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#ifndef STIM_BSQ_H
#define STIM_BSQ_H
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#include <stim/envi/envi_header.h>
#include <stim/envi/hsi.h>
#include <stim/envi/bil.h>
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#include <cstring>
#include <utility>
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#include <vector>
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#include <deque>
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#include <chrono>
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#include <future>
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#include <algorithm>
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namespace stim{
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/**
The BIP class represents a 3-dimensional binary file stored using band sequential (BSQ) image encoding. The binary file is stored
such that X-Y "frames" are stored sequentially to form an image stack along the z-axis. When accessing the data sequentially on disk,
the dimensions read, from fastest to slowest, are X, Y, Z.
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 bsq: public hsi<T> {
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protected:
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//std::vector<double> w; //band wavelengths
unsigned long long offset;
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using binary<T>::R;
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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:
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using binary<T>::open;
using binary<T>::file;
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using binary<T>::read_line_2;
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using binary<T>::read_plane_2;
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bsq(){ hsi<T>::init_bsq(); }
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/// Open a data file for reading using the class interface.
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/// @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
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/// @param wavelengths is an STL vector of size B specifying a numerical label for each band
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bool open(std::string filename,
unsigned long long X,
unsigned long long Y,
unsigned long long B,
unsigned long long header_offset,
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std::vector<double> wavelengths,
stim::iotype io = stim::io_in){
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//copy the wavelengths to the BSQ file structure
w = wavelengths;
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//copy the wavelengths to the structure
offset = header_offset;
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return open(filename, vec<unsigned long long>(X, Y, B), header_offset, io);
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}
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/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
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/// @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){
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return read_plane_2(p, page); //call the binary read_plane function (don't let it update the progress)
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}
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/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
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/// @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){
if(PROGRESS) progress = 0;
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//if there are no wavelengths in the BSQ file
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if(w.size() == 0){
band_index(p, (unsigned long long)wavelength);
if(PROGRESS) progress = 100;
return true;
}
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unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned long long page = 0;
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//get the two neighboring bands (above and below 'wavelength')
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//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);
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if(PROGRESS) progress = 100;
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return true;
}
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while( w[page] < wavelength )
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{
page++;
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//if wavelength is larger than the last wavelength in the header file
// (the wavelength is out of bounds)
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if (page == Z()) {
band_index(p, Z()-1); //return the last band
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if(PROGRESS) progress = 100;
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return true;
}
}
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//when the page counter points to the first band above 'wavelength'
if ( wavelength < w[page] ){
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//do the interpolation
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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);
band_index(p2, page );
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for(unsigned long long i=0; i < XY; i++){
double r = (wavelength - w[page-1]) / (w[page] - w[page-1]);
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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}
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//if the wavelength is equal to a wavelength in header file
else{
band_index(p, page); //return the band
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}
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if(PROGRESS) progress = 100;
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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.
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/// @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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void spectrum(T* p, size_t n, bool PROGRESS){
read_line_2(p, n, PROGRESS);
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}
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void spectrum(T * p, unsigned long long x, unsigned long long y, bool PROGRESS = false){
read_line_2(p, x, y, PROGRESS);
}
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/// Retrieve a single pixel and stores it in pre-allocated memory.
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/// @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 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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file.seekg(n * sizeof(T) + binary<T>::header, std::ios::beg); //point to the certain pixel
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for (unsigned long long i = 0; i < Z(); i++)
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{
file.read((char *)(p + i), sizeof(T));
file.seekg((bandnum - 1) * sizeof(T), std::ios::cur); //go to the next band
}
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return true;
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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.
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/// @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> wls, unsigned char* mask = NULL, bool PROGRESS = false )
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{
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size_t N = wls.size(); //get the number of baseline points
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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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//simplify image resolution
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unsigned long long B = Z(); //calculate the number of bands
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned long long S = XY * sizeof(T); //calculate the number of bytes in a band
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double ai, bi; //stores the two baseline points wavelength surrounding the current band
double ci; //stores the current band's wavelength
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unsigned long long control=0;
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T * a; //pointers to the high and low band images
T * b;
T * c; //pointer to the current image
a = (T*)malloc( S ); //memory allocation
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b = (T*)malloc( S );
c = (T*)malloc( S );
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if (a == NULL || b == NULL || c == NULL){
std::cout<<"ERROR: error allocating memory";
exit(1);
}
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//initialize lownum, highnum, low, high
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ai=w[0];
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//if no baseline point is specified at band 0,
//set the baseline point at band 0 to 0
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if(wls[0] != w[0]){
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bi = wls[control];
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memset(a, (char)0, S);
}
//else get the low band
else{
control += 1;
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band(a, ai);
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bi = wls[control];
}
//get the high band
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band(b, bi);
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//correct every band
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for(unsigned long long cii = 0; cii < B; cii++){
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//update baseline points, if necessary
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if( w[cii] >= bi && cii != B - 1) {
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//if the high band is now on the last BL point?
if (control != N-1) {
control++; //increment the index
std::swap(a, b); //swap the baseline band pointers
ai = bi;
bi = wls[control];
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band(b, bi);
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}
//if the last BL point on the last band of the file?
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else if ( wls[control] < w[B - 1]) {
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std::swap(a, b); //swap the baseline band pointers
memset(b, (char)0, S); //clear the high band
ai = bi;
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bi = w[B - 1];
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}
}
//get the current band
band_index(c, cii);
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ci = w[cii];
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//perform the baseline correction
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for(unsigned long long i=0; i < XY; i++){
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if(mask != NULL && !mask[i]) //if the pixel is excluded by a mask
c[i] = 0; //set the value to zero
else{
double r = (double) (ci - ai) / (double) (bi - ai);
c[i] =(T) ( c[i] - (b[i] - a[i]) * r - a[i] );
}
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}
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target.write(reinterpret_cast<const char*>(c), S); //write the corrected data into destination
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if(PROGRESS)progress = (double)(cii+1) / B * 100;
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}
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//header.save(headername); //save the new header file
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free(a);
free(b);
free(c);
target.close();
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return true;
}
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/// Normalize all spectra based on the value of a single band, storing the result in a new BSQ file.
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/// @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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unsigned long long B = Z(); //calculate the number of bands
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned long long S = XY * sizeof(T); //calculate the number of bytes in a band
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std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
T * b; //pointers to the certain wavelength band
T * c; //pointer to the current image
b = (T*)malloc( S ); //memory allocation
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c = (T*)malloc( S );
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band(b, w); //get the certain band into memory
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for(unsigned long long j = 0; j < B; j++)
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{
band_index(c, j); //get the current band into memory
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for(unsigned long long i = 0; i < XY; i++)
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089d9c81
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Ziqi added normal...
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{
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if(mask != NULL && !mask[i])
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c[i] = (T)0.0;
else
c[i] = c[i] / b[i];
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}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
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if(PROGRESS) progress = (double)(j+1) / B * 100;
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}
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//header.save(headername); //save the new header file
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|
free(b);
free(c);
target.close();
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return true;
}
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|
void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){
size_t B = Z(); //calculate the number of bands
size_t XY = X() * Y(); //calculate the number of pixels in a band
size_t XYb = XY * sizeof(T); //calculate the size of a band in bytes
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file
file.seekg(0, std::ios::beg); //move the pointer to the current file to the beginning
T* len = (T*)malloc(XYb); //allocate space to store the vector length
memset(len, 0, XYb); //initialize the vector length to zero (0)
T* band = (T*) malloc(XYb); //allocate space to store a band image
for(size_t b = 0; b < B; b++){
file.read((char*)band, XYb);
for(size_t xy = 0; xy < XY; xy++){
if(mask == NULL || mask[xy]){
len[xy] += pow(band[xy], 2); //sum the squared value for each pixel value in the band
}
}
if(PROGRESS) progress = (double) (b+1) / (double)B * 50;
}
for(size_t xy = 0; xy < XY; xy++){ //for each pixel, calculate the square root
if(mask == NULL || mask[xy]){
len[xy] += pow(band[xy], 2); //sum the squared value for each pixel value in the band
}
}
file.seekg(0, std::ios::beg); //move the pointer to the current file to the beginning
for(size_t b = 0; b < B; b++){
file.read((char*)band, XYb);
for(size_t xy = 0; xy < XY; xy++){
if(mask == NULL || mask[xy]){
band[xy] /= len[xy]; //divide the band by the vector length
}
}
out.write((char*)band, XYb);
if(PROGRESS) progress = (double) (b+1) / (double)B * 50 + 50;
}
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1a224b6a
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fixed linux compa...
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380
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David Mayerich
added vector norm...
