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#ifndef STIM_BSQ_H
#define STIM_BSQ_H
#include "../envi/envi_header.h"
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#include "../envi/hsi.h"
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#include "../envi/bil.h"
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#include <cstring>
#include <utility>
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#include <vector>
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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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/*unsigned long long X(){
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return R[0];
}
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unsigned long long Y(){
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return R[1];
}
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unsigned long long Z(){
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return R[2];
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}*/
using hsi<T>::w; //use the wavelength array in stim::hsi
using hsi<T>::nnz;
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using binary<T>::progress;
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public:
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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,
std::vector<double> wavelengths){
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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);
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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);
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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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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bool spectrum(T * p, unsigned long long x, unsigned long long y, bool PROGRESS = false){
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return read_line_2(p, x, y, PROGRESS);
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}
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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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}
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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 normalize(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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311
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band(b, w); //get the certain band into memory
|
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|
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for(unsigned long long j = 0; j < B; j++)
|
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Ziqi added normal...
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|
{
band_index(c, j); //get the current band into memory
|
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|
316
|
for(unsigned long long i = 0; i < XY; i++)
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317
|
{
|
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|
318
|
if(mask != NULL && !mask[i])
|
93503ec6
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|
319
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321
|
c[i] = (T)0.0;
else
c[i] = c[i] / b[i];
|
089d9c81
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|
}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
|
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|
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|
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|
if(PROGRESS) progress = (double)(j+1) / B * 100;
|
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|
}
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|
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330
|
//header.save(headername); //save the new header file
|
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|
331
|
|
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|
free(b);
free(c);
target.close();
|
089d9c81
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336
|
return true;
}
|
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|
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338
|
/// Convert the current BSQ file to a BIL file with the specified file name.
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started DOxygen d...
|
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340
|
/// @param outname is the name of the output BIL file to be saved to disk.
|
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added an inverse ...
|
341
|
bool bil(std::string outname, bool PROGRESS = false)
|
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343
|
{
//simplify image resolution
|
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|
unsigned long long jump = (Y() - 1) * X() * sizeof(T);
|
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|
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std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
|
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|
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|
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unsigned long long L = X();
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|
T* line = (T*)malloc(sizeof(T) * L);
|
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|
|
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|
for ( unsigned long long y = 0; y < Y(); y++) //for each y position
|
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353
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{
|
cbce396e
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|
file.seekg(y * X() * sizeof(T), std::ios::beg); //seek to the beginning of the xz slice
|
9d3ba0b1
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|
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|
for ( unsigned long long z = 0; z < Z(); z++ ) //for each band
|
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|
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|
{
|
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|
file.read((char *)line, sizeof(T) * X()); //read a line
target.write((char*)line, sizeof(T) * X()); //write the line to the output file
|
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added support for...
|
359
|
file.seekg(jump, std::ios::cur); //seek to the next band
|
c1078e19
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|
360
|
if(PROGRESS) progress = (double)((y+1) * Z() + z + 1) / (Z() * Y()) * 100; //update the progress counter
|
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|
361
|
}
|
c25e7d0d
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|
362
|
}
|
3150c537
David Mayerich
added further pro...
|
363
|
|
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HSIproc bug fixes...
|
364
|
free(line);
|
c25e7d0d
heziqi
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|
365
|
target.close();
|
3150c537
David Mayerich
added further pro...
|
366
|
|
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speed of bip.base...
|
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368
|
return true;
}
|
20c212c0
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Ziqi added functi...
|
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|
|
a08c98c3
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finished document...
|
370
|
/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
|
77060b79
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started DOxygen d...
|
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375
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|
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lp is a pointer to an array holding the band image for the left baseline point
/// @param rp is a pointer to an array holding the band image for the right baseline point
/// @param wavelength is the label value for the requested baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
|
20c212c0
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Ziqi added functi...
|
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|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
9d3ba0b1
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added stim::hsi a...
|
380
|
unsigned long long XY = X() * Y();
|
20c212c0
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Ziqi added functi...
