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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
if(w.size() == 0)
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return band_index(p, (unsigned long long)wavelength);
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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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}
//if the last BL point on the last band of the file?
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else if ( wls[control] < w[B - 1]) {
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std::swap(a, b); //swap the baseline band pointers
memset(b, (char)0, S); //clear the high band
ai = bi;
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bi = w[B - 1];
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}
}
//get the current band
band_index(c, cii);
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ci = w[cii];
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//perform the baseline correction
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for(unsigned long long i=0; i < XY; i++){
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if(mask != NULL && !mask[i]) //if the pixel is excluded by a mask
c[i] = 0; //set the value to zero
else{
double r = (double) (ci - ai) / (double) (bi - ai);
c[i] =(T) ( c[i] - (b[i] - a[i]) * r - a[i] );
}
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}
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target.write(reinterpret_cast<const char*>(c), S); //write the corrected data into destination
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if(PROGRESS)progress = (double)(cii+1) / B * 100;
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}
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//header.save(headername); //save the new header file
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free(a);
free(b);
free(c);
target.close();
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return true;
}
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/// Normalize all spectra based on the value of a single band, storing the result in a new BSQ file.
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/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
/// @param w is the label specifying the band that the hyperspectral image will be normalized to.
/// @param t is a threshold specified such that a spectrum with a value at w less than t is set to zero. Setting this threshold allows the user to limit division by extremely small numbers.
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bool 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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band(b, w); //get the certain band into memory
|
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for(unsigned long long j = 0; j < B; j++)
|
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{
band_index(c, j); //get the current band into memory
|
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for(unsigned long long i = 0; i < XY; i++)
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{
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315
|
if(mask != NULL && !mask[i])
|
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c[i] = (T)0.0;
else
c[i] = c[i] / b[i];
|
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|
}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
|
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|
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|
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322
|
if(PROGRESS) progress = (double)(j+1) / B * 100;
|
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|
}
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|
//header.save(headername); //save the new header file
|
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|
free(b);
free(c);
target.close();
|
089d9c81
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|
return true;
}
|
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|
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|
/// Convert the current BSQ file to a BIL file with the specified file name.
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|
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|
/// @param outname is the name of the output BIL file to be saved to disk.
|
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|
338
|
bool bil(std::string outname, bool PROGRESS = false)
|
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|
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|
{
//simplify image resolution
|
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341
|
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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|
unsigned long long L = X();
|
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|
347
|
T* line = (T*)malloc(sizeof(T) * L);
|
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|
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|
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added stim::hsi a...
|
349
|
for ( unsigned long long y = 0; y < Y(); y++) //for each y position
|
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|
350
|
{
|
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added support for...
|
351
|
file.seekg(y * X() * sizeof(T), std::ios::beg); //seek to the beginning of the xz slice
|
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|
352
|
for ( unsigned long long z = 0; z < Z(); z++ ) //for each band
|
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|
353
|
{
|
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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...
|
356
|
file.seekg(jump, std::ios::cur); //seek to the next band
|
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|
357
|
if(PROGRESS) progress = (double)((y+1) * Z() + z + 1) / (Z() * Y()) * 100; //update the progress counter
|
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|
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|
}
|
c25e7d0d
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|
359
|
}
|
3150c537
David Mayerich
added further pro...
|
360
|
|
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HSIproc bug fixes...
|
361
|
free(line);
|
c25e7d0d
heziqi
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|
362
|
target.close();
|
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David Mayerich
added further pro...
|
363
|
|
c25e7d0d
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speed of bip.base...
|
364
365
|
return true;
}
|
20c212c0
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Ziqi added functi...
|
366
|
|
a08c98c3
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finished document...
|
367
|
/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
|
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started DOxygen d...
|
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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...
|
377
|
unsigned long long XY = X() * Y();
|
20c212c0
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Ziqi added functi...
|
378
379
380
381
|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
382
|
for(unsigned long long i=0; i < XY; i++){
|
20c212c0
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Ziqi added functi...
|
383
384
385
386
|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
517876d6
heziqi
metrics finished ...
|
387
|
|
a08c98c3
David Mayerich
finished document...
|
388
|
/// 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...
|
389
390
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393
|
/// @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...
|
394
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
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Ziqi added functi...
|
395
396
397
|
T* lp;
T* rp;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
398
399
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
70407ea9
heziqi
Ziqi completed he...
|
400
401
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
402
|
|
70407ea9
heziqi
Ziqi completed he...
|
403
|
band(lp, lb);
|
43dec788
David Mayerich
added code for si...
|
404
|
band(rp, rb);
|
20c212c0
heziqi
Ziqi added functi...
|
405
406
407
|
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
408
409
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
410
411
412
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
413
|
|
a08c98c3
David Mayerich
finished document...
|
414
|
/// 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...
