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#ifndef STIM_BIL_H
#define STIM_BIL_H
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#include "../envi/envi_header.h"
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#include "../envi/binary.h"
#include <cstring>
#include <utility>
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namespace stim{
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/**
The BIL class represents a 3-dimensional binary file stored using band interleaved by line (BIL) image encoding. The binary file is stored
such that X-Z "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 X, Z, 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 bil: public binary<T> {
protected:
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std::vector<double> w; //band wavelength
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unsigned long X(){
return R[0];
}
unsigned long Y(){
return R[2];
}
unsigned long Z(){
return R[1];
}
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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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/// 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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w = wavelengths;
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return open(filename, vec<unsigned int>(X, B, 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_1(p, page);
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unsigned int L = X() * sizeof(T); //caculate the number of bytes in a sample line
unsigned int jump = X() * (Z() - 1) * sizeof(T);
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if (page >= Z()){ //make sure the bank number is right
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std::cout<<"ERROR: page out of range"<<std::endl;
return false;
}
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file.seekg(X() * page * sizeof(T), std::ios::beg);
for (unsigned i = 0; i < Y(); i++)
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{
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file.read((char *)(p + i * X()), L);
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file.seekg( jump, std::ios::cur);
}
return true;
}
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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 int S = XY * sizeof(T); //calculate the number of bytes of a band
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(S); //memory allocation
p2=(T*)malloc(S);
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);
}
return true;
}
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/// Retrieves a band of x values from a given xz plane.
/// @param p is a pointer to pre-allocated memory at least Z * sizeof(T) in size
/// @param c is a pointer to an existing XZ plane (size X*Z*sizeof(T))
/// @param wavelength is the wavelength 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();
unsigned int L = X() * sizeof(T);
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unsigned page=0; //samples around the wavelength
T * p1;
T * p2;
//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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memcpy(p, c, L);
return true;
}
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while( w[page] < wavelength )
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{
page++;
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if (page == B) {
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memcpy(p, c + (B - 1) * X(), L);
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return true;
}
}
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if ( wavelength < w[page] )
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{
p1=(T*)malloc( L ); //memory allocation
p2=(T*)malloc( L );
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memcpy(p1, c + (page - 1) * X(), L);
memcpy(p2, c + page * X(), L);
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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];
}
}
else //if the wavelength is equal to a wavelength in header file
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memcpy(p, c + page * X(), L);
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return true;
}
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/// Retrieve a single spectrum (B-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.
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bool spectrum(T * p, unsigned x, unsigned y){
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return binary<T>::read_line_02(p, x, y);
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}
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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){
//calculate the corresponding x, y
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unsigned int x = n % X();
unsigned int y = n / X();
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//get the pixel
return spectrum(p, x, y);
}
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//given a Y ,return a XZ 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){
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
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);
}
// 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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ai = w[0];
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control=0;
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//if no baseline point is specified at band 0,
//set the baseline point at band 0 to 0
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if(wls[0] != w[0]){
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bi = wls[control];
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memset(a, (char)0, 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++){
//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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ci = w[cii];
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unsigned jump = cii * X();
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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 + jump] =(T) ( c[i + jump] - (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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}//loop for Y slice end
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free(a);
free(b);
free(c);
target.close();
return true;
}
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/// Normalize all spectra based on the value of a single band, storing the result in a new BSQ file.
/// @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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David Mayerich
allowed masking d...
|
336
|
bool normalize(std::string outname, double w, double t = 0.0)
|
c25e7d0d
heziqi
speed of bip.base...
|
337
|
{
|
724ec347
David Mayerich
simplified the EN...
|
338
339
340
|
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
|
c25e7d0d
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speed of bip.base...