|
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382
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384
|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
385
|
for(unsigned long long i=0; i < XY; i++){
|
20c212c0
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Ziqi added functi...
|
386
387
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389
|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
517876d6
heziqi
metrics finished ...
|
390
|
|
a08c98c3
David Mayerich
finished document...
|
391
|
/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
|
77060b79
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started DOxygen d...
|
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393
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396
|
/// @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...
|
397
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
398
399
400
|
T* lp;
T* rp;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
401
402
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
70407ea9
heziqi
Ziqi completed he...
|
403
404
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
405
|
|
70407ea9
heziqi
Ziqi completed he...
|
406
|
band(lp, lb);
|
43dec788
David Mayerich
added code for si...
|
407
|
band(rp, rb);
|
20c212c0
heziqi
Ziqi added functi...
|
408
409
410
|
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
411
412
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
413
414
415
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
416
|
|
a08c98c3
David Mayerich
finished document...
|
417
|
/// 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...
|
418
419
420
421
422
423
|
/// @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...
|
424
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
425
426
427
428
429
|
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...
|
430
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
431
432
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
20c212c0
heziqi
Ziqi added functi...
|
433
434
435
436
437
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
438
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
439
|
//find the wavelength position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
440
441
442
|
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...
|
443
444
445
446
447
448
449
450
|
//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);
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
451
|
//to make sure right bound is bigger than left bound
|
20c212c0
heziqi
Ziqi added functi...
|
452
453
454
455
456
|
else if(lb > rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
exit(1);
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
457
458
|
//find the indices of the left and right baseline points
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
459
460
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
461
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
462
463
464
|
bi--;
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
465
|
band(lp, lb); //get the band images for the left and right baseline points
|
20c212c0
heziqi
Ziqi added functi...
|
466
467
|
band(rp, rb);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
468
469
470
471
472
473
474
|
// 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...
|
475
476
|
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...
|
477
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
478
479
|
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...
|
480
481
|
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...
|
482
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
483
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
484
|
//integrate the main indexed region
|
20c212c0
heziqi
Ziqi added functi...
|
485
|
ai++;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
486
|
for(unsigned long long i = ai; i <= bi ;i++) //for each band in the integral
|
20c212c0
heziqi
Ziqi added functi...
|
487
|
{
|
ba51ae6a
David Mayerich
fixed metric calc...
|
488
489
|
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...
|
490
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
491
492
493
|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
494
|
|
517876d6
heziqi
metrics finished ...
|
495
496
497
498
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
499
500
501
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
502
|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
503
504
505
506
507
508
509
510
|
/// @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...
|
511
|
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...
|
512
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
513
514
515
516
|
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...
|
517
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
518
|
memset(result, 0, XYbytes); //initialize the ratio to zero
|
70407ea9
heziqi
Ziqi completed he...
|
519
520
521
522
|
//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...
|
523
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
524
|
if(mask == NULL || mask[i]){
|
70407ea9
heziqi
Ziqi completed he...
|
525
|
result[i] = p1[i] / p2[i];
|
ba51ae6a
David Mayerich
fixed metric calc...
|
526
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
527
|
}
|
517876d6
heziqi
metrics finished ...
|
528
529
530
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
531
|
return true;
|
70407ea9
heziqi
Ziqi completed he...
|
532
|
}
|
43dec788
David Mayerich
added code for si...
|
533
|
|
a08c98c3
David Mayerich
finished document...
|
534
|
/// Compute the ratio between a peak area and peak height.
|
77060b79
David Mayerich
started DOxygen d...
|
535
536
537
538
539
540
541
542
|
/// @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...
|
543
544
|
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...
|
545
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
546
547
548
|
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...
|
549
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
550
|
memset(result, 0, bytes); //initialize the ratio to zero
|
70407ea9
heziqi
Ziqi completed he...
|
551
552
553
554
|
//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...
|
555
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
556
|
if(mask == NULL || mask[i])
|
70407ea9
heziqi
Ziqi completed he...
|
557
558
|
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
559
560
561
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
562
563
564
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
565
|
/// Compute the ratio between two peak areas.
