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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>
#include <utility>
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//CUDA
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#ifdef CUDA_FOUND
#include <cuda_runtime.h>
#include "cublas_v2.h"
#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++;
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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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}
/// 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);
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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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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, unsigned long long 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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added an inverse ...
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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
len = 0; //initialize the
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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|
|
f6169dea
heziqi
Ziqi completed bi...
|
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|
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a23c4132
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Doxygen comments ...
|
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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.
|
63fc1df8
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added an inverse ...
|
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|
bool bil(std::string outname, bool PROGRESS = false)
|
11f177d5
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Ziqi added functi...
|
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|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
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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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fixed linux compa...
|
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|
|
11f177d5
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Ziqi added functi...
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std::ofstream target(outname.c_str(), std::ios::binary);
|
9d3ba0b1
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//std::string headername = outname + ".hdr";
|
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fixed linux compa...
|
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|
|
f6169dea
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Ziqi completed bi...
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|
T * p; //pointer to the current ZX slice for bip file
|
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Ziqi added functi...
|
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|
p = (T*)malloc(S);
|
f6169dea
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Ziqi completed bi...
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T * q; //pointer to the current XZ slice for bil file
q = (T*)malloc(S);
|
1a224b6a
David Mayerich
fixed linux compa...
|
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|
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9d3ba0b1
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added stim::hsi a...
|
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|
for ( unsigned long long i = 0; i < Y(); i++)
|
1a224b6a
David Mayerich
fixed linux compa...
|
402
|
{
|
724ec347
David Mayerich
simplified the EN...
|
403
|
read_plane_y(p, i);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
404
|
for ( unsigned long long k = 0; k < Z(); k++)
|
f6169dea
heziqi
Ziqi completed bi...
|
405
|
{
|
9d3ba0b1
David Mayerich
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|
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|
unsigned long long ks = k * X();
for ( unsigned long long j = 0; j < X(); j++)
|
724ec347
David Mayerich
simplified the EN...
|
408
|
q[ks + j] = p[k + j * Z()];
|
cbce396e
David Mayerich
added support for...
|
409
|
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63fc1df8
David Mayerich
added an inverse ...
|
410
|
if(PROGRESS) progress = (double)(i * Z() + k+1) / (Y() * Z()) * 100;
|
f6169dea
heziqi
Ziqi completed bi...
|
411
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
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|
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
|
11f177d5
heziqi
Ziqi added functi...
|
413
|
}
|
f6169dea
heziqi
Ziqi completed bi...
|
414
|
|
11f177d5
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Ziqi added functi...
|
415
|
free(p);
|
f6169dea
heziqi
Ziqi completed bi...
|
416
|
free(q);
|
11f177d5
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Ziqi added functi...
|
417
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|
target.close();
return true;
}
|
88c3e636
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Ziqi added big.h
|
420
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
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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.
|
20c212c0
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Ziqi added functi...
|
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|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
431
|
unsigned long long XY = X() * Y();
|
20c212c0
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Ziqi added functi...
|
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433
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435
|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
436
|
for(unsigned long long i=0; i < XY; i++){
|
20c212c0
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Ziqi added functi...
|
437
438
439
440
|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
441
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
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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.
|
70407ea9
heziqi
Ziqi completed he...
|
448
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
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Ziqi added functi...
|
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|
T* lp;
T* rp;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
452
453
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
70407ea9
heziqi
Ziqi completed he...
|
454
455
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
456
|
|
70407ea9
heziqi
Ziqi completed he...
|
457
|
band(lp, lb);
|
1a224b6a
David Mayerich
fixed linux compa...
|
458
|
band(rp, rb);
|
20c212c0
heziqi
Ziqi added functi...
|
459
460
461
|
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
462
463
|
free(lp);
free(rp);
|
20c212c0
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Ziqi added functi...
|
464
465
466
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
467
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
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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
|
70407ea9
heziqi
Ziqi completed he...
|
475
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
476
477
478
479
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|
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
|
20c212c0
heziqi
Ziqi added functi...