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381
382
|
}
|
b31c02eb
David Mayerich
added a --select ...
|
383
384
385
386
387
388
389
390
391
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393
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397
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399
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401
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|
bool select(std::string outfile, std::vector<double> bandlist, unsigned char* mask = NULL, bool PROGRESS = false) {
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file
if (!out) {
std::cout << "ERROR opening output file: " << outfile << std::endl;
return false;
}
file.seekg(0, std::ios::beg); //move the pointer to the current file to the beginning
size_t B = Z(); //calculate the number of bands
size_t XY = X() * Y(); //calculate the number of pixels in a band
size_t in_bytes = XY * sizeof(T); //calculate the size of a band in bytes
T* in = (T*)malloc(in_bytes); //allocate space for the band image
size_t nb = bandlist.size(); //get the number of bands in the output image
for (size_t b = 0; b < nb; b++) {
band(in, bandlist[b]); //get the band associated with the given wavelength
out.write((char*)in, in_bytes); //write the band to the output file
if (PROGRESS) progress = (double)(b + 1) / (double)bandlist.size() * 100;
}
out.close();
free(in);
return true;
}
|
6db250f5
David Mayerich
adaptive streamin...
|
407
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413
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415
|
size_t readlines(T* dest, size_t start, size_t n){
return hsi<T>::read(dest, 0, start, 0, X(), n, Z());
}
size_t writeblock(std::ofstream* f, T* src, size_t n){
auto t0 = std::chrono::high_resolution_clock::now();
f->write((char*)src, n);
auto t1 = std::chrono::high_resolution_clock::now();
return std::chrono::duration_cast<std::chrono::milliseconds>(t1-t0).count();
|
846b3f18
David Mayerich
fixed asynchronou...
|
416
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}
|
cf5b4c92
David Mayerich
simplified asynch...
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418
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/// Convert this BSQ file to a BIL
|
c6251f8b
David Mayerich
allows user to de...
|
419
|
bool bil(std::string outname, bool PROGRESS = false, bool VERBOSE = false, bool OPTIMIZATION = true){
|
8eb07ab6
David Mayerich
edited profiling ...
|
420
|
|
cf5b4c92
David Mayerich
simplified asynch...
|
421
|
const size_t buffers = 4; //number of buffers required for this algorithm
|
0a575bb1
David Mayerich
updated optimizat...
|
422
|
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cf5b4c92
David Mayerich
simplified asynch...
|
423
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425
426
|
size_t mem_per_batch = binary<T>::buffer_size / buffers; //calculate the maximum memory available for a batch
size_t slice_bytes = X() * Z() * sizeof(T); //number of bytes in an input batch slice (Y-slice in this case)
size_t max_slices_per_batch = mem_per_batch / slice_bytes; //maximum number of slices we can process in one batch given memory constraints
|
0a575bb1
David Mayerich
updated optimizat...
|
427
|
|
474c351a
David Mayerich
output timing dat...
|
428
429
|
std::cout<<"maximum memory available for processing: "<<(double)binary<T>::buffer_size/(double)1000000<<" MB"<<std::endl;
std::cout<<" this supports a batch size of "<<max_slices_per_batch<<" Y-axis slices ("<<X()<<" x "<<Z()<<") = "<<X() * Z() * sizeof(T) * max_slices_per_batch/1000000<<" MB"<<std::endl;
|
0a575bb1
David Mayerich
updated optimizat...
|
430
|
|
cf5b4c92
David Mayerich
simplified asynch...
|
431
|
if(max_slices_per_batch == 0){ //if there is insufficient memory for a single slice, throw an error
|
846b3f18
David Mayerich
fixed asynchronou...
|
432
433
434
|
std::cout<<"error, insufficient memory for stim::bsq::bil()"<<std::endl;
exit(1);
}
|
cf5b4c92
David Mayerich
simplified asynch...
|
435
436
|
size_t max_batch_bytes = max_slices_per_batch * slice_bytes; //calculate the amount of memory that will be allocated for all four buffers
|
0a575bb1
David Mayerich
updated optimizat...
|
437
|
stream_optimizer O(1, max_slices_per_batch);
|
6db250f5
David Mayerich
adaptive streamin...
|
438
|
|
cf5b4c92
David Mayerich
simplified asynch...
|
439
440
441
442
443
444
445
446
|
T* src[2]; //source double-buffer for asynchronous batching
src[0] = (T*) malloc(max_batch_bytes);
src[1] = (T*) malloc(max_batch_bytes);
T* dst[2]; //destination double-buffer for asynchronous batching
dst[0] = (T*) malloc(max_batch_bytes);
dst[1] = (T*) malloc(max_batch_bytes);
size_t N[2]; //number of slices stored in buffers 0 and 1
|
d11e2fb6
David Mayerich
fixed async bugs ...
|
447
|
N[0] = N[1] = std::min<size_t>(Y(), max_slices_per_batch); //start with the maximum number of slices that can be stored (may be the entire data set)
|
cf5b4c92
David Mayerich
simplified asynch...
|
448
449
450
451
452
|
std::ofstream target(outname.c_str(), std::ios::binary); //open an output file for writing
//initialize with buffer 0 (used for double buffering)
size_t y_load = 0;
size_t y_proc = 0;
|
6db250f5
David Mayerich
adaptive streamin...
|
453
|
std::future<size_t> rthread;
|
cf5b4c92
David Mayerich
simplified asynch...
|
454
|
std::future<std::ostream&> wthread; //create asynchronous threads for reading and writing
|
846b3f18
David Mayerich
fixed asynchronou...
|
455
|
|
6db250f5
David Mayerich
adaptive streamin...
|
456
457
|
std::chrono::high_resolution_clock::time_point t_start, pt_start; //high-resolution timers
std::chrono::high_resolution_clock::time_point t_end, pt_end;
|
846b3f18
David Mayerich
fixed asynchronou...
|
458
|
size_t t_batch; //number of milliseconds to process a batch
|
6db250f5
David Mayerich
adaptive streamin...
|
459
460
461
462
|
size_t t_total = 0; //total time for operation
size_t pt_total = 0; //total time spent processing data
size_t rt_total = 0; //total time spent reading data
size_t wt_total = 0;
|
c6251f8b
David Mayerich
allows user to de...
|
463
|
size_t dr = 0;
|
5435830b
David Mayerich
linux chrono fixes
|
464
465
|
rt_total += readlines(src[0], 0, N[0]); //read the first batch into the 0 source buffer
|
0a575bb1
David Mayerich
updated optimizat...
|
466
467
|
y_load += N[0]; //increment the loaded slice counter
int b = 1; //initialize the double buffer to 0
|
cf5b4c92
David Mayerich
simplified asynch...
|
468
|
while(y_proc < Y()){ //while there are still slices to be processed
|
846b3f18
David Mayerich
fixed asynchronou...
|
469
|
t_start = std::chrono::high_resolution_clock::now(); //start the timer for this batch
|
cf5b4c92
David Mayerich
simplified asynch...
|
470
|
if(y_load < Y()){ //if there are still slices to be loaded, load them
|
0a575bb1
David Mayerich
updated optimizat...
|
471
472
473
474
|
//if(y_proc > 0){
//}
|
cf5b4c92
David Mayerich
simplified asynch...
|
475
476
|
if(y_load + N[b] > Y()) N[b] = Y() - y_load; //if the next batch would process more than the total slices, adjust the batch size
rthread = std::async(std::launch::async, &stim::bsq<T>::readlines, this, src[b], y_load, N[b]);
|
8933935f
David Mayerich
updated VERBOSE i...
|
477
|
//rt_total += rthread.get();
|
cf5b4c92
David Mayerich
simplified asynch...
|
478
|
y_load += N[b]; //increment the number of loaded slices
|
8b899c24
David Mayerich
fixed asynchronou...
|
479
|
}
|
8b899c24
David Mayerich
fixed asynchronou...
|
480
|
|
cf5b4c92
David Mayerich
simplified asynch...
|
481
|
b = !b; //swap the double-buffer
|
6db250f5
David Mayerich
adaptive streamin...
|
482
|
pt_total += binary<T>::permute(dst[b], src[b], X(), N[b], Z(), 0, 2, 1); //permute the batch to a BIL file
|
6db250f5
David Mayerich
adaptive streamin...
|
483
|
wt_total += writeblock(&target, dst[b], N[b] * slice_bytes); //write the permuted data to the output file
|
cf5b4c92
David Mayerich
simplified asynch...
|
484
485
|
y_proc += N[b]; //increment the counter of processed pixels
if(PROGRESS) progress = (double)( y_proc + 1 ) / Y() * 100; //increment the progress counter based on the number of processed pixels
|
474c351a
David Mayerich
output timing dat...