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|
unsigned int S = XY * sizeof(T); //calculate the number of bytes in a band
unsigned int L = ZX * sizeof(T);
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
T * c; //pointer to the current ZX slice
T * b; //pointer to the standard band
b = (T*)malloc( S ); //memory allocation
c = (T*)malloc( L );
|
e933c14e
David Mayerich
cleaned up the code
|
353
|
band(b, w); //get the certain band into memory
|
c25e7d0d
heziqi
speed of bip.base...
|
354
|
|
724ec347
David Mayerich
simplified the EN...
|
355
|
for(unsigned j = 0; j < Y(); j++)
|
c25e7d0d
heziqi
speed of bip.base...
|
356
|
{
|
724ec347
David Mayerich
simplified the EN...
|
357
|
read_plane_y(c, j);
|
f6169dea
heziqi
Ziqi completed bi...
|
358
|
for(unsigned i = 0; i < B; i++)
|
c25e7d0d
heziqi
speed of bip.base...
|
359
|
{
|
724ec347
David Mayerich
simplified the EN...
|
360
|
for(unsigned m = 0; m < X(); m++)
|
c25e7d0d
heziqi
speed of bip.base...
|
361
|
{
|
724ec347
David Mayerich
simplified the EN...
|
362
363
|
if( b[m + j * X()] < t )
c[m + i * X()] = (T)0.0;
|
93503ec6
David Mayerich
allowed masking d...
|
364
|
else
|
724ec347
David Mayerich
simplified the EN...
|
365
|
c[m + i * X()] = c[m + i * X()] / b[m + j * X()];
|
c25e7d0d
heziqi
speed of bip.base...
|
366
367
368
369
|
}
}
target.write(reinterpret_cast<const char*>(c), L); //write normalized data into destination
}
|
c25e7d0d
heziqi
speed of bip.base...
|
370
371
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373
374
375
376
|
free(b);
free(c);
target.close();
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
377
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|
/// Convert the current BIL 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.
|
c25e7d0d
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speed of bip.base...
|
380
381
|
bool bsq(std::string outname)
{
|
724ec347
David Mayerich
simplified the EN...
|
382
|
unsigned int S = X() * Y() * sizeof(T); //calculate the number of bytes in a band
|
c25e7d0d
heziqi
speed of bip.base...
|
383
384
385
386
387
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|
std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
T * p; //pointer to the current band
p = (T*)malloc(S);
|
724ec347
David Mayerich
simplified the EN...
|
390
|
for ( unsigned i = 0; i < Z(); i++)
|
c25e7d0d
heziqi
speed of bip.base...
|
391
392
393
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|
{
band_index(p, i);
target.write(reinterpret_cast<const char*>(p), S); //write a band data into target file
}
|
6708cc25
heziqi
Ziqi added envi c...
|
395
|
|
c25e7d0d
heziqi
speed of bip.base...
|
396
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|
free(p);
target.close();
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
401
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403
|
/// Convert the current BIL file to a BIP file with the specified file name.
/// @param outname is the name of the output BIP file to be saved to disk.
|
f6169dea
heziqi
Ziqi completed bi...
|
404
405
|
bool bip(std::string outname)
{
|
724ec347
David Mayerich
simplified the EN...
|
406
|
unsigned int S = X() * Z() * sizeof(T); //calculate the number of bytes in a ZX slice
|
f6169dea
heziqi
Ziqi completed bi...
|
407
408
409
410
411
412
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414
415
|
std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
T * p; //pointer to the current XZ slice for bil file
p = (T*)malloc(S);
T * q; //pointer to the current ZX slice for bip file
q = (T*)malloc(S);
|
724ec347
David Mayerich
simplified the EN...
|
416
|
for ( unsigned i = 0; i < Y(); i++)
|
f6169dea
heziqi
Ziqi completed bi...
|
417
|
{
|
724ec347
David Mayerich
simplified the EN...
|
418
419
|
read_plane_y(p, i);
for ( unsigned k = 0; k < Z(); k++)
|
f6169dea
heziqi
Ziqi completed bi...
|
420
|
{
|
724ec347
David Mayerich
simplified the EN...
