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#ifndef STIM_BSQ_H
#define STIM_BSQ_H
#include "../envi/envi_header.h"
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#include "../envi/binary.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>
class bsq: public binary<T> {
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protected:
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std::vector<double> w; //band wavelengths
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unsigned int offset;
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using binary<T>::R;
unsigned long X(){
return R[0];
}
unsigned long Y(){
return R[1];
}
unsigned long Z(){
return R[2];
}
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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_01;
using binary<T>::read_plane_2;
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//using binary<T>::getSlice;
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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
/// @param wavelengths is an optional STL vector of size B specifying a numerical label for each band
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bool open(std::string filename, unsigned int X, unsigned int Y, unsigned int B, unsigned int 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 int>(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 int page){
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return read_plane_2(p, page);
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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){
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//if there are no wavelengths in the BSQ file
if(w.size() == 0)
return band_index(p, (unsigned int)wavelength);
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unsigned int XY = X() * Y(); //calculate the number of pixels in a band
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unsigned 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 );
for(unsigned i=0; i < XY; i++){
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double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
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p[i] = (p2[i] - p1[i]) * r + p1[i];
}
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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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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 x, unsigned y){
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return read_line_01(p, x, y);
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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 n){
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unsigned 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;
}
file.seekg(n * sizeof(T), std::ios::beg); //point to the certain pixel
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for (unsigned 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
}
return true;
}
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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.
/// @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 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 int B = Z(); //calculate the number of bands
unsigned int XY = X() * Y(); //calculate the number of pixels in a band
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unsigned int S = XY * sizeof(T); //calculate the number of bytes in a band
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 control=0;
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
b = (T*)malloc( S );
c = (T*)malloc( S );
if (a == NULL || b == NULL || c == NULL){
std::cout<<"ERROR: error allocating memory";
exit(1);
}
//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];
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
for(unsigned cii = 0; cii < B; cii++){
//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
for(unsigned i=0; i < XY; i++){
double r = (double) (ci - ai) / (double) (bi - ai);
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c[i] =(T) ( c[i] - (b[i] - a[i]) * r - a[i] );
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}
target.write(reinterpret_cast<const char*>(c), S); //write the corrected data into destination
}
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//header.save(headername); //save the new header file
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free(a);
free(b);
free(c);
target.close();
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, double t = 0.0)
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{
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unsigned int B = Z(); //calculate the number of bands
unsigned int XY = X() * Y(); //calculate the number of pixels in a band
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unsigned int S = XY * sizeof(T); //calculate the number of bytes in a band
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
T * b; //pointers to the certain wavelength band
T * c; //pointer to the current image
b = (T*)malloc( S ); //memory allocation
c = (T*)malloc( S );
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band(b, w); //get the certain band into memory
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for(unsigned j = 0; j < B; j++)
{
band_index(c, j); //get the current band into memory
for(unsigned i = 0; i < XY; i++)
{
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if(b[i] < t)
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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//header.save(headername); //save the new header file
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free(b);
free(c);
target.close();
return true;
}
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/// Convert the current BSQ file to a BIP file with the specified file name.
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/// @param outname is the name of the output BIP file to be saved to disk.
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bool bip(std::string outname)
{
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std::string temp = outname + "_temp";
std::string headtemp = temp + ".hdr";
//first creat a temporary bil file and convert bsq file to bil file
bil(temp);
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stim::bil<T> n;
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if(n.open(temp, X(), Y(), Z(), offset, w)==false){ //open infile
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std::cout<<"ERROR: unable to open input file"<<std::endl;
exit(1);
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}
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//then convert bil file to bip file
n.bip(outname);
n.close();
remove(temp.c_str());
remove(headtemp.c_str());
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return true;
}
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/// Convert the current BSQ file to a BIL file with the specified file name.
|
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/// @param outname is the name of the output BIL file to be saved to disk.
