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#ifndef STIM_BIP_H
#define STIM_BIP_H
#include "../envi/envi_header.h"
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#include "../envi/bil.h"
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#include "../envi/binary.h"
#include <cstring>
#include <utility>
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namespace stim{
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/**
The BIP class represents a 3-dimensional binary file stored using band interleaved by pixel (BIP) image encoding. The binary file is stored
such that Z-X "frames" are stored sequentially to form an image stack along the y-axis. When accessing the data sequentially on disk,
the dimensions read, from fastest to slowest, are Z, X, Y.
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 bip: public binary<T> {
protected:
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std::vector<double> w; //band wavelength
unsigned int offset; //header offset
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unsigned long X(){
return R[1];
}
unsigned long Y(){
return R[2];
}
unsigned long Z(){
return R[0];
}
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using binary<T>::thread_data;
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public:
using binary<T>::open;
using binary<T>::file;
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using binary<T>::R;
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using binary<T>::read_line_12;
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/// Open a data file for reading using the class interface.
/// @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;
//copy the offset to the structure
offset = header_offset;
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return open(filename, vec<unsigned int>(B, X, Y), header_offset);
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}
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/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
/// @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 binary<T>::read_plane_0(p, page);
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}
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/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
/// @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; //bands around the wavelength
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//get the bands numbers around the wavelength
//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 (page == Z()) {
band_index(p, Z()-1);
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return true;
}
}
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if ( wavelength < w[page] )
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{
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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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}
else //if the wavelength is equal to a wavelength in header file
{
band_index(p, page);
}
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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.
/// @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.
bool spectrum(T * p, unsigned x, unsigned y){
return read_line_12(p, x, y); //read a line in the binary YZ plane (dimension order for BIP is ZXY)
}
/// Retrieves a band of x values from a given xz plane.
/// @param p is a pointer to pre-allocated memory at least X * sizeof(T) in size
/// @param c is a pointer to an existing XZ plane (size X*Z*sizeof(T))
/// @param wavelength is the wavelength of X values to retrieve
bool read_x_from_xz(T* p, T* c, double wavelength)
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{
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unsigned int B = Z();
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unsigned page=0; //samples around the wavelength
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//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
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if ( w[page] > wavelength ){
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for(unsigned j = 0; j < X(); j++)
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{
p[j] = c[j * B];
}
return true;
}
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while( w[page] < wavelength )
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{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == B) {
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for(unsigned j = 0; j < X(); j++)
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{
p[j] = c[(j + 1) * B - 1];
}
return true;
}
}
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if ( wavelength < w[page] )
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{
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T * p1;
T * p2;
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p1=(T*)malloc( X() * sizeof(T)); //memory allocation
p2=(T*)malloc( X() * sizeof(T));
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//band_index(p1, page - 1);
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for(unsigned j = 0; j < X(); j++)
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{
p1[j] = c[j * B + page - 1];
}
//band_index(p2, page );
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for(unsigned j = 0; j < X(); j++)
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{
p2[j] = c[j * B + page];
}
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for(unsigned i=0; i < X(); 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);
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}
else //if the wavelength is equal to a wavelength in header file
{
//band_index(p, page);
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for(unsigned j = 0; j < X(); j++)
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{
p[j] = c[j * B + page];
}
}
return true;
}
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/// Retrieve a single pixel and stores it in pre-allocated memory.
/// @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;
}
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file.seekg(n * Z() * sizeof(T), std::ios::beg); //point to the certain pixel
file.read((char *)p, sizeof(T) * Z());
return true;
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}
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//given a Y ,return a ZX slice
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bool read_plane_y(T * p, unsigned y){
return binary<T>::read_plane_2(p, y);
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}
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/// Perform baseline correction given a list of baseline points and stores the result in a new BSQ file.
