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#ifndef STIM_BIP_H
#define STIM_BIP_H
#include "../envi/envi_header.h"
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#include "../envi/bil.h"
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#include "../envi/hsi.h"
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#include <cstring>
#include <utility>
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//CUDA
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//#ifdef CUDA_FOUND
#include <stim/cuda/cudatools/error.h>
#include <cuda_runtime.h>
#include "cublas_v2.h"
//#endif
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namespace stim{
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/**
The BIP class represents a 3-dimensional binary file stored using band interleaved by pixel (BIP) image encoding. The binary file is stored
such that Z-X "frames" are stored sequentially to form an image stack along the y-axis. When accessing the data sequentially on disk,
the dimensions read, from fastest to slowest, are Z, X, Y.
This class is optimized for data streaming, and therefore supports extremely large (terabyte-scale) files. Data is loaded from disk
on request. Functions used to access data are written to support efficient reading.
*/
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template <typename T>
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class bip: public hsi<T> {
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protected:
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//std::vector<double> w; //band wavelength
unsigned long long offset; //header offset
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using hsi<T>::w; //use the wavelength array in stim::hsi
using hsi<T>::nnz;
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using binary<T>::progress;
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using hsi<T>::X;
using hsi<T>::Y;
using hsi<T>::Z;
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public:
using binary<T>::open;
using binary<T>::file;
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using binary<T>::R;
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using binary<T>::read_line_0;
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bip(){ hsi<T>::init_bip(); }
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/// Open a data file for reading using the class interface.
/// @param filename is the name of the binary file on disk
/// @param X is the number of samples along dimension 1
/// @param Y is the number of samples (lines) along dimension 2
/// @param B is the number of samples (bands) along dimension 3
/// @param header_offset is the number of bytes (if any) in the binary header
/// @param wavelengths is an optional STL vector of size B specifying a numerical label for each band
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bool open(std::string filename,
unsigned long long X,
unsigned long long Y,
unsigned long long B,
unsigned long long header_offset,
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std::vector<double> wavelengths){
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//copy the wavelengths to the BSQ file structure
w = wavelengths;
//copy the offset to the structure
offset = header_offset;
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return open(filename, vec<unsigned long long>(B, X, Y), header_offset);
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}
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/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
/// @param page <= B is the integer number of the band to be copied.
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bool band_index( T * p, unsigned long long page, bool PROGRESS = false){
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return binary<T>::read_plane_0(p, page, PROGRESS);
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}
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/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
/// @param wavelength is a floating point value (usually a wavelength in spectral data) used as a label for the band to be copied.
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bool band( T * p, double wavelength, bool PROGRESS = false){
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//if there are no wavelengths in the BSQ file
if(w.size() == 0)
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return band_index(p, (unsigned long long)wavelength, PROGRESS);
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unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
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unsigned page=0; //bands around the wavelength
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//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
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if ( w[page] > wavelength ){
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band_index(p, page, PROGRESS);
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return true;
}
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while( w[page] < wavelength )
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{
page++;
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if (page == Z()) {
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band_index(p, Z()-1, PROGRESS);
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return true;
}
}
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if ( wavelength < w[page] )
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{
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T * p1;
T * p2;
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p1=(T*)malloc( XY * sizeof(T)); //memory allocation
p2=(T*)malloc( XY * sizeof(T));
band_index(p1, page - 1);
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band_index(p2, page, PROGRESS);
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for(unsigned long long i=0; i < XY; i++){
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double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
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p[i] = (T)(((double)p2[i] - (double)p1[i]) * r + (double)p1[i]);
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}
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free(p1);
free(p2);
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}
else //if the wavelength is equal to a wavelength in header file
{
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band_index(p, page, PROGRESS);
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}
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return true;
}
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/// Retrieve a single spectrum (Z-axis line) at a given (x, y) location and stores it in pre-allocated memory.
/// @param p is a pointer to pre-allocated memory at least B * sizeof(T) in size.
/// @param x is the x-coordinate (dimension 1) of the spectrum.
/// @param y is the y-coordinate (dimension 2) of the spectrum.
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bool spectrum(T * p, unsigned long long x, unsigned long long y, bool PROGRESS = false){
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return read_line_0(p, x, y, PROGRESS); //read a line in the binary YZ plane (dimension order for BIP is ZXY)
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}
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bool spectrum(T* p, size_t n, bool PROGRESS = false){
size_t y = n / X();
size_t x = n - y * X();
return read_line_0(p, x, y, PROGRESS); //read a line in the binary YZ plane (dimension order for BIP is ZXY)
}
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/// Retrieves a band of x values from a given xz plane.
/// @param p is a pointer to pre-allocated memory at least X * sizeof(T) in size
/// @param c is a pointer to an existing XZ plane (size X*Z*sizeof(T))
/// @param wavelength is the wavelength of X values to retrieve
bool read_x_from_xz(T* p, T* c, double wavelength)
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{
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unsigned long long B = Z();
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unsigned long long page=0; //samples around the wavelength
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//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
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if ( w[page] > wavelength ){
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for(unsigned long long j = 0; j < X(); j++)
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{
p[j] = c[j * B];
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}
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return true;
}
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while( w[page] < wavelength )
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{
page++;
//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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changes for mnf: ...
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|
}
|
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|
}
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|
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Ziqi completed bi...
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Doxygen comments ...
|
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|
/// Convert the current BIP file to a BIL file with the specified file name.
/// @param outname is the name of the output BIL file to be saved to disk.
|
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added an inverse ...
|
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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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added stim::hsi a...
|
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|
unsigned long long S = X() * Z() * sizeof(T); //calculate the number of bytes in a ZX slice
|
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fixed linux compa...
