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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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#include <deque>
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#include <chrono>
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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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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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|
290
|
{
|
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|
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292
293
|
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
|
089d9c81
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296
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298
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300
301
|
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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|
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|
c = (T*)malloc( S );
|
089d9c81
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|
|
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|
304
|
band(b, w); //get the certain band into memory
|
089d9c81
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|
305
|
|
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|
306
|
for(unsigned long long j = 0; j < B; j++)
|
089d9c81
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Ziqi added normal...
|
307
308
|
{
band_index(c, j); //get the current band into memory
|
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added stim::hsi a...
|
309
|
for(unsigned long long i = 0; i < XY; i++)
|
089d9c81
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|
310
|
{
|
798cea97
David Mayerich
added progress ba...
|
311
|
if(mask != NULL && !mask[i])
|
93503ec6
David Mayerich
allowed masking d...
|
312
313
314
|
c[i] = (T)0.0;
else
c[i] = c[i] / b[i];
|
089d9c81
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Ziqi added normal...
|
315
316
|
}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
|
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David Mayerich
added support for...
|
317
|
|
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David Mayerich
added an inverse ...
|
318
|
if(PROGRESS) progress = (double)(j+1) / B * 100;
|
089d9c81
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Ziqi added normal...
|
319
320
|
}
|
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|
321
|
|
cbce396e
David Mayerich
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|
322
|
|
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added a new ENVI ...
|
323
|
//header.save(headername); //save the new header file
|
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|
324
|
|
089d9c81
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Ziqi added normal...
|
325
326
327
|
free(b);
free(c);
target.close();
|
089d9c81
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Ziqi added normal...
|
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329
|
return true;
}
|
43dec788
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|
330
|
|
a08c98c3
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finished document...
|
331
|
/// Convert the current BSQ file to a BIL file with the specified file name.
|
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started DOxygen d...
|
332
333
|
/// @param outname is the name of the output BIL file to be saved to disk.
|
63fc1df8
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added an inverse ...
|
334
|
bool bil(std::string outname, bool PROGRESS = false)
|
c25e7d0d
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speed of bip.base...
|
335
336
|
{
//simplify image resolution
|
9d3ba0b1
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added stim::hsi a...
|
337
|
unsigned long long jump = (Y() - 1) * X() * sizeof(T);
|
43dec788
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added code for si...
|
338
|
|
c25e7d0d
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|
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340
|
std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
|
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added code for si...
|
341
|
|
9d3ba0b1
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added stim::hsi a...
|
342
|
unsigned long long L = X();
|
c1078e19
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HSIproc bug fixes...
|
343
|
T* line = (T*)malloc(sizeof(T) * L);
|
cbce396e
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added support for...
|
344
|
|
9d3ba0b1
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added stim::hsi a...
|
345
|
for ( unsigned long long y = 0; y < Y(); y++) //for each y position
|
c25e7d0d
heziqi
speed of bip.base...
|
346
|
{
|
cbce396e
David Mayerich
added support for...
|
347
|
file.seekg(y * X() * sizeof(T), std::ios::beg); //seek to the beginning of the xz slice
|
9d3ba0b1
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added stim::hsi a...
|
348
|
for ( unsigned long long z = 0; z < Z(); z++ ) //for each band
|
c25e7d0d
heziqi
speed of bip.base...
|
349
|
{
|
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David Mayerich
HSIproc bug fixes...
|
350
351
|
file.read((char *)line, sizeof(T) * X()); //read a line
target.write((char*)line, sizeof(T) * X()); //write the line to the output file
|
cbce396e
David Mayerich
added support for...
|
352
|
file.seekg(jump, std::ios::cur); //seek to the next band
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
353
|
if(PROGRESS) progress = (double)((y+1) * Z() + z + 1) / (Z() * Y()) * 100; //update the progress counter
|
43dec788
David Mayerich
added code for si...
|
354
|
}
|
c25e7d0d
heziqi
speed of bip.base...
|
355
|
}
|
3150c537
David Mayerich
added further pro...
|
356
|
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
357
|
free(line);
|
c25e7d0d
heziqi
speed of bip.base...
