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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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using binary<T>::thread_data;
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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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thread_data = (double)cii / 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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thread_data = 100;
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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, 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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thread_data = (double)j / B * 100;
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}
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//header.save(headername); //save the new header file
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free(b);
free(c);
target.close();
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thread_data = 100; //make sure that the progress bar is full
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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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|
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|
if(n.open(temp, X(), Y(), Z(), offset, w)==false){ //open infile
|
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|
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341
|
std::cout<<"ERROR: unable to open input file"<<std::endl;
exit(1);
|
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|
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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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|
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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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|
/// @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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358
|
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";
|
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|
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367
|
unsigned int xz_bytes = X() * Z() * sizeof(T);
T * xz_slice; //pointer to the current spectrum
xz_slice = (T*)malloc(xz_bytes);
for ( unsigned y = 0; y < Y(); y++) //for each y position
|
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|
{
|
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|
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|
file.seekg(y * X() * sizeof(T), std::ios::beg); //seek to the beginning of the xz slice
for ( unsigned z = 0; z < Z(); z++ ) //for each band
|
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|
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|
{
|
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|
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|
file.read((char *)(xz_slice + z * X()), sizeof(T) * X()); //read a line
file.seekg(jump, std::ios::cur); //seek to the next band
|
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|
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|
thread_data = (double)(y * Z() + z) / (Z() * Y()) * 100; //update the progress counter
|
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|
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|
}
|
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|
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|
target.write(reinterpret_cast<const char*>(xz_slice), xz_bytes); //write the generated XZ slice to the target file
|
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|
}
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381
|
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|
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|
|
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|
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|
thread_data = 100;
free(xz_slice);
|
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|
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|
target.close();
|
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|
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|
|
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|
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|
return true;
}
|
20c212c0
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Ziqi added functi...
|
390
|
|
a08c98c3
David Mayerich
finished document...
|
391
|
/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
|
77060b79
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started DOxygen d...
|
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393
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395
396
397
398
|
/// @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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400
|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
724ec347
David Mayerich
simplified the EN...
|
401
|
unsigned XY = X() * Y();
|
20c212c0
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Ziqi added functi...
|
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403
404
405
406
407
408
409
410
|
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;
}
|
517876d6
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metrics finished ...
|
411
|
|
a08c98c3
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finished document...
|
412
|
/// 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...
|
413
414
415
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417
|
/// @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
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Ziqi completed he...
|
418
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
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Ziqi added functi...
|
419
420
421
|
T* lp;
T* rp;
|
724ec347
David Mayerich
simplified the EN...
|
422
|
unsigned XY = X() * Y();
|
70407ea9
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Ziqi completed he...
|
423
424
425
|
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
426
|
|
70407ea9
heziqi
Ziqi completed he...
|
427
|
band(lp, lb);
|
20c212c0
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Ziqi added functi...
|
428
429
430
431
|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
432
433
|
free(lp);
free(rp);
|
20c212c0
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Ziqi added functi...
|
434
435
436
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
437
|
|
a08c98c3
David Mayerich
finished document...
|
438
|
/// 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...
|
439
440
441
442
443
444
|
/// @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...
|
445
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
446
447
448
449
450
|
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...
|
451
|
|
724ec347
David Mayerich
simplified the EN...
|
452
|
unsigned XY = X() * Y();
|
20c212c0
heziqi
Ziqi added functi...
|
453
454
455
456
457
458
|
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
|
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...
|
481
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
482
483
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
484
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
485
486
487
488
489
490
491
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
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Ziqi completed he...
|
492
493
|
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
494
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
495
|
result[j] += (rab - w[bi]) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
496
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
497
498
|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
499
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
500
|
result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
501
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
502
|
|
20c212c0
heziqi
Ziqi added functi...
|
503
504
505
506
507
508
509
510
511
512
513
|
//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
heziqi
Ziqi completed he...
|
514
|
|
517876d6
heziqi
metrics finished ...
|
515
516
517
518
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
519
520
521
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
522
|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
523
524
525
526
527
528
529
530
|
/// @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...
|
531
|
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
|
20c212c0
heziqi
Ziqi added functi...
|
532
|
|
724ec347
David Mayerich
simplified the EN...