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|
|
11f177d5
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Ziqi added functi...
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std::ofstream target(outname.c_str(), std::ios::binary);
|
9d3ba0b1
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|
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|
//std::string headername = outname + ".hdr";
|
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David Mayerich
fixed linux compa...
|
402
|
|
f6169dea
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Ziqi completed bi...
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|
T * p; //pointer to the current ZX slice for bip file
|
11f177d5
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Ziqi added functi...
|
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|
p = (T*)malloc(S);
|
f6169dea
heziqi
Ziqi completed bi...
|
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|
T * q; //pointer to the current XZ slice for bil file
q = (T*)malloc(S);
|
1a224b6a
David Mayerich
fixed linux compa...
|
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|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
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|
for ( unsigned long long i = 0; i < Y(); i++)
|
1a224b6a
David Mayerich
fixed linux compa...
|
409
|
{
|
724ec347
David Mayerich
simplified the EN...
|
410
|
read_plane_y(p, i);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
411
|
for ( unsigned long long k = 0; k < Z(); k++)
|
f6169dea
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Ziqi completed bi...
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|
{
|
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David Mayerich
added stim::hsi a...
|
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414
|
unsigned long long ks = k * X();
for ( unsigned long long j = 0; j < X(); j++)
|
724ec347
David Mayerich
simplified the EN...
|
415
|
q[ks + j] = p[k + j * Z()];
|
cbce396e
David Mayerich
added support for...
|
416
|
|
63fc1df8
David Mayerich
added an inverse ...
|
417
|
if(PROGRESS) progress = (double)(i * Z() + k+1) / (Y() * Z()) * 100;
|
f6169dea
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Ziqi completed bi...
|
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|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
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|
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
|
11f177d5
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Ziqi added functi...
|
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|
}
|
f6169dea
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Ziqi completed bi...
|
421
|
|
11f177d5
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Ziqi added functi...
|
422
|
free(p);
|
f6169dea
heziqi
Ziqi completed bi...
|
423
|
free(q);
|
11f177d5
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Ziqi added functi...
|
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426
|
target.close();
return true;
}
|
88c3e636
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Ziqi added big.h
|
427
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
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|
/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lp is a pointer to an array holding the band image for the left baseline point
/// @param rp is a pointer to an array holding the band image for the right baseline point
/// @param wavelength is the label value for the requested baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
|
20c212c0
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Ziqi added functi...
|
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437
|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
438
|
unsigned long long XY = X() * Y();
|
20c212c0
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Ziqi added functi...
|
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440
441
442
|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
443
|
for(unsigned long long i=0; i < XY; i++){
|
20c212c0
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Ziqi added functi...
|
444
445
446
447
|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
448
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
449
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|
/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param bandwavelength is the label value for the desired baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
|
70407ea9
heziqi
Ziqi completed he...
|
455
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
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Ziqi added functi...
|
456
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|
T* lp;
T* rp;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
459
460
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
70407ea9
heziqi
Ziqi completed he...
|
461
462
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
463
|
|
70407ea9
heziqi
Ziqi completed he...
|
464
|
band(lp, lb);
|
1a224b6a
David Mayerich
fixed linux compa...
|
465
|
band(rp, rb);
|
20c212c0
heziqi
Ziqi added functi...
|
466
467
468
|
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
469
470
|
free(lp);
free(rp);
|
20c212c0
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Ziqi added functi...
|
471
472
473
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
474
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
475
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|
/// Calculate the area under the spectrum between two specified points and stores the result in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label value for the left bound (start of the integration)
/// @param rab is the label value for the right bound (end of the integration)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
482
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
483
484
485
486
487
|
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
|
20c212c0
heziqi
Ziqi added functi...
|
488
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
489
490
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
20c212c0
heziqi
Ziqi added functi...
|
491
492
493
494
495
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
496
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|
memset(result, (char)0, S);
//find the wavelenght position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
500
501
502
|
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...
|
518
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
519
520
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
521
|
while (rab <= w[bi]){
|
20c212c0
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Ziqi added functi...
|
522
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525
526
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528
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
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Ziqi completed he...
|
529
530
|
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...
|
531
532
|
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...
|
533
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
534
535
|
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...
|
536
|
for(unsigned long long j = 0; j < XY; j++){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
537
|
result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
538
|
}
|
517876d6
heziqi
metrics finished ...
|
539
|
|
20c212c0
heziqi
Ziqi added functi...
|
540
541
|
//calculate the area
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
542
|
for(unsigned long long i = ai; i <= bi ;i++)
|
20c212c0
heziqi
Ziqi added functi...
|
543
544
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
545
|
for(unsigned long long j = 0; j < XY; j++)
|
20c212c0
heziqi
Ziqi added functi...
|
546
|
{
|
1a224b6a
David Mayerich
fixed linux compa...
|
547
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
548
549
550
|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
551
|
|
517876d6
heziqi
metrics finished ...
|
552
553
554
555
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
556
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558
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
559
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|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param pos1 is the label value for the first peak (numerator) position
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param pos2 is the label value for the second peak (denominator) position
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
568
|
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...
|
569
|
|
1a224b6a
David Mayerich
fixed linux compa...
|
570
571
572
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
573
574
575
576
|
//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...
|
577
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
578
579
580
581
582
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
583
584
585
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
586
|
return true;
|
70407ea9
heziqi
Ziqi completed he...
|
587
|
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
588
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
589
590
591
592
593
594
595
596
597
|
/// 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...
|
598
599
|
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...
|
600
601
602
603
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
604
605
606
607
|
//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...
