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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/hsi.h"
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#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>
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class bil: public hsi<T> {
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protected:
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//std::vector<double> w; //band wavelengths
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/*unsigned long long X(){
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return R[0];
}
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unsigned long long Y(){
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return R[2];
}
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unsigned long long Z(){
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return R[1];
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}*/
using hsi<T>::w; //use the wavelength array in stim::hsi
using hsi<T>::nnz;
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using binary<T>::progress;
/// Call the binary nnz() function for the BIL orientation
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//unsigned long long nnz(unsigned char* mask){
// return binary<T>::nnz(mask, X()*Y());
//}
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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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bil(){ hsi<T>::init_bil(); }
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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 long long X,
unsigned long long Y,
unsigned long long B,
unsigned long long header_offset,
std::vector<double> wavelengths){
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w = wavelengths;
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return open(filename, vec<unsigned long long>(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 long long page, bool PROGRESS = false){
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//return binary<T>::read_plane_1(p, page);
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if(PROGRESS) progress = 0;
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unsigned long long L = X() * sizeof(T); //caculate the number of bytes in a sample line
unsigned long long 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);
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for (unsigned long long 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);
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if(PROGRESS) progress = (double)(i+1) / Y() * 100;
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}
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, bool PROGRESS = false){
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//if there are no wavelengths in the BSQ file
if(w.size() == 0)
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return band_index(p, (unsigned long long)wavelength);
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unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned long long S = XY * sizeof(T); //calculate the number of bytes of a band
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unsigned long long 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, PROGRESS);
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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);
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band_index(p2, page, PROGRESS);
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for(unsigned long long i=0; i < XY; i++){
double r = (wavelength - w[page-1]) / (w[page] - w[page-1]);
p[i] = (T)(((double)p2[i] - (double)p1[i]) * r + (double)p1[i]);
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}
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free(p1);
free(p2);
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}
else //if the wavelength is equal to a wavelength in header file
{
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band_index(p, page, PROGRESS);
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}
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 long long B = Z();
unsigned long long L = X() * sizeof(T);
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unsigned long long page=0; //samples around the wavelength
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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 long long 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] = (T)(((double)p2[i] - (double)p1[i]) * r + (double)p1[i]);
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}
}
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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 long long x, unsigned long long y, bool PROGRESS = false){
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return binary<T>::read_line_1(p, x, y, PROGRESS);
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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 long long n){
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//calculate the corresponding x, y
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unsigned long long x = n % X();
unsigned long long 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 long long y){
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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 char* mask = NULL, bool PROGRESS = false){
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unsigned long long N = wls.size(); //get the number of baseline points
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std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
//simplify image resolution
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unsigned long long ZX = Z() * X(); //calculate the number of points in a Y slice
unsigned long long L = ZX * sizeof(T); //calculate the number of bytes of a Y slice
unsigned long long 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 long long 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 long long 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
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for(unsigned long long cii = 0; cii < B; cii++){
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299
300
|
//update baseline points, if necessary
|
6708cc25
heziqi
Ziqi added envi c...
|
301
|
if( w[cii] >= bi && cii != B - 1) {
|
c25e7d0d
heziqi
speed of bip.base...
|
302
303
304
305
306
307
308
309
310
|
//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];
|
724ec347
David Mayerich
simplified the EN...
|
311
|
read_x_from_xz(b, c, bi);
|
c25e7d0d
heziqi
speed of bip.base...
|
312
313
314
|
}
//if the last BL point on the last band of the file?
|
6708cc25
heziqi
Ziqi added envi c...
|
315
|
else if ( wls[control] < w[B - 1]) {
|
c25e7d0d
heziqi
speed of bip.base...
|
316
317
318
|
std::swap(a, b); //swap the baseline band pointers
|
724ec347
David Mayerich
simplified the EN...
|
319
|
memset(b, (char)0, X() * sizeof(T) ); //clear the high band
|
c25e7d0d
heziqi
speed of bip.base...
|
320
321
|
ai = bi;
|
6708cc25
heziqi
Ziqi added envi c...