|
0722eb39
David Mayerich
further updates t...
|
566
567
568
569
570
571
572
573
|
/// @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...
|
574
|
/// @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...
|
575
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
576
577
|
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...
|
578
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
579
580
581
|
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...
|
582
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
583
|
memset(result, 0, bytes); //initialize the ratio result to zero (0)
|
70407ea9
heziqi
Ziqi completed he...
|
584
585
586
587
|
//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...
|
588
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
589
590
|
if(mask == NULL || mask[i]) //if the pixel is masked
result[i] = p1[i] / p2[i]; //calculate the ratio
|
70407ea9
heziqi
Ziqi completed he...
|
591
|
}
|
517876d6
heziqi
metrics finished ...
|
592
593
594
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
595
596
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
597
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
598
|
/// Compute the definite integral of a baseline corrected peak weighted by the corresponding wavelength
|
0722eb39
David Mayerich
further updates t...
|
599
600
601
602
603
604
|
/// @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 ...
|
605
606
607
608
609
610
|
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...
|
611
612
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
613
614
615
616
617
618
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
517876d6
heziqi
metrics finished ...
|
619
|
//find the wavelenght position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
620
621
622
|
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 ...
|
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
|
//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...
|
646
647
|
memset(result, (char)0, S); //initialize the integral to zero (0)
|
517876d6
heziqi
metrics finished ...
|
648
649
650
|
//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...
|
651
652
|
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 ...
|
653
654
655
|
}
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...
|
656
657
|
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 ...
|
658
659
660
661
|
}
//calculate f(x) times x
ai++;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
662
|
for(unsigned long long i = ai; i <= bi ;i++){
|
517876d6
heziqi
metrics finished ...
|
663
|
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
664
665
666
|
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 ...
|
667
668
669
670
671
672
673
674
675
676
677
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
678
|
/// Compute the centroid of a baseline corrected peak.
|
ba51ae6a
David Mayerich
fixed metric calc...
|
679
|
/// Note that the values for the centroid can be outside of [lab, rab] if the spectrum goes negative.
|
0722eb39
David Mayerich
further updates t...
|
680
681
682
683
684
685
|
/// @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...
|
686
687
688
|
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...
|
689
690
|
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
ba51ae6a
David Mayerich
fixed metric calc...
|
691
|
memset(result, 0, bytes); //initialize the ratio result to zero (0)
|
517876d6
heziqi
metrics finished ...
|
692
693
694
695
|
//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...
|
696
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
697
|
if(mask == NULL || mask[i]){
|
517876d6
heziqi
metrics finished ...
|
698
|
result[i] = p1[i] / p2[i];
|
ba51ae6a
David Mayerich
fixed metric calc...
|
699
|
}
|
517876d6
heziqi
metrics finished ...
|
700
701
702
703
|
}
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
704
|
return true;
|
517876d6
heziqi
metrics finished ...
|
705
706
|
}
|
a08c98c3
David Mayerich
finished document...
|
707
|
/// Create a mask based on a given band and threshold value.
|
0722eb39
David Mayerich
further updates t...
|
708
709
710
711
712
713
|
/// All pixels in the
/// specified band greater than the threshold are true and all pixels less than the threshold are false.
/// @param mask_band is the band used to specify the mask
/// @param threshold is the threshold used to determine if the mask value is true or false
/// @param p is a pointer to a pre-allocated array at least X * Y in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
714
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
|
4a6f666c
heziqi
Added mask method
|
715
|
|
724ec347
David Mayerich
simplified the EN...
|
716
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
4a6f666c
heziqi
Added mask method
|
717
718
|
band(temp, mask_band);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
719
|
for (unsigned long long i = 0; i < X() * Y(); i++) {
|
798cea97
David Mayerich
added progress ba...
|
720
|
if (temp[i] < threshold)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
721
|
mask[i] = 0;
|
798cea97
David Mayerich
added progress ba...
|
722
|
else
|
ba51ae6a
David Mayerich
fixed metric calc...
|
723
|
mask[i] = 255;
|
798cea97
David Mayerich
added progress ba...