|
358
|
target.close();
|
3150c537
David Mayerich
added further pro...
|
359
|
|
c25e7d0d
heziqi
speed of bip.base...
|
360
361
|
return true;
}
|
20c212c0
heziqi
Ziqi added functi...
|
362
|
|
a08c98c3
David Mayerich
finished document...
|
363
|
/// 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...
|
364
365
366
367
368
369
370
|
/// @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...
|
371
372
|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
373
|
unsigned long long XY = X() * Y();
|
20c212c0
heziqi
Ziqi added functi...
|
374
375
376
377
|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
378
|
for(unsigned long long i=0; i < XY; i++){
|
20c212c0
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Ziqi added functi...
|
379
380
381
382
|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
517876d6
heziqi
metrics finished ...
|
383
|
|
a08c98c3
David Mayerich
finished document...
|
384
|
/// 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...
|
385
386
387
388
389
|
/// @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...
|
390
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
391
392
393
|
T* lp;
T* rp;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
394
395
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
70407ea9
heziqi
Ziqi completed he...
|
396
397
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
398
|
|
70407ea9
heziqi
Ziqi completed he...
|
399
|
band(lp, lb);
|
43dec788
David Mayerich
added code for si...
|
400
|
band(rp, rb);
|
20c212c0
heziqi
Ziqi added functi...
|
401
402
403
|
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
404
405
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
406
407
408
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
409
|
|
a08c98c3
David Mayerich
finished document...
|
410
|
/// 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...
|
411
412
413
414
415
416
|
/// @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...
|
417
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
418
419
420
421
422
|
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...
|
423
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
424
425
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
20c212c0
heziqi
Ziqi added functi...
|
426
427
428
429
430
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
431
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
432
|
//find the wavelength position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
433
434
435
|
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...
|
436
437
438
439
440
441
442
443
|
//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...
|
444
|
//to make sure right bound is bigger than left bound
|
20c212c0
heziqi
Ziqi added functi...
|
445
446
447
448
449
|
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...
|
450
451
|
//find the indices of the left and right baseline points
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
452
453
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
454
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
455
456
457
|
bi--;
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
458
|
band(lp, lb); //get the band images for the left and right baseline points
|
20c212c0
heziqi
Ziqi added functi...
|
459
460
|
band(rp, rb);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
461
462
463
464
465
466
467
|
// 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...
|
468
469
|
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...
|
470
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
471
472
|
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...
|
473
474
|
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...
|
475
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
476
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
477
|
//integrate the main indexed region
|
20c212c0
heziqi
Ziqi added functi...
|
478
|
ai++;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
479
|
for(unsigned long long i = ai; i <= bi ;i++) //for each band in the integral
|
20c212c0
heziqi
Ziqi added functi...
|
480
|
{
|
ba51ae6a
David Mayerich
fixed metric calc...
|
481
482
|
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...
|
483
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
484
485
486
|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
487
|
|
517876d6
heziqi
metrics finished ...
|
488
489
490
491
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
492
493
494
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
495
|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
496
497
498
499
500
501
502
503
|
/// @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...
|
504
|
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...
|
505
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
506
507
508
509
|
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...
|
510
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
511
|
memset(result, 0, XYbytes); //initialize the ratio to zero
|
70407ea9
heziqi
Ziqi completed he...
|
512
513
514
515
|
//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...
|
516
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
517
|
if(mask == NULL || mask[i]){
|
70407ea9
heziqi
Ziqi completed he...
|
518
|
result[i] = p1[i] / p2[i];
|
ba51ae6a
David Mayerich
fixed metric calc...
|
519
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
520
|
}
|
517876d6
heziqi
metrics finished ...
|
521
522
523
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
524
|
return true;
|
70407ea9
heziqi
Ziqi completed he...
|
525
|
}
|
43dec788
David Mayerich
added code for si...
|
526
|
|
a08c98c3
David Mayerich
finished document...
|
527
|
/// Compute the ratio between a peak area and peak height.
|
77060b79
David Mayerich
started DOxygen d...
|
528
529
530
531
532
533
534
535
|
/// @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...
