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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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}
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bool spectrum(T* p, size_t n, bool PROGRESS = false){
size_t y = n / X();
size_t x = n - y * X();
return read_line_0(p, x, y, PROGRESS); //read a line in the binary YZ plane (dimension order for BIP is ZXY)
}
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/// Retrieves a band of x values from a given xz plane.
/// @param p is a pointer to pre-allocated memory at least X * sizeof(T) in size
/// @param c is a pointer to an existing XZ plane (size X*Z*sizeof(T))
/// @param wavelength is the wavelength of X values to retrieve
bool read_x_from_xz(T* p, T* c, double wavelength)
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{
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unsigned long long B = Z();
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unsigned long long page=0; //samples around the wavelength
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//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
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if ( w[page] > wavelength ){
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for(unsigned long long j = 0; j < X(); j++)
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{
p[j] = c[j * B];
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}
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return true;
}
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while( w[page] < wavelength )
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{
page++;
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if (page == B) {
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for(unsigned long long j = 0; j < X(); j++)
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{
p[j] = c[(j + 1) * B - 1];
}
return true;
}
}
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if ( wavelength < w[page] )
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{
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T * p1;
T * p2;
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p1=(T*)malloc( X() * sizeof(T)); //memory allocation
p2=(T*)malloc( X() * sizeof(T));
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//band_index(p1, page - 1);
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for(unsigned long long j = 0; j < X(); j++)
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{
p1[j] = c[j * B + page - 1];
}
//band_index(p2, page );
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for(unsigned long long j = 0; j < X(); j++)
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{
p2[j] = c[j * B + page];
}
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for(unsigned long long i=0; i < X(); i++){
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double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
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p[i] = (p2[i] - p1[i]) * r + p1[i];
}
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free(p1);
free(p2);
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}
else //if the wavelength is equal to a wavelength in header file
{
//band_index(p, page);
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for(unsigned long long j = 0; j < X(); j++)
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{
p[j] = c[j * B + page];
}
}
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return true;
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}
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/// Retrieve a single pixel and store it in a pre-allocated double array.
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bool pixeld(double* p, unsigned long long n){
unsigned long long bandnum = X() * Y(); //calculate numbers in one band
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if ( n >= bandnum){ //make sure the pixel number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
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unsigned long long B = Z();
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T* temp = (T*) malloc(B * sizeof(T)); //allocate space for the raw pixel data
file.seekg(n * B * sizeof(T), std::ios::beg); //point to the certain pixel
file.read((char *)temp, sizeof(T) * B); //read the spectrum from disk to the temp pointer
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for(unsigned long long i = 0; i < B; i++) //for each element of the spectrum
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p[i] = (double) temp[i]; //cast each element to a double value
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free(temp); //free temporary memory
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return true;
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}
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/// Retrieve a single pixel and stores it in pre-allocated memory.
/// @param p is a pointer to pre-allocated memory at least sizeof(T) in size.
/// @param n is an integer index to the pixel using linear array indexing.
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bool pixel(T * p, unsigned long long n){
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unsigned long long N = X() * Y(); //calculate numbers in one band
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if ( n >= N){ //make sure the pixel number is right
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std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
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file.seekg(n * Z() * sizeof(T), std::ios::beg); //point to the certain pixel
file.read((char *)p, sizeof(T) * Z());
return true;
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}
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//given a Y ,return a ZX slice
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bool read_plane_y(T * p, 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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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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|
/// Convert the current BIP file to a BIL file with the specified file name.
/// @param outname is the name of the output BIL file to be saved to disk.
|
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bool bil(std::string outname, bool PROGRESS = false)
|
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{
|
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unsigned long long S = X() * Z() * sizeof(T); //calculate the number of bytes in a ZX slice
|
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Ziqi added functi...
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std::ofstream target(outname.c_str(), std::ios::binary);
|
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//std::string headername = outname + ".hdr";
|
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T * p; //pointer to the current ZX slice for bip file
|
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Ziqi added functi...
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p = (T*)malloc(S);
|
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T * q; //pointer to the current XZ slice for bil file
q = (T*)malloc(S);
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fixed linux compa...
