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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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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,
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];
}
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];
}
}
return true;
}
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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.
/// @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{
pixel(s, n); //retrieve the spectrum s
base_vals = interp_spectrum(s, base_pts); //get the values at each baseline point
ai = bi = 0;
aw = w[0]; //initialize the current baseline points (assume the spectrum starts at 0)
av = s[0];
bw = base_pts[0];
for(unsigned long long b = 0; b < B; b++){ //for each band in the spectrum
while(bi < base_pts.size() && base_pts[bi] < w[b]) //while the current wavelength is higher than the second baseline point
bi++; //move to the next baseline point
if(bi < base_pts.size()){
bw = base_pts[bi]; //set the wavelength for the upper bound baseline point
bv = base_vals[bi]; //set the value for the upper bound baseline point
}
if(bi == base_pts.size()){ //if we have passed the last baseline point
bw = w[B-1]; //set the outer bound to the last spectral band
bv = s[B-1];
}
if(bi != 0){
ai = bi - 1; //set the lower bound baseline point index
aw = base_pts[ai]; //set the wavelength for the lower bound baseline point
av = base_vals[ai]; //set the value for the lower bound baseline point
}
sbc[b] = s[b] - lerp(w[b], av, aw, bv, bw); //perform the baseline correction and save the new value
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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 normalize(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
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
nv = interp_spectrum(s, w); //find the value of the normalization band
for(unsigned long long b = 0; b < B; b++) //for each band in the spectrum
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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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/// 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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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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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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for ( unsigned long long i = 0; i < Y(); i++)
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{
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read_plane_y(p, i);
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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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q[ks + j] = p[k + j * Z()];
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if(PROGRESS) progress = (double)(i * Z() + k+1) / (Y() * Z()) * 100;
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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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free(p);
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free(q);
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target.close();
return true;
}
|
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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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unsigned long long XY = X() * Y();
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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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for(unsigned long long i=0; i < XY; i++){
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result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
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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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bool height(double lb, double rb, double bandwavelength, T* result){
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T* lp;
T* rp;
|
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unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
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lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
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band(lp, lb);
|
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band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
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free(lp);
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|
return true;
}
|
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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
|
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|
bool area(double lb, double rb, double lab, double rab, T* result){
|
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T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
|
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unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
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lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
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memset(result, (char)0, S);
//find the wavelenght position in the whole band
|
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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
|
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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
|
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|
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|
while (lab >= w[ai]){
|
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|
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|
ai++;
}
|
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|
while (rab <= w[bi]){
|
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|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
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|
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|
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...
|
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|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((rab - w[bi]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
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|
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|
}
|
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|
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|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
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added stim::hsi a...
|
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|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
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|
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|
}
|
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metrics finished ...
|
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|
|
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|
//calculate the area
ai++;
|
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David Mayerich
added stim::hsi a...
|
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|
for(unsigned long long i = ai; i <= bi ;i++)
|
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|
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|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
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|
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|
for(unsigned long long j = 0; j < XY; j++)
|
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Ziqi added functi...
|
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|
{
|
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added stim::hsi a...
|
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|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
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Ziqi added functi...
|
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|
}
std::swap(cur,cur2); //swap the band pointers
}
|
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|
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|
|
517876d6
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metrics finished ...
|
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|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
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|
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|
return true;
}
|
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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...
|
529
|
bool ph_to_ph(T* result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask = NULL){
|
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|
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|
|
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David Mayerich
simplified the EN...
|
531
532
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
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|
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|
//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...
|
538
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
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|
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|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
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|
544
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|
free(p1);
free(p2);
|
70407ea9
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|
547
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|
return true;
}
|
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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...
|
559
560
|
bool pa_to_ph(T* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, unsigned char* mask = NULL){
|
70407ea9
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|
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|
|
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|
562
563
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
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Ziqi completed he...
