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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>
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#include <complex>
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#include <utility>
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//CUDA
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//#ifdef CUDA_FOUND
#include <stim/cuda/cudatools/error.h>
#include <cuda_runtime.h>
#include "cublas_v2.h"
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#include "cufft.h"
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//#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,
stim::iotype io = stim::io_in){
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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, io);
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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++;
//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);
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, size_t 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
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len = 0; //initialize the
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file.read((char*)spec, Bb); //read a spectrum
for(size_t b = 0; b < B; b++) //for each band
len += spec[b]*spec[b]; //add the square of the spectral band
len = sqrt(len); //calculate the square of the sum of squared components
for(size_t b = 0; b < B; b++) //for each band
spec[b] /= len; //divide by the length
}
else
file.seekg(Bb, std::ios::cur); //otherwise skip a spectrum
target.write((char*)spec, Bb); //output the normalized spectrum
if(PROGRESS) progress = (double)(xy + 1) / (double)XY * 100; //update the progress
|
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}
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}
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|
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|
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/// This function loads a specified set of bands and saves them into a new output file
bool select(std::string outfile, std::vector<double> bandlist, unsigned char* mask = NULL, bool PROGRESS = false) {
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
if (!target) {
std::cout << "ERROR opening output file: " << outfile << std::endl;
return false;
}
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 Bout = bandlist.size();
size_t in_bytes = B * sizeof(T); //number of bytes in a spectrum
size_t out_bytes = Bout * sizeof(T); //number of bytes in an output spectrum
T* in = (T*)malloc(in_bytes); //allocate space for the input spectrum
T* out = (T*)malloc(out_bytes); //allocate space for the output spectrum
double wc; //register to store the desired wavelength
double w0, w1; //registers to store the wavelengths surrounding the given band
size_t b0, b1; //indices of the bands surrounding the specified wavelength
for (size_t xy = 0; xy < XY; xy++) { //for each pixel
//memset(out, 0, out_bytes); //set the spectrum to zero
if (mask == NULL || mask[xy]) { //if the pixel is masked
file.read((char*)in, in_bytes); //read an input spectrum
for (size_t b = 0; b < Bout; b++) { //for each band
wc = bandlist[b]; //set the desired wavelength
|
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fixed Linux errors
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|
hsi<T>::band_bounds(wc, b0, b1); //get the surrounding bands
|
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w0 = w[b0]; //get the wavelength for the lower band
w1 = w[b1]; //get the wavelength for the higher band
|
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fixed Linux errors
|
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|
out[b] = hsi<T>::lerp(wc, in[b0], w0, in[b1], w1); //interpolate the spectral values to get the desired output value
|
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}
}
else
file.seekg(Bout, std::ios::cur); //otherwise skip a spectrum
target.write((char*)out, out_bytes); //output the normalized spectrum
if (PROGRESS) progress = (double)(xy + 1) / (double)XY * 100; //update the progress
}
free(in);
free(out);
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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Ziqi added functi...
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{
|
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David Mayerich
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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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|
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Ziqi added functi...
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std::ofstream target(outname.c_str(), std::ios::binary);
|
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|
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|
//std::string headername = outname + ".hdr";
|
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|
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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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|
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|
|
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|
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|
for ( unsigned long long i = 0; i < Y(); i++)
|
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David Mayerich
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|
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|
{
|
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David Mayerich
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|
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|
read_plane_y(p, i);
|
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|
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|
for ( unsigned long long k = 0; k < Z(); k++)
|
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Ziqi completed bi...
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{
|
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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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|
462
|
q[ks + j] = p[k + j * Z()];
|
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David Mayerich
added support for...
|
463
|
|
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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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|
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|
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
|
11f177d5
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Ziqi added functi...
|
467
|
}
|
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Ziqi completed bi...
|
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|
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Ziqi added functi...
|
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|
free(p);
|
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|
470
|
free(q);
|
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Ziqi added functi...
|
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|
target.close();
return true;
}
|
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Ziqi added big.h
|
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|
|
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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.
|
20c212c0
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Ziqi added functi...
|
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|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
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added stim::hsi a...
|
485
|
unsigned long long XY = X() * Y();
|
20c212c0
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Ziqi added functi...
|
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489
|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
490
|
for(unsigned long long i=0; i < XY; i++){
|
20c212c0
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Ziqi added functi...
|
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492
493
494
|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
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|
495
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
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|
/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param bandwavelength is the label value for the desired baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
|
70407ea9
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Ziqi completed he...
|
502
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
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|
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|
T* lp;
T* rp;
|
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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);
|
70407ea9
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Ziqi completed he...
|
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509
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
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Ziqi added functi...
|
510
|
|
70407ea9
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Ziqi completed he...
|
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|
band(lp, lb);
|
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David Mayerich
fixed linux compa...
|
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|
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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|
free(lp);
free(rp);
|
20c212c0
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Ziqi added functi...
|
518
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520
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
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|
|
a23c4132
David Mayerich
Doxygen comments ...
|
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|
/// Calculate the area under the spectrum between two specified points and stores the result in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label value for the left bound (start of the integration)
/// @param rab is the label value for the right bound (end of the integration)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
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Ziqi completed he...
|
529
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
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Ziqi added functi...
|
530
531
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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...
|
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|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
536
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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...
|
538
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541
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|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
543
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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...
|
547
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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
heziqi
Ziqi completed he...
|
565
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
566
567
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
568
|
while (rab <= w[bi]){
|
20c212c0
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Ziqi added functi...
|
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|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
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577
|
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...
|
578
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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);
|
20c212c0
heziqi
Ziqi added functi...
|
580
|
}
|
70407ea9
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Ziqi completed he...
|
581
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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...
|
583
|
for(unsigned long long j = 0; j < XY; j++){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
584
|
result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
585
|
}
|
517876d6
heziqi
metrics finished ...
|
586
|
|
20c212c0
heziqi
Ziqi added functi...
|
587
588
|
//calculate the area
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
589
|
for(unsigned long long i = ai; i <= bi ;i++)
|
20c212c0
heziqi
Ziqi added functi...
|
590
591
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
592
|
for(unsigned long long j = 0; j < XY; j++)
|
20c212c0
heziqi
Ziqi added functi...
|
593
|
{
|
1a224b6a
David Mayerich
fixed linux compa...
|
594
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
595
596
597
|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
598
|
|
517876d6
heziqi
metrics finished ...
|
599
600
601
602
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
603
604
605
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
606
607
608
609
610
611
612
613
614
|
/// 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...
|
615
|
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...
|
616
|
|
1a224b6a
David Mayerich
fixed linux compa...
|
617
618
619
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
620
621
622
623
|
//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...
|
624
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
625
626
627
628
629
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
630
631
632
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
633
|
return true;
|
70407ea9
heziqi
Ziqi completed he...
|
634
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
635
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
636
637
638
639
640
641
642
643
644
|
/// 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...
|
645
646
|
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...
|
647
648
649
650
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
651
652
653
654
|
//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...
|
655
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
656
657
658
659
660
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
661
662
663
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
664
665
666
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
667
668
669
670
671
672
673
674
675
|
/// 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...
|
676
|
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
|
a23c4132
David Mayerich
Doxygen comments ...
|
677
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
678
679
|
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...
|
680
681
682
683
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
684
685
686
687
|
//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...
|
688
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
689
690
691
692
693
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
694
695
696
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
697
698
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
699
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
700
701
702
703
704
705
706
|
/// 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 ...