|
322
|
bi = w[B - 1];
|
c25e7d0d
heziqi
speed of bip.base...
|
323
324
|
}
}
|
c25e7d0d
heziqi
speed of bip.base...
|
325
|
|
6708cc25
heziqi
Ziqi added envi c...
|
326
|
ci = w[cii];
|
c25e7d0d
heziqi
speed of bip.base...
|
327
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
328
|
unsigned long long jump = cii * X();
|
c25e7d0d
heziqi
speed of bip.base...
|
329
|
//perform the baseline correction
|
724ec347
David Mayerich
simplified the EN...
|
330
|
for(unsigned i=0; i < X(); i++)
|
c25e7d0d
heziqi
speed of bip.base...
|
331
332
|
{
double r = (double) (ci - ai) / (double) (bi - ai);
|
92e4cf05
heziqi
include file fixed
|
333
|
c[i + jump] =(T) ( c[i + jump] - (b[i] - a[i]) * r - a[i] );
|
c25e7d0d
heziqi
speed of bip.base...
|
334
335
336
|
}
}//loop for YZ line end
|
c25e7d0d
heziqi
speed of bip.base...
|
337
|
target.write(reinterpret_cast<const char*>(c), L); //write the corrected data into destination
|
cbce396e
David Mayerich
added support for...
|
338
|
|
63fc1df8
David Mayerich
added an inverse ...
|
339
|
if(PROGRESS) progress = (double)(k+1) / Y() * 100;
|
6708cc25
heziqi
Ziqi added envi c...
|
340
|
}//loop for Y slice end
|
c25e7d0d
heziqi
speed of bip.base...
|
341
342
343
344
345
|
free(a);
free(b);
free(c);
target.close();
|
cbce396e
David Mayerich
added support for...
|
346
|
|
c25e7d0d
heziqi
speed of bip.base...
|
347
348
349
350
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
351
352
353
354
355
|
/// 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.
|
c30dd3e6
David Mayerich
added vector norm...
|
356
|
bool ratio(std::string outname, double w, unsigned char* mask = NULL, bool PROGRESS = false)
|
c25e7d0d
heziqi
speed of bip.base...
|
357
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
358
359
360
361
362
|
unsigned long long B = Z(); //calculate the number of bands
unsigned long long ZX = Z() * X();
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned long long S = XY * sizeof(T); //calculate the number of bytes in a band
unsigned long long L = ZX * sizeof(T);
|
c25e7d0d
heziqi
speed of bip.base...
|
363
364
365
366
367
368
369
370
371
372
|
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
|
373
|
band(b, w); //get the certain band into memory
|
c25e7d0d
heziqi
speed of bip.base...
|
374
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
375
|
for(unsigned long long j = 0; j < Y(); j++)
|
c25e7d0d
heziqi
speed of bip.base...
|
376
|
{
|
724ec347
David Mayerich
simplified the EN...
|
377
|
read_plane_y(c, j);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
378
|
for(unsigned long long i = 0; i < B; i++)
|
c25e7d0d
heziqi
speed of bip.base...
|
379
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
380
|
for(unsigned long long m = 0; m < X(); m++)
|
c25e7d0d
heziqi
speed of bip.base...
|
381
|
{
|
798cea97
David Mayerich
added progress ba...
|
382
|
if( mask != NULL && !mask[m + j * X()] )
|
724ec347
David Mayerich
simplified the EN...
|
383
|
c[m + i * X()] = (T)0.0;
|
93503ec6
David Mayerich
allowed masking d...
|
384
|
else
|
724ec347
David Mayerich
simplified the EN...
|
385
|
c[m + i * X()] = c[m + i * X()] / b[m + j * X()];
|
c25e7d0d
heziqi
speed of bip.base...
|
386
387
388
|
}
}
target.write(reinterpret_cast<const char*>(c), L); //write normalized data into destination
|
cbce396e
David Mayerich
added support for...
|
389
|
|
63fc1df8
David Mayerich
added an inverse ...