|
724
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
725
|
if(PROGRESS) progress = (double) (i+1) / (X() * Y()) * 100;
|
4a6f666c
heziqi
Added mask method
|
726
727
|
}
|
517876d6
heziqi
metrics finished ...
|
728
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
729
730
731
|
return true;
}
|
740f8cd2
heziqi
added apply_mask
|
732
|
|
a08c98c3
David Mayerich
finished document...
|
733
|
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
|
0722eb39
David Mayerich
further updates t...
|
734
735
736
|
/// @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...
|
737
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
738
739
740
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
741
742
|
unsigned long long XY = X() * Y(); //calculate number of a band
unsigned long long L = XY * sizeof(T);
|
740f8cd2
heziqi
added apply_mask
|
743
744
745
|
T * temp = (T*)malloc(L);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
746
|
for (unsigned long long i = 0; i < Z(); i++) //for each spectral bin
|
740f8cd2
heziqi
added apply_mask
|
747
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
748
|
band_index(temp, i); //get the specified band (by index)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
749
|
for ( unsigned long long j = 0; j < XY; j++) // for each pixel
|
740f8cd2
heziqi
added apply_mask
|
750
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
751
752
|
if(p[j] == 0){ //if the mask is 0 at that pixel
temp[j] = 0; //set temp to zero
|
740f8cd2
heziqi
added apply_mask
|
753
754
755
756
757
|
}
else{
continue;
}
}
|
e843658b
Brad Deutsch
Previous push did...
|
758
|
target.write(reinterpret_cast<const char*>(temp), L); //write the XY slice at that band to disk
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
759
|
if(PROGRESS) progress = (double)(i + 1) / (double)Z() * 100;
|
740f8cd2
heziqi
added apply_mask
|
760
761
762
763
764
765
|
}
target.close();
free(temp);
return true;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
766
767
768
769
770
771
|
/// Copies all spectra corresponding to nonzero values of a mask into a pre-allocated matrix of size (B x P)
/// where P is the number of masked pixels and B is the number of bands. The allocated memory can be accessed
/// using the following indexing: i = p*B + b
/// @param matrix is the destination for the pixel data
/// @param mask is the mask
bool sift(T* matrix, unsigned char* mask){
|
43dec788
David Mayerich
added code for si...
|
772
773
|
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...
|
774
775
|
//calculate the number of pixels in the mask
|
a2bf1d08
David Mayerich
general bug fixes...
|
776
|
//unsigned long long P = nnz(mask);
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
777
|
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
778
779
780
781
782
783
784
785
786
787
788
|
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++;
|
a2bf1d08
David Mayerich
general bug fixes...
|
789
|
//std::cout<<i<<std::endl;
|
43dec788
David Mayerich
added code for si...
|
790
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
791
|
|
43dec788
David Mayerich
added code for si...
|
792
793
|
}
}
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
794
|
|
43dec788
David Mayerich
added code for si...
|
795
796
|
return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
797
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
798
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
43dec788
David Mayerich
added code for si...
|
799
800
|
/// @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...
|
801
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
e843658b
Brad Deutsch
Previous push did...
|
802
803
|
std::ofstream target(outfile.c_str(), std::ios::binary);
// open a band (XY plane)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
804
805
|
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...
|
806
|
unsigned long long B = Z();
|
e843658b
Brad Deutsch
Previous push did...
|
807
808
809
810
|
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...
|
811
|
for (unsigned long long i = 0; i < B; i++) //for each spectral bin
|
e843658b
Brad Deutsch
Previous push did...
|
812
813
|
{
band_index(temp, i); //get the specified band (XY sheet by index)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
814
|
for (unsigned long long j = 0; j < XY; j++) // for each pixel
|
e843658b
Brad Deutsch
Previous push did...
|
815
816
817
818
819
820
821
|
{
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;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
822
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
823
|
}
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
824
|
if(PROGRESS) progress = (double)(i+1)/ B * 100;
|
e843658b
Brad Deutsch
Previous push did...