/// @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){
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unsigned N = wls.size(); //get the number of baseline points
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
//simplify image resolution
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unsigned int ZX = Z() * X(); //calculate the number of points in a Y slice
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unsigned int L = ZX * sizeof(T); //calculate the number of bytes of a Y slice
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unsigned int B = Z();
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T* c; //pointer to the current Y slice
c = (T*)malloc(L); //memory allocation
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T* a; //pointer to the two YZ lines surrounding the current YZ line
T* b;
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a = (T*)malloc(X() * sizeof(T));
b = (T*)malloc(X() * sizeof(T));
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double ai, bi; //stores the two baseline points wavelength surrounding the current band
double ci; //stores the current band's wavelength
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unsigned control;
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if (a == NULL || b == NULL || c == NULL){
std::cout<<"ERROR: error allocating memory";
exit(1);
}
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// loop start correct every y slice
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for (unsigned k =0; k < Y(); k++)
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{
//get the current y slice
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read_plane_y(c, k);
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//initialize lownum, highnum, low, high
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control=0;
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ai = w[0];
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//if no baseline point is specified at band 0,
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//set the baseline point at band 0 to 0
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if(wls[0] != w[0]){
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bi = wls[control];
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memset(a, (char)0, X() * sizeof(T) );
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}
//else get the low band
else{
control++;
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read_x_from_xz(a, c, ai);
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bi = wls[control];
}
//get the high band
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read_x_from_xz(b, c, bi);
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//correct every YZ line
for(unsigned cii = 0; cii < B; cii++){
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//update baseline points, if necessary
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if( w[cii] >= bi && cii != B - 1) {
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//if the high band is now on the last BL point?
if (control != N-1) {
control++; //increment the index
std::swap(a, b); //swap the baseline band pointers
ai = bi;
bi = wls[control];
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read_x_from_xz(b, c, 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
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memset(b, (char)0, X() * sizeof(T) ); //clear the high band
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ai = bi;
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bi = w[B - 1];
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}
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}
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ci = w[cii];
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//perform the baseline correction
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for(unsigned i=0; i < X(); i++)
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{
double r = (double) (ci - ai) / (double) (bi - ai);
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c[i * B + cii] =(T) ( c[i * B + cii] - (b[i] - a[i]) * r - a[i] );
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}
}//loop for YZ line end
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target.write(reinterpret_cast<const char*>(c), L); //write the corrected data into destination
|
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thread_data = (double)k / Y() * 100;
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}//loop for Y slice end
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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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}
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Doxygen comments ...
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/// Normalize all spectra based on the value of a single band, storing the result in a new BSQ file.
/// @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 ZX = Z() * X();
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
unsigned int L = ZX * sizeof(T);
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std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
|
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T * c; //pointer to the current ZX slice
T * b; //pointer to the standard band
|
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b = (T*)malloc( S ); //memory allocation
|
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c = (T*)malloc( L );
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band(b, w); //get the certain band into memory
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for(unsigned j = 0; j < Y(); j++)
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{
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read_plane_y(c, j);
unsigned jX = j * X(); //to avoid calculating it many times
for(unsigned i = 0; i < X(); i++)
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{
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unsigned iB = i * B;
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for(unsigned m = 0; m < B; m++)
{
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if( b[i+jX] < t )
c[m + iB] = (T)0.0;
else
c[m + iB] = c[m + iB] / b[i + jX]; //perform normalization
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}
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}
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target.write(reinterpret_cast<const char*>(c), L); //write normalized data into destination
|
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thread_data = (double) j / Y() * 100;
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}
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free(b);
free(c);
target.close();
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|
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|
thread_data = 100;
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return true;
}
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Doxygen comments ...
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/// Convert the current BIP file to a BSQ file with the specified file name.
/// @param outname is the name of the output BSQ file to be saved to disk.