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|
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for ( unsigned long long i = 0; i < Y(); i++)
|
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fixed linux compa...
|
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|
{
|
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|
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|
read_plane_y(p, i);
|
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added stim::hsi a...
|
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|
for ( unsigned long long k = 0; k < Z(); k++)
|
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{
|
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unsigned long long ks = k * X();
for ( unsigned long long j = 0; j < X(); j++)
|
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|
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|
q[ks + j] = p[k + j * Z()];
|
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|
415
|
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added an inverse ...
|
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|
if(PROGRESS) progress = (double)(i * Z() + k+1) / (Y() * Z()) * 100;
|
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|
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}
|
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|
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
|
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|
}
|
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Ziqi completed bi...
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Ziqi added functi...
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|
free(p);
|
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|
free(q);
|
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|
target.close();
return true;
}
|
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Ziqi added big.h
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|
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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.
|
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bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
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|
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unsigned long long XY = X() * Y();
|
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Ziqi added functi...
|
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|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
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added stim::hsi a...
|
442
|
for(unsigned long long i=0; i < XY; i++){
|
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Ziqi added functi...
|
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|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
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|
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|
|
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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.
|
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Ziqi completed he...
|
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|
bool height(double lb, double rb, double bandwavelength, T* result){
|
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Ziqi added functi...
|
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|
T* lp;
T* rp;
|
9d3ba0b1
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added stim::hsi a...
|
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|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
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Ziqi completed he...
|
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|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
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Ziqi added functi...
|
462
|
|
70407ea9
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Ziqi completed he...
|
463
|
band(lp, lb);
|
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David Mayerich
fixed linux compa...
|
464
|
band(rp, rb);
|
20c212c0
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Ziqi added functi...
|
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|
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
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metrics finished ...
|
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469
|
free(lp);
free(rp);
|
20c212c0
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Ziqi added functi...
|
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|
return true;
}
|
c359422d
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Ziqi added functi...
|
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|
|
a23c4132
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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
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Ziqi completed he...
|
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|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
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Ziqi added functi...
|
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484
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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
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Ziqi added functi...
|
487
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
488
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|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
20c212c0
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Ziqi added functi...
|
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|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
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Ziqi added functi...
|
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|
memset(result, (char)0, S);
//find the wavelenght position in the whole band
|
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David Mayerich
added stim::hsi a...
|
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|
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long bi = n - 1; //right bound position
|
20c212c0
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Ziqi added functi...
|
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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
|
70407ea9
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Ziqi completed he...
|
517
|
while (lab >= w[ai]){
|
20c212c0
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Ziqi added functi...
|
518
519
|
ai++;
}
|
70407ea9
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Ziqi completed he...
|
520
|
while (rab <= w[bi]){
|
20c212c0
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Ziqi added functi...
|
521
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|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
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Ziqi completed he...
|
528
529
|
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...
|
530
531
|
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...
|
532
|
}
|
70407ea9
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Ziqi completed he...
|
533
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|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
1a224b6a
David Mayerich
fixed linux compa...
|
535
|
for(unsigned long long j = 0; j < XY; j++){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
536
|
result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
537
|
}
|
517876d6
heziqi
metrics finished ...
|
538
|
|
20c212c0
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Ziqi added functi...
|
539
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|
//calculate the area
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
541
|
for(unsigned long long i = ai; i <= bi ;i++)
|
20c212c0
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Ziqi added functi...
|
542
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|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
544
|
for(unsigned long long j = 0; j < XY; j++)
|
20c212c0
heziqi
Ziqi added functi...
|
545
|
{
|
1a224b6a
David Mayerich
fixed linux compa...
|
546
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
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Ziqi added functi...
|
547
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|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
550
|
|
517876d6
heziqi
metrics finished ...
|
551
552
553
554
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
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Ziqi added functi...
|
555
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|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
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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...
|
567
|
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...
|
568
|
|
1a224b6a
David Mayerich
fixed linux compa...
|
569
570
571
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
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Ziqi completed he...