|
707
708
709
710
711
712
|
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...
|
713
714
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
715
716
717
718
719
720
721
722
723
|
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...
|
724
725
726
|
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 ...
|
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
|
//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...
|
753
754
|
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 ...
|
755
756
757
|
}
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...
|
758
|
for(unsigned long long j = 0; j < XY; j++){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
759
|
result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
760
761
762
763
|
}
//calculate f(x) times x
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
764
|
for(unsigned long long i = ai; i <= bi ;i++)
|
517876d6
heziqi
metrics finished ...
|
765
766
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
767
|
for(unsigned long long j = 0; j < XY; j++)
|
517876d6
heziqi
metrics finished ...
|
768
|
{
|
1a224b6a
David Mayerich
fixed linux compa...
|
769
|
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 ...
|
770
771
772
773
774
775
776
777
778
779
780
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
781
782
783
784
785
786
787
|
/// 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...
|
788
|
bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
|
1a224b6a
David Mayerich
fixed linux compa...
|
789
790
791
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
792
793
794
795
|
//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...
|
796
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
797
|
if(mask == NULL || mask[i])
|
517876d6
heziqi
metrics finished ...
|
798
799
800
801
802
|
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
803
|
return true;
|
517876d6
heziqi
metrics finished ...
|
804
805
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
806
807
808
809
810
811
812
|
/// 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
|
e37ce7bf
David Mayerich
added the ability...
|
813
|
bool build_mask(unsigned char* out_mask, double mask_band, double lower, double upper, unsigned char* mask = NULL, bool PROGRESS = false){
|
4a6f666c
heziqi
Added mask method
|
814
|
|
724ec347
David Mayerich
simplified the EN...
|
815
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
798cea97
David Mayerich
added progress ba...
|
816
|
band(temp, mask_band, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
817
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
818
|
for (unsigned long long i = 0; i < X() * Y();i++) {
|
e37ce7bf
David Mayerich
added the ability...
|
819
820
821
822
823
824
825
|
if(mask == NULL || mask[i] != 0){
if(temp[i] > lower && temp[i] < upper){
out_mask[i] = 255;
}
else
out_mask[i] = 0;
}
|
4a6f666c
heziqi
Added mask method
|
826
827
|
}
|
517876d6
heziqi
metrics finished ...
|
828
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
829
830
831
832
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
833
834
835
836
|
/// 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...
|
837
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
838
839
840
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
841
842
|
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
|
843
|
|
1a55a328
David Mayerich
Added comments fo...
|
844
|
T * temp = (T*)malloc(L); //allocate space for that page
|
740f8cd2
heziqi
added apply_mask
|
845
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
846
|
for (unsigned long long i = 0; i < Y(); i++) //for each page (Y in BIP)
|
740f8cd2
heziqi
added apply_mask
|
847
|
{
|
724ec347
David Mayerich
simplified the EN...
|
848
|
read_plane_y(temp, i); //load that page (it's pointed to by temp)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
849
|
for ( unsigned long long j = 0; j < X(); j++) //for each X value
|
740f8cd2
heziqi
added apply_mask
|
850
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
851
|
for (unsigned long long k = 0; k < Z(); k++) //for each B value (band)
|
740f8cd2
heziqi
added apply_mask
|
852
|
{
|
724ec347
David Mayerich
simplified the EN...
|
853
854
|
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...
|
855
|
else //otherwise just continue
|
740f8cd2
heziqi
added apply_mask
|
856
857
858
|
continue;
}
}
|
1a55a328
David Mayerich
Added comments fo...
|
859
|
target.write(reinterpret_cast<const char*>(temp), L); //write the edited band data into target file
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
860
|
if(PROGRESS) progress = (double)(i+1) / (double)Y() * 100;
|
740f8cd2
heziqi
added apply_mask
|
861
|
}
|
1a55a328
David Mayerich
Added comments fo...
|
862
863
864
|
target.close(); //close the target file
free(temp); //free allocated memory
return true; //return true
|
740f8cd2
heziqi
added apply_mask
|
865
866
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
867
868
869
870
871
|
/// 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...
|
872
|
bool sift(T* matrix, unsigned char* mask = NULL, bool PROGRESS = false){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
873
874
875
876
877
|
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...
|
878
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
879
880
|
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...
|
881
|
if(mask == NULL || mask[xy]){ //if the current pixel is masked
|
ba51ae6a
David Mayerich
fixed metric calc...
|
882
883
884
885
886
887
888
889
|
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...
|
890
|
file.seekg(Bbytes, std::ios::cur); //otherwise skip this band
|
814eb271
David Mayerich
fixed problems wi...
|
891
|
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
892
893
894
|
}
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
895
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
896
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
897
|
bool sift(std::string outfile, unsigned char* mask, bool PROGRESS = false){
|
8550e94f
David Mayerich
added sifting and...
|
898
899
|
//reset the file pointer to the beginning of the file
|
1a224b6a
David Mayerich
fixed linux compa...
|
900
|
file.seekg(0, std::ios::beg);
|
8550e94f
David Mayerich
added sifting and...
|
901
902
|
// open an output stream
|
e843658b
Brad Deutsch
Previous push did...
|
903
904
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
8550e94f
David Mayerich
added sifting and...
|
905
|
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
906
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
907
|
T* spectrum = (T*) malloc(B * sizeof(T));
|
e843658b
Brad Deutsch
Previous push did...
|
908
|
|
8550e94f
David Mayerich
added sifting and...
|
909
|
//calculate the number of pixels in a band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
910
|
unsigned long long XY = X() * Y();
|
e843658b
Brad Deutsch
Previous push did...
|
911
|
|
8550e94f
David Mayerich
added sifting and...
|
912
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
913
914
|
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...
|
915
916
917
918
919
|
//if the current pixel isn't masked
if( mask[x] == 0){
//increment the number of skipped pixels
skip++;
|
e843658b
Brad Deutsch
Previous push did...
|
920
|
}
|
8550e94f
David Mayerich
added sifting and...
|
921
922
923
924
925
926
927
928
929
930
931
932
933
934
|
//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...
|
935
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
936
|
if(PROGRESS) progress = (double) (x+1) / XY * 100;
|
8550e94f
David Mayerich
added sifting and...
|
937
|
|
e843658b
Brad Deutsch
Previous push did...
|
938
|
}
|
8550e94f
David Mayerich
added sifting and...
|
939
940
|
//close the output file
|
e843658b
Brad Deutsch
Previous push did...
|
941
|
target.close();
|
8550e94f
David Mayerich
added sifting and...
|
942
|
free(spectrum);
|
cbce396e
David Mayerich
added support for...
|
943
|
|
cbce396e
David Mayerich
added support for...
|
944
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
945
946
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
947
|
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...
|
948
949
950
951
952
|
// 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...
|
953
|
file.seekg(0, std::ios::beg);
|
8550e94f
David Mayerich
added sifting and...
|
954
955
|
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
956
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
957
958
959
960
961
962
963
|
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...
|
964
|
unsigned long long XY = samples * lines;
|
8550e94f
David Mayerich
added sifting and...
|
965
966
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
967
968
|
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...
|
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
|
//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...
|
986
|
if(PROGRESS) progress = (double)(x + 1) / XY * 100;
|
3150c537
David Mayerich
added further pro...
|
987
|
|
8550e94f
David Mayerich
added sifting and...