|
390
|
if(PROGRESS) progress = (double)(j+1) / Y() * 100;
|
c25e7d0d
heziqi
speed of bip.base...
|
391
|
}
|
c25e7d0d
heziqi
speed of bip.base...
|
392
393
394
395
|
free(b);
free(c);
target.close();
|
c25e7d0d
heziqi
speed of bip.base...
|
396
397
|
return true;
}
|
c30dd3e6
David Mayerich
added vector norm...
|
398
399
|
void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){}
|
c25e7d0d
heziqi
speed of bip.base...
|
400
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
401
402
403
|
/// 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.
|
63fc1df8
David Mayerich
added an inverse ...
|
404
|
bool bsq(std::string outname, bool PROGRESS = false)
|
c25e7d0d
heziqi
speed of bip.base...
|
405
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
406
|
unsigned long long S = X() * Y() * sizeof(T); //calculate the number of bytes in a band
|
c25e7d0d
heziqi
speed of bip.base...
|
407
408
409
410
411
412
413
|
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);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
414
|
for ( unsigned long long i = 0; i < Z(); i++)
|
c25e7d0d
heziqi
speed of bip.base...
|
415
416
|
{
band_index(p, i);
|
cbce396e
David Mayerich
added support for...
|
417
418
|
target.write(reinterpret_cast<const char*>(p), S); //write a band data into target file
|
63fc1df8
David Mayerich
added an inverse ...
|
419
|
if(PROGRESS) progress = (double)(i+1) / Z() * 100; //store the progress for the current operation
|
c25e7d0d
heziqi
speed of bip.base...
|
420
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
421
|
|
c25e7d0d
heziqi
speed of bip.base...
|
422
423
424
425
426
|
free(p);
target.close();
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
427
428
429
|
/// 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.
|
63fc1df8
David Mayerich
added an inverse ...
|
430
|
bool bip(std::string outname, bool PROGRESS = false)
|
f6169dea
heziqi
Ziqi completed bi...
|
431
|
{
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
432
|
unsigned long long S = X() * Z() * sizeof(T); //calculate the number of bytes in a ZX slice
|
f6169dea
heziqi
Ziqi completed bi...
|
433
434
435
436
437
438
439
440
441
|
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);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
442
|
for ( unsigned long long i = 0; i < Y(); i++)
|
f6169dea
heziqi
Ziqi completed bi...
|
443
|
{
|
724ec347
David Mayerich
simplified the EN...
|
444
|
read_plane_y(p, i);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
445
|
for ( unsigned long long k = 0; k < Z(); k++)
|
f6169dea
heziqi
Ziqi completed bi...
|
446
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
447
448
|
unsigned long long ks = k * X();
for ( unsigned long long j = 0; j < X(); j++)
|
724ec347
David Mayerich
simplified the EN...
|
449
|
q[k + j * Z()] = p[ks + j];
|
cbce396e
David Mayerich
added support for...
|
450
|
|
63fc1df8
David Mayerich
added an inverse ...
|
451
|
if(PROGRESS) progress = (double)((i+1) * Z() + k+1) / (Z() * Y()) * 100; //store the progress for the current operation
|
f6169dea
heziqi
Ziqi completed bi...
|
452
453
454
455
456
|
}
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
}
|
f6169dea
heziqi
Ziqi completed bi...
|
457
458
459
460
461
462
|
free(p);
free(q);
target.close();
return true;
}
|
20c212c0
heziqi
Ziqi added functi...
|
463
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
464
465
466
467
468
469
470
471
|
/// 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...
|
472
473
|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
474
|
unsigned long long XY = X() * Y();
|
20c212c0
heziqi
Ziqi added functi...
|
475
476
477
478
|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
479
|
for(unsigned long long i=0; i < XY; i++){
|
20c212c0
heziqi
Ziqi added functi...
|
480
481
482
483
|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
484
485
486
487
488
489
490
|
/// 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...
|
491
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
492
493
494
|
T* lp;
T* rp;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
495
496
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
70407ea9
heziqi
Ziqi completed he...