|
421
422
423
|
unsigned ks = k * X();
for ( unsigned j = 0; j < X(); j++)
q[k + j * Z()] = p[ks + j];
|
f6169dea
heziqi
Ziqi completed bi...
|
424
425
426
427
428
|
}
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
}
|
6708cc25
heziqi
Ziqi added envi c...
|
429
|
|
f6169dea
heziqi
Ziqi completed bi...
|
430
431
432
433
434
435
|
free(p);
free(q);
target.close();
return true;
}
|
20c212c0
heziqi
Ziqi added functi...
|
436
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
437
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439
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441
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444
|
/// 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.
|
20c212c0
heziqi
Ziqi added functi...
|
445
446
|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
724ec347
David Mayerich
simplified the EN...
|
447
|
unsigned XY = X() * Y();
|
20c212c0
heziqi
Ziqi added functi...
|
448
449
450
451
452
453
454
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456
|
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;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
457
458
459
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463
|
/// 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.
|
70407ea9
heziqi
Ziqi completed he...
|
464
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
465
466
467
|
T* lp;
T* rp;
|
724ec347
David Mayerich
simplified the EN...
|
468
|
unsigned XY = X() * Y();
|
70407ea9
heziqi
Ziqi completed he...
|
469
470
471
|
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
472
|
|
70407ea9
heziqi
Ziqi completed he...
|
473
|
band(lp, lb);
|
20c212c0
heziqi
Ziqi added functi...
|
474
475
476
477
|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
478
479
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
480
481
482
|
return true;
}
|
70407ea9
heziqi
Ziqi completed he...
|
483
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
484
485
486
487
488
489
490
491
|
/// 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
heziqi
Ziqi completed he...
|
492
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
493
494
495
496
497
|
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...
|
498
|
|
724ec347
David Mayerich
simplified the EN...
|
499
|
unsigned XY = X() * Y();
|
20c212c0
heziqi
Ziqi added functi...
|
500
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503
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505
|
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...
|
506
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508
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510
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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...
|
528
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
529
530
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
531
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
532
533
534
535
536
537
538
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
539
540
|
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
541
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
542
|
result[j] += (rab - w[bi]) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
543
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
544
545
|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
546
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
547
|
result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
548
|
}
|
517876d6
heziqi
metrics finished ...
|
549
|
|
20c212c0
heziqi
Ziqi added functi...
|
550
551
552
553
554
555
556
557
558
559
560
|
//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...
|
561
|
|
517876d6
heziqi
metrics finished ...
|
562
563
564
565
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
566
567
568
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
569
570
571
572
573
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575
576
577
|
/// 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
heziqi
Ziqi completed he...
|
578
579
|
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
|
724ec347
David Mayerich
simplified the EN...
|
580
581
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
582
583
584
585
586
|
//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...
|
587
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
588
589
590
591
592
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
593
594
595
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
596
597
598
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
599
600
601
602
603
604
605
606
607
|
/// 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
heziqi
Ziqi completed he...
|
608
609
610
|
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...
|
611
612
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
613
614
615
616
617
|
//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...
|
618
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
619
620
621
622
623
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
624
625
626
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
627
628
629
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
630
631
632
633
634
635
636
637
638
639
640
|
/// 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...
|
641
642
643
|
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...
|
644
645
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
646
647
648
649
650
|
//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...
|
651
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
652
653
654
655
656
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
657
658
659
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
660
661
662
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
663
664
665
666
667
668
669
|
/// 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 ...
|
670
671
672
673
674
675
|
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...
|
676
|
unsigned XY = X() * Y();
|
517876d6
heziqi
metrics finished ...
|
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
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
|
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 ...
|
744
745
746
747
748
749
750
|
/// 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 ...
|
751
|
bool cpoint(double lb, double rb, double lab, double rab, T* result){
|
724ec347
David Mayerich
simplified the EN...