|
988
989
990
991
992
993
|
}
//close the output file
target.close();
free(spectrum);
|
a2bf1d08
David Mayerich
general bug fixes...
|
994
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
995
|
|
e843658b
Brad Deutsch
Previous push did...
|
996
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
997
998
|
|
e843658b
Brad Deutsch
Previous push did...
|
999
1000
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
1001
1002
1003
1004
|
/// 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
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1005
|
bool mean_spectrum(double* m, double* std = NULL, unsigned char* mask = NULL, bool PROGRESS = false){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1006
1007
|
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
|
35a7195f
David Mayerich
added median spec...
|
1008
1009
1010
|
memset(m, 0, Z() * sizeof(double)); //set the mean spectrum to zero
double* e_x2 = (double*)malloc(Z() * sizeof(double)); //allocate space for E[x^2]
memset(e_x2, 0, Z() * sizeof(double)); //set all values for E[x^2] to zero
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1011
1012
|
unsigned long long count = nnz(mask); //calculate the number of masked pixels
|
35a7195f
David Mayerich
added median spec...
|
1013
|
double x;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1014
1015
1016
1017
|
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
|
35a7195f
David Mayerich
added median spec...
|
1018
1019
1020
|
x = temp[j];
m[j] += x / (double)count; //add the weighted value to the average
e_x2[j] += x*x / (double)count;
|
a43c4fe1
heziqi
Added crop in env...
|
1021
1022
|
}
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1023
|
if(PROGRESS) progress = (double)(i+1) / XY * 100; //increment the progress
|
a43c4fe1
heziqi
Added crop in env...
|
1024
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
1025
|
|
35a7195f
David Mayerich
added median spec...
|
1026
|
//calculate the standard deviation
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1027
1028
1029
1030
|
if (std != NULL) {
for (size_t i = 0; i < Z(); i++)
std[i] = sqrt(e_x2[i] - m[i] * m[i]);
}
|
35a7195f
David Mayerich
added median spec...
|
1031
|
|
a43c4fe1
heziqi
Added crop in env...
|
1032
|
free(temp);
|
a43c4fe1
heziqi
Added crop in env...
|
1033
1034
|
return true;
}
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1035
|
//#ifdef CUDA_FOUND
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1036
|
/// Calculate the covariance matrix for masked pixels using cuBLAS
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1037
|
/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1038
|
int co_matrix_cublas(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1039
|
|
1a224b6a
David Mayerich
fixed linux compa...
|
1040
|
cudaError_t cudaStat;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1041
1042
|
cublasStatus_t stat;
cublasHandle_t handle;
|
1a224b6a
David Mayerich
fixed linux compa...
|
1043
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
|
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...
|
1055
|
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...
|
1056
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1057
1058
1059
1060
|
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
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1061
1062
|
if (stat != CUBLAS_STATUS_SUCCESS) return 1; //test the cuBLAS instance to make sure it is valid
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1063
|
//else std::cout<<"Using cuBLAS to calculate the mean covariance matrix..."<<std::endl;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1064
|
for (unsigned long long xy = 0; xy < XY; xy++){ //for each pixel
|
5a5359da
David Mayerich
fixed - allows th...
|
1065
1066
|
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...
|
1067
1068
1069
|
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...
|
1070
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1071
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
|
5a5359da
David Mayerich
fixed - allows th...
|
1072
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1073
1074
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1075
|
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...
|
1076
1077
1078
1079
1080
|
cudaFree(A_dev); //clean up allocated device memory
cudaFree(s_dev);
cudaFree(avg_dev);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1081
1082
|
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...
|
1083
1084
1085
1086
|
co[B * i + j] = co[B * j + i];
}
}
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1087
|
return 0;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1088
|
}
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1089
|
//#endif
|
1a224b6a
David Mayerich
fixed linux compa...
|
1090
|
|
2aa68315
David Mayerich
major bug fixes f...
|
1091
|
/// Calculate the covariance matrix for all masked pixels in the image with 64-bit floating point precision.
|
a23c4132
David Mayerich
Doxygen comments ...
|
1092
1093
1094
1095
|
/// @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
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1096
|
bool co_matrix(double* co, double* avg, unsigned char *mask, int cuda_device = 0, bool PROGRESS = false){
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1097
|
progress = 0;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1098
|
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1099
|
if(cuda_device >= 0){ //if a CUDA device is specified
|
dc99699e
David Mayerich
implemented a no-...
|
1100
1101
|
int dev_count;
HANDLE_ERROR(cudaGetDeviceCount(&dev_count)); //get the number of CUDA devices
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1102
|
if(dev_count > 0 && dev_count > cuda_device){ //if the first device is not an emulator
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1103
|
cudaDeviceProp prop;
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1104
1105
|
cudaGetDeviceProperties(&prop, cuda_device); //get the property of the requested CUDA device
if (prop.major != 9999) {
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1106
|
std::cout << "Using CUDA device [" << cuda_device << "] to calculate the mean covariance matrix..."<<std::endl;
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1107
1108
1109
1110
|
HANDLE_ERROR(cudaSetDevice(cuda_device));
int status = co_matrix_cublas(co, avg, mask, PROGRESS); //use cuBLAS to calculate the covariance matrix
if (status == 0) return true; //if the cuBLAS function returned correctly, we're done
}
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1111
1112
|
} //otherwise continue using the CPU
std::cout<<"WARNING: cuBLAS failed, using CPU"<<std::endl;
|
dc99699e
David Mayerich
implemented a no-...
|
1113
|
}
|
a43c4fe1
heziqi
Added crop in env...
|
1114
|
//memory allocation
|
2aa68315
David Mayerich
major bug fixes f...
|
1115
1116
|
unsigned long long XY = X() * Y();
unsigned long long B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
1117
|
T* temp = (T*)malloc(sizeof(T) * B);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1118
1119
|
unsigned long long count = nnz(mask); //count the number of masked pixels
|
63fc1df8
David Mayerich
added an inverse ...
|
1120
|
|
2aa68315
David Mayerich
major bug fixes f...
|
1121
1122
1123
1124
|
//initialize covariance matrix
memset(co, 0, B * B * sizeof(double));
//calculate covariance matrix
|
2aa68315
David Mayerich
major bug fixes f...
|
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
|
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...
|
1138
1139
|
}
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1140
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1141
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
1142
1143
1144
1145
|
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...
|
1146
1147
1148
|
}
}
|
a43c4fe1
heziqi
Added crop in env...
|
1149
|
free(temp);
|
2aa68315
David Mayerich
major bug fixes f...
|
1150
|
free(temp_precise);
|
a43c4fe1
heziqi
Added crop in env...
|
1151
1152
1153
|
return true;
}
|
334547d8
sam
changes for mnf: ...
|
1154
|
|
1ee79b84
David Mayerich
more accurate noi...
|
1155
|
int coNoise_matrix_cublas(double* coN, double* avg, unsigned char *mask, bool PROGRESS = false) {
|
334547d8
sam
changes for mnf: ...
|
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
|
cudaError_t cudaStat;
cublasStatus_t stat;
cublasHandle_t handle;
progress = 0; //initialize the progress to zero (0)
unsigned long long XY = X() * Y(); //calculate the number of elements in a band image
unsigned long long B = Z(); //calculate the number of spectral elements
double* s = (double*)malloc(sizeof(double) * B); //allocate space for the spectrum that will be pulled from the file
double* s_dev; //declare a device pointer that will store the spectrum on the GPU
|
1ee79b84
David Mayerich
more accurate noi...