|
415
416
417
418
419
420
|
/// @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...
|
421
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
422
423
424
425
426
|
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...
|
427
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
428
429
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
20c212c0
heziqi
Ziqi added functi...
|
430
431
432
433
434
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
435
436
437
438
|
memset(result, (char)0, S);
//find the wavelenght position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
439
440
441
|
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...
|
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
|
//to make sure the left and the right bound are in the bandwidth
if (lb < w[0] || rb < w[0] || lb > w[n-1] || rb >w[n-1]){
std::cout<<"ERROR: left bound or right bound out of bandwidth"<<std::endl;
exit(1);
}
//to make sure rigth bound is bigger than left bound
else if(lb > rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
exit(1);
}
//get the position of lb and rb
|
70407ea9
heziqi
Ziqi completed he...
|
457
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
458
459
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
460
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
461
462
463
464
465
466
467
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
468
469
|
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...
|
470
471
|
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...
|
472
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
473
474
|
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...
|
475
476
|
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...
|
477
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
478
|
|
20c212c0
heziqi
Ziqi added functi...
|
479
480
|
//calculate the area
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
481
|
for(unsigned long long i = ai; i <= bi ;i++)
|
20c212c0
heziqi
Ziqi added functi...
|
482
483
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
484
|
for(unsigned long long j = 0; j < XY; j++)
|
20c212c0
heziqi
Ziqi added functi...
|
485
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
486
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
487
488
489
|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
490
|
|
517876d6
heziqi
metrics finished ...
|
491
492
493
494
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
495
496
497
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
498
|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
499
500
501
502
503
504
505
506
|
/// @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
|
70407ea9
heziqi
Ziqi completed he...
|
507
|
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
|
20c212c0
heziqi
Ziqi added functi...
|
508
|
|
43dec788
David Mayerich
added code for si...
|
509
510
511
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
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++){
|
70407ea9
heziqi
Ziqi completed he...
|
517
518
519
520
521
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
522
523
524
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
525
|
return true;
|
70407ea9
heziqi
Ziqi completed he...
|
526
|
}
|
43dec788
David Mayerich
added code for si...
|
527
|
|
a08c98c3
David Mayerich
finished document...
|
528
|
/// Compute the ratio between a peak area and peak height.
|
77060b79
David Mayerich
started DOxygen d...
|
529
530
531
532
533
534
535
536
|
/// @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
|
70407ea9
heziqi
Ziqi completed he...
|
537
538
|
bool pa_to_ph(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, T* result){
|
43dec788
David Mayerich
added code for si...
|
539
540
541
542
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
543
544
545
546
|
//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...
|
547
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
548
549
550
551
552
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
553
554
555
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
556
557
558
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
559
|
/// Compute the ratio between two peak areas.
|
0722eb39
David Mayerich
further updates t...
|
560
561
562
563
564
565
566
567
|
/// @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...
|
568
|
/// @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...
|
569
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
570
571
|
bool pa_to_pa(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, T* result){
|
43dec788
David Mayerich
added code for si...
|
572
573
574
575
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
576
577
578
579
|
//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...
|
580
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
581
582
583
584
585
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
586
587
588
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
589
590
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
591
|
|
a08c98c3
David Mayerich
finished document...
|
592
|
/// Compute the definite integral of a baseline corrected peak.
|
0722eb39
David Mayerich
further updates t...
|
593
594
595
596
597
598
|
/// @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 ...
|
599
600
601
602
603
604
|
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...
|
605
606
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
607
608
609
610
611
612
613
614
615
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
memset(result, (char)0, S);
//find the wavelenght position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
616
617
618
|
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 ...
|
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
|
//to make sure the left and the right bound are in the bandwidth
if (lb < w[0] || rb < w[0] || lb > w[n-1] || rb >w[n-1]){
std::cout<<"ERROR: left bound or right bound out of bandwidth"<<std::endl;
exit(1);
}
//to make sure rigth bound is bigger than left bound
else if(lb > rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
exit(1);
}
//get the position of lb and rb
while (lab >= w[ai]){
ai++;
}
while (rab <= w[bi]){
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
645
646
|
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 ...
|
647
648
649
|
}
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...
|
650
651
|
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 ...
|
652
653
654
655
|
}
//calculate f(x) times x
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
656
|
for(unsigned long long i = ai; i <= bi ;i++)
|
517876d6
heziqi
metrics finished ...
|
657
658
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
659
|
for(unsigned long long j = 0; j < XY; j++)
|
517876d6
heziqi
metrics finished ...
|
660
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
661
|
result[j] += (T)((w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
662
663
664
665
666
667
668
669
670
671
672
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
673
|
/// Compute the centroid of a baseline corrected peak.
|
0722eb39
David Mayerich
further updates t...