|
608
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
609
610
611
612
613
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
614
615
616
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
617
618
619
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
620
621
622
623
624
625
626
627
628
|
/// 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...
|
629
|
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
|
a23c4132
David Mayerich
Doxygen comments ...
|
630
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
631
632
|
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...
|
633
634
635
636
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
637
638
639
640
|
//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...
|
641
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
642
643
644
645
646
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
647
648
649
|
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
650
651
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
652
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
653
654
655
656
657
658
659
|
/// 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 ...
|
660
661
662
663
664
665
|
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...
|
666
667
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
668
669
670
671
672
673
674
675
676
|
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...
|
677
678
679
|
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 ...
|
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
|
//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...
|
706
707
|
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 ...
|
708
709
710
|
}
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...
|
711
|
for(unsigned long long j = 0; j < XY; j++){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
712
|
result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
713
714
715
716
|
}
//calculate f(x) times x
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
717
|
for(unsigned long long i = ai; i <= bi ;i++)
|
517876d6
heziqi
metrics finished ...
|
718
719
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
720
|
for(unsigned long long j = 0; j < XY; j++)
|
517876d6
heziqi
metrics finished ...
|
721
|
{
|
1a224b6a
David Mayerich
fixed linux compa...
|
722
|
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 ...
|
723
724
725
726
727
728
729
730
731
732
733
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
734
735
736
737
738
739
740
|
/// 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...
|
741
|
bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
|
1a224b6a
David Mayerich
fixed linux compa...
|
742
743
744
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
745
746
747
748
|
//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...
|
749
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
750
|
if(mask == NULL || mask[i])
|
517876d6
heziqi
metrics finished ...
|
751
752
753
754
755
|
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
|
1a224b6a
David Mayerich
fixed linux compa...
|
756
|
return true;
|
517876d6
heziqi
metrics finished ...
|
757
758
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
759
760
761
762
763
764
765
|
/// 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...
|
766
|
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
|
767
|
|
724ec347
David Mayerich
simplified the EN...
|
768
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
798cea97
David Mayerich
added progress ba...
|
769
|
band(temp, mask_band, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
770
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
771
|
for (unsigned long long i = 0; i < X() * Y();i++) {
|
e37ce7bf
David Mayerich
added the ability...
|
772
773
774
775
776
777
778
|
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
|
779
780
|
}
|
517876d6
heziqi
metrics finished ...
|
781
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
782
783
784
785
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
786
787
788
789
|
/// 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...
|
790
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
791
792
793
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
794
795
|
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
|
796
|
|
1a55a328
David Mayerich
Added comments fo...
|
797
|
T * temp = (T*)malloc(L); //allocate space for that page
|
740f8cd2
heziqi
added apply_mask
|
798
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
799
|
for (unsigned long long i = 0; i < Y(); i++) //for each page (Y in BIP)
|
740f8cd2
heziqi
added apply_mask
|
800
|
{
|
724ec347
David Mayerich
simplified the EN...
|
801
|
read_plane_y(temp, i); //load that page (it's pointed to by temp)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
802
|
for ( unsigned long long j = 0; j < X(); j++) //for each X value
|
740f8cd2
heziqi
added apply_mask
|
803
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
804
|
for (unsigned long long k = 0; k < Z(); k++) //for each B value (band)
|
740f8cd2
heziqi
added apply_mask
|
805
|
{
|
724ec347
David Mayerich
simplified the EN...
|
806
807
|
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...
|
808
|
else //otherwise just continue
|
740f8cd2
heziqi
added apply_mask
|
809
810
811
|
continue;
}
}
|
1a55a328
David Mayerich
Added comments fo...
|
812
|
target.write(reinterpret_cast<const char*>(temp), L); //write the edited band data into target file
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
813
|
if(PROGRESS) progress = (double)(i+1) / (double)Y() * 100;
|
740f8cd2
heziqi
added apply_mask
|
814
|
}
|
1a55a328
David Mayerich
Added comments fo...
|
815
816
817
|
target.close(); //close the target file
free(temp); //free allocated memory
return true; //return true
|
740f8cd2
heziqi
added apply_mask
|
818
819
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
820
821
822
823
824
|
/// 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...
|
825
|
bool sift(T* matrix, unsigned char* mask = NULL, bool PROGRESS = false){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
826
827
828
829
830
|
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...
|
831
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
832
833
|
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...
|
834
|
if(mask == NULL || mask[xy]){ //if the current pixel is masked
|
ba51ae6a
David Mayerich
fixed metric calc...
|
835
836
837
838
839
840
841
842
|
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...
|
843
|
file.seekg(Bbytes, std::ios::cur); //otherwise skip this band
|
814eb271
David Mayerich
fixed problems wi...
|
844
|
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
845
846
847
|
}
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
848
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
849
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
850
|
bool sift(std::string outfile, unsigned char* mask, bool PROGRESS = false){
|
8550e94f
David Mayerich
added sifting and...
|
851
852
|
//reset the file pointer to the beginning of the file
|
1a224b6a
David Mayerich
fixed linux compa...
|
853
|
file.seekg(0, std::ios::beg);
|
8550e94f
David Mayerich
added sifting and...
|
854
855
|
// open an output stream
|
e843658b
Brad Deutsch
Previous push did...
|
856
857
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
8550e94f
David Mayerich
added sifting and...
|
858
|
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
859
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
860
|
T* spectrum = (T*) malloc(B * sizeof(T));
|
e843658b
Brad Deutsch
Previous push did...
|
861
|
|
8550e94f
David Mayerich
added sifting and...