|
572
573
574
575
|
//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...
|
576
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
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Ziqi completed he...
|
577
578
579
580
581
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
582
583
584
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
585
|
return true;
|
70407ea9
heziqi
Ziqi completed he...
|
586
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
587
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
588
589
590
591
592
593
594
595
596
|
/// 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...
|
597
598
|
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...
|
599
600
601
602
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
603
604
605
606
|
//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...
|
607
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
608
609
610
611
612
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
613
614
615
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
616
617
618
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
619
620
621
622
623
624
625
626
627
|
/// 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...
|
628
|
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
|
a23c4132
David Mayerich
Doxygen comments ...
|
629
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
630
631
|
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...
|
632
633
634
635
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
636
637
638
639
|
//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...
|
640
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
641
642
643
644
645
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
646
647
648
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
649
650
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
651
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
652
653
654
655
656
657
658
|
/// 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 ...
|
659
660
661
662
663
664
|
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...
|
665
666
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
667
668
669
670
671
672
673
674
675
|
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...
|
676
677
678
|
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 ...
|
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
|
//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...
|
705
706
|
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 ...
|
707
708
709
|
}
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...
|
710
|
for(unsigned long long j = 0; j < XY; j++){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
711
|
result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
712
713
714
715
|
}
//calculate f(x) times x
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
716
|
for(unsigned long long i = ai; i <= bi ;i++)
|
517876d6
heziqi
metrics finished ...
|
717
718
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
719
|
for(unsigned long long j = 0; j < XY; j++)
|
517876d6
heziqi
metrics finished ...
|
720
|
{
|
1a224b6a
David Mayerich
fixed linux compa...
|
721
|
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 ...
|
722
723
724
725
726
727
728
729
730
731
732
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
733
734
735
736
737
738
739
|
/// 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...
|
740
|
bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
|
1a224b6a
David Mayerich
fixed linux compa...
|
741
742
743
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
744
745
746
747
|
//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...
|
748
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
749
|
if(mask == NULL || mask[i])
|
517876d6
heziqi
metrics finished ...
|
750
751
752
753
754
|
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
755
|
return true;
|
517876d6
heziqi
metrics finished ...
|
756
757
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
758
759
760
761
762
763
764
|
/// 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...
|
765
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
|
4a6f666c
heziqi
Added mask method
|
766
|
|
724ec347
David Mayerich
simplified the EN...
|
767
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
798cea97
David Mayerich
added progress ba...
|
768
|
band(temp, mask_band, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
769
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
770
|
for (unsigned long long i = 0; i < X() * Y();i++) {
|
798cea97
David Mayerich
added progress ba...
|
771
|
if (temp[i] < threshold)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
772
|
mask[i] = 0;
|
798cea97
David Mayerich
added progress ba...
|
773
|
else
|
ba51ae6a
David Mayerich
fixed metric calc...
|
774
|
mask[i] = 255;
|
4a6f666c
heziqi
Added mask method
|
775
776
|
}
|
517876d6
heziqi
metrics finished ...
|
777
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
778
779
780
781
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
782
783
784
785
|
/// 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...
|
786
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
787
788
789
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
790
791
|
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
|
792
|
|
1a55a328
David Mayerich
Added comments fo...
|
793
|
T * temp = (T*)malloc(L); //allocate space for that page
|
740f8cd2
heziqi
added apply_mask
|
794
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
795
|
for (unsigned long long i = 0; i < Y(); i++) //for each page (Y in BIP)
|
740f8cd2
heziqi
added apply_mask
|
796
|
{
|
724ec347
David Mayerich
simplified the EN...
|
797
|
read_plane_y(temp, i); //load that page (it's pointed to by temp)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
798
|
for ( unsigned long long j = 0; j < X(); j++) //for each X value
|
740f8cd2
heziqi
added apply_mask
|
799
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
800
|
for (unsigned long long k = 0; k < Z(); k++) //for each B value (band)
|
740f8cd2
heziqi
added apply_mask
|
801
|
{
|
724ec347
David Mayerich
simplified the EN...