|
486
|
if(y_proc < Y()) rt_total += rthread.get(); //if a new batch was set to load, make sure it loads after calculations
|
846b3f18
David Mayerich
fixed asynchronou...
|
487
488
489
|
t_end = std::chrono::high_resolution_clock::now();
t_batch = std::chrono::duration_cast<std::chrono::milliseconds>(t_end-t_start).count();
t_total += t_batch;
|
c6251f8b
David Mayerich
allows user to de...
|
490
491
492
|
if(OPTIMIZATION)
N[b] = O.update(N[!b] * slice_bytes, t_batch, binary<T>::data_rate, VERBOSE); //set the batch size based on optimization
//binary<T>::data_rate = dr;
|
0a575bb1
David Mayerich
updated optimizat...
|
493
|
//std::cout<<"New N = "<<N[!b]<<" selected with "<<(double)data_rate / 1000000<<" MB/s"<<std::endl;
|
8b899c24
David Mayerich
fixed asynchronou...
|
494
|
}
|
6db250f5
David Mayerich
adaptive streamin...
|
495
|
|
cf5b4c92
David Mayerich
simplified asynch...
|
496
497
498
499
|
free(src[0]); //free buffer resources
free(src[1]);
free(dst[0]);
free(dst[1]);
|
474c351a
David Mayerich
output timing dat...
|
500
|
//if(VERBOSE){
|
6db250f5
David Mayerich
adaptive streamin...
|
501
502
503
504
|
std::cout<<"total time to execute bsq::bil(): "<<t_total<<" ms"<<std::endl;
std::cout<<" total time spent processing: "<<pt_total<<" ms"<<std::endl;
std::cout<<" total time spent reading: "<<rt_total<<" ms"<<std::endl;
std::cout<<" total time spent writing: "<<wt_total<<" ms"<<std::endl;
|
474c351a
David Mayerich
output timing dat...
|
505
|
//}
|
cf5b4c92
David Mayerich
simplified asynch...
|
506
|
return true; //return true
|
8b899c24
David Mayerich
fixed asynchronou...
|
507
508
|
}
|
cf5b4c92
David Mayerich
simplified asynch...
|
509
|
/// Convert this BSQ file to a BIP
|
474c351a
David Mayerich
output timing dat...
|
510
|
bool bip(std::string outname, bool PROGRESS = false, bool VERBOSE = false, bool OPTIMIZATION = true){
|
8b899c24
David Mayerich
fixed asynchronou...
|
511
|
|
cf5b4c92
David Mayerich
simplified asynch...
|
512
|
const size_t buffers = 4; //number of buffers required for this algorithm
|
474c351a
David Mayerich
output timing dat...
|
513
|
|
cf5b4c92
David Mayerich
simplified asynch...
|
514
|
size_t mem_per_batch = binary<T>::buffer_size / buffers; //calculate the maximum memory available for a batch
|
8b899c24
David Mayerich
fixed asynchronou...
|
515
|
|
cf5b4c92
David Mayerich
simplified asynch...
|
516
517
|
size_t slice_bytes = X() * Z() * sizeof(T); //number of bytes in an input batch slice (Y-slice in this case)
size_t max_slices_per_batch = mem_per_batch / slice_bytes; //maximum number of slices we can process in one batch given memory constraints
|
474c351a
David Mayerich
output timing dat...
|
518
519
520
521
|
std::cout<<"maximum memory available for processing: "<<(double)binary<T>::buffer_size/(double)1000000<<" MB"<<std::endl;
std::cout<<" this supports a batch size of "<<max_slices_per_batch<<" Y-axis slices ("<<X()<<" x "<<Z()<<") = "<<X() * Z() * sizeof(T) * max_slices_per_batch/1000000<<" MB"<<std::endl;
|
cf5b4c92
David Mayerich
simplified asynch...
|
522
523
524
|
if(max_slices_per_batch == 0){ //if there is insufficient memory for a single slice, throw an error
std::cout<<"error, insufficient memory for stim::bsq::bil()"<<std::endl;
exit(1);
|
5e1b4869
David Mayerich
BSQ->BIL performa...
|
525
|
}
|
cf5b4c92
David Mayerich
simplified asynch...
|
526
527
|
size_t max_batch_bytes = max_slices_per_batch * slice_bytes; //calculate the amount of memory that will be allocated for all four buffers
|
474c351a
David Mayerich
output timing dat...
|
528
529
|
stream_optimizer O(1, max_slices_per_batch);
|
cf5b4c92
David Mayerich
simplified asynch...
|
530
531
532
533
534
535
536
537
|
T* src[2]; //source double-buffer for asynchronous batching
src[0] = (T*) malloc(max_batch_bytes);
src[1] = (T*) malloc(max_batch_bytes);
T* dst[2]; //destination double-buffer for asynchronous batching
dst[0] = (T*) malloc(max_batch_bytes);
dst[1] = (T*) malloc(max_batch_bytes);
size_t N[2]; //number of slices stored in buffers 0 and 1
|
d11e2fb6
David Mayerich
fixed async bugs ...
|
538
|
N[0] = N[1] = std::min<size_t>(Y(), max_slices_per_batch); //start with the maximum number of slices that can be stored (may be the entire data set)
|
cf5b4c92
David Mayerich
simplified asynch...
|
539
540
541
542
543
|
std::ofstream target(outname.c_str(), std::ios::binary); //open an output file for writing
//initialize with buffer 0 (used for double buffering)
size_t y_load = 0;
size_t y_proc = 0;
|
6db250f5
David Mayerich
adaptive streamin...
|
544
|
std::future<size_t> rthread;
|
cf5b4c92
David Mayerich
simplified asynch...
|
545
|
std::future<std::ostream&> wthread; //create asynchronous threads for reading and writing
|
5e1b4869
David Mayerich
BSQ->BIL performa...
|
546
|
|
474c351a
David Mayerich
output timing dat...
|
547
548
|
std::chrono::high_resolution_clock::time_point t_start, pt_start; //high-resolution timers
std::chrono::high_resolution_clock::time_point t_end, pt_end;
|
cf5b4c92
David Mayerich
simplified asynch...
|
549
|
size_t t_batch; //number of milliseconds to process a batch
|
474c351a
David Mayerich
output timing dat...
|
550
551
552
553
554
555
556
557
558
|
size_t t_total = 0; //total time for operation
size_t pt_total = 0; //total time spent processing data
size_t rt_total = 0; //total time spent reading data
size_t wt_total = 0;
size_t dr = 0;
rt_total += readlines(src[0], 0, N[0]); //read the first batch into the 0 source buffer
y_load += N[0]; //increment the loaded slice counter
int b = 1; //initialize the double buffer to 0
|
cf5b4c92
David Mayerich
simplified asynch...
|
559
560
561
|
while(y_proc < Y()){ //while there are still slices to be processed
t_start = std::chrono::high_resolution_clock::now(); //start the timer for this batch
if(y_load < Y()){ //if there are still slices to be loaded, load them
|
474c351a
David Mayerich
output timing dat...
|
562
563
564
565
|
//if(y_proc > 0){
//}
|
cf5b4c92
David Mayerich
simplified asynch...
|
566
567
|
if(y_load + N[b] > Y()) N[b] = Y() - y_load; //if the next batch would process more than the total slices, adjust the batch size
rthread = std::async(std::launch::async, &stim::bsq<T>::readlines, this, src[b], y_load, N[b]);
|
474c351a
David Mayerich
output timing dat...
|
568
|
//rt_total += rthread.get();
|
cf5b4c92
David Mayerich
simplified asynch...
|
569
|
y_load += N[b]; //increment the number of loaded slices
|
3c25631c
David Mayerich
added a larger bu...
|
570
|
}
|
3c25631c
David Mayerich
added a larger bu...
|
571
|
|
cf5b4c92
David Mayerich
simplified asynch...
|
572
|
b = !b; //swap the double-buffer
|
3a880d1c
David Mayerich
fixed PCA and BIP...
|
573
|
pt_total += binary<T>::permute(dst[b], src[b], X(), N[b], Z(), 2, 0, 1); //permute the batch to a BIL file
|
474c351a
David Mayerich
output timing dat...
|
574
|
wt_total += writeblock(&target, dst[b], N[b] * slice_bytes); //write the permuted data to the output file
|
cf5b4c92
David Mayerich
simplified asynch...
|
575
576
|
y_proc += N[b]; //increment the counter of processed pixels
if(PROGRESS) progress = (double)( y_proc + 1 ) / Y() * 100; //increment the progress counter based on the number of processed pixels
|
474c351a
David Mayerich
output timing dat...
|
577
|
if(y_proc < Y()) rt_total += rthread.get(); //if a new batch was set to load, make sure it loads after calculations
|
cf5b4c92
David Mayerich
simplified asynch...
