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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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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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/// 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++;
//if wavelength is larger than the last wavelength in header file
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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++;
//if wavelength is larger than the last wavelength in header file
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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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;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
338
339
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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.
|
93503ec6
David Mayerich
allowed masking d...
|
343
|
bool normalize(std::string outname, double w, double t = 0.0)
|
c25e7d0d
heziqi
speed of bip.base...
|
344
|
{
|
724ec347
David Mayerich
simplified the EN...
|
345
346
347
|
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
heziqi
speed of bip.base...
|
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349
350
351
352
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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
|
360
|
band(b, w); //get the certain band into memory
|
c25e7d0d
heziqi
speed of bip.base...
|
361
|
|
724ec347
David Mayerich
simplified the EN...
|
362
|
for(unsigned j = 0; j < Y(); j++)
|
c25e7d0d
heziqi
speed of bip.base...
|
363
|
{
|
724ec347
David Mayerich
simplified the EN...
|
364
|
read_plane_y(c, j);
|
f6169dea
heziqi
Ziqi completed bi...
|
365
|
for(unsigned i = 0; i < B; i++)
|
c25e7d0d
heziqi
speed of bip.base...
|
366
|
{
|
724ec347
David Mayerich
simplified the EN...
|
367
|
for(unsigned m = 0; m < X(); m++)
|
c25e7d0d
heziqi
speed of bip.base...
|
368
|
{
|
724ec347
David Mayerich
simplified the EN...
|
369
370
|
if( b[m + j * X()] < t )
c[m + i * X()] = (T)0.0;
|
93503ec6
David Mayerich
allowed masking d...
|
371
|
else
|
724ec347
David Mayerich
simplified the EN...
|
372
|
c[m + i * X()] = c[m + i * X()] / b[m + j * X()];
|
c25e7d0d
heziqi
speed of bip.base...
|
373
374
375
|
}
}
target.write(reinterpret_cast<const char*>(c), L); //write normalized data into destination
|
cbce396e
David Mayerich
added support for...
|
376
377
|
thread_data = (double)j / Y() * 100;
|
c25e7d0d
heziqi
speed of bip.base...
|
378
|
}
|
c25e7d0d
heziqi
speed of bip.base...
|
379
380
381
382
|
free(b);
free(c);
target.close();
|
cbce396e
David Mayerich
added support for...
|
383
|
thread_data = 100;
|
c25e7d0d
heziqi
speed of bip.base...
|
384
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386
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
387
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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
heziqi
speed of bip.base...
|
390
391
|
bool bsq(std::string outname)
{
|
724ec347
David Mayerich
simplified the EN...
|
392
|
unsigned int S = X() * Y() * sizeof(T); //calculate the number of bytes in a band
|
c25e7d0d
heziqi
speed of bip.base...
|
393
394
395
396
397
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399
|
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...
|
400
|
for ( unsigned i = 0; i < Z(); i++)
|
c25e7d0d
heziqi
speed of bip.base...
|
401
402
|
{
band_index(p, i);
|
cbce396e
David Mayerich
added support for...
|
403
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405
|
target.write(reinterpret_cast<const char*>(p), S); //write a band data into target file
thread_data = (double)i / Z() * 100; //store the progress for the current operation
|
c25e7d0d
heziqi
speed of bip.base...
|
406
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
407
|
|
cbce396e
David Mayerich
added support for...
|
408
409
|
thread_data = 100; //set the current progress to 100%
|
c25e7d0d
heziqi
speed of bip.base...
|
410
411
412
413
414
|
free(p);
target.close();
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
415
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417
|
/// 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...
|
418
419
|
bool bip(std::string outname)
{
|
724ec347
David Mayerich
simplified the EN...
|
420
|
unsigned int S = X() * Z() * sizeof(T); //calculate the number of bytes in a ZX slice
|
f6169dea
heziqi
Ziqi completed bi...
|
421
422
423
424
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426
427
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429
|
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...