|
1168
1169
1170
1171
|
double* s2 = (double*)malloc(sizeof(double) * B); //allocate space for the spectrum of second pixel that will be pulled from the file
double* s2_dev; // device pointer on the GPU
cudaStat = cudaMalloc(&s2_dev, B * sizeof(double)); // allocate space on the CUDA device
cudaStat = cudaMemset(s2_dev, 0, B * sizeof(double)); // initialize s2_dev to zero (0)
|
334547d8
sam
changes for mnf: ...
|
1172
1173
1174
1175
1176
1177
1178
1179
1180
|
double* A_dev; //declare a device pointer that will store the covariance matrix on the GPU
double* avg_dev; //declare a device pointer that will store the average spectrum
cudaStat = cudaMalloc(&s_dev, B * sizeof(double)); //allocate space on the CUDA device for the spectrum
cudaStat = cudaMalloc(&A_dev, B * B * sizeof(double)); //allocate space on the CUDA device for the covariance matrix
cudaStat = cudaMemset(A_dev, 0, B * B * sizeof(double)); //initialize the covariance matrix to zero (0)
cudaStat = cudaMalloc(&avg_dev, B * sizeof(double)); //allocate space on the CUDA device for the average spectrum
stat = cublasSetVector((int)B, sizeof(double), avg, 1, avg_dev, 1); //copy the average spectrum to the CUDA device
|
1ee79b84
David Mayerich
more accurate noi...
|
1181
|
double ger_alpha = 1.0 / (double)XY; //scale the outer product by the inverse of the number of samples (mean outer product)
|
334547d8
sam
changes for mnf: ...
|
1182
1183
|
double axpy_alpha = -1; //multiplication factor for the average spectrum (in order to perform a subtraction)
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1184
1185
1186
|
CUBLAS_HANDLE_ERROR(cublasCreate(&handle)); //create a cuBLAS instance
if (stat != CUBLAS_STATUS_SUCCESS) return 1; //test the cuBLAS instance to make sure it is valid
|
1ee79b84
David Mayerich
more accurate noi...
|
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
|
for (unsigned long long xy = 0; xy < XY; xy++) { //for each pixel
if (mask == NULL || mask[xy] != 0) {
pixeld(s, xy); //retreive the spectrum at the current xy pixel location
if (xy < XY - X()) {
pixeld(s2, xy + X()); //retreive the spectrum at the current xy+X pixel location, which is adjacent (bellow) to the pixel at xy location (in y direction)
}
else {
pixeld(s2, xy - X()); //for the last row we consider the the adjacent pixel which is located above pixel xy
}
stat = cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1); //copy the spectrum of first pixel from the host to the device
|
334547d8
sam
changes for mnf: ...
|
1197
1198
|
stat = cublasDaxpy(handle, (int)B, &axpy_alpha, avg_dev, 1, s_dev, 1); //subtract the average spectrum
|
1ee79b84
David Mayerich
more accurate noi...
|
1199
1200
|
stat = cublasSetVector((int)B, sizeof(double), s2, 1, s2_dev, 1); //copy the spectrum of second pixel from the host to the device
stat = cublasDaxpy(handle, (int)B, &axpy_alpha, avg_dev, 1, s2_dev, 1); //subtract the average spectrum
|
334547d8
sam
changes for mnf: ...
|
1201
|
|
1ee79b84
David Mayerich
more accurate noi...
|
1202
|
stat = cublasDaxpy(handle, (int)B, &axpy_alpha, s2_dev, 1, s_dev, 1); //Minimum/Maximum Autocorrelation Factors (MAF) method : subtranct each pixel from adjacent pixel (in y direction)
|
334547d8
sam
changes for mnf: ...
|
1203
1204
1205
|
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)
}
|
1ee79b84
David Mayerich
more accurate noi...
|
1206
|
if (PROGRESS) progress = (double)(xy + 1) / XY * 100; //record the current progress
|
334547d8
sam
changes for mnf: ...
|
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
|
}
cublasGetMatrix((int)B, (int)B, sizeof(double), A_dev, (int)B, coN, (int)B); //copy the result from the GPU to the CPU
cudaFree(A_dev); //clean up allocated device memory
cudaFree(s_dev);
cudaFree(s2_dev);
cudaFree(avg_dev);
|
1ee79b84
David Mayerich
more accurate noi...
|
1217
1218
|
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++) {
|
334547d8
sam
changes for mnf: ...
|
1219
1220
1221
1222
|
coN[B * i + j] = coN[B * j + i];
}
}
|
dc99699e
David Mayerich
implemented a no-...
|
1223
|
return 0;
|
334547d8
sam
changes for mnf: ...
|
1224
|
}
|
1ee79b84
David Mayerich
more accurate noi...
|
1225
|
//#endif
|
334547d8
sam
changes for mnf: ...
|
1226
1227
1228
1229
1230
1231
|
/// Calculate the covariance of noise matrix for all masked pixels in the image with 64-bit floating point precision.
/// @param coN 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
|
1ee79b84
David Mayerich
more accurate noi...
|
1232
|
bool coNoise_matrix(double* coN, double* avg, unsigned char *mask, int cuda_device = 0, bool PROGRESS = false) {
|
dc99699e
David Mayerich
implemented a no-...
|
1233
|
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1234
|
if (cuda_device >= 0) { //if a CUDA device is specified
|
dc99699e
David Mayerich
implemented a no-...
|
1235
1236
|
int dev_count;
HANDLE_ERROR(cudaGetDeviceCount(&dev_count)); //get the number of CUDA devices
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1237
1238
1239
1240
1241
1242
1243
1244
1245
|
if (dev_count > 0 && dev_count > cuda_device) { //if the first device is not an emulator
cudaDeviceProp prop;
cudaGetDeviceProperties(&prop, cuda_device); //get the property of the requested CUDA device
if (prop.major != 9999) {
std::cout << "Using CUDA device [" << cuda_device << "] to calculate the noise covariance matrix..." << std::endl;
HANDLE_ERROR(cudaSetDevice(cuda_device));
int status = coNoise_matrix_cublas(coN, avg, mask, PROGRESS); //use cuBLAS to calculate the covariance matrix
if (status == 0) return true; //if the cuBLAS function returned correctly, we're done
}
|
1ee79b84
David Mayerich
more accurate noi...
|
1246
|
} //otherwise continue using the CPU
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1247
|
std::cout << "WARNING: cuBLAS failed, using CPU" << std::endl;
|
dc99699e
David Mayerich
implemented a no-...
|
1248
|
}
|
334547d8
sam
changes for mnf: ...
|
1249
1250
1251
1252
1253
1254
|
progress = 0;
//memory allocation
unsigned long long XY = X() * Y();
unsigned long long B = Z();
T* temp = (T*)malloc(sizeof(T) * B);
|
1ee79b84
David Mayerich
more accurate noi...
|
1255
|
T* temp2 = (T*)malloc(sizeof(T) * B);
|
334547d8
sam
changes for mnf: ...
|
1256
1257
1258
|
unsigned long long count = nnz(mask); //count the number of masked pixels
|
1ee79b84
David Mayerich
more accurate noi...
|
1259
|
//initialize covariance matrix of noise
|
334547d8
sam
changes for mnf: ...
|
1260
1261
1262
|
memset(coN, 0, B * B * sizeof(double));
//calculate covariance matrix
|
1ee79b84
David Mayerich
more accurate noi...