|
862
|
//calculate the number of pixels in a band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
863
|
unsigned long long XY = X() * Y();
|
e843658b
Brad Deutsch
Previous push did...
|
864
|
|
8550e94f
David Mayerich
added sifting and...
|
865
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
866
867
|
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...
|
868
869
870
871
872
|
//if the current pixel isn't masked
if( mask[x] == 0){
//increment the number of skipped pixels
skip++;
|
e843658b
Brad Deutsch
Previous push did...
|
873
|
}
|
8550e94f
David Mayerich
added sifting and...
|
874
875
876
877
878
879
880
881
882
883
884
885
886
887
|
//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...
|
888
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
889
|
if(PROGRESS) progress = (double) (x+1) / XY * 100;
|
8550e94f
David Mayerich
added sifting and...
|
890
|
|
e843658b
Brad Deutsch
Previous push did...
|
891
|
}
|
8550e94f
David Mayerich
added sifting and...
|
892
893
|
//close the output file
|
e843658b
Brad Deutsch
Previous push did...
|
894
|
target.close();
|
8550e94f
David Mayerich
added sifting and...
|
895
|
free(spectrum);
|
cbce396e
David Mayerich
added support for...
|
896
|
|
cbce396e
David Mayerich
added support for...
|
897
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
898
899
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
900
|
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...
|
901
902
903
904
905
|
// 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...
|
906
|
file.seekg(0, std::ios::beg);
|
8550e94f
David Mayerich
added sifting and...
|
907
908
|
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
909
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
910
911
912
913
914
915
916
|
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...
|
917
|
unsigned long long XY = samples * lines;
|
8550e94f
David Mayerich
added sifting and...
|
918
919
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
920
921
|
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...
|
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
|
//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...
|
939
|
if(PROGRESS) progress = (double)(x + 1) / XY * 100;
|
3150c537
David Mayerich
added further pro...
|
940
|
|
8550e94f
David Mayerich
added sifting and...
|
941
942
943
944
945
946
|
}
//close the output file
target.close();
free(spectrum);
|
a2bf1d08
David Mayerich
general bug fixes...
|
947
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
948
|
|
e843658b
Brad Deutsch
Previous push did...
|
949
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
950
951
|
|
e843658b
Brad Deutsch
Previous push did...
|
952
953
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
954
955
956
957
|
/// 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
|
35a7195f
David Mayerich
added median spec...
|
958
|
bool mean_spectrum(double* m, double* std, unsigned char* mask = NULL, bool PROGRESS = false){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
959
960
|
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...
|
961
962
963
|
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...
|
964
965
|
unsigned long long count = nnz(mask); //calculate the number of masked pixels
|
35a7195f
David Mayerich
added median spec...
|
966
|
double x;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
967
968
969
970
|
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...
|
971
972
973
|
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...
|
974
975
|
}
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
976
|
if(PROGRESS) progress = (double)(i+1) / XY * 100; //increment the progress
|
a43c4fe1
heziqi
Added crop in env...
|
977
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
978
|
|
35a7195f
David Mayerich
added median spec...
|
979
980
981
982
|
//calculate the standard deviation
for(size_t i = 0; i < Z(); i++)
std[i] = sqrt(e_x2[i] - m[i] * m[i]);
|
a43c4fe1
heziqi
Added crop in env...
|
983
|
free(temp);
|
a43c4fe1
heziqi
Added crop in env...
|
984
985
|
return true;
}
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
986
|
//#ifdef CUDA_FOUND
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
987
|
/// Calculate the covariance matrix for masked pixels using cuBLAS
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
988
|
/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
989
|
int co_matrix_cublas(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
990
|
|
1a224b6a
David Mayerich
fixed linux compa...
|
991
|
cudaError_t cudaStat;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
992
993
|
cublasStatus_t stat;
cublasHandle_t handle;
|
1a224b6a
David Mayerich
fixed linux compa...
|
994
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
995
996
997
998
999
1000
1001
1002
1003
1004
1005
|
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...
|
1006
|
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...
|
1007
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1008
1009
1010
1011
|
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...
|
1012
1013
1014
|
if (stat != CUBLAS_STATUS_SUCCESS) return 1; //test the cuBLAS instance to make sure it is valid
else std::cout<<"Using cuBLAS to calculate the mean covariance matrix..."<<std::endl;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1015
|
for (unsigned long long xy = 0; xy < XY; xy++){ //for each pixel
|
5a5359da
David Mayerich
fixed - allows th...
|
1016
1017
|
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...
|
1018
1019
1020
|
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...
|
1021
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1022
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
|
5a5359da
David Mayerich
fixed - allows th...
|
1023
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1024
1025
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1026
|
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...
|
1027
1028
1029
1030
1031
|
cudaFree(A_dev); //clean up allocated device memory
cudaFree(s_dev);
cudaFree(avg_dev);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1032
1033
|
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...
|
1034
1035
1036
1037
|
co[B * i + j] = co[B * j + i];
}
}
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1038
|
return 0;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1039
|
}
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1040
|
//#endif
|
1a224b6a
David Mayerich
fixed linux compa...
|
1041
|
|
2aa68315
David Mayerich
major bug fixes f...
|
1042
|
/// Calculate the covariance matrix for all masked pixels in the image with 64-bit floating point precision.
|
a23c4132
David Mayerich
Doxygen comments ...
|
1043
1044
1045
1046
|
/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
/// @param avg is a pointer to memory of size B that stores the average spectrum
/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
|
63fc1df8
David Mayerich
added an inverse ...
|
1047
|
bool co_matrix(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1048
|
progress = 0;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1049
|
|
b37665a9
David Mayerich
cuBLAS won't run ...