|
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bool bil(std::string outname)
{
//simplify image resolution
|
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|
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|
unsigned int L = X() * Z() * sizeof(T); //calculate the number of bytes of a ZX slice
unsigned int jump = (Y() - 1) * X() * sizeof(T);
|
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|
std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
T * p; //pointer to the current spectrum
p = (T*)malloc(L);
|
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|
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|
for ( unsigned i = 0; i < Y(); i++)
|
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{
|
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|
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file.seekg(X() * i * sizeof(T), std::ios::beg);
for ( unsigned j = 0; j < Z(); j++ )
|
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|
{
|
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|
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|
file.read((char *)(p + j * X()), sizeof(T) * X());
|
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|
file.seekg(jump, std::ios::cur); //go to the next band
}
target.write(reinterpret_cast<const char*>(p), L); //write XZ slice data into target file
}
|
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|
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|
//header.interleave = rts::envi_header::BIL; //change the type of file in header file
//header.save(headername);
|
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free(p);
target.close();
return true;
}
|
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|
|
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|
/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
|
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|
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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.
|
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bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
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|
383
|
unsigned XY = X() * Y();
|
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|
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385
386
387
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390
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|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
for(unsigned i=0; i < XY; i++){
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
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/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
|
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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 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.
|
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bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
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Ziqi added functi...
|
401
402
403
|
T* lp;
T* rp;
|
724ec347
David Mayerich
simplified the EN...
|
404
|
unsigned XY = X() * Y();
|
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Ziqi completed he...
|
405
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407
|
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
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|
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|
|
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|
band(lp, lb);
|
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|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
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|
free(lp);
free(rp);
|
20c212c0
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|
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|
return true;
}
|
c359422d
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|
419
|
|
a08c98c3
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|
420
|
/// 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...
|
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426
|
/// @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
|
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|
427
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
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Ziqi added functi...
|
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430
431
432
|
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
|
20c212c0
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Ziqi added functi...
|
433
|
|
724ec347
David Mayerich
simplified the EN...
|
434
|
unsigned XY = X() * Y();
|
20c212c0
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Ziqi added functi...
|
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436
437
438
439
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|
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
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Ziqi added functi...
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441
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447
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451
452
453
454
455
456
457
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459
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|
memset(result, (char)0, S);
//find the wavelenght position in the whole band
unsigned int n = w.size();
unsigned int ai = 0; //left bound position
unsigned int bi = n - 1; //right bound position
//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...
|
463
|
while (lab >= w[ai]){
|
20c212c0
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Ziqi added functi...
|
464
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|
ai++;
}
|
70407ea9
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Ziqi completed he...
|
466
|
while (rab <= w[bi]){
|
20c212c0
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Ziqi added functi...
|
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468
469
470
471
472
473
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
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Ziqi completed he...
|
474
475
|
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
476
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
477
|
result[j] += (rab - w[bi]) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
478
|
}
|
70407ea9
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Ziqi completed he...
|
479
480
|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
481
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
482
|
result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
483
|
}
|
70407ea9
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Ziqi completed he...
|
484
|
|
20c212c0
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Ziqi added functi...
|
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487
488
489
490
491
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493
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495
|
//calculate the area
ai++;
for(unsigned i = ai; i <= bi ;i++)
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
for(unsigned j = 0; j < XY; j++)
{
result[j] += (w[ai] - w[ai-1]) * (cur[j] + cur2[j]) / 2.0;
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
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Ziqi completed he...
|
496
|
|
517876d6
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metrics finished ...
|
497
498
499
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|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
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Ziqi added functi...
|
501
502
503
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
504
|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
|
77060b79
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started DOxygen d...
|
505
506
507
508
509
510
511
512
|
/// @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
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Ziqi completed he...
|
513
|
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
|
20c212c0
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Ziqi added functi...
|
514
|
|
724ec347
David Mayerich
simplified the EN...
|
515
516
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
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Ziqi completed he...
|
517
518
519
520
521
|
//get the two peak band
height(lb1, rb1, pos1, p1);
height(lb2, rb2, pos2, p2);
//calculate the ratio in result
|
724ec347
David Mayerich
simplified the EN...
|
522
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
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Ziqi completed he...
|
523
524
525
526
527
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
528
529
530
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
531
532
533
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
534
|
/// Compute the ratio between a peak area and peak height.
|
77060b79
David Mayerich
started DOxygen d...
|
535
536
537
538
539
540
541
542
|
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param pos1 is the label value for the first peak (numerator) position
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param pos2 is the label value for the second peak (denominator) position
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
543
544
545
|
bool pa_to_ph(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, T* result){
|
724ec347
David Mayerich
simplified the EN...