|
497
498
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
499
|
|
70407ea9
heziqi
Ziqi completed he...
|
500
|
band(lp, lb);
|
20c212c0
heziqi
Ziqi added functi...
|
501
502
503
504
|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
505
506
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
507
508
509
|
return true;
}
|
70407ea9
heziqi
Ziqi completed he...
|
510
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
511
512
513
514
515
516
517
518
|
/// 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...
|
519
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
520
521
522
523
524
|
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...
|
525
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
526
527
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
20c212c0
heziqi
Ziqi added functi...
|
528
529
530
531
532
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
533
534
535
536
|
memset(result, (char)0, S);
//find the wavelenght position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
537
538
539
|
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long bi = n - 1; //right bound position
|
20c212c0
heziqi
Ziqi added functi...
|
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
|
//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...
|
555
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
556
557
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
558
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
559
560
561
562
563
564
565
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
566
567
|
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
568
569
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((rab - w[bi]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
570
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
571
572
|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
573
574
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
575
|
}
|
517876d6
heziqi
metrics finished ...
|
576
|
|
20c212c0
heziqi
Ziqi added functi...
|
577
578
|
//calculate the area
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
579
|
for(unsigned long long i = ai; i <= bi ;i++)
|
20c212c0
heziqi
Ziqi added functi...
|
580
581
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
582
|
for(unsigned long long j = 0; j < XY; j++)
|
20c212c0
heziqi
Ziqi added functi...
|
583
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
584
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
585
586
587
|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
588
|
|
517876d6
heziqi
metrics finished ...
|
589
590
591
592
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
593
594
595
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
596
597
598
599
600
601
602
603
604
|
/// 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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
605
|
bool ph_to_ph(T* result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask = NULL){
|
70407ea9
heziqi
Ziqi completed he...
|
606
|
|
724ec347
David Mayerich
simplified the EN...
|
607
608
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
609
610
611
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613
|
//get the two peak band
height(lb1, rb1, pos1, p1);
height(lb2, rb2, pos2, p2);
//calculate the ratio in result
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
614
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
615
616
617
618
619
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
620
621
622
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
623
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625
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
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|
/// 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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
635
636
|
bool pa_to_ph(T* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, unsigned char* mask = NULL){
|
70407ea9
heziqi
Ziqi completed he...
|
637
|
|
724ec347
David Mayerich
simplified the EN...
|
638
639
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
640
641
642
643
644
|
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
height(lb2, rb2, pos, p2);
//calculate the ratio in result
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
645
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
646
647
648
649
650
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
651
652
653
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
654
655
656
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
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|
/// 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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
668
669
|
bool pa_to_pa(T* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, unsigned char* mask = NULL){
|
70407ea9
heziqi
Ziqi completed he...
|
670
|
|
724ec347
David Mayerich
simplified the EN...
|
671
672
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
673
674
675
676
677
|
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
area(lb2, rb2, lab2, rab2, p2);
//calculate the ratio in result
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
678
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
679
680
681
682
683
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
684
685
686
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
687
688
689
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
690
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692
693
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696
|
/// 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 ...
|
697
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700
701
702
|
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
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
703
704
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
705
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709
710
711
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713
|
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
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
714
715
716
|
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long bi = n - 1; //right bound position
|
517876d6
heziqi
metrics finished ...
|
717
718
719
720
721
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723
724
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729
730
731
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733
734
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736
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738
739
740
741
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|
//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);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
743
744
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((rab - w[bi]) * (rab + w[bi]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
745
746
747
|
}
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
748
749
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
750
751
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|
}
//calculate f(x) times x
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
754
|
for(unsigned long long i = ai; i <= bi ;i++)
|
517876d6
heziqi
metrics finished ...
|
755
756
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
757
|
for(unsigned long long j = 0; j < XY; j++)
|
517876d6
heziqi
metrics finished ...
|
758
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
759
|
result[j] += (T)((w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
760
761
762
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764
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768
769
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|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
771
772
773
774
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|
/// 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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
778
|
bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
|
724ec347
David Mayerich
simplified the EN...