|
481
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
482
483
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
20c212c0
heziqi
Ziqi added functi...
|
484
485
486
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488
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
489
490
491
492
|
memset(result, (char)0, S);
//find the wavelenght position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
493
494
495
|
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long bi = n - 1; //right bound position
|
20c212c0
heziqi
Ziqi added functi...
|
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506
507
508
509
510
|
//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
|
70407ea9
heziqi
Ziqi completed he...
|
511
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
512
513
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
514
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
515
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517
518
519
520
521
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
522
523
|
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...
|
524
525
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((rab - w[bi]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
526
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
527
528
|
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...
|
529
|
for(unsigned long long j = 0; j < XY; j++){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
530
|
result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
531
|
}
|
517876d6
heziqi
metrics finished ...
|
532
|
|
20c212c0
heziqi
Ziqi added functi...
|
533
534
|
//calculate the area
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
535
|
for(unsigned long long i = ai; i <= bi ;i++)
|
20c212c0
heziqi
Ziqi added functi...
|
536
537
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
538
|
for(unsigned long long j = 0; j < XY; j++)
|
20c212c0
heziqi
Ziqi added functi...
|
539
|
{
|
1a224b6a
David Mayerich
fixed linux compa...
|
540
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
541
542
543
|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
544
|
|
517876d6
heziqi
metrics finished ...
|
545
546
547
548
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
549
550
551
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
552
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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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
561
|
bool ph_to_ph(T* result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask = NULL){
|
70407ea9
heziqi
Ziqi completed he...
|
562
|
|
1a224b6a
David Mayerich
fixed linux compa...
|
563
564
565
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
566
567
568
569
|
//get the two peak band
height(lb1, rb1, pos1, p1);
height(lb2, rb2, pos2, p2);
//calculate the ratio in result
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
570
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
571
572
573
574
575
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
576
577
578
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
579
|
return true;
|
70407ea9
heziqi
Ziqi completed he...
|
580
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
581
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
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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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
591
592
|
bool pa_to_ph(T* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, unsigned char* mask = NULL){
|
1a224b6a
David Mayerich
fixed linux compa...
|
593
594
595
596
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
597
598
599
600
|
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
height(lb2, rb2, pos, p2);
//calculate the ratio in result
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
601
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
602
603
604
605
606
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
607
608
609
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
610
611
612
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
613
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617
618
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621
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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...
|
622
|
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
|
a23c4132
David Mayerich
Doxygen comments ...
|
623
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
624
625
|
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...
|
626
627
628
629
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
630
631
632
633
|
//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...
|
634
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
635
636
637
638
639
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
640
641
642
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
643
644
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
645
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
646
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648
649
650
651
652
|
/// 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
|
517876d6
heziqi
metrics finished ...
|
653
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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...
|
659
660
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
661
662
663
664
665
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667
668
669
|
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...
|
670
671
672
|
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long bi = n - 1; //right bound position
|
517876d6
heziqi
metrics finished ...
|
673
674
675
676
677
678
679
680
681
682
683
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685
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689
690
691
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693
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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...
|
699
700
|
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);
|
517876d6
heziqi
metrics finished ...
|
701
702
703
|
}
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...
|
704
|
for(unsigned long long j = 0; j < XY; j++){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
705
|
result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
706
707
708
709
|
}
//calculate f(x) times x
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
710
|
for(unsigned long long i = ai; i <= bi ;i++)
|
517876d6
heziqi
metrics finished ...
|
711
712
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
713
|
for(unsigned long long j = 0; j < XY; j++)
|
517876d6
heziqi
metrics finished ...
|
714
|
{
|
1a224b6a
David Mayerich
fixed linux compa...
|
715
|
result[j] += (T)((w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
716
717
718
719
720
721
722
723
724
725
726
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
727
728
729
730
731
732
733
|
/// 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...
|
734
|
bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
|
1a224b6a
David Mayerich
fixed linux compa...
|
735
736
737
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
738
739
740
741
|
//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...