|
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|
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
height(lb2, rb2, pos, p2);
//calculate the ratio in result
|
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David Mayerich
added stim::hsi a...
|
569
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
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Ziqi completed he...
|
570
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|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
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metrics finished ...
|
575
576
577
|
free(p1);
free(p2);
|
70407ea9
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Ziqi completed he...
|
578
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|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
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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)
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
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|
592
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|
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){
|
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Ziqi completed he...
|
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|
|
724ec347
David Mayerich
simplified the EN...
|
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|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
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Ziqi completed he...
|
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|
//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...
|
602
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
603
604
605
606
607
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
608
609
610
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
611
612
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
613
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
614
615
616
617
618
619
620
|
/// 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 ...
|
621
622
623
624
625
626
|
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...
|
627
628
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
629
630
631
632
633
634
635
636
637
|
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...
|
638
639
640
|
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 ...
|
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
|
//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...
|
667
668
|
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 ...
|
669
670
671
|
}
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
672
673
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
674
675
676
677
|
}
//calculate f(x) times x
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
678
|
for(unsigned long long i = ai; i <= bi ;i++)
|
517876d6
heziqi
metrics finished ...
|
679
680
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
681
|
for(unsigned long long j = 0; j < XY; j++)
|
517876d6
heziqi
metrics finished ...
|
682
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
683
|
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 ...
|
684
685
686
687
688
689
690
691
692
693
694
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
695
696
697
698
699
700
701
|
/// 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...
|
702
|
bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
|
724ec347
David Mayerich
simplified the EN...
|
703
704
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
705
706
707
708
709
|
//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...
|
710
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
711
|
if(mask == NULL || mask[i])
|
517876d6
heziqi
metrics finished ...
|
712
713
714
715
716
717
718
719
|
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
720
721
722
723
724
725
726
|
/// 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...
|
727
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
|
4a6f666c
heziqi
Added mask method
|
728
|
|
724ec347
David Mayerich
simplified the EN...
|
729
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
798cea97
David Mayerich
added progress ba...
|
730
|
band(temp, mask_band, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
731
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
732
|
for (unsigned long long i = 0; i < X() * Y();i++) {
|
798cea97
David Mayerich
added progress ba...
|
733
|
if (temp[i] < threshold)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
734
|
mask[i] = 0;
|
798cea97
David Mayerich
added progress ba...
|
735
|
else
|
ba51ae6a
David Mayerich
fixed metric calc...
|
736
|
mask[i] = 255;
|
4a6f666c
heziqi
Added mask method
|
737
738
|
}
|
517876d6
heziqi
metrics finished ...
|
739
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
740
741
742
743
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
744
745
746
747
|
/// 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...
|
748
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
749
750
751
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
752
753
|
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
|
754
|
|
1a55a328
David Mayerich
Added comments fo...
|
755
|
T * temp = (T*)malloc(L); //allocate space for that page
|
740f8cd2
heziqi
added apply_mask
|
756
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
757
|
for (unsigned long long i = 0; i < Y(); i++) //for each page (Y in BIP)
|
740f8cd2
heziqi
added apply_mask
|
758
|
{
|
724ec347
David Mayerich
simplified the EN...
|
759
|
read_plane_y(temp, i); //load that page (it's pointed to by temp)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
760
|
for ( unsigned long long j = 0; j < X(); j++) //for each X value
|
740f8cd2
heziqi
added apply_mask
|
761
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
762
|
for (unsigned long long k = 0; k < Z(); k++) //for each B value (band)
|
740f8cd2
heziqi
added apply_mask
|
763
|
{
|
724ec347
David Mayerich
simplified the EN...
|
764
765
|
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...
|
766
|
else //otherwise just continue
|
740f8cd2
heziqi
added apply_mask
|
767
768
769
|
continue;
}
}
|
1a55a328
David Mayerich
Added comments fo...