|
802
803
|
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...
|
804
|
else //otherwise just continue
|
740f8cd2
heziqi
added apply_mask
|
805
806
807
|
continue;
}
}
|
1a55a328
David Mayerich
Added comments fo...
|
808
|
target.write(reinterpret_cast<const char*>(temp), L); //write the edited band data into target file
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
809
|
if(PROGRESS) progress = (double)(i+1) / (double)Y() * 100;
|
740f8cd2
heziqi
added apply_mask
|
810
|
}
|
1a55a328
David Mayerich
Added comments fo...
|
811
812
813
|
target.close(); //close the target file
free(temp); //free allocated memory
return true; //return true
|
740f8cd2
heziqi
added apply_mask
|
814
815
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
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
|
814eb271
David Mayerich
fixed problems wi...
|
821
|
bool sift(T* matrix, unsigned char* mask = NULL, bool PROGRESS = false){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
822
823
824
825
826
|
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...
|
827
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
828
829
|
size_t p = 0; //create counter variables
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
|
d4aa4cf7
David Mayerich
fixed the in-memo...
|
830
|
if(mask == NULL || mask[xy]){ //if the current pixel is masked
|
ba51ae6a
David Mayerich
fixed metric calc...
|
831
832
833
834
835
836
837
838
|
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...
|
839
|
file.seekg(Bbytes, std::ios::cur); //otherwise skip this band
|
814eb271
David Mayerich
fixed problems wi...
|
840
|
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
841
842
843
|
}
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
844
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
845
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
846
|
bool sift(std::string outfile, unsigned char* mask, bool PROGRESS = false){
|
8550e94f
David Mayerich
added sifting and...
|
847
848
|
//reset the file pointer to the beginning of the file
|
1a224b6a
David Mayerich
fixed linux compa...
|
849
|
file.seekg(0, std::ios::beg);
|
8550e94f
David Mayerich
added sifting and...
|
850
851
|
// open an output stream
|
e843658b
Brad Deutsch
Previous push did...
|
852
853
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
8550e94f
David Mayerich
added sifting and...
|
854
|
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
855
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
856
|
T* spectrum = (T*) malloc(B * sizeof(T));
|
e843658b
Brad Deutsch
Previous push did...
|
857
|
|
8550e94f
David Mayerich
added sifting and...
|
858
|
//calculate the number of pixels in a band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
859
|
unsigned long long XY = X() * Y();
|
e843658b
Brad Deutsch
Previous push did...
|
860
|
|
8550e94f
David Mayerich
added sifting and...
|
861
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
862
863
|
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...
|
864
865
866
867
868
|
//if the current pixel isn't masked
if( mask[x] == 0){
//increment the number of skipped pixels
skip++;
|
e843658b
Brad Deutsch
Previous push did...
|
869
|
}
|
8550e94f
David Mayerich
added sifting and...
|
870
871
872
873
874
875
876
877
878
879
880
881
882
883
|
//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...
|
884
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
885
|
if(PROGRESS) progress = (double) (x+1) / XY * 100;
|
8550e94f
David Mayerich
added sifting and...
|
886
|
|
e843658b
Brad Deutsch
Previous push did...
|
887
|
}
|
8550e94f
David Mayerich
added sifting and...
|
888
889
|
//close the output file
|
e843658b
Brad Deutsch
Previous push did...
|
890
|
target.close();
|
8550e94f
David Mayerich
added sifting and...
|
891
|
free(spectrum);
|
cbce396e
David Mayerich
added support for...
|
892
|
|
cbce396e
David Mayerich
added support for...
|
893
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
894
895
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
896
|
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...
|
897
898
899
900
901
|
// 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...
|
902
|
file.seekg(0, std::ios::beg);
|
8550e94f
David Mayerich
added sifting and...
|
903
904
|
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
905
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
906
907
908
909
910
911
912
|
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...
|
913
|
unsigned long long XY = samples * lines;
|
8550e94f
David Mayerich
added sifting and...
|
914
915
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
916
917
|
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...
|
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
|
//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...