|
752
753
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
754
755
756
757
758
|
//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...
|
759
|
for(unsigned i = 0; i < X() * Y(); i++){
|
517876d6
heziqi
metrics finished ...
|
760
761
762
763
764
765
766
767
768
769
770
|
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 ...
|
771
772
773
774
775
776
777
|
/// 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...
|
778
|
bool build_mask(double mask_band, double threshold, unsigned char* p){
|
4a6f666c
heziqi
Added mask method
|
779
|
|
724ec347
David Mayerich
simplified the EN...
|
780
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
4a6f666c
heziqi
Added mask method
|
781
782
|
band(temp, mask_band);
|
724ec347
David Mayerich
simplified the EN...
|
783
|
for (unsigned int i = 0; i < X() * Y(); i++) {
|
4a6f666c
heziqi
Added mask method
|
784
785
786
787
788
789
|
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
}
|
517876d6
heziqi
metrics finished ...
|
790
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
791
792
793
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
794
795
796
797
|
/// 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
|
798
799
800
801
|
bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
|
1a55a328
David Mayerich
Added comments fo...
|
802
|
//I THINK THIS IS WRONG
|
724ec347
David Mayerich
simplified the EN...
|
803
|
unsigned XZ = X() * Z(); //calculate the number of values in a page on disk
|
1a55a328
David Mayerich
Added comments fo...
|
804
|
unsigned L = XZ * sizeof(T); //calculate the size of the page (in bytes)
|
740f8cd2
heziqi
added apply_mask
|
805
|
|
1a55a328
David Mayerich
Added comments fo...
|
806
|
T * temp = (T*)malloc(L); //allocate memory for a temporary page
|
740f8cd2
heziqi
added apply_mask
|
807
|
|
724ec347
David Mayerich
simplified the EN...
|
808
|
for (unsigned i = 0; i < Y(); i++) //for each value in Y() (BIP should be X)
|
740f8cd2
heziqi
added apply_mask
|
809
|
{
|
724ec347
David Mayerich
simplified the EN...
|
810
811
|
read_plane_y(temp, i); //retrieve an ZX slice, stored in temp
for ( unsigned j = 0; j < Z(); j++) //for each Z() (Y)
|
740f8cd2
heziqi
added apply_mask
|
812
|
{
|
724ec347
David Mayerich
simplified the EN...
|
813
|
for (unsigned k = 0; k < X(); k++) //for each band
|
740f8cd2
heziqi
added apply_mask
|
814
|
{
|
724ec347
David Mayerich
simplified the EN...
|
815
816
|
if(p[i * X() + k] == 0)
temp[j * X() + k] = 0;
|
740f8cd2
heziqi
added apply_mask
|
817
818
819
820
821
822
823
824
825
826
827
|
else
continue;
}
}
target.write(reinterpret_cast<const char*>(temp), L); //write a band data into target file
}
target.close();
free(temp);
return true;
}
|
f7e99517
David Mayerich
added sifting for...
|
828
829
|
/// Saves to disk only those spectra corresponding to mask values != 0
/// Unlike the BIP and BSQ versions of this function, this version saves a different format: the BIL file is saved as a BIP
|
2fcab4f0
David Mayerich
added unsifting f...
|
830
|
bool sift(std::string outfile, unsigned char* p){
|
724ec347
David Mayerich
simplified the EN...
|
831
|
// Assume X() = X, Y() = Y, Z() = Z.
|
e843658b
Brad Deutsch
Previous push did...
|
832
833
834
|
std::ofstream target(outfile.c_str(), std::ios::binary);
//for loading pages:
|
724ec347
David Mayerich
simplified the EN...
|
835
|
unsigned XZ = X() * Z(); //calculate the number of values in an XZ page on disk
|
f7e99517
David Mayerich
added sifting for...
|
836
|
unsigned int B = Z(); //calculate the number of bands
|
e843658b
Brad Deutsch
Previous push did...