|
536
537
|
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...
|
538
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
539
540
541
|
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...
|
542
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
543
|
memset(result, 0, bytes); //initialize the ratio to zero
|
70407ea9
heziqi
Ziqi completed he...
|
544
545
546
547
|
//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...
|
548
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
549
|
if(mask == NULL || mask[i])
|
70407ea9
heziqi
Ziqi completed he...
|
550
551
|
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
552
553
554
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
555
556
557
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
558
|
/// Compute the ratio between two peak areas.
|
0722eb39
David Mayerich
further updates t...
|
559
560
561
562
563
564
565
566
|
/// @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...
|
567
|
/// @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...
|
568
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
569
570
|
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...
|
571
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
572
573
574
|
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...
|
575
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
576
|
memset(result, 0, bytes); //initialize the ratio result to zero (0)
|
70407ea9
heziqi
Ziqi completed he...
|
577
578
579
580
|
//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...
|
581
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
582
583
|
if(mask == NULL || mask[i]) //if the pixel is masked
result[i] = p1[i] / p2[i]; //calculate the ratio
|
70407ea9
heziqi
Ziqi completed he...
|
584
|
}
|
517876d6
heziqi
metrics finished ...
|
585
586
587
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
588
589
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
590
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
591
|
/// Compute the definite integral of a baseline corrected peak weighted by the corresponding wavelength
|
0722eb39
David Mayerich
further updates t...
|
592
593
594
595
596
597
|
/// @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 ...
|
598
599
600
601
602
603
|
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...
|
604
605
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
606
607
608
609
610
611
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
517876d6
heziqi
metrics finished ...
|
612
|
//find the wavelenght position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
613
614
615
|
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 ...
|
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
|
//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...
|
639
640
|
memset(result, (char)0, S); //initialize the integral to zero (0)
|
517876d6
heziqi
metrics finished ...
|
641
642
643
|
//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...
|
644
645
|
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 ...
|
646
647
648
|
}
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...
|
649
650
|
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 ...
|
651
652
653
654
|
}
//calculate f(x) times x
ai++;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
655
|
for(unsigned long long i = ai; i <= bi ;i++){
|
517876d6
heziqi
metrics finished ...
|
656
|
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
657
658
659
|
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 ...
|
660
661
662
663
664
665
666
667
668
669
670
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
671
|
/// Compute the centroid of a baseline corrected peak.
|
ba51ae6a
David Mayerich
fixed metric calc...
|
672
|
/// Note that the values for the centroid can be outside of [lab, rab] if the spectrum goes negative.
|
0722eb39
David Mayerich
further updates t...
|
673
674
675
676
677
678
|
/// @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...
|
679
680
681
|
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...
|
682
683
|
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
ba51ae6a
David Mayerich
fixed metric calc...
|
684
|
memset(result, 0, bytes); //initialize the ratio result to zero (0)
|
517876d6
heziqi
metrics finished ...
|
685
686
687
688
|
//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...
|
689
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
690
|
if(mask == NULL || mask[i]){
|
517876d6
heziqi
metrics finished ...
|
691
|
result[i] = p1[i] / p2[i];
|
ba51ae6a
David Mayerich
fixed metric calc...
|
692
|
}
|
517876d6
heziqi
metrics finished ...
|
693
694
695
696
|
}
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
697
|
return true;
|
517876d6
heziqi
metrics finished ...
|
698
699
|
}
|
a08c98c3
David Mayerich
finished document...
|
700
|
/// Create a mask based on a given band and threshold value.
|
0722eb39
David Mayerich
further updates t...
|
701
702
703
704
705
706
|
/// 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...
|
707
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
|
4a6f666c
heziqi
Added mask method
|
708
|
|
724ec347
David Mayerich
simplified the EN...
|
709
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
4a6f666c
heziqi
Added mask method
|
710
711
|
band(temp, mask_band);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
712
|
for (unsigned long long i = 0; i < X() * Y(); i++) {
|
798cea97
David Mayerich
added progress ba...
|
713
|
if (temp[i] < threshold)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
714
|
mask[i] = 0;
|
798cea97
David Mayerich
added progress ba...