|
430
|
for ( unsigned i = 0; i < Y(); i++)
|
f6169dea
heziqi
Ziqi completed bi...
|
431
|
{
|
724ec347
David Mayerich
simplified the EN...
|
432
433
|
read_plane_y(p, i);
for ( unsigned k = 0; k < Z(); k++)
|
f6169dea
heziqi
Ziqi completed bi...
|
434
|
{
|
724ec347
David Mayerich
simplified the EN...
|
435
436
437
|
unsigned ks = k * X();
for ( unsigned j = 0; j < X(); j++)
q[k + j * Z()] = p[ks + j];
|
cbce396e
David Mayerich
added support for...
|
438
439
|
thread_data = (double)(i * Z() + k) / (Z() * Y()) * 100; //store the progress for the current operation
|
f6169dea
heziqi
Ziqi completed bi...
|
440
441
442
443
444
|
}
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
}
|
cbce396e
David Mayerich
added support for...
|
445
446
|
thread_data = 100;
|
6708cc25
heziqi
Ziqi added envi c...
|
447
|
|
f6169dea
heziqi
Ziqi completed bi...
|
448
449
450
451
452
453
|
free(p);
free(q);
target.close();
return true;
}
|
20c212c0
heziqi
Ziqi added functi...
|
454
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
455
456
457
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459
460
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462
|
/// 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...
|
463
464
|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
724ec347
David Mayerich
simplified the EN...
|
465
|
unsigned XY = X() * Y();
|
20c212c0
heziqi
Ziqi added functi...
|
466
467
468
469
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471
472
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474
|
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 ...
|
475
476
477
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481
|
/// 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...
|
482
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
483
484
485
|
T* lp;
T* rp;
|
724ec347
David Mayerich
simplified the EN...
|
486
|
unsigned XY = X() * Y();
|
70407ea9
heziqi
Ziqi completed he...
|
487
488
489
|
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
490
|
|
70407ea9
heziqi
Ziqi completed he...
|
491
|
band(lp, lb);
|
20c212c0
heziqi
Ziqi added functi...
|
492
493
494
495
|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
496
497
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
498
499
500
|
return true;
}
|
70407ea9
heziqi
Ziqi completed he...
|
501
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
502
503
504
505
506
507
508
509
|
/// 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...
|
510
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
511
512
513
514
515
|
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...
|
516
|
|
724ec347
David Mayerich
simplified the EN...
|
517
|
unsigned XY = X() * Y();
|
20c212c0
heziqi
Ziqi added functi...
|
518
519
520
521
522
523
|
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...
|
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
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543
544
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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...
|
546
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
547
548
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
549
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
550
551
552
553
554
555
556
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
557
558
|
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
559
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
560
|
result[j] += (rab - w[bi]) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
561
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
562
563
|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
564
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
565
|
result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
566
|
}
|
517876d6
heziqi
metrics finished ...
|
567
|
|
20c212c0
heziqi
Ziqi added functi...
|
568
569
570
571
572
573
574
575
576
577
578
|
//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...
|
579
|
|
517876d6
heziqi
metrics finished ...
|
580
581
582
583
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
584
585
586
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
587
588
589
590
591
592
593
594
595
|
/// 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...
|
596
597
|
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
|
724ec347
David Mayerich
simplified the EN...
|
598
599
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
600
601
602
603
604
|
//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...
|
605
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
606
607
608
609
610
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
611
612
613
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
614
615
616
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
617
618
619
620
621
622
623
624
625
|
/// 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...
|
626
627
628
|
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...
|
629
630
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
631
632
633
634
635
|
//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...
|
636
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
637
638
639
640
641
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
642
643
644
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
645
646
647
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
648
649
650
651
652
653
654
655
656
657
658
|
/// 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...
|
659
660
661
|
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...
|
662
663
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
664
665
666
667
668
|
//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...
|
669
|
for(unsigned i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
670
671
672
673
674
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
675
676
677
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
678
679
680
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
681
682
683
684
685
686
687
|
/// 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 ...