|
1263
1264
1265
|
double* coN_half = (double*)malloc(B * B * sizeof(double)); //allocate space for a higher-precision intermediate matrix
double* temp_precise = (double*)malloc(B * sizeof(double));
double* temp_precise2 = (double*)malloc(B * sizeof(double));
|
334547d8
sam
changes for mnf: ...
|
1266
1267
|
memset(coN_half, 0, B * B * sizeof(double)); //initialize the high-precision matrix with zeros
unsigned long long idx; //stores i*B to speed indexing
|
1ee79b84
David Mayerich
more accurate noi...
|
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
|
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
if (xy < XY - X()) {
pixel(temp2, xy + X()); //retreive the spectrum at the current xy+X pixel location, which is adjacent (bellow) to the pixel at xy location (in y direction)
}
else {
pixel(temp2, xy - X()); //for the last row we consider the the adjacent pixel which is located above pixel xy
}
for (unsigned long long b = 0; b < B; b++) { //subtract the mean from this spectrum and increase the precision
|
334547d8
sam
changes for mnf: ...
|
1278
|
temp_precise[b] = (double)temp[b] - (double)avg[b];
|
1ee79b84
David Mayerich
more accurate noi...
|
1279
1280
|
temp_precise2[b] = (double)temp2[b] - (double)avg[b];
}
|
334547d8
sam
changes for mnf: ...
|
1281
|
|
1ee79b84
David Mayerich
more accurate noi...
|
1282
1283
|
for (unsigned long long b2 = 0; b2 < B; b2++) //Minimum/Maximum Autocorrelation Factors (MAF) method : subtranct each pixel from adjacent pixel (in y direction)
temp_precise[b2] -= temp_precise2[b2];
|
334547d8
sam
changes for mnf: ...
|
1284
1285
|
idx = 0;
|
1ee79b84
David Mayerich
more accurate noi...
|
1286
|
for (unsigned long long b0 = 0; b0 < B; b0++) { //for each band
|
334547d8
sam
changes for mnf: ...
|
1287
1288
1289
1290
|
for (unsigned long long b1 = b0; b1 < B; b1++)
coN_half[idx++] += temp_precise[b0] * temp_precise[b1];
}
}
|
1ee79b84
David Mayerich
more accurate noi...
|
1291
|
if (PROGRESS) progress = (double)(xy + 1) / XY * 100;
|
334547d8
sam
changes for mnf: ...
|
1292
1293
|
}
idx = 0;
|
1ee79b84
David Mayerich
more accurate noi...
|
1294
1295
1296
|
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++) {
coN[j * B + i] = coN[i * B + j] = coN_half[idx++] / (double)count;
|
334547d8
sam
changes for mnf: ...
|
1297
1298
1299
1300
|
}
}
free(temp);
|
1ee79b84
David Mayerich
more accurate noi...
|
1301
|
free(temp2);
|
334547d8
sam
changes for mnf: ...
|
1302
|
free(temp_precise);
|
1ee79b84
David Mayerich
more accurate noi...
|
1303
|
free(temp_precise2);
|
334547d8
sam
changes for mnf: ...
|
1304
1305
1306
|
return true;
}
|
334547d8
sam
changes for mnf: ...
|
1307
1308
1309
1310
1311
1312
1313
1314
|
/// 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
bool project_cublas(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask = NULL, bool PROGRESS = false){
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1315
1316
|
//cudaError_t cudaStat;
//cublasStatus_t stat;
|
334547d8
sam
changes for mnf: ...
|
1317
1318
1319
|
cublasHandle_t handle;
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
|
334547d8
sam
changes for mnf: ...
|
1320
1321
1322
1323
1324
1325
1326
|
progress = 0; //initialize the progress to zero (0)
unsigned long long XY = X() * Y(); //calculate the number of elements in a band image
unsigned long long B = Z(); //calculate the number of spectral elements
double* s = (double*)malloc(sizeof(double) * B); //allocate space for the spectrum that will be pulled from the file
double* s_dev; //declare a device pointer that will store the spectrum on the GPU
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1327
|
HANDLE_ERROR(cudaMalloc(&s_dev, B * sizeof(double))); //allocate space on the CUDA device for the spectrum
|
334547d8
sam
changes for mnf: ...
|
1328
1329
1330
|
double* basis_dev; // device pointer on the GPU
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1331
1332
|
HANDLE_ERROR(cudaMalloc(&basis_dev, M * B * sizeof(double))); // allocate space on the CUDA device
HANDLE_ERROR(cudaMemset(basis_dev, 0, M * B * sizeof(double))); // initialize basis_dev to zero (0)
|
334547d8
sam
changes for mnf: ...
|
1333
1334
1335
1336
1337
1338
1339
1340
|
/// transposing basis matrix (because cuBLAS is column-major)
double *basis_Transposed = (double*)malloc(M * B * sizeof(double));
memset(basis_Transposed, 0, M * B * sizeof(double));
for (int i = 0; i<M; i++)
for (int j = 0; j<B; j++)
basis_Transposed[i+j*M] = basis[i*B+j];
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1341
1342
|
//copy the basis_Transposed matrix to the CUDA device (both matrices are stored in column-major format)
CUBLAS_HANDLE_ERROR(cublasSetMatrix((int)M, (int)B, sizeof(double),basis_Transposed, (int)M, basis_dev, (int)M));
|
334547d8
sam
changes for mnf: ...
|
1343
|
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1344
1345
1346
|
double* center_dev; //declare a device pointer that will store the center (average)
HANDLE_ERROR(cudaMalloc(¢er_dev, B * sizeof(double))); //allocate space on the CUDA device for the center (average)
CUBLAS_HANDLE_ERROR(cublasSetVector((int)B, sizeof(double), center, 1, center_dev, 1)); //copy the center vector (average) to the CUDA device (from host to device)
|
334547d8
sam
changes for mnf: ...
|
1347
1348
|
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1349
1350
1351
1352
|
double* A = (double*)malloc(sizeof(double) * M); //allocate space for the projected pixel on the host
double* A_dev; //declare a device pointer that will store the projected pixel on the GPU
HANDLE_ERROR(cudaMalloc(&A_dev,M * sizeof(double))); //allocate space on the CUDA device for the projected pixel
HANDLE_ERROR(cudaMemset(A_dev, 0,M * sizeof(double))); //initialize the projected pixel to zero (0)
|
334547d8
sam
changes for mnf: ...
|
1353
1354
1355
1356
1357
|
double axpy_alpha = -1; //multiplication factor for the center (in order to perform a subtraction)
double axpy_alpha2 = 1; //multiplication factor for the matrix-vector multiplication
double axpy_beta = 0; //multiplication factor for the matrix-vector multiplication (there is no second scalor)
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1358
|
CUBLAS_HANDLE_ERROR(cublasCreate(&handle)); //create a cuBLAS instance
|
334547d8
sam
changes for mnf: ...
|
1359
|
|
08d1c3b9
David Mayerich
fixed casting war...
|
1360
1361
1362
|
T* temp = (T*)malloc(sizeof(T) * M); //allocate space for the projected pixel to be written on the disc
size_t i;
for (unsigned long long xy = 0; xy < XY; xy++){ //for each pixel
|
334547d8
sam
changes for mnf: ...
|
1363
|
if (mask == NULL || mask[xy] != 0){
|
08d1c3b9
David Mayerich
fixed casting war...