|
770
|
target.write(reinterpret_cast<const char*>(temp), L); //write the edited band data into target file
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
771
|
if(PROGRESS) progress = (double)(i+1) / (double)Y() * 100;
|
740f8cd2
heziqi
added apply_mask
|
772
|
}
|
1a55a328
David Mayerich
Added comments fo...
|
773
774
775
|
target.close(); //close the target file
free(temp); //free allocated memory
return true; //return true
|
740f8cd2
heziqi
added apply_mask
|
776
777
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
|
/// 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
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
file.seekg(Bbytes, std::ios::cur); //otherwise skip this band
}
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
805
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
806
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
807
|
bool sift(std::string outfile, unsigned char* mask, bool PROGRESS = false){
|
8550e94f
David Mayerich
added sifting and...
|
808
809
810
811
812
|
//reset the file pointer to the beginning of the file
file.seekg(0, std::ios::beg);
// open an output stream
|
e843658b
Brad Deutsch
Previous push did...
|
813
814
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
8550e94f
David Mayerich
added sifting and...
|
815
|
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
816
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
817
|
T* spectrum = (T*) malloc(B * sizeof(T));
|
e843658b
Brad Deutsch
Previous push did...
|
818
|
|
8550e94f
David Mayerich
added sifting and...
|
819
|
//calculate the number of pixels in a band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
820
|
unsigned long long XY = X() * Y();
|
e843658b
Brad Deutsch
Previous push did...
|
821
|
|
8550e94f
David Mayerich
added sifting and...
|
822
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
823
824
|
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...
|
825
826
827
828
829
|
//if the current pixel isn't masked
if( mask[x] == 0){
//increment the number of skipped pixels
skip++;
|
e843658b
Brad Deutsch
Previous push did...
|
830
|
}
|
8550e94f
David Mayerich
added sifting and...
|
831
832
833
834
835
836
837
838
839
840
841
842
843
844
|
//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...
|
845
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
846
|
if(PROGRESS) progress = (double) (x+1) / XY * 100;
|
8550e94f
David Mayerich
added sifting and...
|
847
|
|
e843658b
Brad Deutsch
Previous push did...
|
848
|
}
|
8550e94f
David Mayerich
added sifting and...
|
849
850
|
//close the output file
|
e843658b
Brad Deutsch
Previous push did...
|
851
|
target.close();
|
8550e94f
David Mayerich
added sifting and...
|
852
|
free(spectrum);
|
cbce396e
David Mayerich
added support for...
|
853
|
|
cbce396e
David Mayerich
added support for...
|
854
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
855
856
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
857
|
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...
|
858
859
860
861
862
863
864
865
|
// open an output stream
std::ofstream target(outfile.c_str(), std::ios::binary);
//reset the file pointer to the beginning of the file
file.seekg(0, std::ios::beg);
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
866
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
867
868
869
870
871
872
873
|
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...
|
874
|
unsigned long long XY = samples * lines;
|
8550e94f
David Mayerich
added sifting and...
|
875
876
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
877
878
|
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...
|
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
|
//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...
|
896
|
if(PROGRESS) progress = (double)(x + 1) / XY * 100;
|
3150c537
David Mayerich
added further pro...
|
897
|
|
8550e94f
David Mayerich
added sifting and...
|
898
899
900
901
902
903
|
}
//close the output file
target.close();
free(spectrum);
|
a2bf1d08
David Mayerich
general bug fixes...
|
904
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
905
|
|
e843658b
Brad Deutsch
Previous push did...
|
906
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
907
908
|
|
e843658b
Brad Deutsch
Previous push did...
|
909
910
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
911
912
913
914
|
/// 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 ...
|
915
|
bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
916
917
918
919
920
921
922
923
924
925
926
927
928
929
|
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...
|
930
931
|
}
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
932
|
if(PROGRESS) progress = (double)(i+1) / XY * 100; //increment the progress
|
a43c4fe1
heziqi
Added crop in env...