|
578
579
580
|
t_end = std::chrono::high_resolution_clock::now();
t_batch = std::chrono::duration_cast<std::chrono::milliseconds>(t_end-t_start).count();
t_total += t_batch;
|
474c351a
David Mayerich
output timing dat...
|
581
582
583
584
|
if(OPTIMIZATION)
N[b] = O.update(N[!b] * slice_bytes, t_batch, binary<T>::data_rate, VERBOSE); //set the batch size based on optimization
//binary<T>::data_rate = dr;
//std::cout<<"New N = "<<N[!b]<<" selected with "<<(double)data_rate / 1000000<<" MB/s"<<std::endl;
|
6db250f5
David Mayerich
adaptive streamin...
|
585
|
}
|
474c351a
David Mayerich
output timing dat...
|
586
|
|
cf5b4c92
David Mayerich
simplified asynch...
|
587
588
589
590
|
free(src[0]); //free buffer resources
free(src[1]);
free(dst[0]);
free(dst[1]);
|
35a7195f
David Mayerich
added median spec...
|
591
|
if(VERBOSE){
|
474c351a
David Mayerich
output timing dat...
|
592
593
594
595
|
std::cout<<"total time to execute bsq::bip(): "<<t_total<<" ms"<<std::endl;
std::cout<<" total time spent processing: "<<pt_total<<" ms"<<std::endl;
std::cout<<" total time spent reading: "<<rt_total<<" ms"<<std::endl;
std::cout<<" total time spent writing: "<<wt_total<<" ms"<<std::endl;
|
35a7195f
David Mayerich
added median spec...
|
596
|
}
|
cf5b4c92
David Mayerich
simplified asynch...
|
597
598
|
return true; //return true
}
|
20c212c0
heziqi
Ziqi added functi...
|
599
|
|
a08c98c3
David Mayerich
finished document...
|
600
|
/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
601
602
603
604
605
606
607
|
/// @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
heziqi
Ziqi added functi...
|
608
609
|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
610
|
unsigned long long XY = X() * Y();
|
20c212c0
heziqi
Ziqi added functi...
|
611
612
613
614
|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
615
|
for(unsigned long long i=0; i < XY; i++){
|
20c212c0
heziqi
Ziqi added functi...
|
616
617
618
619
|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
517876d6
heziqi
metrics finished ...
|
620
|
|
a08c98c3
David Mayerich
finished document...
|
621
|
/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
622
623
624
625
626
|
/// @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...
|
627
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
628
629
630
|
T* lp;
T* rp;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
631
632
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
70407ea9
heziqi
Ziqi completed he...
|
633
634
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
635
|
|
70407ea9
heziqi
Ziqi completed he...
|
636
|
band(lp, lb);
|
43dec788
David Mayerich
added code for si...
|
637
|
band(rp, rb);
|
20c212c0
heziqi
Ziqi added functi...
|
638
639
640
|
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
641
642
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
643
644
645
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
646
|
|
a08c98c3
David Mayerich
finished document...
|
647
|
/// Calculate the area under the spectrum between two specified points and stores the result in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
648
649
650
651
652
653
|
/// @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...
|
654
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
655
656
657
658
659
|
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...
|
660
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
661
662
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
20c212c0
heziqi
Ziqi added functi...
|
663
664
665
666
667
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
668
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
669
|
//find the wavelength position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
670
671
672
|
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long bi = n - 1; //right bound position
|
20c212c0
heziqi
Ziqi added functi...
|
673
674
675
676
677
|
//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]){
|
11ff9d7e
David Mayerich
improved user out...
|
678
679
680
681
682
683
684
685
686
687
688
689
690
|
if (lb < w[0]) {
std::cout << "bsq::area ERROR - left bound " << lb << " is below the minimum available wavelength " << w[0] << std::endl;
}
if (rb < w[0]) {
std::cout << "bsq::area ERROR - right bound " << rb << " is below the minimum available wavelength " << w[0] << std::endl;
}
if (lb > w[n - 1]) {
std::cout << "bsq::area ERROR - left bound " << lb << " is above the maximum available wavelength " << w[n - 1] << std::endl;
}
if (rb > w[n - 1]) {
std::cout << "bsq::area ERROR - right bound " << rb << " is above the maximum available wavelength " << w[0] << std::endl;
}
return false;
|
20c212c0
heziqi
Ziqi added functi...
|
691
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
692
|
//to make sure right bound is bigger than left bound
|
20c212c0
heziqi
Ziqi added functi...
|
693
|
else if(lb > rb){
|
11ff9d7e
David Mayerich
improved user out...
|
694
695
|
std::cout << "bsq::area ERROR - right bound " << rb << " should be larger than left bound " << lb << std::endl;
return false;
|
20c212c0
heziqi
Ziqi added functi...
|
696
697
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
698
|
//find the indices of the left and right baseline points
|
1a224b6a
David Mayerich
fixed linux compa...
|
699
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
700
701
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
702
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
703
704
705
|
bi--;
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
706
|
band(lp, lb); //get the band images for the left and right baseline points
|
20c212c0
heziqi
Ziqi added functi...
|
707
708
|
band(rp, rb);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
709
710
711
712
713
714
715
|
// calculate the average value of the indexed region
memset(result, 0, S); //initialize the integral to zero (0)
//integrate the region between the specified bands and the closest indexed band
// this integrates the "tails" of the spectrum that lie outside the main indexed region
baseline_band(lb, rb, lp, rp, rab, cur2); //calculate the image for the right-most band in the integral
baseline_band(lb, rb, lp, rp, w[bi], cur); //calculate the image for the right-most indexed band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
716
717
|
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...
|
718
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
719
720
|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
721
722
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
723
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
724
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
725
|
//integrate the main indexed region
|
20c212c0
heziqi
Ziqi added functi...
|
726
|
ai++;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
727
|
for(unsigned long long i = ai; i <= bi ;i++) //for each band in the integral
|
20c212c0
heziqi
Ziqi added functi...
|
728
|
{
|
ba51ae6a
David Mayerich
fixed metric calc...
|
729
730
|
baseline_band(lb, rb, lp, rp, w[ai], cur2); //get the baselined band
for(unsigned long long j = 0; j < XY; j++){ //for each pixel in that band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
731
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
732
733
734
|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
735
|
|
517876d6
heziqi
metrics finished ...
|
736
737
738
739
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
740
741
742
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
743
|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
744
745
746
747
748
749
750
751
|
/// @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...
|
752
|
bool ph_to_ph(T* result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask = NULL){
|
20c212c0
heziqi
Ziqi added functi...
|
753
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
754
755
756
757
|
size_t XYbytes = X() * Y() * sizeof(T); //calculate the size of the band image (in bytes)
T* p1 = (T*)malloc(XYbytes); //allocate space for both bands in the ratio
T* p2 = (T*)malloc(XYbytes);
|
43dec788
David Mayerich
added code for si...
|
758
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
759
|
memset(result, 0, XYbytes); //initialize the ratio to zero
|
70407ea9
heziqi
Ziqi completed he...
|
760
761
762
763
|
//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...
|
764
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
765
|
if(mask == NULL || mask[i]){
|
70407ea9
heziqi
Ziqi completed he...
|
766
|
result[i] = p1[i] / p2[i];
|
ba51ae6a
David Mayerich
fixed metric calc...
|
767
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
768
|
}
|
517876d6
heziqi
metrics finished ...
|
769
770
771
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
772
|
return true;
|
70407ea9
heziqi
Ziqi completed he...
|
773
|
}
|
43dec788
David Mayerich
added code for si...
|
774
|
|
a08c98c3
David Mayerich
finished document...
|
775
|
/// Compute the ratio between a peak area and peak height.
|
77060b79
David Mayerich
started DOxygen d...
|
776
777
778
779
780
781
782
783
|
/// @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...
|
784
785
|
bool pa_to_ph(T* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, unsigned char* mask = NULL){
|
43dec788
David Mayerich
added code for si...
|
786
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
787
788
789
|
size_t bytes = X() * Y() * sizeof(T);
T* p1 = (T*)malloc(bytes); //allocate space for both ratio components
T* p2 = (T*)malloc(bytes);
|
43dec788
David Mayerich
added code for si...
|
790
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
791
|
memset(result, 0, bytes); //initialize the ratio to zero
|
70407ea9
heziqi
Ziqi completed he...
|
792
793
794
795
|
//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...
|
796
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
797
|
if(mask == NULL || mask[i])
|
70407ea9
heziqi
Ziqi completed he...
|
798
799
|
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
800
801
802
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
803
804
805
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
806
|
/// Compute the ratio between two peak areas.