|
688
689
690
691
692
693
|
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...
|
694
|
unsigned XY = X() * Y();
|
517876d6
heziqi
metrics finished ...
|
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
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
|
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 ...
|
762
763
764
765
766
767
768
|
/// 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 ...
|
769
|
bool cpoint(double lb, double rb, double lab, double rab, T* result){
|
724ec347
David Mayerich
simplified the EN...
|
770
771
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
772
773
774
775
776
|
//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...
|
777
|
for(unsigned i = 0; i < X() * Y(); i++){
|
517876d6
heziqi
metrics finished ...
|
778
779
780
781
782
783
784
785
786
787
788
|
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 ...
|
789
790
791
792
793
794
795
|
/// 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...
|
796
|
bool build_mask(double mask_band, double threshold, unsigned char* p){
|
4a6f666c
heziqi
Added mask method
|
797
|
|
724ec347
David Mayerich
simplified the EN...
|
798
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
4a6f666c
heziqi
Added mask method
|
799
800
|
band(temp, mask_band);
|
724ec347
David Mayerich
simplified the EN...
|
801
|
for (unsigned int i = 0; i < X() * Y(); i++) {
|
4a6f666c
heziqi
Added mask method
|
802
803
804
805
806
807
|
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
}
|
517876d6
heziqi
metrics finished ...
|
808
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
809
810
811
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
812
813
814
815
|
/// 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
|
816
817
818
819
|
bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
|
1a55a328
David Mayerich
Added comments fo...
|
820
|
//I THINK THIS IS WRONG
|
724ec347
David Mayerich
simplified the EN...
|
821
|
unsigned XZ = X() * Z(); //calculate the number of values in a page on disk
|
1a55a328
David Mayerich
Added comments fo...
|
822
|
unsigned L = XZ * sizeof(T); //calculate the size of the page (in bytes)
|
740f8cd2
heziqi
added apply_mask
|
823
|
|
1a55a328
David Mayerich
Added comments fo...
|
824
|
T * temp = (T*)malloc(L); //allocate memory for a temporary page
|
740f8cd2
heziqi
added apply_mask
|
825
|
|
724ec347
David Mayerich
simplified the EN...
|
826
|
for (unsigned i = 0; i < Y(); i++) //for each value in Y() (BIP should be X)
|
740f8cd2
heziqi
added apply_mask
|
827
|
{
|
724ec347
David Mayerich
simplified the EN...
|
828
829
|
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
|
830
|
{
|
724ec347
David Mayerich
simplified the EN...
|
831
|
for (unsigned k = 0; k < X(); k++) //for each band
|
740f8cd2
heziqi
added apply_mask
|
832
|
{
|
724ec347
David Mayerich
simplified the EN...
|
833
834
|
if(p[i * X() + k] == 0)
temp[j * X() + k] = 0;
|
740f8cd2
heziqi
added apply_mask
|
835
836
837
838
839
840
841
842
843
844
845
|
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...
|
846
847
|
/// 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...
|
848
|
bool sift(std::string outfile, unsigned char* p){
|
724ec347
David Mayerich
simplified the EN...
|
849
|
// Assume X() = X, Y() = Y, Z() = Z.
|
e843658b
Brad Deutsch
Previous push did...
|
850
851
852
|
std::ofstream target(outfile.c_str(), std::ios::binary);
//for loading pages:
|
3150c537
David Mayerich
added further pro...
|
853
854
855
|
unsigned long XZ = X() * Z(); //calculate the number of values in an XZ page on disk
unsigned long B = Z(); //calculate the number of bands
unsigned long L = XZ * sizeof(T); //calculate the size of the page (in bytes)
|
e843658b
Brad Deutsch
Previous push did...
|
856
|
|
f7e99517
David Mayerich
added sifting for...
|
857
858
859
860
861
|
//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...
|
862
|
|
f7e99517
David Mayerich
added sifting for...
|
863
|
//for each slice along the y axis
|
3150c537
David Mayerich
added further pro...