|
546
547
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
548
549
550
551
552
|
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
height(lb2, rb2, pos, p2);
//calculate the ratio in result
|
724ec347
David Mayerich
simplified the EN...
|
553
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
554
555
556
557
558
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
559
560
561
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
562
563
564
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
565
|
/// Compute the ratio between two peak areas.
|
0722eb39
David Mayerich
further updates t...
|
566
567
568
569
570
571
572
573
574
575
|
/// @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)
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
576
577
578
|
bool pa_to_pa(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, T* result){
|
724ec347
David Mayerich
simplified the EN...
|
579
580
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
581
582
583
584
585
|
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
area(lb2, rb2, lab2, rab2, p2);
//calculate the ratio in result
|
724ec347
David Mayerich
simplified the EN...
|
586
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
587
588
589
590
591
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
592
593
594
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
595
596
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
597
|
|
a08c98c3
David Mayerich
finished document...
|
598
|
/// Compute the definite integral of a baseline corrected peak.
|
0722eb39
David Mayerich
further updates t...
|
599
600
601
602
603
604
|
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label for the start of the definite integral
/// @param rab is the label for the end of the definite integral
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
517876d6
heziqi
metrics finished ...
|
605
606
607
608
609
610
|
bool x_area(double lb, double rb, double lab, double rab, T* result){
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
|
724ec347
David Mayerich
simplified the EN...
|
611
|
unsigned XY = X() * Y();
|
517876d6
heziqi
metrics finished ...
|
612
613
614
615
616
617
618
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
645
646
647
648
649
650
651
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653
654
655
656
657
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660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
|
unsigned S = XY * sizeof(T);
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
unsigned int n = w.size();
unsigned int ai = 0; //left bound position
unsigned int bi = n - 1; //right bound position
//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);
for(unsigned j = 0; j < XY; j++){
result[j] += (rab - w[bi]) * (rab + w[bi]) * (cur[j] + cur2[j]) / 4.0;
}
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
for(unsigned j = 0; j < XY; j++){
result[j] += (w[ai] - lab) * (w[ai] + lab) * (cur[j] + cur2[j]) / 4.0;
}
//calculate f(x) times x
ai++;
for(unsigned i = ai; i <= bi ;i++)
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
for(unsigned j = 0; j < XY; j++)
{
result[j] += (w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * (cur[j] + cur2[j]) / 4.0;
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
679
|
/// Compute the centroid of a baseline corrected peak.
|
0722eb39
David Mayerich
further updates t...
|
680
681
682
683
684
685
|
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label for the start of the peak
/// @param rab is the label for the end of the peak
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
517876d6
heziqi
metrics finished ...
|
686
|
bool cpoint(double lb, double rb, double lab, double rab, T* result){
|
724ec347
David Mayerich
simplified the EN...
|
687
688
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
689
690
691
692
693
|
//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
|
724ec347
David Mayerich
simplified the EN...
|
694
|
for(unsigned i = 0; i < X() * Y(); i++){
|
517876d6
heziqi
metrics finished ...
|
695
696
697
698
699
700
701
702
703
704
705
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
706
|
/// Create a mask based on a given band and threshold value.
|
0722eb39
David Mayerich
further updates t...
|
707
708
709
710
711
712
|
/// 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
|
f4c5d71b
David Mayerich
started working w...
|
713
|
bool build_mask(double mask_band, double threshold, unsigned char* p = NULL){
|
4a6f666c
heziqi
Added mask method
|
714
|
|
724ec347
David Mayerich
simplified the EN...
|
715
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
4a6f666c
heziqi
Added mask method
|
716
717
|
band(temp, mask_band);
|
724ec347
David Mayerich
simplified the EN...
|
718
|
for (unsigned int i = 0; i < X() * Y(); i++) {
|
4a6f666c
heziqi
Added mask method
|
719
720
721
722
723
724
|
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
}
|
517876d6
heziqi
metrics finished ...
|
725
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
726
727
728
|
return true;
}
|
740f8cd2
heziqi
added apply_mask
|
729
|
|
a08c98c3
David Mayerich
finished document...