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bool bsq(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 bip file to bil file
bil(temp);
|
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|
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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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|
std::cout<<"ERROR: unable to open input file"<<std::endl;
exit(1);
}
//then convert bil file to bsq file
n.bsq(outname);
n.close();
remove(temp.c_str());
remove(headtemp.c_str());
return true;
}
|
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Doxygen comments ...
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/// Convert the current BIP file to a BIL file with the specified file name.
/// @param outname is the name of the output BIL file to be saved to disk.
|
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bool bil(std::string outname)
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{
|
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|
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unsigned int S = X() * Z() * sizeof(T); //calculate the number of bytes in a ZX slice
|
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|
std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
|
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T * p; //pointer to the current ZX slice for bip file
|
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|
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|
p = (T*)malloc(S);
|
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T * q; //pointer to the current XZ slice for bil file
q = (T*)malloc(S);
|
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|
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|
|
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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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|
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|
read_plane_y(p, i);
for ( unsigned k = 0; k < Z(); k++)
|
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|
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{
|
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|
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|
unsigned ks = k * X();
for ( unsigned j = 0; j < X(); j++)
q[ks + j] = p[k + j * Z()];
|
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|
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|
thread_data = (double)(i * Z() + k) / (Y() * Z()) * 100;
|
f6169dea
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|
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|
}
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
|
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}
|
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David Mayerich
added support for...
|
452
|
thread_data = 100;
|
11f177d5
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Ziqi added functi...
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|
free(p);
|
f6169dea
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Ziqi completed bi...
|
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|
free(q);
|
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|
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|
target.close();
return true;
}
|
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|
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|
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David Mayerich
Doxygen comments ...
|
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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.
/// @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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David Mayerich
simplified the EN...
|
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|
unsigned XY = X() * Y();
|
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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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|
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|
|
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Doxygen comments ...
|
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|
/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
/// @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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|
487
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
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|
488
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|
T* lp;
T* rp;
|
724ec347
David Mayerich
simplified the EN...
|
491
|
unsigned XY = X() * Y();
|
70407ea9
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|
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|
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
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|
495
|
|
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|
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|
band(lp, lb);
|
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|
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|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
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metrics finished ...
|
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|
free(lp);
free(rp);
|
20c212c0
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|
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|
return true;
}
|
c359422d
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|
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|
|
a23c4132
David Mayerich
Doxygen comments ...
|
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|
/// Calculate the area under the spectrum between two specified points and stores the result in a pre-allocated array.
/// @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
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Ziqi completed he...
|
514
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
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|
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|
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...
|
520
|
|
724ec347
David Mayerich
simplified the EN...
|
521
|
unsigned XY = X() * Y();
|
20c212c0
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|
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523
524
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526
527
|
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...
|
528
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531
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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...
|
550
|
while (lab >= w[ai]){
|
20c212c0
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Ziqi added functi...
|
551
552
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
553
|
while (rab <= w[bi]){
|
20c212c0
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Ziqi added functi...
|
554
555
556
557
558
559
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|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
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Ziqi completed he...
|
561
562
|
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
563
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
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Ziqi completed he...
|
564
|
result[j] += (rab - w[bi]) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
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Ziqi added functi...
|
565
|
}
|
70407ea9
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Ziqi completed he...
|
566
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|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
20c212c0
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Ziqi added functi...
|
568
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
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Ziqi completed he...
|
569
|
result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
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Ziqi added functi...
|
570
|
}
|
517876d6
heziqi
metrics finished ...
|
571
|
|
20c212c0
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Ziqi added functi...
|
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575
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577
578
579
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581
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|
//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...
|
583
|
|
517876d6
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metrics finished ...
|
584
585
586
587
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
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Ziqi added functi...
|
588
589
590
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
591
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|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
/// @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...
|
600
601
|
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
|
724ec347
David Mayerich
simplified the EN...
|
602
603
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
604
605
606
607
608
|
//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...
|
609
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
610
611
612
613
614
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
615
616
617
|
free(p1);
free(p2);
|
70407ea9
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Ziqi completed he...
|
618
619
620
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
621
622
623
624
625
626
627
628
629
|
/// Compute the ratio between a peak area and peak height.