|
742
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
743
|
if(mask == NULL || mask[i])
|
517876d6
heziqi
metrics finished ...
|
744
745
746
747
748
|
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
749
|
return true;
|
517876d6
heziqi
metrics finished ...
|
750
751
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
752
753
754
755
756
757
758
|
/// 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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
759
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
|
4a6f666c
heziqi
Added mask method
|
760
|
|
724ec347
David Mayerich
simplified the EN...
|
761
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
798cea97
David Mayerich
added progress ba...
|
762
|
band(temp, mask_band, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
763
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
764
|
for (unsigned long long i = 0; i < X() * Y();i++) {
|
798cea97
David Mayerich
added progress ba...
|
765
|
if (temp[i] < threshold)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
766
|
mask[i] = 0;
|
798cea97
David Mayerich
added progress ba...
|
767
|
else
|
ba51ae6a
David Mayerich
fixed metric calc...
|
768
|
mask[i] = 255;
|
4a6f666c
heziqi
Added mask method
|
769
770
|
}
|
517876d6
heziqi
metrics finished ...
|
771
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
772
773
774
775
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
776
777
778
779
|
/// 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...
|
780
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
781
782
783
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
784
785
|
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
|
786
|
|
1a55a328
David Mayerich
Added comments fo...
|
787
|
T * temp = (T*)malloc(L); //allocate space for that page
|
740f8cd2
heziqi
added apply_mask
|
788
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
789
|
for (unsigned long long i = 0; i < Y(); i++) //for each page (Y in BIP)
|
740f8cd2
heziqi
added apply_mask
|
790
|
{
|
724ec347
David Mayerich
simplified the EN...
|
791
|
read_plane_y(temp, i); //load that page (it's pointed to by temp)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
792
|
for ( unsigned long long j = 0; j < X(); j++) //for each X value
|
740f8cd2
heziqi
added apply_mask
|
793
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
794
|
for (unsigned long long k = 0; k < Z(); k++) //for each B value (band)
|
740f8cd2
heziqi
added apply_mask
|
795
|
{
|
724ec347
David Mayerich
simplified the EN...
|
796
797
|
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...
|
798
|
else //otherwise just continue
|
740f8cd2
heziqi
added apply_mask
|
799
800
801
|
continue;
}
}
|
1a55a328
David Mayerich
Added comments fo...
|
802
|
target.write(reinterpret_cast<const char*>(temp), L); //write the edited band data into target file
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
803
|
if(PROGRESS) progress = (double)(i+1) / (double)Y() * 100;
|
740f8cd2
heziqi
added apply_mask
|
804
|
}
|
1a55a328
David Mayerich
Added comments fo...
|
805
806
807
|
target.close(); //close the target file
free(temp); //free allocated memory
return true; //return true
|
740f8cd2
heziqi
added apply_mask
|
808
809
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
810
811
812
813
814
815
816
817
818
819
820
|
/// Copies all spectra corresponding to nonzero values of a mask into a pre-allocated matrix of size (B x P)
/// where P is the number of masked pixels and B is the number of bands. The allocated memory can be accessed
/// using the following indexing: i = p*B + b
/// @param matrix is the destination for the pixel data
/// @param mask is the mask
bool sift(T* matrix, unsigned char* mask){
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...
|
821
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
822
823
824
825
826
827
828
829
830
831
832
|
size_t p = 0; //create counter variables
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
if(mask[xy]){ //if the current pixel is masked
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...
|
833
|
file.seekg(Bbytes, std::ios::cur); //otherwise skip this band
|
ba51ae6a
David Mayerich
fixed metric calc...
|
834
835
836
|
}
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
837
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
838
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
839
|
bool sift(std::string outfile, unsigned char* mask, bool PROGRESS = false){
|
8550e94f
David Mayerich
added sifting and...
|
840
841
|
//reset the file pointer to the beginning of the file
|
1a224b6a
David Mayerich
fixed linux compa...