|
730
|
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
|
0722eb39
David Mayerich
further updates t...
|
731
732
733
|
/// @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
|
734
735
736
737
|
bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
|
724ec347
David Mayerich
simplified the EN...
|
738
|
unsigned XY = X() * Y(); //calculate number of a band
|
740f8cd2
heziqi
added apply_mask
|
739
740
741
742
|
unsigned L = XY * sizeof(T);
T * temp = (T*)malloc(L);
|
724ec347
David Mayerich
simplified the EN...
|
743
|
for (unsigned i = 0; i < Z(); i++) //for each spectral bin
|
740f8cd2
heziqi
added apply_mask
|
744
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
745
746
|
band_index(temp, i); //get the specified band (by index)
for ( unsigned j = 0; j < XY; j++) // for each pixel
|
740f8cd2
heziqi
added apply_mask
|
747
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
748
749
|
if(p[j] == 0){ //if the mask is 0 at that pixel
temp[j] = 0; //set temp to zero
|
740f8cd2
heziqi
added apply_mask
|
750
751
752
753
754
|
}
else{
continue;
}
}
|
e843658b
Brad Deutsch
Previous push did...
|
755
|
target.write(reinterpret_cast<const char*>(temp), L); //write the XY slice at that band to disk
|
740f8cd2
heziqi
added apply_mask
|
756
757
758
759
760
761
|
}
target.close();
free(temp);
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
762
763
764
765
|
///Saves to disk only those spectra corresponding to mask values != 0
bool sift_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
// open a band (XY plane)
|
724ec347
David Mayerich
simplified the EN...
|
766
|
unsigned XY = X() * Y(); //Number of XY pixels
|
e843658b
Brad Deutsch
Previous push did...
|
767
768
769
770
771
|
unsigned L = XY * sizeof(T); //size of XY pixels
T * temp = (T*)malloc(L); //allocate memory for a band
T * temp_vox = (T*)malloc(sizeof(T)); //allocate memory for one voxel
|
724ec347
David Mayerich
simplified the EN...
|
772
|
for (unsigned i = 0; i < Z(); i++) //for each spectral bin
|
e843658b
Brad Deutsch
Previous push did...
|
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
|
{
band_index(temp, i); //get the specified band (XY sheet by index)
for (unsigned j = 0; j < XY; j++) // for each pixel
{
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;
}
}
}
target.close();
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
792
|
/// Calculate the mean band value (average along B) at each pixel location.
|
0722eb39
David Mayerich
further updates t...
|
793
794
|
/// @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...
|
795
|
bool band_avg(T* p){
|
724ec347
David Mayerich
simplified the EN...
|
796
|
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
797
798
799
800
|
T* temp = (T*)malloc(sizeof(T) * XY);
//initialize p
band_index(p, 0);
for (unsigned j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
801
|
p[j] /= (T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
802
803
|
}
//get every band and add them all
|
724ec347
David Mayerich
simplified the EN...
|
804
|
for (unsigned i = 1; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
805
806
|
band_index(temp, i);
for (unsigned j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
807
|
p[j] += temp[j]/(T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
808
809
810
811
812
813
|
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
814
815
816
817
|
/// 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
|
a43c4fe1
heziqi
Added crop in env...
|
818
|
bool avg_band(T*p, unsigned char* mask){
|
724ec347
David Mayerich
simplified the EN...
|
819
|
unsigned long long XY = X() * Y();
|
a08c98c3
David Mayerich
finished document...
|
820
|
unsigned count = 0; //count will store the number of masked pixels
|
a43c4fe1
heziqi
Added crop in env...
|
821
|
T* temp = (T*)malloc(sizeof(T) * XY);
|
a08c98c3
David Mayerich
finished document...
|
822
|
//calculate this loop counts the number of true pixels in the mask
|
a43c4fe1
heziqi
Added crop in env...
|
823
824
825
826
827
|
for (unsigned j = 0; j < XY; j++){
if (mask[j] != 0){
count++;
}
}
|
724ec347
David Mayerich
simplified the EN...
|
828
|
//this loops goes through each band in B (Z())
|
a08c98c3
David Mayerich
finished document...