|
0722eb39
David Mayerich
further updates t...
|
807
808
809
810
811
812
813
814
|
/// @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)
|
43dec788
David Mayerich
added code for si...
|
815
|
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
|
0722eb39
David Mayerich
further updates t...
|
816
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
817
818
|
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){
|
43dec788
David Mayerich
added code for si...
|
819
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
820
821
822
|
size_t bytes = X() * Y() * sizeof(T);
T* p1 = (T*)malloc(bytes); //allocate space for each of the operands
T* p2 = (T*)malloc(bytes);
|
43dec788
David Mayerich
added code for si...
|
823
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
824
|
memset(result, 0, bytes); //initialize the ratio result to zero (0)
|
70407ea9
heziqi
Ziqi completed he...
|
825
826
827
828
|
//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...
|
829
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
830
831
|
if(mask == NULL || mask[i]) //if the pixel is masked
result[i] = p1[i] / p2[i]; //calculate the ratio
|
70407ea9
heziqi
Ziqi completed he...
|
832
|
}
|
517876d6
heziqi
metrics finished ...
|
833
834
835
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
836
837
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
838
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
839
|
/// Compute the definite integral of a baseline corrected peak weighted by the corresponding wavelength
|
0722eb39
David Mayerich
further updates t...
|
840
841
842
843
844
845
|
/// @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 ...
|
846
847
848
849
850
851
|
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...
|
852
853
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
854
855
856
857
858
859
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
517876d6
heziqi
metrics finished ...
|
860
|
//find the wavelenght position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
861
862
863
|
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 ...
|
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
|
//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);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
887
888
|
memset(result, (char)0, S); //initialize the integral to zero (0)
|
517876d6
heziqi
metrics finished ...
|
889
890
891
|
//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...
|
892
893
|
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 ...
|
894
895
896
|
}
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
897
898
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
899
900
901
902
|
}
//calculate f(x) times x
ai++;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
903
|
for(unsigned long long i = ai; i <= bi ;i++){
|
517876d6
heziqi
metrics finished ...
|
904
|
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
905
906
907
|
for(unsigned long long j = 0; j < XY; j++){
T v = (T)((w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
result[j] += v;
|
517876d6
heziqi
metrics finished ...
|
908
909
910
911
912
913
914
915
916
917
918
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
919
|
/// Compute the centroid of a baseline corrected peak.
|
ba51ae6a
David Mayerich
fixed metric calc...
|
920
|
/// Note that the values for the centroid can be outside of [lab, rab] if the spectrum goes negative.
|
0722eb39
David Mayerich
further updates t...
|
921
922
923
924
925
926
|
/// @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...
|
927
928
929
|
bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
size_t bytes = X() * Y() * sizeof(T); //calculate the number of bytes in a band image
T* p1 = (T*)malloc(X() * Y() * sizeof(T)); //allocate space for both operands
|
43dec788
David Mayerich
added code for si...
|
930
931
|
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
ba51ae6a
David Mayerich
fixed metric calc...
|
932
|
memset(result, 0, bytes); //initialize the ratio result to zero (0)
|
517876d6
heziqi
metrics finished ...
|
933
934
935
936
|
//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...
|
937
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
938
|
if(mask == NULL || mask[i]){
|
517876d6
heziqi
metrics finished ...
|
939
|
result[i] = p1[i] / p2[i];
|
ba51ae6a
David Mayerich
fixed metric calc...
|
940
|
}
|
517876d6
heziqi
metrics finished ...
|
941
942
943
944
|
}
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
945
|
return true;
|
517876d6
heziqi
metrics finished ...
|
946
947
|
}
|
a08c98c3
David Mayerich
finished document...
|
948
|
/// Create a mask based on a given band and threshold value.
|
0722eb39
David Mayerich
further updates t...
|
949
950
951
952
953
954
|
/// 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...
|
955
956
|
bool build_mask(unsigned char* out_mask, double mask_band, double lower, double upper, unsigned char* mask = NULL, bool PROGRESS = false){
memset(out_mask, 0, X() * Y()); //initialize the mask to zero
|
4a6f666c
heziqi
Added mask method
|
957
|
|
724ec347
David Mayerich
simplified the EN...
|
958
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
4a6f666c
heziqi
Added mask method
|
959
960
|
band(temp, mask_band);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
961
|
for (unsigned long long i = 0; i < X() * Y(); i++) {
|
e37ce7bf
David Mayerich
added the ability...
|
962
963
964
965
966
967
968
|
if(mask == NULL || mask[i] != 0){
if(temp[i] > lower && temp[i] < upper){
out_mask[i] = 255;
}
else
out_mask[i] = 0;
}
|
798cea97
David Mayerich
added progress ba...
|
969
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
970
|
if(PROGRESS) progress = (double) (i+1) / (X() * Y()) * 100;
|
4a6f666c
heziqi
Added mask method
|
971
972
|
}
|
517876d6
heziqi
metrics finished ...
|
973
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
974
975
976
|
return true;
}
|
740f8cd2
heziqi
added apply_mask
|
977
|
|
a08c98c3
David Mayerich
finished document...
|
978
|
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
|
0722eb39
David Mayerich
further updates t...
|
979
980
981
|
/// @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...
|
982
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
983
984
985
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
986
987
|
unsigned long long XY = X() * Y(); //calculate number of a band
unsigned long long L = XY * sizeof(T);
|
740f8cd2
heziqi
added apply_mask
|
988
989
990
|
T * temp = (T*)malloc(L);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
991
|
for (unsigned long long i = 0; i < Z(); i++) //for each spectral bin
|
740f8cd2
heziqi
added apply_mask
|
992
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
993
|
band_index(temp, i); //get the specified band (by index)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
994
|
for ( unsigned long long j = 0; j < XY; j++) // for each pixel
|
740f8cd2
heziqi
added apply_mask
|
995
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
996
997
|
if(p[j] == 0){ //if the mask is 0 at that pixel
temp[j] = 0; //set temp to zero
|
740f8cd2
heziqi
added apply_mask
|
998
999
1000
1001
1002
|
}
else{
continue;
}
}
|
e843658b
Brad Deutsch
Previous push did...
|
1003
|
target.write(reinterpret_cast<const char*>(temp), L); //write the XY slice at that band to disk
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
1004
|
if(PROGRESS) progress = (double)(i + 1) / (double)Z() * 100;
|
740f8cd2
heziqi
added apply_mask
|
1005
1006
1007
1008
1009
1010
|
}
target.close();
free(temp);
return true;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
1011
1012
1013
1014
1015
|
/// 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...
|
1016
|
bool sift(T* matrix, unsigned char* mask = NULL, bool PROGRESS = false){
|
43dec788
David Mayerich
added code for si...
|
1017
1018
|
unsigned long long XY = X() * Y(); //Number of XY pixels
unsigned long long L = XY * sizeof(T); //size of XY plane (in bytes)
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
1019
1020
|
//calculate the number of pixels in the mask
|
a2bf1d08
David Mayerich
general bug fixes...
|
1021
|
//unsigned long long P = nnz(mask);
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
1022
|
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
|
T* band_image = (T*) malloc( XY * sizeof(T)); //allocate space for a single band
unsigned long long i; //pixel index into the sifted array
for(unsigned long long b = 0; b < Z(); b++){ //for each band in the data set
band_index(band_image, b); //retrieve an image of that band
i = 0;
for(unsigned long long xy = 0; xy < XY; xy++){
if(mask == NULL || mask[xy] != 0){ //if the pixel is valid
matrix[i*Z() + b] = band_image[xy]; //copy it to the appropriate point in the values[] array
i++;
|
43dec788
David Mayerich
added code for si...
|
1034
|
}
|
78578186
David Mayerich
fixed a bug in th...
|
1035
|
if(PROGRESS) progress = (double)(b * XY + xy+1) / (double)(XY * Z()) * 100;
|
43dec788
David Mayerich
added code for si...
|
1036
1037
|
}
}
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
1038
|
|
43dec788
David Mayerich
added code for si...
|
1039
1040
|
return true;
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
1041
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
1042
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
43dec788
David Mayerich
added code for si...
|
1043
1044
|
/// @param outfile is the name of the sifted ENVI file to be written to disk
/// @param unsigned char* p is the mask file used for sifting
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
1045
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
e843658b
Brad Deutsch
Previous push did...
|
1046
1047
|
std::ofstream target(outfile.c_str(), std::ios::binary);
// open a band (XY plane)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1048
1049
|
unsigned long long XY = X() * Y(); //Number of XY pixels
unsigned long long L = XY * sizeof(T); //size of XY pixels
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
1050
|
unsigned long long B = Z();
|
e843658b
Brad Deutsch
Previous push did...