|
842
|
file.seekg(0, std::ios::beg);
|
8550e94f
David Mayerich
added sifting and...
|
843
844
|
// open an output stream
|
e843658b
Brad Deutsch
Previous push did...
|
845
846
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
8550e94f
David Mayerich
added sifting and...
|
847
|
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
848
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
849
|
T* spectrum = (T*) malloc(B * sizeof(T));
|
e843658b
Brad Deutsch
Previous push did...
|
850
|
|
8550e94f
David Mayerich
added sifting and...
|
851
|
//calculate the number of pixels in a band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
852
|
unsigned long long XY = X() * Y();
|
e843658b
Brad Deutsch
Previous push did...
|
853
|
|
8550e94f
David Mayerich
added sifting and...
|
854
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
855
856
|
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...
|
857
858
859
860
861
|
//if the current pixel isn't masked
if( mask[x] == 0){
//increment the number of skipped pixels
skip++;
|
e843658b
Brad Deutsch
Previous push did...
|
862
|
}
|
8550e94f
David Mayerich
added sifting and...
|
863
864
865
866
867
868
869
870
871
872
873
874
875
876
|
//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...
|
877
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
878
|
if(PROGRESS) progress = (double) (x+1) / XY * 100;
|
8550e94f
David Mayerich
added sifting and...
|
879
|
|
e843658b
Brad Deutsch
Previous push did...
|
880
|
}
|
8550e94f
David Mayerich
added sifting and...
|
881
882
|
//close the output file
|
e843658b
Brad Deutsch
Previous push did...
|
883
|
target.close();
|
8550e94f
David Mayerich
added sifting and...
|
884
|
free(spectrum);
|
cbce396e
David Mayerich
added support for...
|
885
|
|
cbce396e
David Mayerich
added support for...
|
886
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
887
888
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
889
|
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...
|
890
891
892
893
894
|
// 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...
|
895
|
file.seekg(0, std::ios::beg);
|
8550e94f
David Mayerich
added sifting and...
|
896
897
|
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
898
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
899
900
901
902
903
904
905
|
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...
|
906
|
unsigned long long XY = samples * lines;
|
8550e94f
David Mayerich
added sifting and...
|
907
908
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
909
910
|
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...
|
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
|
//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...
|
928
|
if(PROGRESS) progress = (double)(x + 1) / XY * 100;
|
3150c537
David Mayerich
added further pro...
|
929
|
|
8550e94f
David Mayerich
added sifting and...
|
930
931
932
933
934
935
|
}
//close the output file
target.close();
free(spectrum);
|
a2bf1d08
David Mayerich
general bug fixes...
|
936
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
937
|
|
e843658b
Brad Deutsch
Previous push did...
|
938
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
939
940
|
|
e843658b
Brad Deutsch
Previous push did...
|
941
942
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
943
944
945
946
|
/// 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
|
63fc1df8
David Mayerich
added an inverse ...
|
947
|
bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
948
949
950
951
952
953
954
955
956
957
958
959
960
961
|
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
|
a43c4fe1
heziqi
Added crop in env...
|
962
963
|
}
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
964
|
if(PROGRESS) progress = (double)(i+1) / XY * 100; //increment the progress
|
a43c4fe1
heziqi
Added crop in env...
|
965
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
966
|
|
a43c4fe1
heziqi
Added crop in env...
|
967
|
free(temp);
|
a43c4fe1
heziqi
Added crop in env...
|
968
969
|
return true;
}
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
970
971
|
#ifdef CUDA_FOUND
/// Calculate the covariance matrix for masked pixels using cuBLAS
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
972
|
/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
|
63fc1df8
David Mayerich
added an inverse ...
|
973
|
bool co_matrix_cublas(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
974
|
|
1a224b6a
David Mayerich
fixed linux compa...
|
975
|
cudaError_t cudaStat;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
976
977
|
cublasStatus_t stat;
cublasHandle_t handle;
|
1a224b6a
David Mayerich
fixed linux compa...
|
978
|
|
63fc1df8
David Mayerich
added an inverse ...