|
674
675
676
677
678
679
|
/// @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
|
517876d6
heziqi
metrics finished ...
|
680
|
bool cpoint(double lb, double rb, double lab, double rab, T* result){
|
43dec788
David Mayerich
added code for si...
|
681
682
683
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
684
685
686
687
|
//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...
|
688
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
517876d6
heziqi
metrics finished ...
|
689
690
691
692
693
694
695
696
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
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
|
798cea97
David Mayerich
added progress ba...
|
707
|
bool build_mask(double mask_band, double threshold, unsigned char* p = NULL, 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
714
715
716
717
|
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
|
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.
|
740f8cd2
heziqi
added apply_mask
|
730
731
732
733
|
bool apply_mask(std::string outfile, unsigned char* p){
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
|
740f8cd2
heziqi
added apply_mask
|
752
753
754
755
756
757
|
}
target.close();
free(temp);
return true;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
758
759
760
761
762
763
|
/// 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...
|
764
765
|
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...
|
766
767
|
//calculate the number of pixels in the mask
|
a2bf1d08
David Mayerich
general bug fixes...
|
768
|
//unsigned long long P = nnz(mask);
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
769
|
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
770
771
772
773
774
775
776
777
778
779
780
|
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...
|
781
|
//std::cout<<i<<std::endl;
|
43dec788
David Mayerich
added code for si...
|
782
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
783
|
|
43dec788
David Mayerich
added code for si...
|
784
785
|
}
}
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
786
|
|
43dec788
David Mayerich
added code for si...
|
787
788
|
return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
789
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
790
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
43dec788
David Mayerich
added code for si...
|
791
792
|
/// @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...
|
793
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
e843658b
Brad Deutsch
Previous push did...
|
794
795
|
std::ofstream target(outfile.c_str(), std::ios::binary);
// open a band (XY plane)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
796
797
|
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...
|
798
|
unsigned long long B = Z();
|
e843658b
Brad Deutsch
Previous push did...
|
799
800
801
802
|
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...
|
803
|
for (unsigned long long i = 0; i < B; i++) //for each spectral bin
|
e843658b
Brad Deutsch
Previous push did...
|
804
805
|
{
band_index(temp, i); //get the specified band (XY sheet by index)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
806
|
for (unsigned long long j = 0; j < XY; j++) // for each pixel
|
e843658b
Brad Deutsch
Previous push did...
|
807
808
809
810
811
812
813
|
{
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...
|
814
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
815
|
}
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
816
|
if(PROGRESS) progress = (double)(i+1)/ B * 100;
|
e843658b
Brad Deutsch
Previous push did...
|
817
818
819
|
}
target.close();
free(temp);
|
3150c537
David Mayerich
added further pro...
|
820
|
|
63fc1df8
David Mayerich
added an inverse ...
|
821
|
progress = 100;
|
3150c537
David Mayerich
added further pro...
|
822
|
|
e843658b
Brad Deutsch
Previous push did...
|
823
824
825
|
return true;
}
|
2fcab4f0
David Mayerich
added unsifting f...
|
826
|
/// Generates a spectral image from a matrix of spectral values in lexicographic order and a mask
|
a2bf1d08
David Mayerich
general bug fixes...
|
827
|
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...
|
828
829
830
831
832
833
834
835
836
837
838
839
840
|
//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...
|
841
842
843
|
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...
|
844
845
846
847
848
849
850
851
|
// 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...
|
852
|
for(unsigned long long b = 0; b < B; b++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
853
854
|
//set the unsifted index value to zero
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
855
|
unsigned long long i = 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
856
857
858
859
860
|
//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...
|
861
|
for(unsigned long long xi = 0; xi < XY; xi++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
862
863
864
865
866
867
|
if( p[xi] == 0 )
unsifted[xi] = 0;
else{
unsifted[xi] = sifted[i];
i++;
}
|
3150c537
David Mayerich
added further pro...
|
868
|
//std::cout<<xi<<"/"<<XY<<", "<<b<<"/"<<B<<std::endl;
|
a2bf1d08
David Mayerich
general bug fixes...
|
869
|
if(PROGRESS) progress = (double)((b + 1) * XY + xi + 1) / (B * XY) * 100;
|
2fcab4f0
David Mayerich
added unsifting f...
|
870
|
}
|
3150c537
David Mayerich
added further pro...
|
871
|
//std::cout<<b*XY<<"/"<<B*XY<<" "<<B<<"-"<<XY<<std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
872
873
874
875
|
//write the band image to disk
target.write(reinterpret_cast<const char*>(unsifted), sizeof(T) * XY);
}
|
3150c537
David Mayerich
added further pro...
|
876
|
//std::cout<<"unsifted"<<std::endl;
|
a2bf1d08
David Mayerich
general bug fixes...