|
779
780
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
781
782
783
784
785
|
//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
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
786
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
787
|
if(mask == NULL || mask[i])
|
517876d6
heziqi
metrics finished ...
|
788
789
790
791
792
793
794
795
|
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
796
797
798
799
800
801
802
|
/// 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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
803
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
|
4a6f666c
heziqi
Added mask method
|
804
|
|
724ec347
David Mayerich
simplified the EN...
|
805
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
798cea97
David Mayerich
added progress ba...
|
806
|
band(temp, mask_band, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
807
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
808
|
for (unsigned long long i = 0; i < X() * Y(); i++) {
|
798cea97
David Mayerich
added progress ba...
|
809
|
if (temp[i] < threshold)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
810
|
mask[i] = 0;
|
798cea97
David Mayerich
added progress ba...
|
811
|
else
|
ba51ae6a
David Mayerich
fixed metric calc...
|
812
|
mask[i] = 255;
|
4a6f666c
heziqi
Added mask method
|
813
814
|
}
|
517876d6
heziqi
metrics finished ...
|
815
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
816
817
818
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
819
820
821
822
|
/// 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.
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
823
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
824
825
826
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
1a55a328
David Mayerich
Added comments fo...
|
827
|
//I THINK THIS IS WRONG
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
828
829
|
unsigned long long XZ = X() * Z(); //calculate the number of values in a page on disk
unsigned long long L = XZ * sizeof(T); //calculate the size of the page (in bytes)
|
740f8cd2
heziqi
added apply_mask
|
830
|
|
1a55a328
David Mayerich
Added comments fo...
|
831
|
T * temp = (T*)malloc(L); //allocate memory for a temporary page
|
740f8cd2
heziqi
added apply_mask
|
832
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
833
|
for (unsigned long long i = 0; i < Y(); i++) //for each value in Y() (BIP should be X)
|
740f8cd2
heziqi
added apply_mask
|
834
|
{
|
724ec347
David Mayerich
simplified the EN...
|
835
|
read_plane_y(temp, i); //retrieve an ZX slice, stored in temp
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
836
|
for ( unsigned long long j = 0; j < Z(); j++) //for each Z() (Y)
|
740f8cd2
heziqi
added apply_mask
|
837
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
838
|
for (unsigned long long k = 0; k < X(); k++) //for each band
|
740f8cd2
heziqi
added apply_mask
|
839
|
{
|
724ec347
David Mayerich
simplified the EN...
|
840
841
|
if(p[i * X() + k] == 0)
temp[j * X() + k] = 0;
|
740f8cd2
heziqi
added apply_mask
|
842
843
844
845
846
|
else
continue;
}
}
target.write(reinterpret_cast<const char*>(temp), L); //write a band data into target file
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
847
|
if(PROGRESS) progress = (double)(i+1) / (double)Y() * 100;
|
740f8cd2
heziqi
added apply_mask
|
848
849
850
851
852
853
|
}
target.close();
free(temp);
return true;
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
|
/// Copies all spectra corresponding to nonzero values of a mask into a pre-allocated matrix of size (B x P)
/// where P is the number of masked pixels and B is the number of bands. The allocated memory can be accessed
/// using the following indexing: i = p*B + b
/// @param matrix is the destination for the pixel data
/// @param mask is the mask
bool sift(T* matrix, unsigned char* mask){
size_t Lbytes = sizeof(T) * X();
T* line = (T*) malloc( Lbytes ); //allocate space for a line
file.seekg(0, std::ios::beg); //seek to the beginning of the file
size_t pl;
size_t p = 0; //create counter variables
for(size_t y = 0; y < Y(); y++){ //for each line in the data set
for(size_t b = 0; b < Z(); b++){ //for each band in the data set
pl = 0; //initialize the pixel offset for the current line to zero (0)
file.read( (char*)line, Lbytes ); //read the current line
for(size_t x = 0; x < X(); x++){
if(mask[y * X() + x]){ //if the current pixel is masked
size_t i = (p + pl) * Z() + b; //calculate the index in the sifted matrix
matrix[i] = line[x]; //store the current value in the line at the correct matrix location
pl++; //increment the pixel pointer
}
}
}
p += pl; //add the line increment to the running pixel index
}
return true;
}
|
f7e99517
David Mayerich
added sifting for...