|
533
534
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
535
536
537
538
539
|
//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...
|
540
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
541
542
543
544
545
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
546
547
548
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
549
550
551
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
552
|
/// Compute the ratio between a peak area and peak height.
|
77060b79
David Mayerich
started DOxygen d...
|
553
554
555
556
557
558
559
560
|
/// @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...
|
561
562
563
|
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...
|
564
565
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
566
567
568
569
570
|
//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...
|
571
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
572
573
574
575
576
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
577
578
579
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
580
581
582
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
583
|
/// Compute the ratio between two peak areas.
|
0722eb39
David Mayerich
further updates t...
|
584
585
586
587
588
589
590
591
592
593
|
/// @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...
|
594
595
596
|
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...
|
597
598
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
599
600
601
602
603
|
//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...
|
604
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
605
606
607
608
609
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
610
611
612
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
613
614
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
615
|
|
a08c98c3
David Mayerich
finished document...
|
616
|
/// Compute the definite integral of a baseline corrected peak.
|
0722eb39
David Mayerich
further updates t...
|
617
618
619
620
621
622
|
/// @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 ...
|
623
624
625
626
627
628
|
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...
|
629
|
unsigned XY = X() * Y();
|
517876d6
heziqi
metrics finished ...
|
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
|
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...
|
697
|
/// Compute the centroid of a baseline corrected peak.
|
0722eb39
David Mayerich
further updates t...
|
698
699
700
701
702
703
|
/// @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 ...
|
704
|
bool cpoint(double lb, double rb, double lab, double rab, T* result){
|
724ec347
David Mayerich
simplified the EN...
|
705
706
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
707
708
709
710
711
|
//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...
|
712
|
for(unsigned i = 0; i < X() * Y(); i++){
|
517876d6
heziqi
metrics finished ...
|
713
714
715
716
717
718
719
720
721
722
723
|
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...
|
724
|
/// Create a mask based on a given band and threshold value.
|
0722eb39
David Mayerich
further updates t...
|
725
726
727
728
729
730
|
/// 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...
|
731
|
bool build_mask(double mask_band, double threshold, unsigned char* p = NULL){
|
4a6f666c
heziqi
Added mask method
|
732
|
|
724ec347
David Mayerich
simplified the EN...
|
733
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
4a6f666c
heziqi
Added mask method
|
734
735
|
band(temp, mask_band);
|
724ec347
David Mayerich
simplified the EN...
|
736
|
for (unsigned int i = 0; i < X() * Y(); i++) {
|
4a6f666c
heziqi
Added mask method
|
737
738
739
740
741
742
|
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
}
|
517876d6
heziqi
metrics finished ...
|
743
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
744
745
746
|
return true;
}
|
740f8cd2
heziqi
added apply_mask
|
747
|
|
a08c98c3
David Mayerich
finished document...
|
748
|
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
|
0722eb39
David Mayerich
further updates t...
|
749
750
751
|
/// @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
|
752
753
754
755
|
bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
|
724ec347
David Mayerich
simplified the EN...
|
756
|
unsigned XY = X() * Y(); //calculate number of a band
|
740f8cd2
heziqi
added apply_mask
|
757
758
759
760
|
unsigned L = XY * sizeof(T);
T * temp = (T*)malloc(L);
|
724ec347
David Mayerich
simplified the EN...
|
761
|
for (unsigned i = 0; i < Z(); i++) //for each spectral bin
|
740f8cd2
heziqi
added apply_mask
|
762
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
763
764
|
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
|
765
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
766
767
|
if(p[j] == 0){ //if the mask is 0 at that pixel
temp[j] = 0; //set temp to zero
|
740f8cd2
heziqi
added apply_mask
|
768
769
770
771
772
|
}
else{
continue;
}
}
|
e843658b
Brad Deutsch
Previous push did...
|
773
|
target.write(reinterpret_cast<const char*>(temp), L); //write the XY slice at that band to disk
|
740f8cd2
heziqi
added apply_mask
|
774
775
776
777
778
779
|
}
target.close();
free(temp);
return true;
}
|
2fcab4f0
David Mayerich
added unsifting f...