|
1364
|
pixeld(s, xy); //retreive the spectrum at the current xy pixel location
|
334547d8
sam
changes for mnf: ...
|
1365
|
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1366
1367
1368
1369
1370
|
CUBLAS_HANDLE_ERROR(cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1)); //copy the spectrum from the host to the device
CUBLAS_HANDLE_ERROR(cublasDaxpy(handle, (int)B, &axpy_alpha, center_dev, 1, s_dev, 1)); //subtract the center (average)
CUBLAS_HANDLE_ERROR(cublasDgemv(handle,CUBLAS_OP_N,(int)M,(int)B,&axpy_alpha2,basis_dev,(int)M,s_dev,1,&axpy_beta,A_dev,1)); //performs the matrix-vector multiplication
CUBLAS_HANDLE_ERROR(cublasGetVector((int)M, sizeof(double), A_dev, 1, A, 1)); //copy the projected pixel to the host (from GPU to CPU)
|
08d1c3b9
David Mayerich
fixed casting war...
|
1371
|
for(i = 0; i < M; i++) temp[i] = (T)A[i]; //casting projected pixel from double to whatever T is
|
334547d8
sam
changes for mnf: ...
|
1372
|
}
|
3a880d1c
David Mayerich
fixed PCA and BIP...
|
1373
1374
|
else
memset(temp, 0, sizeof(T) * M);
|
334547d8
sam
changes for mnf: ...
|
1375
1376
1377
1378
1379
1380
1381
|
target.write(reinterpret_cast<const char*>(temp), sizeof(T) * M); //write the projected vector
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
}
//clean up allocated device memory
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1382
1383
1384
1385
1386
|
HANDLE_ERROR(cudaFree(A_dev));
HANDLE_ERROR(cudaFree(s_dev));
HANDLE_ERROR(cudaFree(basis_dev));
HANDLE_ERROR(cudaFree(center_dev));
CUBLAS_HANDLE_ERROR(cublasDestroy(handle));
|
334547d8
sam
changes for mnf: ...
|
1387
1388
1389
1390
|
free(A);
free(s);
free(temp);
target.close(); //close the output file
|
08d1c3b9
David Mayerich
fixed casting war...
|
1391
|
|
334547d8
sam
changes for mnf: ...
|
1392
1393
|
return true;
}
|
334547d8
sam
changes for mnf: ...
|
1394
|
|
812a2741
David Mayerich
added documentati...
|
1395
1396
1397
1398
1399
1400
|
/// 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
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1401
|
bool project(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask = NULL, int cuda_device = 0, bool PROGRESS = false){
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1402
1403
1404
|
if (cuda_device >= 0) { //if a CUDA device is specified
int dev_count;
HANDLE_ERROR(cudaGetDeviceCount(&dev_count)); //get the number of CUDA devices
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1405
|
if (dev_count > 0 && dev_count > cuda_device) { //if the first device is not an emulator
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1406
|
cudaDeviceProp prop;
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1407
1408
|
cudaGetDeviceProperties(&prop, cuda_device); //get the property of the requested CUDA device
if (prop.major != 9999) {
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1409
|
std::cout << "Using CUDA device [" << cuda_device << "] to perform a basis projection..." << std::endl;
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1410
|
HANDLE_ERROR(cudaSetDevice(cuda_device));
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1411
|
return project_cublas(outfile, center, basis, M, mask, PROGRESS);
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1412
|
}
|
1c92dffe
David Mayerich
simplified CUDA i...
|
1413
1414
|
} //otherwise continue using the CPU
std::cout << "WARNING: cuBLAS failed, using CPU" << std::endl;
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1415
1416
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1417
|
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1418
|
//std::string headername = outfile + ".hdr"; //the header file name
|
63fc1df8
David Mayerich
added an inverse ...
|
1419
1420
1421
1422
1423
1424
1425
1426
1427
|
//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...
|
1428
1429
1430
1431
1432
1433
1434
1435
|
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 ...
|
1436
1437
|
}
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
1438
|
|
63fc1df8
David Mayerich
added an inverse ...
|
1439
1440
1441
1442
1443
1444
1445
|
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
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08d1c3b9
David Mayerich
fixed casting war...
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63fc1df8
David Mayerich
added an inverse ...
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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
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1a224b6a
David Mayerich
fixed linux compa...
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for(unsigned long long b = 0; b < B; b++){ //for each component of the basis vector
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9d3ba0b1
David Mayerich
added stim::hsi a...
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1469
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s[b] += (T)((double)coeff[c] * bv[b] + center[b]); //calculate the contribution of each element of the basis vector in the final spectrum
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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;
}
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0df38ff3
heziqi
fixed head detached
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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
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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,
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David Mayerich
added an inverse ...
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unsigned long long b1,
bool PROGRESS = false){
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a43c4fe1
heziqi
Added crop in env...
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3033b886
David Mayerich
implemented spect...
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//calculate the new number of samples, lines, and bands
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fixed BIP croppin...
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unsigned long long samples = x1 - x0 + 1;
unsigned long long lines = y1 - y0 + 1;
unsigned long long bands = b1 - b0 + 1;
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David Mayerich
implemented spect...
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//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
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f78ceb64
David Mayerich
fixed BIP croppin...
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char* temp = (char*)malloc(L);
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3033b886
David Mayerich
implemented spect...
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//open an output file for binary writing
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a43c4fe1
heziqi
Added crop in env...
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std::ofstream out(outfile.c_str(), std::ios::binary);
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3033b886
David Mayerich
implemented spect...
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//seek to the first pixel in the cropped image
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David Mayerich
fixed BIP croppin...
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size_t startx = x0 * Z();
size_t starty = y0 * X() * Z();
size_t startb = b0;
file.seekg( (starty + startx + startb) * sizeof(T), std::ios::beg);
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3033b886
David Mayerich
implemented spect...
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//distance between sample spectra in the same line
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f78ceb64
David Mayerich
fixed BIP croppin...
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size_t dist_between_samples = Z() - bands;
size_t jump_sample = dist_between_samples * sizeof(T);
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3033b886
David Mayerich
implemented spect...
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//distance between sample spectra in adjacent lines
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f78ceb64
David Mayerich
fixed BIP croppin...
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//unsigned long long jump_line = ( X() - x1 + x0 ) * Z() * sizeof(T);
size_t dist_between_lines = X() - samples;
size_t jump_line = dist_between_lines * Z() * sizeof(T);
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3033b886
David Mayerich
implemented spect...
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//unsigned long long sp = y0 * X() + x0; //start pixel
//for each pixel in the image
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David Mayerich
fixed BIP croppin...
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for (unsigned y = 0; y < lines; y++) {
for (unsigned x = 0; x < samples; x++) {
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3033b886
David Mayerich
implemented spect...
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//read the cropped spectral region
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f78ceb64
David Mayerich
fixed BIP croppin...
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1538
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file.read(temp, L );
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3033b886
David Mayerich
implemented spect...
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1539
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//pixel(temp, sp + x + y * X());
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f78ceb64
David Mayerich
fixed BIP croppin...
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out.write(temp, L); //write slice data into target file
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3150c537
David Mayerich
added further pro...
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3033b886
David Mayerich
implemented spect...
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file.seekg(jump_sample, std::ios::cur);
|
dd5aab2f
David Mayerich
fixed errors in s...
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1544
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if(PROGRESS) progress = (double)(y * samples + x + 1) / (lines * samples) * 100;
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a43c4fe1
heziqi
Added crop in env...