|
829
|
// masked (or valid) pixels from that band are averaged and the average is stored in p
|
724ec347
David Mayerich
simplified the EN...
|
830
|
for (unsigned i = 0; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
831
|
p[i] = 0;
|
a08c98c3
David Mayerich
finished document...
|
832
833
|
band_index(temp, i); //get the band image and store it in temp
for (unsigned j = 0; j < XY; j++){ //loop through temp, averaging valid pixels
|
a43c4fe1
heziqi
Added crop in env...
|
834
835
836
837
838
839
840
841
842
|
if (mask[j] != 0){
p[i] += temp[j] / (T)count;
}
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
843
844
845
846
847
|
/// Calculate the covariance matrix for all masked pixels in the image.
/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
/// @param avg is a pointer to memory of size B that stores the average spectrum
/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
|
a43c4fe1
heziqi
Added crop in env...
|
848
849
|
bool co_matrix(T* co, T* avg, unsigned char *mask){
//memory allocation
|
724ec347
David Mayerich
simplified the EN...
|
850
851
|
unsigned long long xy = X() * Y();
unsigned int B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
|
T* bandi = (T*)malloc(sizeof(T) * xy);
T* bandj = (T*)malloc(sizeof(T) * xy);
//count vaild pixels in a band
unsigned count = 0;
for (unsigned j = 0; j < xy; j++){
if (mask[j] != 0){
count++;
}
}
//calculate correlation coefficient matrix
for (unsigned i = 0; i < B; i++)
{
band_index(bandi, i);
for (unsigned j = i; j < B; j++){
band_index(bandj, j);
T numerator = 0; //to calculate element in correlation coefficient matrix, numerator part
//calculate the R(i,j) in correlation coeffient matrix
for (unsigned k = 0; k < xy; k++){
if (mask[k] != 0){
numerator += (bandi[k] - avg[i]) * (bandj[k] - avg[j]) / count;
}
}
co[i*B + j] = numerator;
co[j*B + i] = numerator; //because correlated matrix is a symmetric matrix
}
}
free(bandi);
free(bandj);
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
883
|
|
a43c4fe1
heziqi
Added crop in env...
|
884
|
|
a08c98c3
David Mayerich
finished document...
|
885
886
887
888
889
890
891
|
/// 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
|
a43c4fe1
heziqi
Added crop in env...
|
892
893
894
895
896
897
898
899
900
|
bool crop(std::string outfile, unsigned x0, unsigned y0, unsigned x1, unsigned y1){
//calculate the new number of samples and lines
unsigned long long sam = x1 - x0; //samples
unsigned long long lin = y1 - y0; //lines
unsigned long long L = sam * lin * sizeof(T);
//get specified band and save
T* temp = (T*)malloc(L);
std::ofstream out(outfile.c_str(), std::ios::binary);
|
724ec347
David Mayerich
simplified the EN...
|
901
902
|
unsigned long long jumpb = X() * (Y() - lin) * sizeof(T); //jump pointer to the next band
unsigned long long jumpl = (X() - sam) * sizeof(T); //jump pointer to the next line
|
a43c4fe1
heziqi
Added crop in env...
|
903
|
//get start
|
724ec347
David Mayerich
simplified the EN...
|
904
905
|
file.seekg((y0 * X() + x0) * sizeof(T), std::ios::beg);
for (unsigned i = 0; i < Z(); i++)
|
a43c4fe1
heziqi
Added crop in env...
|
906
907
908
909
910
911
912
913
914
915
916
917
|
{
for (unsigned j = 0; j < lin; j++)
{
file.read((char *)(temp + j * sam), sizeof(T) * sam);
file.seekg(jumpl, std::ios::cur); //go to the next band
}
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
file.seekg(jumpb, std::ios::cur);
}
free(temp);
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
918
|
|
740f8cd2
heziqi
added apply_mask
|
919
|
|
a08c98c3
David Mayerich
finished document...
|
920
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
921
922
923
924
|
bool close(){
file.close();
return true;
}
|
31394e2a
heziqi
Ziqi added method...
|
925
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
926
927
|
};
}
|
31394e2a
heziqi
Ziqi added method...
|
928
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
929
930
|
#endif
|
fc712213
David Mayerich
code simplifications
|
931
|
|