|
1050
|
int dev_count;
|
ebd02452
David Mayerich
added cuBLAS erro...
|
1051
1052
|
HANDLE_ERROR(cudaGetDeviceCount(&dev_count)); //get the number of CUDA devices
std::cout<<"Number of CUDA devices: "<<dev_count<<std::endl; //output the number of CUDA devices
|
b37665a9
David Mayerich
cuBLAS won't run ...
|
1053
|
cudaDeviceProp prop;
|
ebd02452
David Mayerich
added cuBLAS erro...
|
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
|
int best_device_id = 0; //stores the best CUDA device
float best_device_cc = 0.0f; //stores the compute capability of the best device
std::cout<<"CUDA devices:"<<std::endl;
for(int d = 0; d < dev_count; d++){ //for each CUDA device
cudaGetDeviceProperties(&prop, d); //get the property of the first device
float cc = prop.major + prop.minor / 10.0f; //calculate the compute capability
std::cout<<d<<": ("<<prop.major<<"."<<prop.minor<<") "<<prop.name<<std::endl; //display the device information
if(cc > best_device_cc){
best_device_cc = cc; //if this is better than the previous device, use it
best_device_id = d;
}
}
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1067
|
if(dev_count > 0 && prop.major != 9999){ //if the first device is not an emulator
|
ebd02452
David Mayerich
added cuBLAS erro...
|
1068
1069
|
std::cout<<"Using device "<<best_device_id<<std::endl;
HANDLE_ERROR(cudaSetDevice(best_device_id));
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1070
1071
1072
|
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
} //otherwise continue using the CPU
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1073
|
|
ebd02452
David Mayerich
added cuBLAS erro...
|
1074
|
std::cout<<"No supported CUDA devices found or cuBLAS failed. Using CPU"<<std::endl;
|
a43c4fe1
heziqi
Added crop in env...
|
1075
|
//memory allocation
|
2aa68315
David Mayerich
major bug fixes f...
|
1076
1077
|
unsigned long long XY = X() * Y();
unsigned long long B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
1078
|
T* temp = (T*)malloc(sizeof(T) * B);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1079
1080
|
unsigned long long count = nnz(mask); //count the number of masked pixels
|
63fc1df8
David Mayerich
added an inverse ...
|
1081
|
|
2aa68315
David Mayerich
major bug fixes f...
|
1082
1083
1084
1085
|
//initialize covariance matrix
memset(co, 0, B * B * sizeof(double));
//calculate covariance matrix
|
2aa68315
David Mayerich
major bug fixes f...
|
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
|
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...
|
1099
1100
|
}
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1101
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1102
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
1103
1104
1105
1106
|
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...
|
1107
1108
1109
|
}
}
|
a43c4fe1
heziqi
Added crop in env...
|
1110
|
free(temp);
|
2aa68315
David Mayerich
major bug fixes f...
|
1111
|
free(temp_precise);
|
a43c4fe1
heziqi
Added crop in env...
|
1112
1113
1114
|
return true;
}
|
334547d8
sam
changes for mnf: ...
|
1115
|
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1116
|
//#ifdef CUDA_FOUND
|
334547d8
sam
changes for mnf: ...
|
1117
1118
|
/// Calculate the covariance matrix of Noise for masked pixels using cuBLAS
/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1119
|
int coNoise_matrix_cublas(double* coN, double* avg, unsigned char *mask, bool PROGRESS = false){
|
334547d8
sam
changes for mnf: ...
|
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
|
cudaError_t cudaStat;
cublasStatus_t stat;
cublasHandle_t handle;
progress = 0; //initialize the progress to zero (0)
unsigned long long XY = X() * Y(); //calculate the number of elements in a band image
unsigned long long B = Z(); //calculate the number of spectral elements
double* s = (double*)malloc(sizeof(double) * B); //allocate space for the spectrum that will be pulled from the file
double* s_dev; //declare a device pointer that will store the spectrum on the GPU
double* 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)
double* A_dev; //declare a device pointer that will store the covariance matrix on the GPU
double* avg_dev; //declare a device pointer that will store the average spectrum
cudaStat = cudaMalloc(&s_dev, B * sizeof(double)); //allocate space on the CUDA device for the spectrum
cudaStat = cudaMalloc(&A_dev, B * B * sizeof(double)); //allocate space on the CUDA device for the covariance matrix
cudaStat = cudaMemset(A_dev, 0, B * B * sizeof(double)); //initialize the covariance matrix to zero (0)
cudaStat = cudaMalloc(&avg_dev, B * sizeof(double)); //allocate space on the CUDA device for the average spectrum
stat = cublasSetVector((int)B, sizeof(double), avg, 1, avg_dev, 1); //copy the average spectrum to the CUDA device
double ger_alpha = 1.0/(double)XY; //scale the outer product by the inverse of the number of samples (mean outer product)
double axpy_alpha = -1; //multiplication factor for the average spectrum (in order to perform a subtraction)
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1147
1148
1149
|
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
|
334547d8
sam
changes for mnf: ...
|
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
|
for (unsigned long long xy = 0; xy < XY; xy++){ //for each pixel
if (mask == NULL || mask[xy] != 0){
pixeld(s, xy); //retreive the spectrum at the current xy pixel location
stat = cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1); //copy the spectrum from the host to the device
stat = cublasDaxpy(handle, (int)B, &axpy_alpha, avg_dev, 1, s_dev, 1); //subtract the average spectrum
cudaMemcpy(s2_dev, s_dev + 1 , (B-1) * sizeof(double), cudaMemcpyDeviceToDevice); //copy B-1 elements from shifted source data (s_dev) to device pointer (s2_dev )
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 (z direction is choosed to do so , which is almost the same as x or y direction or even average of them )
stat = cublasDsyr(handle, CUBLAS_FILL_MODE_UPPER, (int)B, &ger_alpha, s_dev, 1, A_dev, (int)B); //calculate the covariance matrix (symmetric outer product)
}
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
}
cublasGetMatrix((int)B, (int)B, sizeof(double), A_dev, (int)B, 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);
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++){
coN[B * i + j] = coN[B * j + i];
}
}
return true;
}
|
2781a48c
David Mayerich
fixed cuBLAS func...