|
780
781
|
/// Saves to disk only those spectra corresponding to mask values != 0
bool sift(std::string outfile, unsigned char* p){
|
e843658b
Brad Deutsch
Previous push did...
|
782
783
|
std::ofstream target(outfile.c_str(), std::ios::binary);
// open a band (XY plane)
|
3150c537
David Mayerich
added further pro...
|
784
785
|
unsigned long XY = X() * Y(); //Number of XY pixels
unsigned long L = XY * sizeof(T); //size of XY pixels
|
e843658b
Brad Deutsch
Previous push did...
|
786
787
788
789
|
T * temp = (T*)malloc(L); //allocate memory for a band
T * temp_vox = (T*)malloc(sizeof(T)); //allocate memory for one voxel
|
3150c537
David Mayerich
added further pro...
|
790
|
for (unsigned long i = 0; i < Z(); i++) //for each spectral bin
|
e843658b
Brad Deutsch
Previous push did...
|
791
792
|
{
band_index(temp, i); //get the specified band (XY sheet by index)
|
3150c537
David Mayerich
added further pro...
|
793
|
for (unsigned long j = 0; j < XY; j++) // for each pixel
|
e843658b
Brad Deutsch
Previous push did...
|
794
795
796
797
798
799
800
801
|
{
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;
}
|
3150c537
David Mayerich
added further pro...
|
802
803
|
thread_data = (double)(i * XY + j) / (XY * Z()) * 100;
|
e843658b
Brad Deutsch
Previous push did...
|
804
805
806
807
|
}
}
target.close();
free(temp);
|
3150c537
David Mayerich
added further pro...
|
808
809
810
|
thread_data = 100;
|
e843658b
Brad Deutsch
Previous push did...
|
811
812
813
|
return true;
}
|
2fcab4f0
David Mayerich
added unsifting f...
|
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
|
/// Generates a spectral image from a matrix of spectral values in lexicographic order and a mask
bool unsift(std::string outfile, unsigned char* p, unsigned int samples, unsigned int lines){
//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
|
3150c537
David Mayerich
added further pro...
|
829
830
831
|
unsigned long P = X(); //Number of pixels
unsigned long B = Z(); //number of bands
unsigned long XY = samples * lines; //total number of pixels in an unsifted image
|
2fcab4f0
David Mayerich
added unsifting f...
|
832
833
834
835
836
837
838
839
|
// 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
|
3150c537
David Mayerich
added further pro...
|
840
|
for(unsigned long b = 0; b < B; b++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
841
842
|
//set the unsifted index value to zero
|
3150c537
David Mayerich
added further pro...
|
843
|
unsigned long i = 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
844
845
846
847
848
|
//retrieve the sifted band (masked pixels only)
band_index(sifted, b);
//for each pixel in the final image (treat it as a 1D image)
|
3150c537
David Mayerich
added further pro...
|
849
|
for(unsigned long xi = 0; xi < XY; xi++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
850
851
852
853
854
855
|
if( p[xi] == 0 )
unsifted[xi] = 0;
else{
unsifted[xi] = sifted[i];
i++;
}
|
3150c537
David Mayerich
added further pro...
|
856
857
|
//std::cout<<xi<<"/"<<XY<<", "<<b<<"/"<<B<<std::endl;
thread_data = (double)(b * XY + xi) / (B * XY) * 100;
|
2fcab4f0
David Mayerich
added unsifting f...
|
858
|
}
|
3150c537
David Mayerich
added further pro...
|
859
|
//std::cout<<b*XY<<"/"<<B*XY<<" "<<B<<"-"<<XY<<std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
860
861
862
863
|
//write the band image to disk
target.write(reinterpret_cast<const char*>(unsifted), sizeof(T) * XY);
}
|
3150c537
David Mayerich
added further pro...
|
864
865
866
|
//std::cout<<"unsifted"<<std::endl;
thread_data = 100;
|
2fcab4f0
David Mayerich
added unsifting f...
|
867
868
869
|
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
870
|
|
a08c98c3
David Mayerich
finished document...
|
871
|
/// Calculate the mean band value (average along B) at each pixel location.
|
0722eb39
David Mayerich
further updates t...
|
872
873
|
/// @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...
|
874
|
bool band_avg(T* p){
|
724ec347
David Mayerich
simplified the EN...