|
884
885
|
/// 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
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
886
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
887
|
// Assume X() = X, Y() = Y, Z() = Z.
|
e843658b
Brad Deutsch
Previous push did...
|
888
889
890
|
std::ofstream target(outfile.c_str(), std::ios::binary);
//for loading pages:
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
891
892
893
|
unsigned long long XZ = X() * Z(); //calculate the number of values in an XZ page on disk
unsigned long long B = Z(); //calculate the number of bands
unsigned long long L = XZ * sizeof(T); //calculate the size of the page (in bytes)
|
e843658b
Brad Deutsch
Previous push did...
|
894
|
|
f7e99517
David Mayerich
added sifting for...
|
895
896
897
898
899
|
//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...
|
900
|
|
f7e99517
David Mayerich
added sifting for...
|
901
|
//for each slice along the y axis
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
902
|
for (unsigned long long y = 0; y < Y(); y++) //Select a page by choosing Y coordinate, Y()
|
e843658b
Brad Deutsch
Previous push did...
|
903
|
{
|
f7e99517
David Mayerich
added sifting for...
|
904
905
906
|
read_plane_y(slice, y); //retrieve an ZX page, store in "slice"
//for each sample along X
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
907
|
for (unsigned long long x = 0; x < X(); x++) //Select a pixel by choosing X coordinate in the page, X()
|
e843658b
Brad Deutsch
Previous push did...
|
908
|
{
|
f7e99517
David Mayerich
added sifting for...
|
909
910
|
//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...
|
911
|
{
|
f7e99517
David Mayerich
added sifting for...
|
912
|
//for each band at that pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
913
|
for (unsigned long long b = 0; b < B; b++) //Select a voxel by choosing Z coordinate at the pixel
|
e843658b
Brad Deutsch
Previous push did...
|
914
|
{
|
f7e99517
David Mayerich
added sifting for...
|
915
|
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...
|
916
|
}
|
f7e99517
David Mayerich
added sifting for...
|
917
|
target.write((char*)spec, B * sizeof(T)); //write that spectrum to disk. Size is L2.
|
e843658b
Brad Deutsch
Previous push did...
|
918
|
}
|
3150c537
David Mayerich
added further pro...
|
919
|
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
920
|
if(PROGRESS) progress = (double) ((y+1) * X() + x+1) / (Y() * X()) * 100;
|
e843658b
Brad Deutsch
Previous push did...
|
921
922
923
|
}
}
target.close();
|
f7e99517
David Mayerich
added sifting for...
|
924
925
|
free(slice);
free(spec);
|
3150c537
David Mayerich
added further pro...
|
926
|
|
e843658b
Brad Deutsch
Previous push did...
|
927
928
929
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
930
931
932
|
/// 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...
|
933
|
bool band_avg(T* p){
|
724ec347
David Mayerich
simplified the EN...
|
934
|
unsigned long long XZ = X() * Z();
|
a43c4fe1
heziqi
Added crop in env...
|
935
|
T* temp = (T*)malloc(sizeof(T) * XZ);
|
724ec347
David Mayerich
simplified the EN...
|
936
|
T* line = (T*)malloc(sizeof(T) * X());
|
a43c4fe1
heziqi
Added crop in env...
|
937
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
938
|
for (unsigned long long i = 0; i < Y(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
939
940
|
getY(temp, i);
//initialize x-line
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
941
|
for (unsigned long long j = 0; j < X(); j++){
|
a43c4fe1
heziqi
Added crop in env...
|
942
943
|
line[j] = 0;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
944
945
946
|
unsigned long long c = 0;
for (unsigned long long j = 0; j < Z(); j++){
for (unsigned long long k = 0; k < X(); k++){
|
724ec347
David Mayerich
simplified the EN...