|
933
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
934
|
|
a43c4fe1
heziqi
Added crop in env...
|
935
|
free(temp);
|
a43c4fe1
heziqi
Added crop in env...
|
936
937
|
return true;
}
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
938
939
|
#ifdef CUDA_FOUND
/// Calculate the covariance matrix for masked pixels using cuBLAS
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
940
|
/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
|
63fc1df8
David Mayerich
added an inverse ...
|
941
|
bool co_matrix_cublas(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
942
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945
946
|
cudaError_t cudaStat;
cublasStatus_t stat;
cublasHandle_t handle;
|
63fc1df8
David Mayerich
added an inverse ...
|
947
|
progress = 0; //initialize the progress to zero (0)
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
948
949
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|
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...
|
959
|
stat = cublasSetVector((int)B, sizeof(double), avg, 1, avg_dev, 1); //copy the average spectrum to the CUDA device
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
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|
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...
|
970
971
|
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...
|
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|
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...
|
975
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}
|
63fc1df8
David Mayerich
added an inverse ...
|
976
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
|
5a5359da
David Mayerich
fixed - allows th...
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c6f526c2
David Mayerich
added cuBLAS supp...
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979
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}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
980
|
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...
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cudaFree(A_dev); //clean up allocated device memory
cudaFree(s_dev);
cudaFree(avg_dev);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
986
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|
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...
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988
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co[B * i + j] = co[B * j + i];
}
}
|
c6f526c2
David Mayerich
added cuBLAS supp...
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994
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return true;
}
#endif
|
a23c4132
David Mayerich
Doxygen comments ...
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995
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2aa68315
David Mayerich
major bug fixes f...
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996
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/// Calculate the covariance matrix for all masked pixels in the image with 64-bit floating point precision.
|
a23c4132
David Mayerich
Doxygen comments ...
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/// @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 ...
|
1001
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bool co_matrix(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
c6f526c2
David Mayerich
added cuBLAS supp...
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#ifdef CUDA_FOUND
|
63fc1df8
David Mayerich
added an inverse ...
|
1004
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return co_matrix_cublas(co, avg, mask, PROGRESS); //if CUDA is available, use cuBLAS to calculate the covariance matrix
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c6f526c2
David Mayerich
added cuBLAS supp...
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1005
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#endif
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63fc1df8
David Mayerich
added an inverse ...
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progress = 0;
|
a43c4fe1
heziqi
Added crop in env...
|
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//memory allocation
|
2aa68315
David Mayerich
major bug fixes f...
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unsigned long long XY = X() * Y();
unsigned long long B = Z();
|
a43c4fe1
heziqi
Added crop in env...
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T* temp = (T*)malloc(sizeof(T) * B);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
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unsigned long long count = nnz(mask); //count the number of masked pixels
|
63fc1df8
David Mayerich
added an inverse ...
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1013
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2aa68315
David Mayerich
major bug fixes f...
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//initialize covariance matrix
memset(co, 0, B * B * sizeof(double));
//calculate covariance matrix
|
2aa68315
David Mayerich
major bug fixes f...
|
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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...
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}
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1033
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if(PROGRESS) progress = (double)(xy+1) / XY * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1034
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}
|
2aa68315
David Mayerich
major bug fixes f...
|
1035
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|
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...
|
1039
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}
}
|
a43c4fe1
heziqi
Added crop in env...
|
1042
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free(temp);
|
2aa68315
David Mayerich
major bug fixes f...
|
1043
|
free(temp_precise);
|
a43c4fe1
heziqi
Added crop in env...
|
1044
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return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1047
|
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 ...
|
1048
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std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1050
|
//std::string headername = outfile + ".hdr"; //the header file name
|
63fc1df8
David Mayerich
added an inverse ...
|
1051
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|
//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...
|
1060
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|
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 ...
|
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}
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
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63fc1df8
David Mayerich
added an inverse ...