|
864
|
for (unsigned long y = 0; y < Y(); y++) //Select a page by choosing Y coordinate, Y()
|
e843658b
Brad Deutsch
Previous push did...
|
865
|
{
|
f7e99517
David Mayerich
added sifting for...
|
866
867
868
|
read_plane_y(slice, y); //retrieve an ZX page, store in "slice"
//for each sample along X
|
3150c537
David Mayerich
added further pro...
|
869
|
for (unsigned long x = 0; x < X(); x++) //Select a pixel by choosing X coordinate in the page, X()
|
e843658b
Brad Deutsch
Previous push did...
|
870
|
{
|
f7e99517
David Mayerich
added sifting for...
|
871
872
|
//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...
|
873
|
{
|
f7e99517
David Mayerich
added sifting for...
|
874
|
//for each band at that pixel
|
3150c537
David Mayerich
added further pro...
|
875
|
for (unsigned long b = 0; b < B; b++) //Select a voxel by choosing Z coordinate at the pixel
|
e843658b
Brad Deutsch
Previous push did...
|
876
|
{
|
f7e99517
David Mayerich
added sifting for...
|
877
|
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...
|
878
|
}
|
f7e99517
David Mayerich
added sifting for...
|
879
|
target.write((char*)spec, B * sizeof(T)); //write that spectrum to disk. Size is L2.
|
e843658b
Brad Deutsch
Previous push did...
|
880
|
}
|
3150c537
David Mayerich
added further pro...
|
881
882
|
thread_data = (double) (y * X() + x) / (Y() * X()) * 100;
|
e843658b
Brad Deutsch
Previous push did...
|
883
884
885
|
}
}
target.close();
|
f7e99517
David Mayerich
added sifting for...
|
886
887
|
free(slice);
free(spec);
|
3150c537
David Mayerich
added further pro...
|
888
889
|
thread_data = 100;
|
e843658b
Brad Deutsch
Previous push did...
|
890
891
892
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
893
894
895
|
/// 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...
|
896
|
bool band_avg(T* p){
|
724ec347
David Mayerich
simplified the EN...
|
897
|
unsigned long long XZ = X() * Z();
|
a43c4fe1
heziqi
Added crop in env...
|
898
|
T* temp = (T*)malloc(sizeof(T) * XZ);
|
724ec347
David Mayerich
simplified the EN...
|
899
|
T* line = (T*)malloc(sizeof(T) * X());
|
a43c4fe1
heziqi
Added crop in env...
|
900
|
|
724ec347
David Mayerich
simplified the EN...
|
901
|
for (unsigned i = 0; i < Y(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
902
903
|
getY(temp, i);
//initialize x-line
|
724ec347
David Mayerich
simplified the EN...
|
904
|
for (unsigned j = 0; j < X(); j++){
|
a43c4fe1
heziqi
Added crop in env...
|
905
906
907
|
line[j] = 0;
}
unsigned c = 0;
|
724ec347
David Mayerich
simplified the EN...
|
908
909
910
|
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...
|
911
912
913
|
c++;
}
}
|
724ec347
David Mayerich
simplified the EN...
|
914
915
|
for (unsigned j = 0; j < X(); j++){
p[j + i * X()] = line[j];
|
a43c4fe1
heziqi
Added crop in env...
|
916
917
918
919
920
921
|
}
}
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
922
923
924
925
|
/// 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...
|
926
|
bool avg_band(T*p, unsigned char* mask){
|
724ec347
David Mayerich
simplified the EN...
|
927
928
|
unsigned long long XZ = X() * Z();
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
929
|
T* temp = (T*)malloc(sizeof(T) * XZ);
|
724ec347
David Mayerich
simplified the EN...
|
930
|
for (unsigned j = 0; j < Z(); j++){
|
a43c4fe1
heziqi
Added crop in env...
|
931
932
933
934
935
936
937
938
939
|
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...
|
940
941
942
943
|
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...