|
935
|
if(PROGRESS) progress = (double)(x + 1) / XY * 100;
|
3150c537
David Mayerich
added further pro...
|
936
|
|
8550e94f
David Mayerich
added sifting and...
|
937
938
939
940
941
942
|
}
//close the output file
target.close();
free(spectrum);
|
a2bf1d08
David Mayerich
general bug fixes...
|
943
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
944
|
|
e843658b
Brad Deutsch
Previous push did...
|
945
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
946
947
|
|
e843658b
Brad Deutsch
Previous push did...
|
948
949
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
950
951
952
953
|
/// 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 ...
|
954
|
bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
955
956
957
958
959
960
961
962
963
964
965
966
967
968
|
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...
|
969
970
|
}
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
971
|
if(PROGRESS) progress = (double)(i+1) / XY * 100; //increment the progress
|
a43c4fe1
heziqi
Added crop in env...
|
972
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
973
|
|
a43c4fe1
heziqi
Added crop in env...
|
974
|
free(temp);
|
a43c4fe1
heziqi
Added crop in env...
|
975
976
|
return true;
}
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
977
978
|
#ifdef CUDA_FOUND
/// Calculate the covariance matrix for masked pixels using cuBLAS
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
979
|
/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
|
63fc1df8
David Mayerich
added an inverse ...
|
980
|
bool co_matrix_cublas(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
981
|
|
1a224b6a
David Mayerich
fixed linux compa...
|
982
|
cudaError_t cudaStat;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
983
984
|
cublasStatus_t stat;
cublasHandle_t handle;
|
1a224b6a
David Mayerich
fixed linux compa...
|
985
|
|
63fc1df8
David Mayerich
added an inverse ...
|
986
|
progress = 0; //initialize the progress to zero (0)
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
987
988
989
990
991
992
993
994
995
996
997
|
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...
|
998
|
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...
|
999
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1000
1001
1002
1003
1004
1005
1006
1007
1008
|
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...
|
1009
1010
|
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...
|
1011
1012
1013
|
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...
|
1014
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1015
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
|
5a5359da
David Mayerich
fixed - allows th...
|
1016
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1017
1018
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1019
|
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...
|
1020
1021
1022
1023
1024
|
cudaFree(A_dev); //clean up allocated device memory
cudaFree(s_dev);
cudaFree(avg_dev);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1025
1026
|
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...
|
1027
1028
1029
1030
|
co[B * i + j] = co[B * j + i];
}
}
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1031
1032
1033
|
return true;
}
#endif
|
1a224b6a
David Mayerich
fixed linux compa...
|
1034
|
|
2aa68315
David Mayerich
major bug fixes f...
|
1035
|
/// Calculate the covariance matrix for all masked pixels in the image with 64-bit floating point precision.
|
a23c4132
David Mayerich
Doxygen comments ...
|
1036
1037
1038
1039
|
/// @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 ...
|
1040
|
bool co_matrix(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1041
1042
|
#ifdef CUDA_FOUND
|
b37665a9
David Mayerich
cuBLAS won't run ...
|
1043
1044
1045
1046
1047
1048
|
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...
|
1049
|
#endif
|
63fc1df8
David Mayerich
added an inverse ...
|
1050
|
progress = 0;
|
a43c4fe1
heziqi
Added crop in env...
|
1051
|
//memory allocation
|
2aa68315
David Mayerich
major bug fixes f...
|
1052
1053
|
unsigned long long XY = X() * Y();
unsigned long long B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
1054
|
T* temp = (T*)malloc(sizeof(T) * B);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1055
1056
|
unsigned long long count = nnz(mask); //count the number of masked pixels
|
63fc1df8
David Mayerich
added an inverse ...
|
1057
|
|
2aa68315
David Mayerich
major bug fixes f...
|
1058
1059
1060
1061
|
//initialize covariance matrix
memset(co, 0, B * B * sizeof(double));
//calculate covariance matrix
|
2aa68315
David Mayerich
major bug fixes f...
|
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
|
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...
|
1075
1076
|
}
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1077
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1078
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
1079
1080
1081
1082
|
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...