|
1182
|
//#endif
|
334547d8
sam
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/// 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
bool coNoise_matrix(double* coN, double* avg, unsigned char *mask, bool PROGRESS = false){
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int dev_count;
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HANDLE_ERROR(cudaGetDeviceCount(&dev_count)); //get the number of CUDA devices
std::cout<<"Number of CUDA devices: "<<dev_count<<std::endl; //output the number of CUDA devices
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cudaDeviceProp prop;
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int best_device_id = 0; //stores the best CUDA device
float best_device_cc = 0.0f; //stores the compute capability of the best device
std::cout<<"CUDA devices:"<<std::endl;
for(int d = 0; d < dev_count; d++){ //for each CUDA device
cudaGetDeviceProperties(&prop, d); //get the property of the first device
float cc = prop.major + prop.minor / 10.0f; //calculate the compute capability
std::cout<<d<<": ("<<prop.major<<"."<<prop.minor<<") "<<prop.name<<std::endl; //display the device information
if(cc > best_device_cc){
best_device_cc = cc; //if this is better than the previous device, use it
best_device_id = d;
}
}
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2781a48c
David Mayerich
fixed cuBLAS func...
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if(dev_count > 0 && prop.major != 9999){ //if the first device is not an emulator
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added cuBLAS erro...
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std::cout<<"Using device "<<best_device_id<<std::endl;
HANDLE_ERROR(cudaSetDevice(best_device_id));
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David Mayerich
fixed cuBLAS func...
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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
} //otherwise continue using the CPU
|
ebd02452
David Mayerich
added cuBLAS erro...
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std::cout<<"cuBLAS initialization failed - using CPU"<<std::endl;
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334547d8
sam
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progress = 0;
//memory allocation
unsigned long long XY = X() * Y();
unsigned long long B = Z();
T* temp = (T*)malloc(sizeof(T) * B);
unsigned long long count = nnz(mask); //count the number of masked pixels
//initialize covariance matrix of noise
memset(coN, 0, B * B * sizeof(double));
//calculate covariance matrix
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));
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
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];
for(unsigned long long b2 = 0; b2 < B-1; b2++) //Minimum/Maximum Autocorrelation Factors (MAF) method : subtranct each pixel from adjacent pixel (z direction is choosed to do so , which is almost the same as x or y direction or even average of them )
temp_precise[b2] -= temp_precise[b2+1];
idx = 0;
for (unsigned long long b0 = 0; b0 < B; b0++){ //for each band
for (unsigned long long b1 = b0; b1 < B; b1++)
coN_half[idx++] += temp_precise[b0] * temp_precise[b1];
}
}
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
idx = 0;
for (unsigned long long i = 0; i < B; i++){ //copy the precision matrix to both halves of the output matrix
for (unsigned long long j = i; j < B; j++){
coN[j * B + i] = coN[i * B + j] = coN_half[idx++] / (double) count;
}
}
free(temp);
free(temp_precise);
return true;
}
#ifdef CUDA_FOUND
/// 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){
cudaError_t cudaStat;
cublasStatus_t stat;
cublasHandle_t handle;
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
|
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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
cudaStat = cudaMalloc(&s_dev, B * sizeof(double)); //allocate space on the CUDA device for the spectrum
double* basis_dev; // device pointer on the GPU
cudaStat = cudaMalloc(&basis_dev, M * B * sizeof(double)); // allocate space on the CUDA device
cudaStat = cudaMemset(basis_dev, 0, M * B * sizeof(double)); // initialize basis_dev to zero (0)
/// 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];
stat = cublasSetMatrix((int)M, (int)B, sizeof(double),basis_Transposed, (int)M, basis_dev, (int)M); //copy the basis_Transposed matrix to the CUDA device (both matrices are stored in column-major format)
double* center_dev; //declare a device pointer that will store the center (average)
cudaStat = cudaMalloc(¢er_dev, B * sizeof(double)); //allocate space on the CUDA device for the center (average)
stat = cublasSetVector((int)B, sizeof(double), center, 1, center_dev, 1); //copy the center vector (average) to the CUDA device (from host to device)
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
cudaStat = cudaMalloc(&A_dev,M * sizeof(double)); //allocate space on the CUDA device for the projected pixel
cudaStat = cudaMemset(A_dev, 0,M * sizeof(double)); //initialize the projected pixel to zero (0)
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)
stat = cublasCreate(&handle); //create a cuBLAS instance
if (stat != CUBLAS_STATUS_SUCCESS) { //test the cuBLAS instance to make sure it is valid
printf ("CUBLAS initialization failed\n");
return EXIT_FAILURE;
}
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08d1c3b9
David Mayerich
fixed casting war...
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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: ...
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if (mask == NULL || mask[xy] != 0){
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08d1c3b9
David Mayerich
fixed casting war...
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pixeld(s, xy); //retreive the spectrum at the current xy pixel location
|
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sam
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stat = cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1); //copy the spectrum from the host to the device
stat = cublasDaxpy(handle, (int)B, &axpy_alpha, center_dev, 1, s_dev, 1); //subtract the center (average)
stat = 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
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3a880d1c
David Mayerich
fixed PCA and BIP...