|
979
|
progress = 0; //initialize the progress to zero (0)
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
980
981
982
983
984
985
986
987
988
989
990
|
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...
|
991
|
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...
|
992
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
993
994
995
996
997
998
999
1000
1001
|
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
|
5a5359da
David Mayerich
fixed - allows th...
|
1002
1003
|
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...
|
1004
1005
1006
|
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...
|
1007
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1008
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
|
5a5359da
David Mayerich
fixed - allows th...
|
1009
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1010
1011
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1012
|
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...
|
1013
1014
1015
1016
1017
|
cudaFree(A_dev); //clean up allocated device memory
cudaFree(s_dev);
cudaFree(avg_dev);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1018
1019
|
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...
|
1020
1021
1022
1023
|
co[B * i + j] = co[B * j + i];
}
}
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1024
1025
1026
|
return true;
}
#endif
|
1a224b6a
David Mayerich
fixed linux compa...
|
1027
|
|
2aa68315
David Mayerich
major bug fixes f...
|
1028
|
/// Calculate the covariance matrix for all masked pixels in the image with 64-bit floating point precision.
|
a23c4132
David Mayerich
Doxygen comments ...
|
1029
1030
1031
1032
|
/// @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
|
63fc1df8
David Mayerich
added an inverse ...
|
1033
|
bool co_matrix(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1034
1035
|
#ifdef CUDA_FOUND
|
b37665a9
David Mayerich
cuBLAS won't run ...
|
1036
1037
1038
1039
1040
1041
|
int dev_count;
cudaGetDeviceCount(&dev_count); //get the number of CUDA devices
cudaDeviceProp prop;
cudaGetDeviceProperties(&prop, 0); //get the property of the first device
if(dev_count > 0 && prop.major != 9999) //if the first device is not an emulator
return co_matrix_cublas(co, avg, mask, PROGRESS); //use cuBLAS to calculate the covariance matrix
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1042
|
#endif
|
63fc1df8
David Mayerich
added an inverse ...
|
1043
|
progress = 0;
|
a43c4fe1
heziqi
Added crop in env...
|
1044
|
//memory allocation
|
2aa68315
David Mayerich
major bug fixes f...
|
1045
1046
|
unsigned long long XY = X() * Y();
unsigned long long B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
1047
|
T* temp = (T*)malloc(sizeof(T) * B);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1048
1049
|
unsigned long long count = nnz(mask); //count the number of masked pixels
|
63fc1df8
David Mayerich
added an inverse ...
|
1050
|
|
2aa68315
David Mayerich
major bug fixes f...
|
1051
1052
1053
1054
|
//initialize covariance matrix
memset(co, 0, B * B * sizeof(double));
//calculate covariance matrix
|
2aa68315
David Mayerich
major bug fixes f...
|
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
|
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...
|
1068
1069
|
}
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1070
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1071
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
1072
1073
1074
1075
|
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...
|
1076
1077
1078
|
}
}
|
a43c4fe1
heziqi
Added crop in env...
|
1079
|
free(temp);
|
2aa68315
David Mayerich
major bug fixes f...
|
1080
|
free(temp_precise);
|
a43c4fe1
heziqi
Added crop in env...
|
1081
1082
1083
|
return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1084
|
bool project(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask = NULL, bool PROGRESS = false){
|
63fc1df8
David Mayerich
added an inverse ...
|
1085
1086
|
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1087
|
//std::string headername = outfile + ".hdr"; //the header file name
|
63fc1df8
David Mayerich
added an inverse ...
|
1088
1089
1090
1091
1092
1093
1094
1095
1096
|
//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...
|
1097
1098
1099
1100
1101
1102
1103
1104
|
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 ...
|
1105
1106
|
}
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
1107
|
|
63fc1df8
David Mayerich
added an inverse ...
|
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
|
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
|
1a224b6a
David Mayerich
fixed linux compa...
|
1137
|
for(unsigned long long b = 0; b < B; b++){ //for each component of the basis vector
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1138
|
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 ...