|
1051
1052
1053
1054
|
T * temp = (T*)malloc(L); //allocate memory for a band
T * temp_vox = (T*)malloc(sizeof(T)); //allocate memory for one voxel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1055
|
for (unsigned long long i = 0; i < B; i++) //for each spectral bin
|
e843658b
Brad Deutsch
Previous push did...
|
1056
1057
|
{
band_index(temp, i); //get the specified band (XY sheet by index)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1058
|
for (unsigned long long j = 0; j < XY; j++) // for each pixel
|
e843658b
Brad Deutsch
Previous push did...
|
1059
1060
1061
1062
1063
1064
1065
|
{
if (p[j] != 0){ //if the mask is != 0 at that pixel
temp_vox[0] = temp[j];
target.write(reinterpret_cast<const char*>(temp_vox), sizeof(T)); //write the XY slice at that band to disk
}
else{
continue;
|
1a224b6a
David Mayerich
fixed linux compa...
|
1066
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
1067
|
}
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
1068
|
if(PROGRESS) progress = (double)(i+1)/ B * 100;
|
e843658b
Brad Deutsch
Previous push did...
|
1069
1070
1071
|
}
target.close();
free(temp);
|
3150c537
David Mayerich
added further pro...
|
1072
|
|
63fc1df8
David Mayerich
added an inverse ...
|
1073
|
progress = 100;
|
3150c537
David Mayerich
added further pro...
|
1074
|
|
e843658b
Brad Deutsch
Previous push did...
|
1075
1076
1077
|
return true;
}
|
2fcab4f0
David Mayerich
added unsifting f...
|
1078
|
/// Generates a spectral image from a matrix of spectral values in lexicographic order and a mask
|
a2bf1d08
David Mayerich
general bug fixes...
|
1079
|
bool unsift(std::string outfile, unsigned char* p, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
|
2fcab4f0
David Mayerich
added unsifting f...
|
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
|
//create a binary output stream
std::ofstream target(outfile.c_str(), std::ios::binary);
//make sure that there's only one line
if(Y() != 1){
std::cout<<"ERROR in stim::bsq::sift() - number of lines does not equal 1"<<std::endl;
return false;
}
std::cout<<"started sifting"<<std::endl;
//get the number of pixels and bands in the input image
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1093
1094
1095
|
unsigned long long P = X(); //Number of pixels
unsigned long long B = Z(); //number of bands
unsigned long long XY = samples * lines; //total number of pixels in an unsifted image
|
2fcab4f0
David Mayerich
added unsifting f...
|
1096
1097
1098
1099
1100
1101
1102
1103
|
// allocate memory for a sifted band
T * sifted = (T*)malloc(P * sizeof(T)); //allocate memory for a band
//allocate memory for an unsifted band image
T* unsifted = (T*) malloc(XY * sizeof(T));
//for each band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1104
|
for(unsigned long long b = 0; b < B; b++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
1105
1106
|
//set the unsifted index value to zero
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1107
|
unsigned long long i = 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1108
1109
1110
1111
1112
|
//retrieve the sifted band (masked pixels only)
band_index(sifted, b);
//for each pixel in the final image (treat it as a 1D image)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1113
|
for(unsigned long long xi = 0; xi < XY; xi++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
1114
1115
1116
1117
1118
1119
|
if( p[xi] == 0 )
unsifted[xi] = 0;
else{
unsifted[xi] = sifted[i];
i++;
}
|
3150c537
David Mayerich
added further pro...
|
1120
|
//std::cout<<xi<<"/"<<XY<<", "<<b<<"/"<<B<<std::endl;
|
a2bf1d08
David Mayerich
general bug fixes...
|
1121
|
if(PROGRESS) progress = (double)((b + 1) * XY + xi + 1) / (B * XY) * 100;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1122
|
}
|
3150c537
David Mayerich
added further pro...
|
1123
|
//std::cout<<b*XY<<"/"<<B*XY<<" "<<B<<"-"<<XY<<std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1124
1125
1126
1127
|
//write the band image to disk
target.write(reinterpret_cast<const char*>(unsifted), sizeof(T) * XY);
}
|
3150c537
David Mayerich
added further pro...
|
1128
|
//std::cout<<"unsifted"<<std::endl;
|
a2bf1d08
David Mayerich
general bug fixes...
|
1129
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
1130
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
1131
1132
1133
|
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
1134
|
|
a08c98c3
David Mayerich
finished document...
|
1135
|
/// Calculate the mean band value (average along B) at each pixel location.
|
0722eb39
David Mayerich
further updates t...
|
1136
1137
|
/// @param p is a pointer to memory of size X * Y * sizeof(T) that will store the band averages.
|
a43c4fe1
heziqi
Added crop in env...
|
1138
|
bool band_avg(T* p){
|
724ec347
David Mayerich
simplified the EN...
|
1139
|
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
1140
1141
1142
|
T* temp = (T*)malloc(sizeof(T) * XY);
//initialize p
band_index(p, 0);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1143
|
for (unsigned long long j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
1144
|
p[j] /= (T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
1145
1146
|
}
//get every band and add them all
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1147
|
for (unsigned long long i = 1; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
1148
|
band_index(temp, i);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1149
|
for (unsigned long long j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
1150
|
p[j] += temp[j]/(T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
1151
1152
1153
1154
1155
1156
|
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
1157
1158
1159
1160
|
/// 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...
|
1161
|
bool mean_spectrum(double* m, double* std, unsigned char* mask = NULL, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
1162
|
unsigned long long XY = X() * Y();
|
35a7195f
David Mayerich
added median spec...
|
1163
|
unsigned long long count = nnz(mask); //count will store the number of masked pixels
|
a43c4fe1
heziqi
Added crop in env...
|
1164
|
T* temp = (T*)malloc(sizeof(T) * XY);
|
35a7195f
David Mayerich
added median spec...
|
1165
|
|
724ec347
David Mayerich
simplified the EN...
|
1166
|
//this loops goes through each band in B (Z())
|
a08c98c3
David Mayerich
finished document...
|
1167
|
// masked (or valid) pixels from that band are averaged and the average is stored in p
|
35a7195f
David Mayerich
added median spec...
|
1168
1169
1170
|
double e_x; //stores E[x]^2
double e_x2; //stores E[x^2]
double x;
|
2aa68315
David Mayerich
major bug fixes f...
|
1171
|
for (unsigned long long i = 0; i < Z(); i++){
|
35a7195f
David Mayerich
added median spec...
|
1172
1173
|
e_x = 0;
e_x2 = 0;
|
a08c98c3
David Mayerich
finished document...
|
1174
|
band_index(temp, i); //get the band image and store it in temp
|
2aa68315
David Mayerich
major bug fixes f...
|
1175
1176
|
for (unsigned long long j = 0; j < XY; j++){ //loop through temp, averaging valid pixels
if (mask == NULL || mask[j] != 0){
|
35a7195f
David Mayerich
added median spec...
|
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
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1190
1191
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|
x = (double)temp[j];
e_x += x / (double)count; //sum the expected value of x
e_x2 += (x * x) / (double)count; //sum the expected value of x^2
}
}
m[i] = e_x; //store the mean
std[i] = sqrt(e_x2 - e_x * e_x); //calculate the standard deviation
if(PROGRESS) progress = (double)(i+1) / Z() * 100; //update the progress counter
}
free(temp);
return true;
}
/// Calculate the median value for all masked (or valid) pixels in a band and returns the median 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
bool median_spectrum(double* m, unsigned char* mask = NULL, bool PROGRESS = false){
size_t XY = X() * Y();
size_t count = nnz(mask); //count will store the number of masked pixels
T* temp = (T*)malloc(sizeof(T) * XY);
std::vector<T> band_values(count); //create an STD vector of band values
//this loops goes through each band in B (Z())
// masked (or valid) pixels from that band are averaged and the average is stored in p
size_t k;
for (size_t i = 0; i < Z(); i++){ //for each band
band_index(temp, i); //get the band image and store it in temp
k = 0; //initialize the band_value index to zero
for (size_t j = 0; j < XY; j++){ //loop through temp, averaging valid pixels
if (mask == NULL || mask[j] != 0){
band_values[k] = temp[j]; //store the value in the band_values array
k++; //increment the band_values index
|
43dec788
David Mayerich
added code for si...
|
1211
|
}
|
a43c4fe1
heziqi
Added crop in env...
|
1212
|
}
|
35a7195f
David Mayerich
added median spec...
|
1213
1214
1215
|
std::sort(band_values.begin(), band_values.end()); //sort all of the values in the band
m[i] = band_values[ count/2 ]; //store the center value in the array
if(PROGRESS) progress = (double)(i+1) / Z() * 100; //update the progress counter
|
a43c4fe1
heziqi
Added crop in env...