|
944
|
if (mask[kx + i] != 0){
|
724ec347
David Mayerich
simplified the EN...
|
945
946
|
for (unsigned j = 0; j < Z(); j++){
p[j] += temp[j * X() + i] / (T)count;
|
a43c4fe1
heziqi
Added crop in env...
|
947
948
949
950
951
952
953
954
|
}
}
}
}
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
955
956
957
958
959
|
/// 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...
|
960
961
|
bool co_matrix(T* co, T* avg, unsigned char *mask){
//memory allocation
|
724ec347
David Mayerich
simplified the EN...
|
962
963
|
unsigned long long xy = X() * Y();
unsigned int B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
|
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
|
1000
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1001
1002
1003
1004
1005
1006
1007
|
/// Crop a region of the image and save it to a new file.
/// @param outfile is the file name for the new cropped image
/// @param x0 is the lower-left x pixel coordinate to be included in the cropped image
/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
|
e9bddc57
David Mayerich
added band croppi...
|
1008
1009
1010
1011
1012
1013
|
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){
|
a43c4fe1
heziqi
Added crop in env...
|
1014
|
|
3033b886
David Mayerich
implemented spect...
|
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
|
//calculate the new image parameters
unsigned long long samples = x1 - x0;
unsigned long long lines = y1 - y0;
unsigned long long bands = b1 - b0;
//calculate the size of a line
unsigned long long L = samples * sizeof(T);
//allocate space for a line
T* temp = (T*)malloc(bands * L);
//create an output stream to store the cropped file
|
a43c4fe1
heziqi
Added crop in env...
|
1028
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
3033b886
David Mayerich
implemented spect...
|
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
|
//calculate the distance between bands
unsigned long long jumpb = (X() - samples) * sizeof(T);
//distance needed to jump from the previous line of the last band to the next line of the first band
unsigned long long longjump = ((Z() - b1) * X() + b0 * X()) * sizeof(T);
//set the start position for the cropped region
file.seekg((y0 * X() * Z() + b0 * X() + x0) * sizeof(T), std::ios::beg);
for (unsigned x = 0; x < lines; x++)
|
a43c4fe1
heziqi
Added crop in env...
|
1040
|
{
|
3033b886
David Mayerich
implemented spect...
|
1041
|
for (unsigned z = b0; z < b1; z++)
|
a43c4fe1
heziqi
Added crop in env...
|
1042
|
{
|
3033b886
David Mayerich
implemented spect...
|
1043
|
file.read((char *)(temp + z * samples), sizeof(T) * samples);
|
a43c4fe1
heziqi
Added crop in env...
|
1044
|
file.seekg(jumpb, std::ios::cur); //go to the next band
|
3150c537
David Mayerich
added further pro...
|
1045
|
|
3033b886
David Mayerich
implemented spect...
|
1046
|
thread_data = (double)(x * Z() + z) / (lines * Z()) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1047
|
}
|
3033b886
David Mayerich
implemented spect...
|
1048
1049
1050
1051
1052
1053
|
//write slice data into target file
out.write(reinterpret_cast<const char*>(temp), bands * L);
//seek to the beginning of the next X-Z slice
file.seekg(longjump, std::ios::cur);
|
a43c4fe1
heziqi
Added crop in env...
|
1054
|
}
|
3033b886
David Mayerich
implemented spect...
|
1055
1056
|
//free the temporary frame
|
a43c4fe1
heziqi
Added crop in env...
|
1057
|
free(temp);
|
3150c537
David Mayerich
added further pro...
|
1058
1059
1060
|
thread_data = 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1061
1062
1063
|
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
1064
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1065
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
1066
1067
1068
1069
1070
|
bool close(){
file.close();
return true;
}
|
c25e7d0d
heziqi
speed of bip.base...
|
1071
|
};
|
cac62fd3
David Mayerich
modified to work ...
|
1072
|
}
|
6aa04ba2
David Mayerich
interleave types
|
1073
1074
|
#endif
|