|
877
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
878
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
879
880
881
|
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
882
|
|
a08c98c3
David Mayerich
finished document...
|
883
|
/// Calculate the mean band value (average along B) at each pixel location.
|
0722eb39
David Mayerich
further updates t...
|
884
885
|
/// @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...
|
886
|
bool band_avg(T* p){
|
724ec347
David Mayerich
simplified the EN...
|
887
|
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
888
889
890
|
T* temp = (T*)malloc(sizeof(T) * XY);
//initialize p
band_index(p, 0);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
891
|
for (unsigned long long j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
892
|
p[j] /= (T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
893
894
|
}
//get every band and add them all
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
895
|
for (unsigned long long i = 1; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
896
|
band_index(temp, i);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
897
|
for (unsigned long long j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
898
|
p[j] += temp[j]/(T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
899
900
901
902
903
904
|
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
905
906
907
908
|
/// 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 ...
|
909
|
bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
910
|
unsigned long long XY = X() * Y();
|
2aa68315
David Mayerich
major bug fixes f...
|
911
|
unsigned long long count = 0; //count will store the number of masked pixels
|
a43c4fe1
heziqi
Added crop in env...
|
912
|
T* temp = (T*)malloc(sizeof(T) * XY);
|
a08c98c3
David Mayerich
finished document...
|
913
|
//calculate this loop counts the number of true pixels in the mask
|
a43c4fe1
heziqi
Added crop in env...
|
914
|
for (unsigned j = 0; j < XY; j++){
|
2aa68315
David Mayerich
major bug fixes f...
|
915
|
if (mask == NULL || mask[j] != 0){
|
a43c4fe1
heziqi
Added crop in env...
|
916
917
918
|
count++;
}
}
|
724ec347
David Mayerich
simplified the EN...
|
919
|
//this loops goes through each band in B (Z())
|
a08c98c3
David Mayerich
finished document...
|
920
|
// masked (or valid) pixels from that band are averaged and the average is stored in p
|
2aa68315
David Mayerich
major bug fixes f...
|
921
|
for (unsigned long long i = 0; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
922
|
p[i] = 0;
|
a08c98c3
David Mayerich
finished document...
|
923
|
band_index(temp, i); //get the band image and store it in temp
|
2aa68315
David Mayerich
major bug fixes f...
|
924
925
926
|
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...
|
927
|
}
|
a43c4fe1
heziqi
Added crop in env...
|
928
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
929
|
if(PROGRESS) progress = (double)(i+1) / Z() * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
930
931
932
933
|
}
free(temp);
return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
934
|
|
a08c98c3
David Mayerich
finished document...
|
935
936
937
938
939
940
941
|
/// 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...
|
942
943
944
945
946
|
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 ...
|
947
948
|
unsigned long long b1,
bool PROGRESS = false){
|
e9bddc57
David Mayerich
added band croppi...
|
949
950
951
952
953
954
955
956
957
958
|
//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...
|
959
|
T* temp = (T*)malloc(L);
|
e9bddc57
David Mayerich
added band croppi...
|
960
961
|
//create an output stream to store the output file
|
a43c4fe1
heziqi
Added crop in env...
|
962
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
e9bddc57
David Mayerich
added band croppi...
|
963
964
965
966
967
968
969
970
971
972
973
974
|
//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...
|
975
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
976
|
for (unsigned long long y = 0; y < lines; y++)
|
a43c4fe1
heziqi
Added crop in env...
|
977
|
{
|
e9bddc57
David Mayerich
added band croppi...
|
978
|
file.read((char *)(temp + y * samples), sizeof(T) * samples);
|
43dec788
David Mayerich
added code for si...
|
979
|
file.seekg(jumpl, std::ios::cur); //go to the next band
|
3150c537
David Mayerich
added further pro...
|
980
|
|
63fc1df8
David Mayerich
added an inverse ...
|
981
|
if(PROGRESS) progress = (double)((z+1) * lines + y + 1) / ((b1 - b0) * lines) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
982
|
}
|
43dec788
David Mayerich
added code for si...
|
983
|
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
|
a43c4fe1
heziqi
Added crop in env...
|
984
985
986
|
file.seekg(jumpb, std::ios::cur);
}
free(temp);
|
3150c537
David Mayerich
added further pro...
|
987
|
|
a43c4fe1
heziqi
Added crop in env...
|
988
989
|
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
990
|
|
740f8cd2
heziqi
added apply_mask
|
991
|
|
a08c98c3
David Mayerich
finished document...
|
992
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
993
994
995
996
|
bool close(){
file.close();
return true;
}
|
31394e2a
heziqi
Ziqi added method...
|
997
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
998
999
|
};
}
|
31394e2a
heziqi
Ziqi added method...
|
1000
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1001
|
#endif
|
43dec788
David Mayerich
added code for si...
|
|
|