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stat = cublasGetVector((int)M, sizeof(double), A_dev, 1, A, 1); //copy the projected pixel to the host (from GPU to CPU)
//stat = cublasGetVector((int)B, sizeof(double), s_dev, 1, A, 1); //copy the projected pixel to the host (from GPU to CPU)
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sam
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David Mayerich
fixed casting war...
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//std::copy<double*, T*>(A, A + M, temp);
for(i = 0; i < M; i++) temp[i] = (T)A[i]; //casting projected pixel from double to whatever T is
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334547d8
sam
changes for mnf: ...
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}
|
3a880d1c
David Mayerich
fixed PCA and BIP...
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else
memset(temp, 0, sizeof(T) * M);
|
334547d8
sam
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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
cudaFree(A_dev);
cudaFree(s_dev);
cudaFree(basis_dev);
cudaFree(center_dev);
free(A);
free(s);
free(temp);
target.close(); //close the output file
|
08d1c3b9
David Mayerich
fixed casting war...
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334547d8
sam
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return true;
}
#endif
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812a2741
David Mayerich
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/// Project the spectra onto a set of basis functions
/// @param outfile is the name of the new binary output file that will be created
/// @param center is a spectrum about which the data set will be rotated (ex. when performing mean centering)
/// @param basis a set of basis vectors that the data set will be projected onto (after centering)
/// @param M is the number of basis vectors
/// @param mask is a character mask used to limit processing to valid pixels
|
9d3ba0b1
David Mayerich
added stim::hsi a...
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1364
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bool project(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask = NULL, bool PROGRESS = false){
|
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David Mayerich
added an inverse ...
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#ifdef CUDA_FOUND
int dev_count;
cudaGetDeviceCount(&dev_count); //get the number of CUDA devices
cudaDeviceProp prop;
cudaGetDeviceProperties(&prop, 0); //get the property of the first device
if(dev_count > 0 && prop.major != 9999) //if the first device is not an emulator
return project_cublas(outfile,center,basis,M,mask,PROGRESS); //use cuBLAS to calculate the covariance matrix
#endif
|
63fc1df8
David Mayerich
added an inverse ...
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std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
|
9d3ba0b1
David Mayerich
added stim::hsi a...
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//std::string headername = outfile + ".hdr"; //the header file name
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//memory allocation
unsigned long long XY = X() * Y();
unsigned long long B = Z();
T* s = (T*)malloc(sizeof(T) * B); //allocate space for the spectrum
T* rs = (T*)malloc(sizeof(T) * M); //allocate space for the projected spectrum
double* bv; //pointer to the current projection vector
for(unsigned long long xy = 0; xy < XY; xy++){ //for each spectrum in the image
|
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David Mayerich
added stim::hsi a...
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memset(rs, 0, sizeof(T) * M);
if(mask == NULL || mask[xy]){
pixel(s, xy); //load the spectrum
for(unsigned long long m = 0; m < M; m++){ //for each basis vector
bv = &basis[m * B]; //assign 'bv' to the beginning of the basis vector
for(unsigned long long b = 0; b < B; b++){ //for each band
rs[m] += (T)(((double)s[b] - center[b]) * bv[b]); //center the spectrum and perform the projection
}
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David Mayerich
added an inverse ...
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}
}
|
1a224b6a
David Mayerich
fixed linux compa...
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David Mayerich
added an inverse ...
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target.write(reinterpret_cast<const char*>(rs), sizeof(T) * M); //write the projected vector
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
free(s); //free temporary storage arrays
free(rs);
target.close(); //close the output file
|
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
|
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
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1426
|
s[b] += (T)((double)coeff[c] * bv[b] + center[b]); //calculate the contribution of each element of the basis vector in the final spectrum
|
63fc1df8
David Mayerich
added an inverse ...
|
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}
}
target.write(reinterpret_cast<const char*>(s), sizeof(T) * B); //write the projected vector
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
free(coeff); //free temporary storage arrays
free(s);
target.close(); //close the output file
return true;
}
|
0df38ff3
heziqi
fixed head detached
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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
|
e9bddc57
David Mayerich
added band croppi...
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bool crop(std::string outfile, unsigned long long x0,
unsigned long long y0,
unsigned long long x1,
unsigned long long y1,
unsigned long long b0,
|
63fc1df8
David Mayerich
added an inverse ...
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unsigned long long b1,
bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
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David Mayerich
implemented spect...
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//calculate the new number of samples, lines, and bands
unsigned long long samples = x1 - x0;
unsigned long long lines = y1 - y0;
unsigned long long bands = b1 - b0;
//calculate the length of one cropped spectrum
unsigned long long L = bands * sizeof(T);
//unsigned long long L = Z() * sizeof(T);
//allocate space for the spectrum
|
a43c4fe1
heziqi
Added crop in env...
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T* temp = (T*)malloc(L);
|
3033b886
David Mayerich
implemented spect...
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//open an output file for binary writing
|
a43c4fe1
heziqi
Added crop in env...
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std::ofstream out(outfile.c_str(), std::ios::binary);
|
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David Mayerich
implemented spect...
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//seek to the first pixel in the cropped image
file.seekg( (y0 * X() * Z() + x0 * Z() + b0) * sizeof(T), std::ios::beg);
//distance between sample spectra in the same line
unsigned long long jump_sample = ( (Z() - b1) + b0 ) * sizeof(T);
//distance between sample spectra in adjacent lines
|
e6d6e994
David Mayerich
fixed cropping bu...