|
837
|
unsigned L = XZ * sizeof(T); //calculate the size of the page (in bytes)
|
e843658b
Brad Deutsch
Previous push did...
|
838
|
|
f7e99517
David Mayerich
added sifting for...
|
839
840
841
842
843
|
//allocate temporary memory for a XZ slice
T* slice = (T*) malloc(L);
//allocate temporary memory for a spectrum
T* spec = (T*) malloc(B * sizeof(T));
|
e843658b
Brad Deutsch
Previous push did...
|
844
|
|
f7e99517
David Mayerich
added sifting for...
|
845
846
|
//for each slice along the y axis
for (unsigned int y = 0; y < Y(); y++) //Select a page by choosing Y coordinate, Y()
|
e843658b
Brad Deutsch
Previous push did...
|
847
|
{
|
f7e99517
David Mayerich
added sifting for...
|
848
849
850
851
|
read_plane_y(slice, y); //retrieve an ZX page, store in "slice"
//for each sample along X
for (unsigned x = 0; x < X(); x++) //Select a pixel by choosing X coordinate in the page, X()
|
e843658b
Brad Deutsch
Previous push did...
|
852
|
{
|
f7e99517
David Mayerich
added sifting for...
|
853
854
|
//if the mask != 0 at that xy pixel
if (p[y * X() + x] != 0) //if the mask != 0 at that XY pixel
|
e843658b
Brad Deutsch
Previous push did...
|
855
|
{
|
f7e99517
David Mayerich
added sifting for...
|
856
857
|
//for each band at that pixel
for (unsigned int b = 0; b < B; b++) //Select a voxel by choosing Z coordinate at the pixel
|
e843658b
Brad Deutsch
Previous push did...
|
858
|
{
|
f7e99517
David Mayerich
added sifting for...
|
859
|
spec[b] = slice[b*X() + x]; //Pass the correct spectral value from XZ page into the spectrum to be saved.
|
e843658b
Brad Deutsch
Previous push did...
|
860
|
}
|
f7e99517
David Mayerich
added sifting for...
|
861
|
target.write((char*)spec, B * sizeof(T)); //write that spectrum to disk. Size is L2.
|
e843658b
Brad Deutsch
Previous push did...
|
862
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
863
864
865
|
}
}
target.close();
|
f7e99517
David Mayerich
added sifting for...
|
866
867
|
free(slice);
free(spec);
|
e843658b
Brad Deutsch
Previous push did...
|
868
869
870
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
871
872
873
|
/// Calculate the mean band value (average along B) at each pixel location.
/// @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 XZ = X() * Z();
|
a43c4fe1
heziqi
Added crop in env...
|
876
|
T* temp = (T*)malloc(sizeof(T) * XZ);
|
724ec347
David Mayerich
simplified the EN...
|
877
|
T* line = (T*)malloc(sizeof(T) * X());
|
a43c4fe1
heziqi
Added crop in env...
|
878
|
|
724ec347
David Mayerich
simplified the EN...
|
879
|
for (unsigned i = 0; i < Y(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
880
881
|
getY(temp, i);
//initialize x-line
|
724ec347
David Mayerich
simplified the EN...
|
882
|
for (unsigned j = 0; j < X(); j++){
|
a43c4fe1
heziqi
Added crop in env...
|
883
884
885
|
line[j] = 0;
}
unsigned c = 0;
|
724ec347
David Mayerich
simplified the EN...
|
886
887
888
|
for (unsigned j = 0; j < Z(); j++){
for (unsigned k = 0; k < X(); k++){
line[k] += temp[c] / (T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
889
890
891
|
c++;
}
}
|
724ec347
David Mayerich
simplified the EN...
|
892
893
|
for (unsigned j = 0; j < X(); j++){
p[j + i * X()] = line[j];
|
a43c4fe1
heziqi
Added crop in env...
|
894
895
896
897
898
899
|
}
}
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
900
901
902
903
|
/// 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...