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1545
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}
|
3033b886
David Mayerich
implemented spect...
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file.seekg(jump_line, std::ios::cur);
|
a43c4fe1
heziqi
Added crop in env...
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}
free(temp);
|
f78ceb64
David Mayerich
fixed BIP croppin...
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1550
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out.close();
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3150c537
David Mayerich
added further pro...
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1551
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a43c4fe1
heziqi
Added crop in env...
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1552
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return true;
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
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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...
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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...
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1622
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if(PROGRESS) progress = (double)( (y+1) * S[0] + 1) / (double) (S[0] * S[1]) * 100;
|
2ce6954b
David Mayerich
added the ability...
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1623
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}
}
|
82a7c08c
David Mayerich
added an append c...
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///Append two files together along the band dimension
void append(std::string outfile, bip<T>* C, 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 a_bytes = Z() * sizeof(T); //calculate the number of bytes in a single plane of this file
size_t b_bytes = C->Z() * sizeof(T); //calculate the number of bytes in a single plane of the appending file
T* a = (T*)malloc(a_bytes); //allocate space for a plane of the current file
T* b = (T*)malloc(b_bytes); //allocate space for a plane of the appended file
if (PROGRESS) progress = 0;
for (size_t xy = 0; xy < X()*Y(); xy++) {
spectrum(a, xy); //read a plane from the current file
out.write((char*)a, a_bytes); //write the plane to disk
C->spectrum(b, xy); //read a plane from the appending file
out.write((char*)b, b_bytes);
if (PROGRESS) progress = (double)(xy + 1) / (double)(X() * Y()) * 100;
}
out.close();
}
|
9b2a5d71
David Mayerich
implemented finit...
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/// Convolve the given band range with a kernel specified by a vector of coefficients.
/// @param outfile is an already open stream to the output file
/// @param C is an array of coefficients
/// @param start is the band to start processing (the first coefficient starts here)
/// @param nbands is the number of bands to process
/// @param center is the index for the center coefficient for the kernel (used to set the wavelengths in the output file)
|
9d77bbd9
David Mayerich
updates for HSIvi...
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1654
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void convolve(std::string outfile, std::vector<double> C, size_t start, size_t end, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1655
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
|
1a224b6a
David Mayerich
fixed linux compa...
|
1656
|
|
9b2a5d71
David Mayerich
implemented finit...
|
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size_t N = end - start + 1; //number of bands in the output spectrum
size_t Nb = N * sizeof(T); //size of the output spectrum in bytes
size_t B = Z(); //calculate the number of values in a spectrum
size_t Bb = B * sizeof(T); //calculate the size of a spectrum in bytes
file.seekg(0, std::ios::beg); //move to the beginning of the input file
size_t nC = C.size(); //get the number of bands that the kernel spans
T* inspec = (T*)malloc(Bb); //allocate space for the input spectrum
T* outspec = (T*)malloc(Nb); //allocate space for the output spectrum
size_t XY = X() * Y(); //number of pixels in the image
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
file.read((char*)inspec, Bb); //read an input spectrum
memset(outspec, 0, Nb); //set the output spectrum to zero (0)
|
9d77bbd9
David Mayerich
updates for HSIvi...
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if(mask == NULL || mask[xy]){
for(size_t b = 0; b < N; b++){ //for each component of the spectrum
for(size_t c = 0; c < nC; c++){ //for each coefficient in the kernel
outspec[b] += (T)(inspec[b + start + c] * C[c]); //perform the sum/multiply part of the convolution
}
|
9b2a5d71
David Mayerich
implemented finit...
|
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}
}
out.write((char*)outspec, Nb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1684
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void deriv(std::string outfile, size_t d, size_t order, const std::vector<double> w, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1685
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std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
|
1a224b6a
David Mayerich
fixed linux compa...
|
1686
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9b2a5d71
David Mayerich
implemented finit...
|
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size_t B = Z(); //calculate the number of values in a spectrum
size_t Bb = B * sizeof(T); //calculate the size of a spectrum in bytes
bool UNIFORM = true;
double ds = w[1] - w[0]; //initialize ds
for(size_t b = 1; b < B; b++) //test to see if the spectral spacing is uniform (if it is, convolution is much faster)
if(w[b] - w[b-1] != ds) UNIFORM = false;
size_t nC = order + d; //approximating a derivative requires order + d samples
file.seekg(0, std::ios::beg); //move to the beginning of the input file
T* inspec = (T*)malloc(Bb); //allocate space for the input spectrum
T* outspec = (T*)malloc(Bb); //allocate space for the output spectrum
size_t XY = X() * Y(); //number of pixels in the image
size_t mid = (size_t)(nC / 2); //calculate the mid point of the kernel
size_t iw; //index to the first wavelength used to evaluate the derivative at this band
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
file.read((char*)inspec, Bb); //read an input spectrum
memset(outspec, 0, Bb); //set the output spectrum to zero (0)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1709
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if(mask == NULL || mask[xy]){
iw = 0;
for(size_t b = 0; b < mid; b++){ //for each component of the spectrum
|
9b2a5d71
David Mayerich
implemented finit...
|
1712
1713
|
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
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for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
}
std::vector<double> w_pts(w.begin(), w.begin() + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[0], w_pts, d); //get the optimal sample weights
for(size_t b = mid; b <= B - (nC - mid); b++){
iw = b - mid;
if(!UNIFORM){ //if the spacing is non-uniform, we have to re-calculate these points every iteration
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
}
for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
}
iw = B - nC;
for(size_t b = B - (nC - mid) + 1; b < B; b++){
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
|
9b2a5d71
David Mayerich
implemented finit...
|
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}
|
9b2a5d71
David Mayerich
implemented finit...
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}
|
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David Mayerich
implemented finit...
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out.write((char*)outspec, Bb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
|
278c622b
David Mayerich
finished Windows ...
