
ai++;
}
while (rab <= w[bi]){
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((rab - w[bi]) * (rab + w[bi]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
}
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
}
//calculate f(x) times x
ai++;
for(unsigned long long i = ai; i <= bi ;i++)
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
for(unsigned long long j = 0; j < XY; j++)
{
result[j] += (T)((w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
/// Compute the centroid of a baseline corrected peak.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label for the start of the peak
/// @param rab is the label for the end of the peak
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
bool cpoint(double lb, double rb, double lab, double rab, T* result){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
//get the area and the peak band
x_area(lb, rb, lab, rab, p1);
area(lb, rb, lab, rab, p2);
//calculate the ratio in result
for(unsigned long long i = 0; i < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// Create a mask based on a given band and threshold value.
/// All pixels in the
/// specified band greater than the threshold are true and all pixels less than the threshold are false.
/// @param mask_band is the band used to specify the mask
/// @param threshold is the threshold used to determine if the mask value is true or false
/// @param p is a pointer to a pre-allocated array at least X * Y in size
bool build_mask(double mask_band, double threshold, unsigned char* p, bool PROGRESS = false){
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
band(temp, mask_band, PROGRESS);
for (unsigned long long i = 0; i < X() * Y();i++) {
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
}
free(temp);
return true;
}
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
/// @param outfile is the name of the masked output file
/// @param p is a pointer to memory of size X * Y, where p(i) = 0 for pixels that will be set to zero.
bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
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
T * temp = (T*)malloc(L); //allocate space for that page
for (unsigned long long i = 0; i < Y(); i++) //for each page (Y in BIP)
{
read_plane_y(temp, i); //load that page (it's pointed to by temp)
for ( unsigned long long j = 0; j < X(); j++) //for each X value
{
for (unsigned long long k = 0; k < Z(); k++) //for each B value (band)
{
if (p[i * X() + j] == 0) //if the mask value is zero
temp[j * Z() + k] = 0; //set the pixel value to zero
else //otherwise just continue
continue;
}
}
target.write(reinterpret_cast<const char*>(temp), L); //write the edited band data into target file
}
target.close(); //close the target file
free(temp); //free allocated memory
return true; //return true
}
/// Saves to disk only those spectra corresponding to mask values != 0
bool sift(std::string outfile, unsigned char* mask, bool PROGRESS = false){
//reset the file pointer to the beginning of the file
file.seekg(0, std::ios::beg);
// open an output stream
std::ofstream target(outfile.c_str(), std::ios::binary);
//allocate space for a single spectrum
unsigned long long B = Z();
T* spectrum = (T*) malloc(B * sizeof(T));
//calculate the number of pixels in a band
unsigned long long XY = X() * Y();
//for each pixel
unsigned long long skip = 0; //number of spectra to skip
for(unsigned long long x = 0; x < XY; x++){
//if the current pixel isn't masked
if( mask[x] == 0){
//increment the number of skipped pixels
skip++;
}
//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));
}
if(PROGRESS) progress = (double) (x+1) / XY * 100;
}
//close the output file
target.close();
free(spectrum);
return true;
}
bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines){
// open an output stream
std::ofstream target(outfile.c_str(), std::ios::binary);
//reset the file pointer to the beginning of the file
file.seekg(0, std::ios::beg);
//allocate space for a single spectrum
unsigned long long B = Z();
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
unsigned long long XY = samples * lines;
//for each pixel
unsigned long long skip = 0; //number of spectra to skip
for(unsigned long long x = 0; x < XY; x++){
//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));
}
progress = (double)x / XY * 100;
}
//close the output file
target.close();
free(spectrum);
progress = 100;
return true;
}
/// Calculate the mean value for all masked (or valid) pixels in a band and returns the average spectrum
/// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
unsigned long long XY = X() * Y(); //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
memset(p, 0, sizeof(double) * Z()); //initialize the average spectrum to zero (0)
//for (unsigned j = 0; j < Z(); j++){
// p[j] = 0;
//}
unsigned long long count = nnz(mask); //calculate the number of masked pixels
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
p[j] += (double)temp[j] / (double)count; //add the weighted value to the average
}
}
if(PROGRESS) progress = (double)(i+1) / XY * 100; //increment the progress
}
free(temp);
return true;
}
#ifdef CUDA_FOUND
/// Calculate the covariance matrix for masked pixels using cuBLAS
/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
bool co_matrix_cublas(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
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
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
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
if (stat != CUBLAS_STATUS_SUCCESS) { //test the cuBLAS instance to make sure it is valid
printf ("CUBLAS initialization failed\n");
return EXIT_FAILURE;
}
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
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)
}
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
}
cublasGetMatrix((int)B, (int)B, sizeof(double), A_dev, (int)B, co, (int)B); //copy the result from the GPU to the CPU
cudaFree(A_dev); //clean up allocated device memory
cudaFree(s_dev);
cudaFree(avg_dev);
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++){
co[B * i + j] = co[B * j + i];
}
}
return true;
}
#endif
/// Calculate the covariance matrix for all masked pixels in the image with 64-bit floating point precision.