|
1216
1217
1218
1219
|
}
free(temp);
return true;
}
|
1a224b6a
David Mayerich
fixed linux compa...
|
1220
|
|
a08c98c3
David Mayerich
finished document...
|
1221
1222
1223
1224
1225
1226
1227
|
/// 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...
|
1228
1229
1230
1231
1232
|
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 ...
|
1233
1234
|
unsigned long long b1,
bool PROGRESS = false){
|
e9bddc57
David Mayerich
added band croppi...
|
1235
1236
|
//calculate the new number of samples, lines, and bands
|
be1064b1
David Mayerich
fixed cropping er...
|
1237
1238
1239
|
unsigned long long samples = x1 - x0 + 1;
unsigned long long lines = y1 - y0 + 1;
unsigned long long bands = b1 - b0 + 1;
|
e9bddc57
David Mayerich
added band croppi...
|
1240
1241
1242
1243
1244
|
//calculate the size of a single band
unsigned long long L = samples * lines * sizeof(T);
//allocate space for a single band
|
a43c4fe1
heziqi
Added crop in env...
|
1245
|
T* temp = (T*)malloc(L);
|
e9bddc57
David Mayerich
added band croppi...
|
1246
1247
|
//create an output stream to store the output file
|
a43c4fe1
heziqi
Added crop in env...
|
1248
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
e9bddc57
David Mayerich
added band croppi...
|
1249
1250
1251
1252
1253
1254
1255
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1257
1258
1259
|
//calculate the distance required to jump from the end of one band to the beginning of another
unsigned long long jumpb = X() * (Y() - lines) * sizeof(T);
//calculate the distance required to jump from the end of one line to the beginning of another
unsigned long long jumpl = (X() - samples) * sizeof(T);
//seek to the start of the cropped region in the input file
file.seekg( (b0 * X() * Y() + y0 * X() + x0) * sizeof(T), std::ios::beg);
//for each band
|
be1064b1
David Mayerich
fixed cropping er...
|
1260
|
for (unsigned long long z = b0; z <= b1; z++)
|
a43c4fe1
heziqi
Added crop in env...
|
1261
|
{
|
963d0676
David Mayerich
bug fixes related...
|
1262
|
//std::cout<<z<<std::endl;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1263
|
for (unsigned long long y = 0; y < lines; y++)
|
a43c4fe1
heziqi
Added crop in env...
|
1264
|
{
|
e9bddc57
David Mayerich
added band croppi...
|
1265
|
file.read((char *)(temp + y * samples), sizeof(T) * samples);
|
43dec788
David Mayerich
added code for si...
|
1266
|
file.seekg(jumpl, std::ios::cur); //go to the next band
|
3150c537
David Mayerich
added further pro...
|
1267
|
|
be1064b1
David Mayerich
fixed cropping er...
|
1268
|
if(PROGRESS) progress = (double)((z - b0) * lines + y + 1) / ((b1 - b0 + 1) * lines) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1269
|
}
|
43dec788
David Mayerich
added code for si...
|
1270
|
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
|
a43c4fe1
heziqi
Added crop in env...
|
1271
1272
1273
|
file.seekg(jumpb, std::ios::cur);
}
free(temp);
|
3150c537
David Mayerich
added further pro...
|
1274
|
|
a43c4fe1
heziqi
Added crop in env...
|
1275
1276
|
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
1277
|
|
bb61cb18
David Mayerich
added subimage fu...
|
1278
1279
1280
1281
1282
1283
1284
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1286
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|
///Crop out several subimages and assemble a new image from these concatenated subimages
/// @param outfile is the file name for the output image
/// @param sx is the width of each subimage
/// @param sy is the height of each subimage
/// @mask is the mask used to define subimage positions extracted from the input file
void subimages(std::string outfile, size_t sx, size_t sy, unsigned char* mask, bool PROGRESS = false){
size_t N = nnz(mask); //get the number of subimages
T* dst = (T*) malloc(N * sx * sy * sizeof(T)); //allocate space for a single band of the output image
memset(dst, 0, N*sx*sy*sizeof(T)); //initialize the band image to zero
std::ofstream out(outfile, std::ios::binary); //open a file for writing
T* src = (T*) malloc(X() * Y() * sizeof(T));
for(size_t b = 0; b < Z(); b++){ //for each band
band_index(src, b); //load the band image
size_t i = 0; //create an image index and initialize it to zero
size_t n = 0;
while(n < N){ //for each subimage
if(mask[i]){ //if the pixel is masked, copy the surrounding pixels into the destination band
size_t yi = i / X(); //determine the y position of the current pixel
size_t xi = i - yi * X(); //determine the x position of the current pixel
if( xi > sx/2 && xi < X() - sx/2 && //if the subimage is completely within the bounds of the original image
yi > sy/2 && yi < Y() - sy/2){
size_t cx = xi - sx/2; //calculate the corner position for the subimage
size_t cy = yi - sy/2;
|
bb61cb18
David Mayerich
added subimage fu...
|
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
|
for(size_t syi = 0; syi < sy; syi++){ //for each line in the subimage
size_t src_i = (cy + syi) * X() + cx;
//size_t dst_i = syi * (N * sx) + n * sx;
size_t dst_i = (n * sy + syi) * sx;
memcpy(&dst[dst_i], &src[src_i], sx * sizeof(T)); //copy one line from the subimage to the destination image
}
n++;
}
}
i++;
if(PROGRESS) progress = (double)( (n+1) * (b+1) ) / (N * Z()) * 100;
}//end while n
out.write((const char*)dst, N * sx * sy * sizeof(T)); //write the band to memory
}
free(dst); //free memory
free(src);
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1324
1325
1326
1327
1328
|
/// 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){
|
1a224b6a
David Mayerich
fixed linux compa...
|
1329
|
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
|
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 XY = X() * Y(); //calculate the number of elements in a band
size_t XYb = XY * sizeof(T); //calculate the number of bytes in a band
T* temp = (T*)malloc(XYb); //allocate space to store a band
size_t i = 0; //store the first index into the band array
for(size_t b = 0; b < Z(); b++){ //for each band
if(b != band_array[i]){ //if this band is not trimmed
file.read((char*)temp, XYb); //read the band
out.write((char*)temp, XYb); //output the band
}
else{
file.seekg(XYb, std::ios::cur); //otherwise, skip the band
i++;
}
if(PROGRESS) progress = (double)(b+1) / (double) Z() * 100;
}
free(temp); //free the scratch space for the band
}
|
2ce6954b
David Mayerich
added the ability...
|
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
|
/// Combine two BSQ 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, bsq<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 line_bytes = X() * sizeof(T);
size_t band_bytes = X() * Y() * sizeof(T);
T* cur = (T*)malloc(X() * Y() * sizeof(T)); //allocate space for a band of the current image
size_t line_src_bytes = C->X() * sizeof(T);
size_t band_src_bytes = C->X() * C->Y() * sizeof(T);
T* src = (T*)malloc(C->X() * C->Y() * sizeof(T)); //allocate space for a band of the source image
size_t line_dst_bytes = S[0] * sizeof(T);
size_t band_dst_bytes = S[0] * S[1] * sizeof(T);
T* dst = (T*)malloc(band_dst_bytes); //allocate space for a band of the destination image
memset(dst, 0, band_dst_bytes); //set all values to zero (0) in the destination image
for(size_t b = 0; b < Z(); b++){ //for each band in both images
file.read((char*)cur, band_bytes); //read a band from the current image
C->file.read((char*)src, band_src_bytes); //read a band from the source image
for(size_t y = 0; y < Y(); y++)
memcpy( &dst[ (p0[1]+y) * S[0] + p0[0] ], &cur[ y * X() ], line_bytes); //copy the line from the current to the destination image
//memset( &dst[ (p0[1]+y) * S[0] + p0[0] ], 0, line_dst_bytes);
for(size_t y = 0; y < C->Y(); y++)
memcpy( &dst[ (p1[1]+y) * S[0] + p1[0] ], &src[ y * C->X() ], line_src_bytes); //copy the line from the source to the destination image
out.write((char*)dst, band_dst_bytes); //write the combined image to an output file
if(PROGRESS) progress = (double)(b + 1) / (double) Z() * 100;
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1395
1396
1397
|
out.close();
}
|
82a7c08c
David Mayerich
added an append c...
|
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
|
/// Append an image to this one along the band dimension
void append(std::string outfile, bsq<T>* C, bool PROGRESS = false) {
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
file.seekg(0, std::ios::beg); //move to the beginning of both files
C->file.seekg(0, std::ios::beg);
if (PROGRESS) progress = 0;
out << file.rdbuf(); //copy the data from this ENVI file
if (PROGRESS) progress = (double)(Z() + 1) / (double)(Z() + C->Z()) * 100;
out << C->file.rdbuf(); //copy the data from the appending file
if (PROGRESS) progress = 100;
out.close();
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1412
1413
1414
1415
1416
1417
1418
1419
|
/// Convolve the given band range with a kernel specified by a vector of coefficients.