|
1083
1084
1085
|
}
}
|
a43c4fe1
heziqi
Added crop in env...
|
1086
|
free(temp);
|
2aa68315
David Mayerich
major bug fixes f...
|
1087
|
free(temp_precise);
|
a43c4fe1
heziqi
Added crop in env...
|
1088
1089
1090
|
return true;
}
|
812a2741
David Mayerich
added documentati...
|
1091
1092
1093
1094
1095
1096
|
/// Project the spectra onto a set of basis functions
/// @param outfile is the name of the new binary output file that will be created
/// @param center is a spectrum about which the data set will be rotated (ex. when performing mean centering)
/// @param basis a set of basis vectors that the data set will be projected onto (after centering)
/// @param M is the number of basis vectors
/// @param mask is a character mask used to limit processing to valid pixels
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1097
|
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 ...
|
1098
1099
|
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1100
|
//std::string headername = outfile + ".hdr"; //the header file name
|
63fc1df8
David Mayerich
added an inverse ...
|
1101
1102
1103
1104
1105
1106
1107
1108
1109
|
//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...
|
1110
1111
1112
1113
1114
1115
1116
1117
|
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 ...
|
1118
1119
|
}
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
1120
|
|
63fc1df8
David Mayerich
added an inverse ...
|
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
|
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...
|
1150
|
for(unsigned long long b = 0; b < B; b++){ //for each component of the basis vector
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1151
|
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 ...
|
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
|
}
}
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
|
1166
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1167
1168
1169
1170
1171
1172
1173
|
/// 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...
|
1174
1175
1176
1177
1178
|
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 ...
|
1179
1180
|
unsigned long long b1,
bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1181
|
|
3033b886
David Mayerich
implemented spect...
|
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
|
//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...
|
1193
|
T* temp = (T*)malloc(L);
|
3033b886
David Mayerich
implemented spect...
|
1194
1195
|
//open an output file for binary writing
|
a43c4fe1
heziqi
Added crop in env...
|
1196
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
3033b886
David Mayerich
implemented spect...
|
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
|
//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...
|
1212
|
{
|
3033b886
David Mayerich
implemented spect...
|
1213
|
for (unsigned x = 0; x < samples; x++)
|
a43c4fe1
heziqi
Added crop in env...
|
1214
|
{
|
3033b886
David Mayerich
implemented spect...
|
1215
1216
1217
|
//read the cropped spectral region
file.read( (char*) temp, L );
//pixel(temp, sp + x + y * X());
|
1a224b6a
David Mayerich
fixed linux compa...
|
1218
|
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
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3150c537
David Mayerich
added further pro...
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1219
|
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3033b886
David Mayerich
implemented spect...
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1220
1221
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file.seekg(jump_sample, std::ios::cur);
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63fc1df8
David Mayerich
added an inverse ...
|
1222
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if(PROGRESS) progress = (double)((y+1) * samples + x + 1) / (lines * samples) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1223
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}
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3033b886
David Mayerich
implemented spect...
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1224
1225
|
file.seekg(jump_line, std::ios::cur);
|
a43c4fe1
heziqi
Added crop in env...
|
1226
1227
|
}
free(temp);
|
3150c537
David Mayerich
added further pro...
|
1228
|
|
a43c4fe1
heziqi
Added crop in env...
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1229
1230
1231
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return true;
}
|
dc8eb8aa
David Mayerich
added band trimmi...