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bool multiply(std::string outname, double v, unsigned char* mask = NULL, bool PROGRESS = false){
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
unsigned long long N = X() * Y(); //calculate the total number of pixels to be processed
unsigned long long B = Z(); //get the number of bands
T* s = (T*)malloc(sizeof(T) * B); //allocate memory to store a pixel
for(unsigned long long n = 0; n < N; n++){ //for each pixel in the image
if(mask == NULL || mask[n]){ //if the pixel is masked
for(size_t b = 0; b < B; b++) //for each band in the spectrum
s[b] *= (T)v; //multiply
}
if(PROGRESS) progress = (double)(n+1) / N * 100; //set the current progress
target.write((char*)s, sizeof(T) * B); //write the corrected data into destination
} //end for each pixel
free(s); //free the spectrum
target.close(); //close the output file
return true;
}
bool add(std::string outname, double v, unsigned char* mask = NULL, bool PROGRESS = false){
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
unsigned long long N = X() * Y(); //calculate the total number of pixels to be processed
unsigned long long B = Z(); //get the number of bands
T* s = (T*)malloc(sizeof(T) * B); //allocate memory to store a pixel
for(unsigned long long n = 0; n < N; n++){ //for each pixel in the image
if(mask == NULL || mask[n]){ //if the pixel is masked
for(size_t b = 0; b < B; b++) //for each band in the spectrum
s[b] += (T)v; //multiply
}
if(PROGRESS) progress = (double)(n+1) / N * 100; //set the current progress
target.write((char*)s, sizeof(T) * B); //write the corrected data into destination
} //end for each pixel
free(s); //free the spectrum
target.close(); //close the output file
return true;
}
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int fft(std::string outname, size_t bandmin, size_t bandmax, size_t samples = 0, T* ratio = NULL, size_t rx = 0, size_t ry = 0, bool PROGRESS = false, int device = 0){
if(device == -1){
std::cout<<"ERROR: GPU required for FFT (uses cuFFT)."<<std::endl;
exit(1);
}
if(samples == 0) samples = Z(); //if samples are specified, use all of them
if(samples > Z()){
std::cout<<"ERROR: stim::envi doesn't support FFT padding just yet."<<std::endl;
exit(1);
}
int nd; //stores the number of CUDA devices
HANDLE_ERROR(cudaGetDeviceCount(&nd)); //get the number of CUDA devices
if(device >= nd){ //test for the existence of the requested device
std::cout<<"ERROR: requested CUDA device for stim::envi::fft() doesn't exist"<<std::endl;
exit(1);
}
HANDLE_ERROR(cudaSetDevice(device)); //set the CUDA device
cudaDeviceProp prop;
HANDLE_ERROR(cudaGetDeviceProperties(&prop, device)); //get the CUDA device properties
size_t B = Z();
size_t S = samples;
size_t fft_size = S * sizeof(T); //number of bytes for each FFT
size_t cuda_bytes = prop.totalGlobalMem; //get the number of bytes of global memory available
size_t cuda_use = (size_t)floor(cuda_bytes * 0.2); //only use 80%
size_t nS = cuda_use / fft_size; //calculate the number of spectra that can be loaded onto the GPU as a single batch
size_t batch_bytes = nS * fft_size; //calculate the size of a batch (in bytes)
size_t fft_bytes = nS * (S/2 + 1) * sizeof(cufftComplex);
T* batch = (T*) malloc(batch_bytes); //allocate space in host memory to store a batch
memset(batch, 0, batch_bytes);
std::complex<T>* batch_fft = (std::complex<T>*) malloc(fft_bytes);
T* gpu_batch; //device pointer to the batch
HANDLE_ERROR(cudaMalloc(&gpu_batch, batch_bytes)); //allocate space on the device for the FFT batch
cufftComplex* gpu_batch_fft; //allocate space for the FFT result
HANDLE_ERROR(cudaMalloc(&gpu_batch_fft, fft_bytes));
int N[1]; //create an array with the interferogram size (required for cuFFT input)
N[0] = (int)S; //set the only array value to the interferogram size
//if a background is provided for a ratio
std::complex<T>* ratio_fft = NULL; //create a pointer for the FFT of the ratio image (if it exists)
if(ratio){
size_t bkg_bytes = rx * ry * S * sizeof(T); //calculate the total number of bytes in the background image
T* bkg_copy = (T*) malloc(bkg_bytes); //allocate space to copy the background
if(S == Z()) memcpy(bkg_copy, ratio, bkg_bytes); //if the number of samples used in processing equals the number of available samples
else{
for(size_t xyi = 0; xyi < rx*ry; xyi++)
memcpy(&bkg_copy[xyi * S], &ratio[xyi * B], S * sizeof(T));
}
T* gpu_ratio;
HANDLE_ERROR(cudaMalloc(&gpu_ratio, bkg_bytes));
HANDLE_ERROR(cudaMemcpy(gpu_ratio, bkg_copy, bkg_bytes, cudaMemcpyHostToDevice));
cufftHandle bkg_plan;
CUFFT_HANDLE_ERROR(cufftPlanMany(&bkg_plan, 1, N, NULL, 1, N[0], NULL, 1, N[0], CUFFT_R2C, (int)(rx * ry)));
size_t bkg_fft_bytes = rx * ry * (S / 2 + 1) * sizeof(cufftComplex);
T* gpu_ratio_fft;
HANDLE_ERROR(cudaMalloc(&gpu_ratio_fft, bkg_fft_bytes));
CUFFT_HANDLE_ERROR(cufftExecR2C(bkg_plan, (cufftReal*)gpu_ratio, (cufftComplex*)gpu_ratio_fft));
ratio_fft = (std::complex<T>*) malloc(bkg_fft_bytes);
HANDLE_ERROR(cudaMemcpy(ratio_fft, gpu_ratio_fft, bkg_fft_bytes, cudaMemcpyDeviceToHost));
HANDLE_ERROR(cudaFree(gpu_ratio));
HANDLE_ERROR(cudaFree(gpu_ratio_fft));
CUFFT_HANDLE_ERROR(cufftDestroy(bkg_plan));
}
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cufftHandle plan; //create a CUFFT plan
CUFFT_HANDLE_ERROR(cufftPlanMany(&plan, 1, N, NULL, 1, N[0], NULL, 1, N[0], CUFFT_R2C, (int)nS));
std::ofstream outfile(outname, std::ios::binary); //open a file for writing
size_t XY = X() * Y(); //calculate the number of spectra
size_t xy = 0;
size_t bs; //stores the number of spectra in the current batch
size_t s, b;
size_t S_fft = S/2 + 1;
size_t bandkeep = bandmax - bandmin + 1;
size_t x, y;
size_t ratio_i;
T* temp_spec = (T*) malloc(Z() * sizeof(T)); //allocate space to hold a single pixel
while(xy < XY){ //while there are unprocessed spectra
bs = min(XY - xy, nS); //calculate the number of spectra to include in the batch
for(s = 0; s < bs; s++){ //for each spectrum in the batch
pixel(temp_spec, xy + s); //read a pixel from disk
memcpy(&batch[s * S], temp_spec, S * sizeof(T));
//pixel(&batch[s * S], xy + s); //read the next spectrum
}
HANDLE_ERROR(cudaMemcpy(gpu_batch, batch, batch_bytes, cudaMemcpyHostToDevice));
CUFFT_HANDLE_ERROR(cufftExecR2C(plan, (cufftReal*)gpu_batch, gpu_batch_fft)); //execute the (implicitly forward) transform
HANDLE_ERROR(cudaMemcpy(batch_fft, gpu_batch_fft, fft_bytes, cudaMemcpyDeviceToHost)); //copy the data back to the GPU
for(s = 0; s < bs; s++){ //for each spectrum in the batch
y = (xy + s)/X();
x = xy + s - y * X();
if(ratio_fft) ratio_i = (y % ry) * rx + (x % rx); //if a background is used, calculate the coordinates into it
for(b = 0; b < S/2 + 1; b++){ //for each sample
if(ratio_fft)
batch[s * S + b] = -log(abs(batch_fft[s * S_fft + b]) / abs(ratio_fft[ratio_i * S_fft + b]));
else
batch[s * S + b] = abs(batch_fft[s * S_fft + b]); //calculate the magnitude of the spectrum
}
outfile.write((char*)&batch[s * S + bandmin], bandkeep * sizeof(T)); //save the resulting spectrum
}
xy += bs; //increment xy by the number of spectra processed
if(PROGRESS) progress = (double)xy / (double)XY * 100;
}
outfile.close();
free(ratio_fft);
free(batch_fft);
free(batch);
HANDLE_ERROR(cudaFree(gpu_batch));
HANDLE_ERROR(cudaFree(gpu_batch_fft));
return 0;
}
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Doxygen comments ...
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/// Close the file.
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bool close(){
file.close();
return true;
}
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};
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David Mayerich
interleave types
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}
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#endif
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