/// @param outfile is an already open stream to the output file
/// @param C is an array of coefficients
/// @param start is the band to start processing (the first coefficient starts here)
/// @param nbands is the number of bands to process
/// @param center is the index for the center coefficient for the kernel (used to set the wavelengths in the output file)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1420
|
void convolve(std::ofstream& out, std::vector<double> C, size_t start, size_t end, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
|
size_t nbands = end - start + 1;
size_t XY = X() * Y(); //calculate the number of values in a band
size_t XYb = XY * sizeof(T); //calculate the size of a band (frame) in bytes
file.seekg(XYb * start, std::ios::beg); //move to the beginning of the 'start' band
size_t nframes = C.size(); //get the number of bands that the kernel spans
std::deque<T*> frame(nframes, NULL); //create an array to store pointers to each frame
for(size_t f = 0; f < nframes; f++){ //for each frame
frame[f] = (T*)malloc(XYb); //allocate space for the frame
file.read((char*)frame[f], XYb); //load the frame
}
T* outband = (T*)malloc(XYb); //allocate space for the output band
//Implementation: In order to minimize reads from secondary storage, each band is only loaded once into the 'frame' deque.
// When a new band is loaded, the last band is popped, a new frame is copied to the pointer, and it is
// re-inserted into the deque.
for(size_t b = 0; b < nbands; b++){ //for each band
memset(outband, 0, XYb); //set the output band to zero (0)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1441
1442
1443
1444
1445
1446
1447
1448
|
size_t c, xy;
double coeff;
for(c = 0; c < nframes; c++){ //for each frame (corresponding to each coefficient)
coeff = C[c];
for(xy = 0; xy < XY; xy++){ //for each pixel
if(mask == NULL || mask[xy]){
outband[xy] += (T)(coeff * frame[c][xy]); //calculate the contribution of the current frame (scaled by the corresponding coefficient)
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
|
}
}
out.write((char*)outband, XYb); //output the band
file.read((char*)frame[0], XYb); //read the next band
frame.push_back(frame.front()); //put the first element in the back
frame.pop_front(); //pop the first element
if(PROGRESS) progress = (double)(b+1) / (double)nbands * 100;
}
}
/// Performs a single convolution and saves it to an output file
/// @param outfile is the convolved file to be output
/// @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
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1465
|
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...
|
1466
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1467
|
convolve(out, C, start, end, mask, PROGRESS); //start the convolution
|
9b2a5d71
David Mayerich
implemented finit...
|
1468
1469
1470
1471
1472
1473
1474
1475
1476
|
out.close();
}
/// Performs a set of convolutions and chains the results together in a single file
/// @param outfile is the convolved file to be output
/// @param C is an array containing an array of coefficients for each kernel
/// @param start is the list of start bands for each kernel
/// @param end is the list of end bands for each kernel
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1477
|
void convolve(std::string outfile, std::vector< std::vector<double> > C, std::vector<size_t> start, std::vector<size_t> end, unsigned char* mask = NULL, bool PROGRESS = false){
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9b2a5d71
David Mayerich
implemented finit...
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std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
size_t K = C.size(); //get the number of kernels
for(size_t k = 0; k < K; k++){
size_t b0 = start[k]; //calculate the range of the convolution
size_t b1 = end[k];
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9d77bbd9
David Mayerich
updates for HSIvi...
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convolve(out, C[k], b0, b1, mask, PROGRESS); //perform the convolution with the current kernel in the given range
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9b2a5d71
David Mayerich
implemented finit...
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}
out.close();
}
/// Approximate the spectral derivative of the image
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9d77bbd9
David Mayerich
updates for HSIvi...
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void deriv(std::string outfile, size_t d, size_t order, const std::vector<double> w = std::vector<double>(), unsigned char* mask = NULL, bool PROGRESS = false){
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9b2a5d71
David Mayerich
implemented finit...
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std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
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1a224b6a
David Mayerich
fixed linux compa...
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1493
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9b2a5d71
David Mayerich
implemented finit...
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size_t XY = X() * Y(); //calculate the number of values in a band
size_t XYb = XY * sizeof(T); //calculate the size of a band (frame) in bytes
size_t B = Z();
file.seekg(0, std::ios::beg); //move to the beginning of the file
size_t N = order + d; //approximating a derivative requires order + d samples
std::deque<T*> frame(N, NULL); //create an array to store pointers to each frame
for(size_t f = 0; f < N; f++){ //for each frame
frame[f] = (T*)malloc(XYb); //allocate space for the frame
file.read((char*)frame[f], XYb); //load the frame
}
T* outband = (T*)malloc(XYb); //allocate space for the output band
//Implementation: In order to minimize reads from secondary storage, each band is only loaded once into the 'frame' deque.
// When a new band is loaded, the last band is popped, a new frame is copied to the pointer, and it is
// re-inserted into the deque.
size_t mid = (size_t)(N / 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 b = 0; b < B; b++){ //for each band
if(b < mid) //calculate the first wavelength used to evaluate the derivative at this band
iw = 0;
else if(b > B - (N - mid + 1))
iw = B - N;
else{
iw = b - mid;
file.read((char*)frame[0], XYb); //read the next band
frame.push_back(frame.front()); //put the first element in the back
frame.pop_front(); //pop the first element
}
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + N); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
memset(outband, 0, XYb); //set the output band to zero (0)
for(size_t c = 0; c < N; c++){ //for each frame (corresponding to each coefficient)
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
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9d77bbd9
David Mayerich
updates for HSIvi...
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1530
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if(mask == NULL || mask[xy]){
outband[xy] += (T)(C[c] * frame[c][xy]); //calculate the contribution of the current frame (scaled by the corresponding coefficient)
}
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9b2a5d71
David Mayerich
implemented finit...
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}
}
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1a224b6a
David Mayerich
fixed linux compa...
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1535
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out.write((char*)outband, XYb); //output the band
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9b2a5d71
David Mayerich
implemented finit...
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if(PROGRESS) progress = (double)(b+1) / (double)B * 100;
}
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2ce6954b
David Mayerich
added the ability...
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1538
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278c622b
David Mayerich
finished Windows ...
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} //end deriv
bool multiply(std::string outname, double v, unsigned char* mask = NULL, bool PROGRESS = false){
unsigned long long B = Z(); //calculate the number of bands
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned long long S = XY * sizeof(T); //calculate the number of bytes in a band
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
T * c; //pointer to the current image
c = (T*)malloc( S ); //allocate memory for the band image
for(unsigned long long j = 0; j < B; j++){ //for each band
band_index(c, j); //load the current band
for(unsigned long long i = 0; i < XY; i++){ //for each pixel
if(mask == NULL || mask[i]) //if the pixel is masked
c[i] *= (T)v; //perform the multiplication
}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
if(PROGRESS) progress = (double)(j+1) / B * 100; //update the progress
}
free(c); //free the band
target.close(); //close the output file
return true;
}
bool add(std::string outname, double v, unsigned char* mask = NULL, bool PROGRESS = false){
unsigned long long B = Z(); //calculate the number of bands
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned long long S = XY * sizeof(T); //calculate the number of bytes in a band
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
T * c; //pointer to the current image
c = (T*)malloc( S ); //allocate memory for the band image
for(unsigned long long j = 0; j < B; j++){ //for each band
band_index(c, j); //load the current band
for(unsigned long long i = 0; i < XY; i++){ //for each pixel
if(mask == NULL || mask[i]) //if the pixel is masked
c[i] += (T)v; //perform the multiplication
}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
if(PROGRESS) progress = (double)(j+1) / B * 100; //update the progress
}
free(c); //free the band
target.close(); //close the output file
return true;
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2ce6954b
David Mayerich
added the ability...
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1593
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}
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740f8cd2
heziqi
added apply_mask
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1595
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a08c98c3
David Mayerich
finished document...
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1596
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/// Close the file.
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f6169dea
heziqi
Ziqi completed bi...
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bool close(){
file.close();
return true;
}
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31394e2a
heziqi
Ziqi added method...
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1601
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3fc1d461
heziqi
Ziqi added saveBa...
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1602
1603
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};
}
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31394e2a
heziqi
Ziqi added method...
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1604
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e8eb202f
David Mayerich
added a new ENVI ...
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1605
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#endif
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43dec788
David Mayerich
added code for si...
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