/// @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...
|
630
631
632
|
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...
|
633
634
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
635
636
637
638
639
|
//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...
|
640
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
641
642
643
644
645
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
646
647
648
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
649
650
651
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
652
653
654
655
656
657
658
659
660
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662
|
/// Compute the ratio between two peak areas.
/// @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...
|
663
664
665
|
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...
|
666
667
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
668
669
670
671
672
|
//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...
|
673
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
674
675
676
677
678
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
679
680
681
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
682
683
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
684
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
685
686
687
688
689
690
691
|
/// Compute the definite integral of a baseline corrected peak.
/// @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 ...
|
692
693
694
695
696
697
|
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...
|
698
|
unsigned XY = X() * Y();
|
517876d6
heziqi
metrics finished ...
|
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
|
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;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
766
767
768
769
770
771
772
|
/// Compute the centroid of a baseline corrected peak.
/// @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 ...
|
773
|
bool cpoint(double lb, double rb, double lab, double rab, T* result){
|
724ec347
David Mayerich
simplified the EN...
|
774
775
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
776
777
778
779
780
|
//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...
|
781
|
for(unsigned i = 0; i < X() * Y(); i++){
|
517876d6
heziqi
metrics finished ...
|
782
783
784
785
786
787
788
789
790
791
792
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
793
794
795
796
797
798
799
|
/// Create a mask based on a given band and threshold value.
/// 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...
|
800
|
bool build_mask(double mask_band, double threshold, unsigned char* p){
|
4a6f666c
heziqi
Added mask method
|
801
|
|
724ec347
David Mayerich
simplified the EN...
|
802
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
4a6f666c
heziqi
Added mask method
|
803
804
|
band(temp, mask_band);
|
724ec347
David Mayerich
simplified the EN...
|
805
|
for (unsigned int i = 0; i < X() * Y();i++) {
|
4a6f666c
heziqi
Added mask method
|
806
807
808
809
810
811
|
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
}
|
517876d6
heziqi
metrics finished ...
|
812
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
813
814
815
816
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
817
818
819
820
|
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
/// @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
|
821
822
823
824
|
bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
|
724ec347
David Mayerich
simplified the EN...
|
825
|
unsigned ZX = Z() * X(); //calculate the number of values in a page (XZ in BIP)
|
1a55a328
David Mayerich
Added comments fo...
|
826
|
unsigned L = ZX * sizeof(T); //calculate the number of bytes in a page
|
740f8cd2
heziqi
added apply_mask
|
827
|
|
1a55a328
David Mayerich
Added comments fo...
|
828
|
T * temp = (T*)malloc(L); //allocate space for that page
|
740f8cd2
heziqi
added apply_mask
|
829
|
|
724ec347
David Mayerich
simplified the EN...
|
830
|
for (unsigned i = 0; i < Y(); i++) //for each page (Y in BIP)
|
740f8cd2
heziqi
added apply_mask
|
831
|
{
|
724ec347
David Mayerich
simplified the EN...
|
832
833
|
read_plane_y(temp, i); //load that page (it's pointed to by temp)
for ( unsigned j = 0; j < X(); j++) //for each X value
|
740f8cd2
heziqi
added apply_mask
|
834
|
{
|
724ec347
David Mayerich
simplified the EN...
|
835
|
for (unsigned k = 0; k < Z(); k++) //for each B value (band)
|
740f8cd2
heziqi
added apply_mask
|
836
|
{
|
724ec347
David Mayerich
simplified the EN...
|
837
838
|
if (p[i * X() + j] == 0) //if the mask value is zero
temp[j * Z() + k] = 0; //set the pixel value to zero
|
1a55a328
David Mayerich
Added comments fo...