|
875
|
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
876
877
878
879
|
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...
|
880
|
p[j] /= (T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
881
882
|
}
//get every band and add them all
|
724ec347
David Mayerich
simplified the EN...
|
883
|
for (unsigned i = 1; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
884
885
|
band_index(temp, i);
for (unsigned j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
886
|
p[j] += temp[j]/(T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
887
888
889
890
891
892
|
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
893
894
895
896
|
/// 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...
|
897
|
bool avg_band(T*p, unsigned char* mask){
|
724ec347
David Mayerich
simplified the EN...
|
898
|
unsigned long long XY = X() * Y();
|
a08c98c3
David Mayerich
finished document...
|
899
|
unsigned count = 0; //count will store the number of masked pixels
|
a43c4fe1
heziqi
Added crop in env...
|
900
|
T* temp = (T*)malloc(sizeof(T) * XY);
|
a08c98c3
David Mayerich
finished document...
|
901
|
//calculate this loop counts the number of true pixels in the mask
|
a43c4fe1
heziqi
Added crop in env...
|
902
903
904
905
906
|
for (unsigned j = 0; j < XY; j++){
if (mask[j] != 0){
count++;
}
}
|
724ec347
David Mayerich
simplified the EN...
|
907
|
//this loops goes through each band in B (Z())
|
a08c98c3
David Mayerich
finished document...
|
908
|
// masked (or valid) pixels from that band are averaged and the average is stored in p
|
724ec347
David Mayerich
simplified the EN...
|
909
|
for (unsigned i = 0; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
910
|
p[i] = 0;
|
a08c98c3
David Mayerich
finished document...
|
911
912
|
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...
|
913
914
915
916
917
918
919
920
921
|
if (mask[j] != 0){
p[i] += temp[j] / (T)count;
}
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
922
923
924
925
926
|
/// 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...
|
927
928
|
bool co_matrix(T* co, T* avg, unsigned char *mask){
//memory allocation
|
724ec347
David Mayerich
simplified the EN...
|
929
930
|
unsigned long long xy = X() * Y();
unsigned int B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
|
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
|
962
|
|
a43c4fe1
heziqi
Added crop in env...
|
963
|
|
a08c98c3
David Mayerich
finished document...
|
964
965
966
967
968
969
970
|
/// 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...
|
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
|
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,
unsigned long long b1){
//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...
|
987
|
T* temp = (T*)malloc(L);
|
e9bddc57
David Mayerich
added band croppi...
|
988
989
|
//create an output stream to store the output file
|
a43c4fe1
heziqi
Added crop in env...
|
990
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
e9bddc57
David Mayerich
added band croppi...
|
991
992
993
994
995
996
997
998
999
1000
1001
1002
|
//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...
|
1003
|
{
|
e9bddc57
David Mayerich
added band croppi...
|
1004
|
for (unsigned y = 0; y < lines; y++)
|
a43c4fe1
heziqi
Added crop in env...
|
1005
|
{
|
e9bddc57
David Mayerich
added band croppi...
|
1006
|
file.read((char *)(temp + y * samples), sizeof(T) * samples);
|
a43c4fe1
heziqi
Added crop in env...
|
1007
|
file.seekg(jumpl, std::ios::cur); //go to the next band
|
3150c537
David Mayerich
added further pro...
|
1008
|
|
e9bddc57
David Mayerich
added band croppi...
|
1009
|
thread_data = (double)(z * lines + y) / (Z() * lines) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1010
1011
1012
1013
1014
|
}
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
file.seekg(jumpb, std::ios::cur);
}
free(temp);
|
3150c537
David Mayerich
added further pro...
|
1015
1016
1017
|
thread_data = 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1018
1019
|
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
1020
|
|
740f8cd2
heziqi
added apply_mask
|
1021
|
|
a08c98c3
David Mayerich
finished document...
|
1022
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
1023
1024
1025
1026
|
bool close(){
file.close();
return true;
}
|
31394e2a
heziqi
Ziqi added method...
|
1027
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
1028
1029
|
};
}
|
31394e2a
heziqi
Ziqi added method...
|
1030
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1031
1032
|
#endif
|
fc712213
David Mayerich
code simplifications
|
1033
|
|