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unsigned long long jump_line = ( X() - x1 + x0 ) * Z() * sizeof(T);
|
3033b886
David Mayerich
implemented spect...
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//unsigned long long sp = y0 * X() + x0; //start pixel
//for each pixel in the image
for (unsigned y = 0; y < lines; y++)
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heziqi
Added crop in env...
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{
|
3033b886
David Mayerich
implemented spect...
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for (unsigned x = 0; x < samples; x++)
|
a43c4fe1
heziqi
Added crop in env...
|
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{
|
3033b886
David Mayerich
implemented spect...
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//read the cropped spectral region
file.read( (char*) temp, L );
//pixel(temp, sp + x + y * X());
|
1a224b6a
David Mayerich
fixed linux compa...
|
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out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
|
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);
|
63fc1df8
David Mayerich
added an inverse ...
|
1497
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if(PROGRESS) progress = (double)((y+1) * samples + x + 1) / (lines * samples) * 100;
|
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heziqi
Added crop in env...
|
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}
|
3033b886
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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);
|
3150c537
David Mayerich
added further pro...
|
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a43c4fe1
heziqi
Added crop in env...
|
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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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1543
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/// Combine two BIP images along the Y axis
/// @param outfile is the combined file to be output
/// @param infile is the input file stream for the image to combine with this one
/// @param Sx is the size of the second image along X
/// @param Sy is the size of the second image along Y
/// @param offset is a shift (negative or positive) in the combined image to the left or right
void combine(std::string outfile, bip<T>* C, long long xp, long long yp, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
file.seekg(0, std::ios::beg); //move to the beginning of both files
C->file.seekg(0, std::ios::beg);
size_t S[2]; //size of the output band image
size_t p0[2]; //position of the current image in the output
size_t p1[2]; //position of the source image in the output
hsi<T>::calc_combined_size(xp, yp, C->X(), C->Y(), S[0], S[1], p0[0], p0[1], p1[0], p1[1]); //calculate the image placement parameters
size_t spec_bytes = Z() * sizeof(T); //calculate the number of bytes in a spectrum
T* spec = (T*)malloc(spec_bytes); //allocate space for a spectrum
for(size_t y = 0; y < S[1]; y++){ //for each pixel in the destination image
for(size_t x = 0; x < S[0]; x++){
if(x >= p0[0] && x < p0[0] + X() && y >= p0[1] && y < p0[1] + Y()) //if this pixel is in the current image
file.read((char*)spec, spec_bytes);
else if(x >= p1[0] && x < p1[0] + C->X() && y >= p1[1] && y < p1[1] + C->Y()) //if this pixel is in the source image
C->file.read((char*)spec, spec_bytes);
else
memset(spec, 0, spec_bytes);
out.write((char*)spec, spec_bytes); //write to the output file
}
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1a224b6a
David Mayerich
fixed linux compa...
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1574
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if(PROGRESS) progress = (double)( (y+1) * S[0] + 1) / (double) (S[0] * S[1]) * 100;
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2ce6954b
David Mayerich
added the ability...
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1575
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}
}
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9b2a5d71
David Mayerich
implemented finit...
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/// Convolve the given band range with a kernel specified by a vector of coefficients.
/// @param outfile is an already open stream to the output file
/// @param C is an array of coefficients
/// @param start is the band to start processing (the first coefficient starts here)
/// @param nbands is the number of bands to process
/// @param center is the index for the center coefficient for the kernel (used to set the wavelengths in the output file)
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9d77bbd9
David Mayerich
updates for HSIvi...
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1586
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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...
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1587
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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...
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1588
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9b2a5d71
David Mayerich
implemented finit...
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size_t N = end - start + 1; //number of bands in the output spectrum
size_t Nb = N * sizeof(T); //size of the output spectrum in bytes
size_t B = Z(); //calculate the number of values in a spectrum
size_t Bb = B * sizeof(T); //calculate the size of a spectrum in bytes
file.seekg(0, std::ios::beg); //move to the beginning of the input file
size_t nC = C.size(); //get the number of bands that the kernel spans
T* inspec = (T*)malloc(Bb); //allocate space for the input spectrum
T* outspec = (T*)malloc(Nb); //allocate space for the output spectrum
size_t XY = X() * Y(); //number of pixels in the image
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
file.read((char*)inspec, Bb); //read an input spectrum
memset(outspec, 0, Nb); //set the output spectrum to zero (0)
|
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...
|
1616
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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...
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1617
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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...
|
1618
1619
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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...
|
1641
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1643
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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...
|
1644
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std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
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for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
}
std::vector<double> w_pts(w.begin(), w.begin() + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[0], w_pts, d); //get the optimal sample weights
for(size_t b = mid; b <= B - (nC - mid); b++){
iw = b - mid;
if(!UNIFORM){ //if the spacing is non-uniform, we have to re-calculate these points every iteration
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
}
for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
}
iw = B - nC;
for(size_t b = B - (nC - mid) + 1; b < B; b++){
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
|
9b2a5d71
David Mayerich
implemented finit...
|
1666
|
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1667
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}
|
9b2a5d71
David Mayerich
implemented finit...
|
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out.write((char*)outspec, Bb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
|
278c622b
David Mayerich
finished Windows ...
|
1673
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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;
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1719
|
|
0df38ff3
heziqi
fixed head detached
|
1720
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1721
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/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
1722
1723
1724
1725
1726
|
bool close(){
file.close();
return true;
}
|
88c3e636
heziqi
Ziqi added big.h
|
1727
|
};
|
6aa04ba2
David Mayerich
interleave types
|
1728
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}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1729
1730
|
#endif
|