|
839
|
else //otherwise just continue
|
740f8cd2
heziqi
added apply_mask
|
840
841
842
|
continue;
}
}
|
1a55a328
David Mayerich
Added comments fo...
|
843
|
target.write(reinterpret_cast<const char*>(temp), L); //write the edited band data into target file
|
740f8cd2
heziqi
added apply_mask
|
844
|
}
|
1a55a328
David Mayerich
Added comments fo...
|
845
846
847
|
target.close(); //close the target file
free(temp); //free allocated memory
return true; //return true
|
740f8cd2
heziqi
added apply_mask
|
848
849
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
850
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
851
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
8550e94f
David Mayerich
added sifting and...
|
852
853
854
855
856
857
|
bool sift(std::string outfile, unsigned char* mask){
//reset the file pointer to the beginning of the file
file.seekg(0, std::ios::beg);
// open an output stream
|
e843658b
Brad Deutsch
Previous push did...
|
858
859
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
8550e94f
David Mayerich
added sifting and...
|
860
|
//allocate space for a single spectrum
|
3150c537
David Mayerich
added further pro...
|
861
|
unsigned long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
862
|
T* spectrum = (T*) malloc(B * sizeof(T));
|
e843658b
Brad Deutsch
Previous push did...
|
863
|
|
8550e94f
David Mayerich
added sifting and...
|
864
|
//calculate the number of pixels in a band
|
3150c537
David Mayerich
added further pro...
|
865
|
unsigned long XY = X() * Y();
|
e843658b
Brad Deutsch
Previous push did...
|
866
|
|
8550e94f
David Mayerich
added sifting and...
|
867
|
//for each pixel
|
3150c537
David Mayerich
added further pro...
|
868
869
|
unsigned long skip = 0; //number of spectra to skip
for(unsigned long x = 0; x < XY; x++){
|
8550e94f
David Mayerich
added sifting and...
|
870
871
872
873
874
|
//if the current pixel isn't masked
if( mask[x] == 0){
//increment the number of skipped pixels
skip++;
|
e843658b
Brad Deutsch
Previous push did...
|
875
|
}
|
8550e94f
David Mayerich
added sifting and...
|
876
877
878
879
880
881
882
883
884
885
886
887
888
889
|
//if the current pixel is masked
else{
//skip the intermediate pixels
file.seekg(skip * B * sizeof(T), std::ios::cur);
//set the skip value to zero
skip = 0;
//read this pixel into memory
file.read((char *)spectrum, B * sizeof(T));
//write this pixel out
target.write((char *)spectrum, B * sizeof(T));
|
3150c537
David Mayerich
added further pro...
|
890
891
|
thread_data = (double) x / XY * 100;
|
8550e94f
David Mayerich
added sifting and...
|
892
893
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
894
|
}
|
8550e94f
David Mayerich
added sifting and...
|
895
896
|
//close the output file
|
e843658b
Brad Deutsch
Previous push did...
|
897
|
target.close();
|
8550e94f
David Mayerich
added sifting and...
|
898
|
free(spectrum);
|
cbce396e
David Mayerich
added support for...
|
899
|
|
3150c537
David Mayerich
added further pro...
|
900
901
|
thread_data = 100;
|
cbce396e
David Mayerich
added support for...
|
902
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
903
904
905
906
907
908
909
910
911
912
913
|
}
bool unsift(std::string outfile, unsigned char* mask, unsigned int samples, unsigned int lines){
// open an output stream
std::ofstream target(outfile.c_str(), std::ios::binary);
//reset the file pointer to the beginning of the file
file.seekg(0, std::ios::beg);
//allocate space for a single spectrum
|
3150c537
David Mayerich
added further pro...
|
914
|
unsigned long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
915
916
917
918
919
920
921
|
T* spectrum = (T*) malloc(B * sizeof(T));
//allocate space for a spectrum of zeros
T* zeros = (T*) malloc(B * sizeof(T));
memset(zeros, 0, B * sizeof(T));
//calculate the number of pixels in a band
|
3150c537
David Mayerich
added further pro...