|
825
826
827
|
}
target.close();
free(temp);
|
3150c537
David Mayerich
added further pro...
|
828
|
|
63fc1df8
David Mayerich
added an inverse ...
|
829
|
progress = 100;
|
3150c537
David Mayerich
added further pro...
|
830
|
|
e843658b
Brad Deutsch
Previous push did...
|
831
832
833
|
return true;
}
|
2fcab4f0
David Mayerich
added unsifting f...
|
834
|
/// Generates a spectral image from a matrix of spectral values in lexicographic order and a mask
|
a2bf1d08
David Mayerich
general bug fixes...
|
835
|
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...
|
836
837
838
839
840
841
842
843
844
845
846
847
848
|
//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...
|
849
850
851
|
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...
|
852
853
854
855
856
857
858
859
|
// 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...
|
860
|
for(unsigned long long b = 0; b < B; b++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
861
862
|
//set the unsifted index value to zero
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
863
|
unsigned long long i = 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
864
865
866
867
868
|
//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...
|
869
|
for(unsigned long long xi = 0; xi < XY; xi++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
870
871
872
873
874
875
|
if( p[xi] == 0 )
unsifted[xi] = 0;
else{
unsifted[xi] = sifted[i];
i++;
}
|
3150c537
David Mayerich
added further pro...
|
876
|
//std::cout<<xi<<"/"<<XY<<", "<<b<<"/"<<B<<std::endl;
|
a2bf1d08
David Mayerich
general bug fixes...
|
877
|
if(PROGRESS) progress = (double)((b + 1) * XY + xi + 1) / (B * XY) * 100;
|
2fcab4f0
David Mayerich
added unsifting f...
|
878
|
}
|
3150c537
David Mayerich
added further pro...
|
879
|
//std::cout<<b*XY<<"/"<<B*XY<<" "<<B<<"-"<<XY<<std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
880
881
882
883
|
//write the band image to disk
target.write(reinterpret_cast<const char*>(unsifted), sizeof(T) * XY);
}
|
3150c537
David Mayerich
added further pro...
|
884
|
//std::cout<<"unsifted"<<std::endl;
|
a2bf1d08
David Mayerich
general bug fixes...
|
885
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
886
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
887
888
889
|
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
890
|
|
a08c98c3
David Mayerich
finished document...
|
891
|
/// Calculate the mean band value (average along B) at each pixel location.
|
0722eb39
David Mayerich
further updates t...
|
892
893
|
/// @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...
|
894
|
bool band_avg(T* p){
|
724ec347
David Mayerich
simplified the EN...
|
895
|
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
896
897
898
|
T* temp = (T*)malloc(sizeof(T) * XY);
//initialize p
band_index(p, 0);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
899
|
for (unsigned long long j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
900
|
p[j] /= (T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
901
902
|
}
//get every band and add them all
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
903
|
for (unsigned long long i = 1; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
904
|
band_index(temp, i);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
905
|
for (unsigned long long j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
906
|
p[j] += temp[j]/(T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
907
908
909
910
911
912
|
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
913
914
915
916
|
/// Calculate the mean value for all masked (or valid) pixels in a band and returns the average spectrum
/// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
|
63fc1df8
David Mayerich
added an inverse ...
|
917
|
bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
918
|
unsigned long long XY = X() * Y();
|
2aa68315
David Mayerich
major bug fixes f...
|
919
|
unsigned long long count = 0; //count will store the number of masked pixels
|
a43c4fe1
heziqi
Added crop in env...
|
920
|
T* temp = (T*)malloc(sizeof(T) * XY);
|
a08c98c3
David Mayerich
finished document...
|
921
|
//calculate this loop counts the number of true pixels in the mask
|
a43c4fe1
heziqi
Added crop in env...
|
922
|
for (unsigned j = 0; j < XY; j++){
|
2aa68315
David Mayerich
major bug fixes f...
|
923
|
if (mask == NULL || mask[j] != 0){
|
a43c4fe1
heziqi
Added crop in env...
|
924
925
926
|
count++;
}
}
|
724ec347
David Mayerich
simplified the EN...