|
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target.write(reinterpret_cast<const char*>(rs), sizeof(T) * M); //write the projected vector
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
free(s); //free temporary storage arrays
free(rs);
target.close(); //close the output file
return true;
}
bool inverse(std::string outfile, double* center, double* basis, unsigned long long B, unsigned long long C = 0, bool PROGRESS = false){
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
std::string headername = outfile + ".hdr"; //the header file name
//memory allocation
unsigned long long XY = X() * Y();
if(C == 0) C = Z(); //if no coefficient number is given, assume all are used
C = std::min<unsigned long long>(C, Z()); //set the number of coefficients (the user can specify fewer)
T* coeff = (T*)malloc(sizeof(T) * Z()); //allocate space for the coefficients
T* s = (T*)malloc(sizeof(T) * B); //allocate space for the spectrum
double* bv; //pointer to the current projection vector
for(unsigned long long xy = 0; xy < XY; xy++){ //for each pixel in the image (expressed as a set of coefficients)
pixel(coeff, xy); //load the coefficients
memset(s, 0, sizeof(T) * B); //initialize the spectrum to zero (0)
for(unsigned long long c = 0; c < C; c++){ //for each basis vector coefficient
bv = &basis[c * B]; //assign 'bv' to the beginning of the basis vector
for(unsigned long long b = 0; b < B; b++){ //for each component of the basis vector
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1101
|
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 ...
|
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}
}
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
|
1116
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
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|
/// 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...
|
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|
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 ...
|
1129
1130
|
unsigned long long b1,
bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1131
|
|
3033b886
David Mayerich
implemented spect...
|
1132
1133
1134
1135
1136
1137
1138
1139
1140
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1142
|
//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...
|
1143
|
T* temp = (T*)malloc(L);
|
3033b886
David Mayerich
implemented spect...
|
1144
1145
|
//open an output file for binary writing
|
a43c4fe1
heziqi
Added crop in env...
|
1146
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
3033b886
David Mayerich
implemented spect...
|
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
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1159
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1161
|
//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...
|
1162
|
{
|
3033b886
David Mayerich
implemented spect...
|
1163
|
for (unsigned x = 0; x < samples; x++)
|
a43c4fe1
heziqi
Added crop in env...
|
1164
|
{
|
3033b886
David Mayerich
implemented spect...
|
1165
1166
1167
|
//read the cropped spectral region
file.read( (char*) temp, L );
//pixel(temp, sp + x + y * X());
|
a43c4fe1
heziqi
Added crop in env...
|
1168
|
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
|
3150c537
David Mayerich
added further pro...
|
1169
|
|
3033b886
David Mayerich
implemented spect...
|
1170
1171
|
file.seekg(jump_sample, std::ios::cur);
|
63fc1df8
David Mayerich
added an inverse ...
|
1172
|
if(PROGRESS) progress = (double)((y+1) * samples + x + 1) / (lines * samples) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1173
|
}
|
3033b886
David Mayerich
implemented spect...
|
1174
1175
|
file.seekg(jump_line, std::ios::cur);
|
a43c4fe1
heziqi
Added crop in env...
|
1176
1177
|
}
free(temp);
|
3150c537
David Mayerich
added further pro...
|
1178
|
|
a43c4fe1
heziqi
Added crop in env...
|
1179
1180
1181
|
return true;
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1182
1183
1184
1185
1186
1187
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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...
|
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
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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
}
if(PROGRESS) progress = (double)( (y+1) * S[0] + 1) / (double) (S[0] * S[1]) * 100;
}
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1253
|
|
0df38ff3
heziqi
fixed head detached
|
1254
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1255
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
1256
1257
1258
1259
1260
|
bool close(){
file.close();
return true;
}
|
88c3e636
heziqi
Ziqi added big.h
|
1261
|
};
|
6aa04ba2
David Mayerich
interleave types
|
1262
|
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1263
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|
#endif
|