|
715
|
else
|
ba51ae6a
David Mayerich
fixed metric calc...
|
716
|
mask[i] = 255;
|
798cea97
David Mayerich
added progress ba...
|
717
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
718
|
if(PROGRESS) progress = (double) (i+1) / (X() * Y()) * 100;
|
4a6f666c
heziqi
Added mask method
|
719
720
|
}
|
517876d6
heziqi
metrics finished ...
|
721
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
722
723
724
|
return true;
}
|
740f8cd2
heziqi
added apply_mask
|
725
|
|
a08c98c3
David Mayerich
finished document...
|
726
|
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
|
0722eb39
David Mayerich
further updates t...
|
727
728
729
|
/// @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...
|
730
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
731
732
733
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
734
735
|
unsigned long long XY = X() * Y(); //calculate number of a band
unsigned long long L = XY * sizeof(T);
|
740f8cd2
heziqi
added apply_mask
|
736
737
738
|
T * temp = (T*)malloc(L);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
739
|
for (unsigned long long i = 0; i < Z(); i++) //for each spectral bin
|
740f8cd2
heziqi
added apply_mask
|
740
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
741
|
band_index(temp, i); //get the specified band (by index)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
742
|
for ( unsigned long long j = 0; j < XY; j++) // for each pixel
|
740f8cd2
heziqi
added apply_mask
|
743
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
744
745
|
if(p[j] == 0){ //if the mask is 0 at that pixel
temp[j] = 0; //set temp to zero
|
740f8cd2
heziqi
added apply_mask
|
746
747
748
749
750
|
}
else{
continue;
}
}
|
e843658b
Brad Deutsch
Previous push did...
|
751
|
target.write(reinterpret_cast<const char*>(temp), L); //write the XY slice at that band to disk
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
752
|
if(PROGRESS) progress = (double)(i + 1) / (double)Z() * 100;
|
740f8cd2
heziqi
added apply_mask
|
753
754
755
756
757
758
|
}
target.close();
free(temp);
return true;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
759
760
761
762
763
764
|
/// 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...
|
765
766
|
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...
|
767
768
|
//calculate the number of pixels in the mask
|
a2bf1d08
David Mayerich
general bug fixes...
|
769
|
//unsigned long long P = nnz(mask);
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
770
|
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
771
772
773
774
775
776
777
778
779
780
781
|
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...
|
782
|
//std::cout<<i<<std::endl;
|
43dec788
David Mayerich
added code for si...
|
783
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
784
|
|
43dec788
David Mayerich
added code for si...
|
785
786
|
}
}
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
787
|
|
43dec788
David Mayerich
added code for si...
|
788
789
|
return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
790
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
791
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
43dec788
David Mayerich
added code for si...
|
792
793
|
/// @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...
|
794
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
e843658b
Brad Deutsch
Previous push did...
|
795
796
|
std::ofstream target(outfile.c_str(), std::ios::binary);
// open a band (XY plane)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
797
798
|
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...
|
799
|
unsigned long long B = Z();
|
e843658b
Brad Deutsch
Previous push did...
|
800
801
802
803
|
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...
|
804
|
for (unsigned long long i = 0; i < B; i++) //for each spectral bin
|
e843658b
Brad Deutsch
Previous push did...
|
805
806
|
{
band_index(temp, i); //get the specified band (XY sheet by index)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
807
|
for (unsigned long long j = 0; j < XY; j++) // for each pixel
|
e843658b
Brad Deutsch
Previous push did...
|
808
809
810
811
812
813
814
|
{
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...
|
815
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
816
|
}
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
817
|
if(PROGRESS) progress = (double)(i+1)/ B * 100;
|
e843658b
Brad Deutsch
Previous push did...
|
818
819
820
|
}
target.close();
free(temp);
|
3150c537
David Mayerich
added further pro...
|
821
|
|
63fc1df8
David Mayerich
added an inverse ...
|
822
|
progress = 100;
|
3150c537
David Mayerich
added further pro...
|
823
|
|
e843658b
Brad Deutsch
Previous push did...