|
922
|
unsigned long XY = samples * lines;
|
8550e94f
David Mayerich
added sifting and...
|
923
924
|
//for each pixel
|
3150c537
David Mayerich
added further pro...
|
925
926
|
unsigned long skip = 0; //number of spectra to skip
for(unsigned long x = 0; x < XY; x++){
|
8550e94f
David Mayerich
added sifting and...
|
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
|
//if the current pixel isn't masked
if( mask[x] == 0){
//write a bunch of zeros
target.write((char *)zeros, B * sizeof(T));
}
//if the current pixel is masked
else{
//read a pixel into memory
file.read((char *)spectrum, B * sizeof(T));
//write this pixel out
target.write((char *)spectrum, B * sizeof(T));
}
|
3150c537
David Mayerich
added further pro...
|
944
945
|
thread_data = (double)x / XY * 100;
|
8550e94f
David Mayerich
added sifting and...
|
946
947
948
949
950
951
|
}
//close the output file
target.close();
free(spectrum);
|
3150c537
David Mayerich
added further pro...
|
952
953
|
thread_data = 100;
|
e843658b
Brad Deutsch
Previous push did...
|
954
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
955
956
|
|
e843658b
Brad Deutsch
Previous push did...
|
957
958
959
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
960
961
|
/// @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...
|
962
|
bool band_avg(T* p){
|
724ec347
David Mayerich
simplified the EN...
|
963
|
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
964
|
//get every pixel and calculate average value
|
724ec347
David Mayerich
simplified the EN...
|
965
|
T* temp = (T*)malloc(sizeof(T) * Z());
|
a43c4fe1
heziqi
Added crop in env...
|
966
967
968
969
970
|
T sum;
for (unsigned i = 0; i < XY; i++){
pixel(temp, i);
//calculate the sum value of every value
sum = 0; //initialize sum value
|
724ec347
David Mayerich
simplified the EN...
|
971
972
|
for (unsigned j = 0; j < Z(); j++){
sum += temp[j]/(T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
973
974
975
976
977
978
979
|
}
p[i] = sum;
}
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
980
981
982
983
|
/// 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...
|
984
|
bool avg_band(T*p, unsigned char* mask){
|
724ec347
David Mayerich
simplified the EN...
|
985
986
|
unsigned long long XY = X() * Y();
T* temp = (T*)malloc(sizeof(T) * Z());
|
a43c4fe1
heziqi
Added crop in env...
|
987
|
//Iinitialize
|
724ec347
David Mayerich
simplified the EN...
|
988
|
for (unsigned j = 0; j < Z(); j++){
|
a43c4fe1
heziqi
Added crop in env...
|
989
990
991
992
993
994
995
996
997
998
999
1000
1001
|
p[j] = 0;
}
//calculate vaild number in a band
unsigned count = 0;
for (unsigned j = 0; j < XY; j++){
if (mask[j] != 0){
count++;
}
}
//calculate average number of a band
for (unsigned i = 0; i < XY; i++){
if (mask[i] != 0){
pixel(temp, i);
|
724ec347
David Mayerich
simplified the EN...
|
1002
|
for (unsigned j = 0; j < Z(); j++){
|
a43c4fe1
heziqi
Added crop in env...
|
1003
1004
1005
1006
1007
1008
1009
|
p[j] += temp[j] / (T)count;
}
}
}
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
1010
1011
1012
1013
1014
1015
|
/// 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...
|
1016
1017
|
bool co_matrix(T* co, T* avg, unsigned char *mask){
//memory allocation
|
724ec347
David Mayerich
simplified the EN...