|
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
|
}
}
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
|
1153
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1154
1155
1156
1157
1158
1159
1160
|
/// 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...
|
1161
1162
1163
1164
1165
|
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 ...
|
1166
1167
|
unsigned long long b1,
bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1168
|
|
3033b886
David Mayerich
implemented spect...
|
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
|
//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
|
a43c4fe1
heziqi
Added crop in env...
|
1180
|
T* temp = (T*)malloc(L);
|
3033b886
David Mayerich
implemented spect...
|
1181
1182
|
//open an output file for binary writing
|
a43c4fe1
heziqi
Added crop in env...
|
1183
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
3033b886
David Mayerich
implemented spect...
|
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
|
//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++)
|
a43c4fe1
heziqi
Added crop in env...
|
1199
|
{
|
3033b886
David Mayerich
implemented spect...
|
1200
|
for (unsigned x = 0; x < samples; x++)
|
a43c4fe1
heziqi
Added crop in env...
|
1201
|
{
|
3033b886
David Mayerich
implemented spect...
|
1202
1203
1204
|
//read the cropped spectral region
file.read( (char*) temp, L );
//pixel(temp, sp + x + y * X());
|
1a224b6a
David Mayerich
fixed linux compa...
|
1205
|
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
|
3150c537
David Mayerich
added further pro...
|
1206
|
|
3033b886
David Mayerich
implemented spect...
|
1207
1208
|
file.seekg(jump_sample, std::ios::cur);
|
63fc1df8
David Mayerich
added an inverse ...
|
1209
|
if(PROGRESS) progress = (double)((y+1) * samples + x + 1) / (lines * samples) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1210
|
}
|
3033b886
David Mayerich
implemented spect...
|
1211
1212
|
file.seekg(jump_line, std::ios::cur);
|
a43c4fe1
heziqi
Added crop in env...
|
1213
1214
|
}
free(temp);
|
3150c537
David Mayerich
added further pro...
|
1215
|
|
a43c4fe1
heziqi
Added crop in env...
|
1216
1217
1218
|
return true;
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1219
1220
1221
1222
1223
1224
1225
1226
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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);
}
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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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1a224b6a
David Mayerich
fixed linux compa...
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1286
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if(PROGRESS) progress = (double)( (y+1) * S[0] + 1) / (double) (S[0] * S[1]) * 100;
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2ce6954b
David Mayerich
added the ability...
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}
}
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9b2a5d71
David Mayerich
implemented finit...
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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)
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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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9b2a5d71
David Mayerich
implemented finit...
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std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
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1a224b6a
David Mayerich
fixed linux compa...
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9b2a5d71
David Mayerich
implemented finit...
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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)
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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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9b2a5d71
David Mayerich
implemented finit...
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}
}
out.write((char*)outspec, Nb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
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9d77bbd9
David Mayerich
updates for HSIvi...
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1328
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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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9b2a5d71
David Mayerich
implemented finit...
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std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
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1a224b6a
David Mayerich
fixed linux compa...
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9b2a5d71
David Mayerich
implemented finit...
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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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9b2a5d71
David Mayerich
implemented finit...
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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
|
9d77bbd9
David Mayerich
updates for HSIvi...
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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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9b2a5d71
David Mayerich
implemented finit...
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}
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9b2a5d71
David Mayerich
implemented finit...
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}
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9b2a5d71
David Mayerich
implemented finit...
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out.write((char*)outspec, Bb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
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dc8eb8aa
David Mayerich
added band trimmi...
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1385
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0df38ff3
heziqi
fixed head detached
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1386
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a23c4132
David Mayerich
Doxygen comments ...
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1387
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/// Close the file.
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f6169dea
heziqi
Ziqi completed bi...
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bool close(){
file.close();
return true;
}
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88c3e636
heziqi
Ziqi added big.h
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1393
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};
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6aa04ba2
David Mayerich
interleave types
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}
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e8eb202f
David Mayerich
added a new ENVI ...
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#endif
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