|
824
825
826
|
return true;
}
|
2fcab4f0
David Mayerich
added unsifting f...
|
827
|
/// Generates a spectral image from a matrix of spectral values in lexicographic order and a mask
|
a2bf1d08
David Mayerich
general bug fixes...
|
828
|
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...
|
829
830
831
832
833
834
835
836
837
838
839
840
841
|
//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...
|
842
843
844
|
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...
|
845
846
847
848
849
850
851
852
|
// 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...
|
853
|
for(unsigned long long b = 0; b < B; b++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
854
855
|
//set the unsifted index value to zero
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
856
|
unsigned long long i = 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
857
858
859
860
861
|
//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...
|
862
|
for(unsigned long long xi = 0; xi < XY; xi++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
863
864
865
866
867
868
|
if( p[xi] == 0 )
unsifted[xi] = 0;
else{
unsifted[xi] = sifted[i];
i++;
}
|
3150c537
David Mayerich
added further pro...
|
869
|
//std::cout<<xi<<"/"<<XY<<", "<<b<<"/"<<B<<std::endl;
|
a2bf1d08
David Mayerich
general bug fixes...
|
870
|
if(PROGRESS) progress = (double)((b + 1) * XY + xi + 1) / (B * XY) * 100;
|
2fcab4f0
David Mayerich
added unsifting f...
|
871
|
}
|
3150c537
David Mayerich
added further pro...
|
872
|
//std::cout<<b*XY<<"/"<<B*XY<<" "<<B<<"-"<<XY<<std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
873
874
875
876
|
//write the band image to disk
target.write(reinterpret_cast<const char*>(unsifted), sizeof(T) * XY);
}
|
3150c537
David Mayerich
added further pro...
|
877
|
//std::cout<<"unsifted"<<std::endl;
|
a2bf1d08
David Mayerich
general bug fixes...
|
878
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
879
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
880
881
882
|
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
883
|
|
a08c98c3
David Mayerich
finished document...
|
884
|
/// Calculate the mean band value (average along B) at each pixel location.
|
0722eb39
David Mayerich
further updates t...
|
885
886
|
/// @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...
|
887
|
bool band_avg(T* p){
|
724ec347
David Mayerich
simplified the EN...
|
888
|
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
889
890
891
|
T* temp = (T*)malloc(sizeof(T) * XY);
//initialize p
band_index(p, 0);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
892
|
for (unsigned long long j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
893
|
p[j] /= (T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
894
895
|
}
//get every band and add them all
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
896
|
for (unsigned long long i = 1; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
897
|
band_index(temp, i);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
898
|
for (unsigned long long j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
899
|
p[j] += temp[j]/(T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
900
901
902
903
904
905
|
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
906
907
908
909
|
/// 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 ...
|
910
|
bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
911
|
unsigned long long XY = X() * Y();
|
2aa68315
David Mayerich
major bug fixes f...
|
912
|
unsigned long long count = 0; //count will store the number of masked pixels
|
a43c4fe1
heziqi
Added crop in env...
|
913
|
T* temp = (T*)malloc(sizeof(T) * XY);
|
a08c98c3
David Mayerich
finished document...
|
914
|
//calculate this loop counts the number of true pixels in the mask
|
a43c4fe1
heziqi
Added crop in env...
|
915
|
for (unsigned j = 0; j < XY; j++){
|
2aa68315
David Mayerich
major bug fixes f...
|
916
|
if (mask == NULL || mask[j] != 0){
|
a43c4fe1
heziqi
Added crop in env...
|
917
918
919
|
count++;
}
}
|
724ec347
David Mayerich
simplified the EN...
|
920
|
//this loops goes through each band in B (Z())
|
a08c98c3
David Mayerich
finished document...
|
921
|
// masked (or valid) pixels from that band are averaged and the average is stored in p
|
2aa68315
David Mayerich
major bug fixes f...
|
922
|
for (unsigned long long i = 0; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
923
|
p[i] = 0;
|
a08c98c3
David Mayerich
finished document...
|
924
|
band_index(temp, i); //get the band image and store it in temp
|
2aa68315
David Mayerich
major bug fixes f...