|
1018
1019
|
unsigned long long xy = X() * Y();
unsigned int B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
|
T* temp = (T*)malloc(sizeof(T) * B);
//count vaild pixels in a band
unsigned count = 0;
for (unsigned j = 0; j < xy; j++){
if (mask[j] != 0){
count++;
}
}
//initialize correlation matrix
for (unsigned i = 0; i < B; i++){
for (unsigned k = 0; k < B; k++){
co[i * B + k] = 0;
}
}
//calculate correlation coefficient matrix
for (unsigned j = 0; j < xy; j++){
if (mask[j] != 0){
pixel(temp, j);
for (unsigned i = 0; i < B; i++){
for (unsigned k = i; k < B; k++){
co[i * B + k] += (temp[i] - avg[i]) * (temp[k] - avg[k]) / count;
}
}
}
}
//because correlation matrix is symmetric
for (unsigned i = 0; i < B; i++){
for (unsigned k = i + 1; k < B; k++){
co[k * B + i] = co[i * B + k];
}
}
free(temp);
return true;
}
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0df38ff3
heziqi
fixed head detached
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1056
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a23c4132
David Mayerich
Doxygen comments ...
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/// 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
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e9bddc57
David Mayerich
added band croppi...
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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){
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a43c4fe1
heziqi
Added crop in env...
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1070
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3033b886
David Mayerich
implemented spect...
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//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 length of one cropped spectrum
unsigned long long L = bands * sizeof(T);
//unsigned long long L = Z() * sizeof(T);
//allocate space for the spectrum
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a43c4fe1
heziqi
Added crop in env...
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T* temp = (T*)malloc(L);
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3033b886
David Mayerich
implemented spect...
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//open an output file for binary writing
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a43c4fe1
heziqi
Added crop in env...
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1085
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std::ofstream out(outfile.c_str(), std::ios::binary);
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3033b886
David Mayerich
implemented spect...
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//seek to the first pixel in the cropped image
file.seekg( (y0 * X() * Z() + x0 * Z() + b0) * sizeof(T), std::ios::beg);
//distance between sample spectra in the same line
unsigned long long jump_sample = ( (Z() - b1) + b0 ) * sizeof(T);
//distance between sample spectra in adjacent lines
unsigned long long jump_line = (X() - x1) * Z() * sizeof(T);
//unsigned long long sp = y0 * X() + x0; //start pixel
//for each pixel in the image
for (unsigned y = 0; y < lines; y++)
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a43c4fe1
heziqi
Added crop in env...
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1101
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{
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3033b886
David Mayerich
implemented spect...
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for (unsigned x = 0; x < samples; x++)
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a43c4fe1
heziqi
Added crop in env...
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1103
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{
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3033b886
David Mayerich
implemented spect...
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//read the cropped spectral region
file.read( (char*) temp, L );
//pixel(temp, sp + x + y * X());
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a43c4fe1
heziqi
Added crop in env...
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1107
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out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
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3150c537
David Mayerich
added further pro...
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1108
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3033b886
David Mayerich
implemented spect...
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file.seekg(jump_sample, std::ios::cur);
thread_data = (double)(y * samples + x) / (lines * samples) * 100;
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a43c4fe1
heziqi
Added crop in env...
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1112
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}
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3033b886
David Mayerich
implemented spect...
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file.seekg(jump_line, std::ios::cur);
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a43c4fe1
heziqi
Added crop in env...
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1115
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}
free(temp);
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3150c537
David Mayerich
added further pro...
|
1117
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thread_data = 100;
|
a43c4fe1
heziqi
Added crop in env...
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1119
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return true;
}
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0df38ff3
heziqi
fixed head detached
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1122
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|
a23c4132
David Mayerich
Doxygen comments ...
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1123
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/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
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bool close(){
file.close();
return true;
}
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88c3e636
heziqi
Ziqi added big.h
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1129
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};
|
6aa04ba2
David Mayerich
interleave types
|
1130
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}
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e8eb202f
David Mayerich
added a new ENVI ...
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1131
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#endif
|