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1232
1233
1234
1235
1236
1237
1238
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/// Remove a list of bands from the ENVI file
/// @param outfile is the file name for the output hyperspectral image (with trimmed bands)
/// @param b is an array of bands to be eliminated
void trim(std::string outfile, std::vector<size_t> band_array, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
file.seekg(0, std::ios::beg); //move to the beginning of the input file
size_t B = Z(); //calculate the number of elements in a spectrum
size_t Bdst = Z() - band_array.size(); //calculate the number of elements in an output spectrum
size_t Bb = B * sizeof(T); //calculate the number of bytes in a spectrum
size_t XY = X() * Y(); //calculate the number of pixels in the image
T* src = (T*)malloc(Bb); //allocate space to store an input spectrum
T* dst = (T*)malloc(Bdst * sizeof(T)); //allocate space to store an output spectrum
size_t i; //index into the band array
size_t bdst; //index into the output array
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
i = 0;
bdst = 0;
file.read((char*)src, Bb); //read a spectrum
for(size_t b = 0; b < B; b++){ //for each band
if(b != band_array[i]){ //if the band isn't trimmed
dst[bdst] = src[b]; //copy the band value to the output spectrum
bdst++;
}
else i++; //otherwise increment i
}
out.write((char*)dst, Bdst * sizeof(T)); //write the output spectrum
if(PROGRESS) progress = (double)(xy + 1) / (double) XY * 100;
}
free(src);
free(dst);
}
|
2ce6954b
David Mayerich
added the ability...
|
1268
1269
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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
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
1299
|
if(PROGRESS) progress = (double)( (y+1) * S[0] + 1) / (double) (S[0] * S[1]) * 100;
|
2ce6954b
David Mayerich
added the ability...
|
1300
1301
1302
|
}
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1303
1304
1305
1306
1307
1308
1309
1310
|
/// Convolve the given band range with a kernel specified by a vector of coefficients.
/// @param outfile is an already open stream to the output file
/// @param C is an array of coefficients
/// @param start is the band to start processing (the first coefficient starts here)
/// @param nbands is the number of bands to process
/// @param center is the index for the center coefficient for the kernel (used to set the wavelengths in the output file)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1311
|
void convolve(std::string outfile, std::vector<double> C, size_t start, size_t end, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1312
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
|
1a224b6a
David Mayerich
fixed linux compa...
|
1313
|
|
9b2a5d71
David Mayerich
implemented finit...
|
1314
1315
1316
1317
1318
1319
1320
1321
1322
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1327
1328
|
size_t N = end - start + 1; //number of bands in the output spectrum
size_t Nb = N * sizeof(T); //size of the output spectrum in bytes
size_t B = Z(); //calculate the number of values in a spectrum
size_t Bb = B * sizeof(T); //calculate the size of a spectrum in bytes
file.seekg(0, std::ios::beg); //move to the beginning of the input file
size_t nC = C.size(); //get the number of bands that the kernel spans
T* inspec = (T*)malloc(Bb); //allocate space for the input spectrum
T* outspec = (T*)malloc(Nb); //allocate space for the output spectrum
size_t XY = X() * Y(); //number of pixels in the image
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
file.read((char*)inspec, Bb); //read an input spectrum
memset(outspec, 0, Nb); //set the output spectrum to zero (0)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1329
1330
1331
1332
1333
|
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
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1334
1335
1336
1337
1338
1339
1340
|
}
}
out.write((char*)outspec, Nb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1341
|
void deriv(std::string outfile, size_t d, size_t order, const std::vector<double> w, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1342
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
|
1a224b6a
David Mayerich
fixed linux compa...
|
1343
1344
|
|
9b2a5d71
David Mayerich
implemented finit...
|
1345
1346
1347
1348
1349
1350
1351
1352
1353
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1355
1356
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1358
1359
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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...
|
1366
1367
1368
|
if(mask == NULL || mask[xy]){
iw = 0;
for(size_t b = 0; b < mid; b++){ //for each component of the spectrum
|
9b2a5d71
David Mayerich
implemented finit...
|
1369
1370
|
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...
|
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
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1382
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1384
1385
1386
1387
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1390
|
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
|
9b2a5d71
David Mayerich
implemented finit...
|
1391
|
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1392
|
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1393
1394
1395
1396
1397
|
out.write((char*)outspec, Bb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1398
|
|
0df38ff3
heziqi
fixed head detached
|
1399
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1400
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
1401
1402
1403
1404
1405
|
bool close(){
file.close();
return true;
}
|
88c3e636
heziqi
Ziqi added big.h
|
1406
|
};
|
6aa04ba2
David Mayerich
interleave types
|
1407
|
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1408
1409
|
#endif
|