/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
/// @param avg is a pointer to memory of size B that stores the average spectrum
/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
bool co_matrix(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
#ifdef CUDA_FOUND
return co_matrix_cublas(co, avg, mask, PROGRESS); //if CUDA is available, use cuBLAS to calculate the covariance matrix
#endif
progress = 0;
//memory allocation
unsigned long long XY = X() * Y();
unsigned long long B = Z();
T* temp = (T*)malloc(sizeof(T) * B);
unsigned long long count = nnz(mask); //count the number of masked pixels
//initialize covariance matrix
memset(co, 0, B * B * sizeof(double));
//calculate covariance matrix
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];
}
}
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
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;
}
}
free(temp);
free(temp_precise);
return true;
}
bool project(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask = NULL, 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();
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
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
}
}
}
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
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
for(unsigned long long b = 0; b < B; b++){ //for each component of the basis vector
s[b] += (T)((double)coeff[c] * bv[b] + center[b]); //calculate the contribution of each element of the basis vector in the final spectrum
}
}
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;
}
/// Crop a region of the image and save it to a new file.
/// @param outfile is the file name for the new cropped image
/// @param x0 is the lower-left x pixel coordinate to be included in the cropped image
/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
bool crop(std::string outfile, unsigned long long x0,
unsigned long long y0,
unsigned long long x1,
unsigned long long y1,
unsigned long long b0,
unsigned long long b1,
bool PROGRESS = false){
//calculate the new number of samples, lines, and bands
unsigned long long samples = x1 - x0;
unsigned long long lines = y1 - y0;
unsigned long long bands = b1 - b0;
//calculate the length of one cropped spectrum
unsigned long long L = bands * sizeof(T);
//unsigned long long L = Z() * sizeof(T);
//allocate space for the spectrum
T* temp = (T*)malloc(L);
//open an output file for binary writing
std::ofstream out(outfile.c_str(), std::ios::binary);
//seek to the first pixel in the cropped image
file.seekg( (y0 * X() * Z() + x0 * Z() + b0) * sizeof(T), std::ios::beg);
//distance between sample spectra in the same line
unsigned long long jump_sample = ( (Z() - b1) + b0 ) * sizeof(T);
//distance between sample spectra in adjacent lines
unsigned long long jump_line = (X() - x1) * Z() * sizeof(T);
//unsigned long long sp = y0 * X() + x0; //start pixel
//for each pixel in the image
for (unsigned y = 0; y < lines; y++)
{
for (unsigned x = 0; x < samples; x++)
{
//read the cropped spectral region
file.read( (char*) temp, L );
//pixel(temp, sp + x + y * X());
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
file.seekg(jump_sample, std::ios::cur);
if(PROGRESS) progress = (double)((y+1) * samples + x + 1) / (lines * samples) * 100;
}
file.seekg(jump_line, std::ios::cur);
}
free(temp);
return true;
}
/// Close the file.
bool close(){
file.close();
return true;
}
};
}
#endif