|
925
926
927
|
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...
|
928
|
}
|
a43c4fe1
heziqi
Added crop in env...
|
929
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
930
|
if(PROGRESS) progress = (double)(i+1) / Z() * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
931
932
933
934
|
}
free(temp);
return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
935
|
|
a08c98c3
David Mayerich
finished document...
|
936
937
938
939
940
941
942
|
/// 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...
|
943
944
945
946
947
|
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 ...
|
948
949
|
unsigned long long b1,
bool PROGRESS = false){
|
e9bddc57
David Mayerich
added band croppi...
|
950
951
952
953
954
955
956
957
958
959
|
//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...
|
960
|
T* temp = (T*)malloc(L);
|
e9bddc57
David Mayerich
added band croppi...
|
961
962
|
//create an output stream to store the output file
|
a43c4fe1
heziqi
Added crop in env...
|
963
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
e9bddc57
David Mayerich
added band croppi...
|
964
965
966
967
968
969
970
971
972
973
974
975
|
//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...
|
976
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
977
|
for (unsigned long long y = 0; y < lines; y++)
|
a43c4fe1
heziqi
Added crop in env...
|
978
|
{
|
e9bddc57
David Mayerich
added band croppi...
|
979
|
file.read((char *)(temp + y * samples), sizeof(T) * samples);
|
43dec788
David Mayerich
added code for si...
|
980
|
file.seekg(jumpl, std::ios::cur); //go to the next band
|
3150c537
David Mayerich
added further pro...
|
981
|
|
63fc1df8
David Mayerich
added an inverse ...
|
982
|
if(PROGRESS) progress = (double)((z+1) * lines + y + 1) / ((b1 - b0) * lines) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
983
|
}
|
43dec788
David Mayerich
added code for si...
|
984
|
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
|
a43c4fe1
heziqi
Added crop in env...
|
985
986
987
|
file.seekg(jumpb, std::ios::cur);
}
free(temp);
|
3150c537
David Mayerich
added further pro...
|
988
|
|
a43c4fe1
heziqi
Added crop in env...
|
989
990
|
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
991
|
|
dc8eb8aa
David Mayerich
added band trimmi...
|
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
|
/// 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
}
|
2ce6954b
David Mayerich
added the ability...
|
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
|
/// 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...
|
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
|
out.close();
}
/// 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...
|
1074
|
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...
|
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
|
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...
|
1095
1096
1097
1098
1099
1100
1101
1102
|
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...
|
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
|
}
}
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...
|
1119
|
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...
|
1120
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1121
|
convolve(out, C, start, end, mask, PROGRESS); //start the convolution
|
9b2a5d71
David Mayerich
implemented finit...
|
1122
1123
1124
1125
1126
1127
1128
1129
1130
|
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...
|
1131
|
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){
|
9b2a5d71
David Mayerich
implemented finit...
|
1132
1133
1134
1135
1136
1137
|
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];
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1138
|
convolve(out, C[k], b0, b1, mask, PROGRESS); //perform the convolution with the current kernel in the given range
|
9b2a5d71
David Mayerich
implemented finit...
|
1139
1140
1141
1142
1143
1144
|
}
out.close();
}
/// Approximate the spectral derivative of the image
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1145
|
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){
|
9b2a5d71
David Mayerich
implemented finit...
|
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
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
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1184
1185
1186
|
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)
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1187
1188
1189
1190
1191
|
}
}
out.write((char*)outband, XYb); //output the band
if(PROGRESS) progress = (double)(b+1) / (double)B * 100;
}
|
2ce6954b
David Mayerich
added the ability...
|
1192
1193
1194
|
}
|
740f8cd2
heziqi
added apply_mask
|
1195
|
|
a08c98c3
David Mayerich
finished document...
|
1196
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
1197
1198
1199
1200
|
bool close(){
file.close();
return true;
}
|
31394e2a
heziqi
Ziqi added method...
|
1201
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
1202
1203
|
};
}
|
31394e2a
heziqi
Ziqi added method...
|
1204
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1205
|
#endif
|
43dec788
David Mayerich
added code for si...
|
|
|