|
927
|
//this loops goes through each band in B (Z())
|
a08c98c3
David Mayerich
finished document...
|
928
|
// masked (or valid) pixels from that band are averaged and the average is stored in p
|
2aa68315
David Mayerich
major bug fixes f...
|
929
|
for (unsigned long long i = 0; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
930
|
p[i] = 0;
|
a08c98c3
David Mayerich
finished document...
|
931
|
band_index(temp, i); //get the band image and store it in temp
|
2aa68315
David Mayerich
major bug fixes f...
|
932
933
934
|
for (unsigned long long j = 0; j < XY; j++){ //loop through temp, averaging valid pixels
if (mask == NULL || mask[j] != 0){
p[i] += (double)temp[j] / (double)count;
|
43dec788
David Mayerich
added code for si...
|
935
|
}
|
a43c4fe1
heziqi
Added crop in env...
|
936
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
937
|
if(PROGRESS) progress = (double)(i+1) / Z() * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
938
939
940
941
|
}
free(temp);
return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
942
|
|
a08c98c3
David Mayerich
finished document...
|
943
944
945
946
947
948
949
|
/// 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...
|
950
951
952
953
954
|
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 ...
|
955
956
|
unsigned long long b1,
bool PROGRESS = false){
|
e9bddc57
David Mayerich
added band croppi...
|
957
958
959
960
961
962
963
964
965
966
|
//calculate the new number of samples, lines, and bands
unsigned long long samples = x1 - x0;
unsigned long long lines = y1 - y0;
unsigned long long bands = b1 - b0;
//calculate the 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...
|
967
|
T* temp = (T*)malloc(L);
|
e9bddc57
David Mayerich
added band croppi...
|
968
969
|
//create an output stream to store the output file
|
a43c4fe1
heziqi
Added crop in env...
|
970
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
e9bddc57
David Mayerich
added band croppi...
|
971
972
973
974
975
976
977
978
979
980
981
982
|
//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
for (unsigned long long z = b0; z < b1; z++)
|
a43c4fe1
heziqi
Added crop in env...
|
983
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
984
|
for (unsigned long long y = 0; y < lines; y++)
|
a43c4fe1
heziqi
Added crop in env...
|
985
|
{
|
e9bddc57
David Mayerich
added band croppi...
|
986
|
file.read((char *)(temp + y * samples), sizeof(T) * samples);
|
43dec788
David Mayerich
added code for si...
|
987
|
file.seekg(jumpl, std::ios::cur); //go to the next band
|
3150c537
David Mayerich
added further pro...
|
988
|
|
63fc1df8
David Mayerich
added an inverse ...
|
989
|
if(PROGRESS) progress = (double)((z+1) * lines + y + 1) / ((b1 - b0) * lines) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
990
|
}
|
43dec788
David Mayerich
added code for si...
|
991
|
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
|
a43c4fe1
heziqi
Added crop in env...
|
992
993
994
|
file.seekg(jumpb, std::ios::cur);
}
free(temp);
|
3150c537
David Mayerich
added further pro...
|
995
|
|
a43c4fe1
heziqi
Added crop in env...
|
996
997
|
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
998
|
|
dc8eb8aa
David Mayerich
added band trimmi...
|
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
|
/// Remove a list of bands from the ENVI file
/// @param outfile is the file name for the output hyperspectral image (with trimmed bands)
/// @param b is an array of bands to be eliminated
void trim(std::string outfile, std::vector<size_t> band_array, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
file.seekg(0, std::ios::beg); //move to the beginning of the input file
size_t 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
}
|
740f8cd2
heziqi
added apply_mask
|
1028
|
|
a08c98c3
David Mayerich
finished document...
|
1029
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
1030
1031
1032
1033
|
bool close(){
file.close();
return true;
}
|
31394e2a
heziqi
Ziqi added method...
|
1034
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
1035
1036
|
};
}
|
31394e2a
heziqi
Ziqi added method...
|
1037
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1038
|
#endif
|
43dec788
David Mayerich
added code for si...
|
|
|