|
904
|
bool avg_band(T*p, unsigned char* mask){
|
724ec347
David Mayerich
simplified the EN...
|
905
906
|
unsigned long long XZ = X() * Z();
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
907
|
T* temp = (T*)malloc(sizeof(T) * XZ);
|
724ec347
David Mayerich
simplified the EN...
|
908
|
for (unsigned j = 0; j < Z(); j++){
|
a43c4fe1
heziqi
Added crop in env...
|
909
910
911
912
913
914
915
916
917
|
p[j] = 0;
}
//calculate vaild number in a band
unsigned count = 0;
for (unsigned j = 0; j < XY; j++){
if (mask[j] != 0){
count++;
}
}
|
724ec347
David Mayerich
simplified the EN...
|
918
919
920
921
|
for (unsigned k = 0; k < Y(); k++){
read_plane_y(temp, k);
unsigned kx = k * X();
for (unsigned i = 0; i < X(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
922
|
if (mask[kx + i] != 0){
|
724ec347
David Mayerich
simplified the EN...
|
923
924
|
for (unsigned j = 0; j < Z(); j++){
p[j] += temp[j * X() + i] / (T)count;
|
a43c4fe1
heziqi
Added crop in env...
|
925
926
927
928
929
930
931
932
|
}
}
}
}
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
933
934
935
936
937
|
/// 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...
|
938
939
|
bool co_matrix(T* co, T* avg, unsigned char *mask){
//memory allocation
|
724ec347
David Mayerich
simplified the EN...
|
940
941
|
unsigned long long xy = X() * Y();
unsigned int B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
|
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;
}
|
0df38ff3
heziqi
fixed head detached
|
978
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
979
980
981
982
983
984
985
|
/// Crop a region of the image and save it to a new file.
/// @param outfile is the file name for the new cropped image
/// @param x0 is the lower-left x pixel coordinate to be included in the cropped image
/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
|
a43c4fe1
heziqi
Added crop in env...
|
986
987
988
989
990
|
bool crop(std::string outfile, unsigned x0, unsigned y0, unsigned x1, unsigned y1){
//calculate the new number of samples and lines
unsigned long long sam = x1 - x0; //samples
unsigned long long lin = y1 - y0; //lines
|
724ec347
David Mayerich
simplified the EN...
|
991
|
unsigned long long L = sam * Z() * sizeof(T);
|
a43c4fe1
heziqi
Added crop in env...
|
992
993
994
|
//get specified band and save
T* temp = (T*)malloc(L);
std::ofstream out(outfile.c_str(), std::ios::binary);
|
724ec347
David Mayerich
simplified the EN...
|
995
|
unsigned long long jumpb = (X() - sam) * sizeof(T); //jump pointer to the next band
|
a43c4fe1
heziqi
Added crop in env...
|
996
|
//get start
|
724ec347
David Mayerich
simplified the EN...
|
997
|
file.seekg((y0 * X() * Z() + x0) * sizeof(T), std::ios::beg);
|
a43c4fe1
heziqi
Added crop in env...
|
998
999
|
for (unsigned i = 0; i < lin; i++)
{
|
724ec347
David Mayerich
simplified the EN...
|
1000
|
for (unsigned j = 0; j < Z(); j++)
|
a43c4fe1
heziqi
Added crop in env...
|
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
|
{
file.read((char *)(temp + j * sam), sizeof(T) * sam);
file.seekg(jumpb, std::ios::cur); //go to the next band
}
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
}
free(temp);
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
1011
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1012
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
1013
1014
1015
1016
1017
|
bool close(){
file.close();
return true;
}
|
c25e7d0d
heziqi
speed of bip.base...
|
1018
|
};
|
cac62fd3
David Mayerich
modified to work ...
|
1019
|
}
|
6aa04ba2
David Mayerich
interleave types
|
1020
1021
|
#endif
|