|
947
|
line[k] += temp[c] / (T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
948
949
950
|
c++;
}
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
951
|
for (unsigned long long j = 0; j < X(); j++){
|
724ec347
David Mayerich
simplified the EN...
|
952
|
p[j + i * X()] = line[j];
|
a43c4fe1
heziqi
Added crop in env...
|
953
954
955
956
957
958
|
}
}
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
959
960
961
962
|
/// 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
|
63fc1df8
David Mayerich
added an inverse ...
|
963
|
bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
964
965
|
unsigned long long XZ = X() * Z();
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
966
|
T* temp = (T*)malloc(sizeof(T) * XZ);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
967
|
for (unsigned long long j = 0; j < Z(); j++){
|
a43c4fe1
heziqi
Added crop in env...
|
968
969
970
|
p[j] = 0;
}
//calculate vaild number in a band
|
2aa68315
David Mayerich
major bug fixes f...
|
971
972
973
|
unsigned long long count = 0;
for (unsigned long long j = 0; j < XY; j++){
if (mask == NULL || mask[j] != 0){
|
a43c4fe1
heziqi
Added crop in env...
|
974
975
976
|
count++;
}
}
|
2aa68315
David Mayerich
major bug fixes f...
|
977
|
for (unsigned long long k = 0; k < Y(); k++){
|
724ec347
David Mayerich
simplified the EN...
|
978
|
read_plane_y(temp, k);
|
2aa68315
David Mayerich
major bug fixes f...
|
979
980
981
982
983
|
unsigned long long kx = k * X();
for (unsigned long long i = 0; i < X(); i++){
if (mask == NULL || mask[kx + i] != 0){
for (unsigned long long j = 0; j < Z(); j++){
p[j] += temp[j * X() + i] / (double)count;
|
a43c4fe1
heziqi
Added crop in env...
|
984
985
986
|
}
}
}
|
63fc1df8
David Mayerich
added an inverse ...
|
987
|
if(PROGRESS) progress = (double)(k+1) / Y() * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
988
989
990
991
992
|
}
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
993
994
995
996
997
|
/// 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
|
63fc1df8
David Mayerich
added an inverse ...
|
998
999
|
bool co_matrix(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
progress = 0;
|
a43c4fe1
heziqi
Added crop in env...
|
1000
|
//memory allocation
|
724ec347
David Mayerich
simplified the EN...
|
1001
|
unsigned long long xy = X() * Y();
|
2aa68315
David Mayerich
major bug fixes f...
|
1002
|
unsigned long long B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
1003
1004
|
T* temp = (T*)malloc(sizeof(T) * B);
//count vaild pixels in a band
|
2aa68315
David Mayerich
major bug fixes f...
|
1005
1006
1007
|
unsigned long long count = 0;
for (unsigned long long j = 0; j < xy; j++){
if (mask == NULL || mask[j] != 0){
|
a43c4fe1
heziqi
Added crop in env...
|
1008
1009
1010
1011
|
count++;
}
}
//initialize correlation matrix
|
2aa68315
David Mayerich
major bug fixes f...
|
1012
1013
|
for (unsigned long long i = 0; i < B; i++){
for (unsigned long long k = 0; k < B; k++){
|
a43c4fe1
heziqi
Added crop in env...
|
1014
1015
1016
1017
|
co[i * B + k] = 0;
}
}
//calculate correlation coefficient matrix
|
2aa68315
David Mayerich
major bug fixes f...
|
1018
1019
|
for (unsigned long long j = 0; j < xy; j++){
if (mask == NULL || mask[j] != 0){
|
a43c4fe1
heziqi
Added crop in env...
|
1020
|
pixel(temp, j);
|
2aa68315
David Mayerich
major bug fixes f...
|
1021
1022
1023
|
for (unsigned long long i = 0; i < B; i++){
for (unsigned long long k = i; k < B; k++){
co[i * B + k] += ((double)temp[i] - (double)avg[i]) * ((double)temp[k] - (double)avg[k]) / (double)count;
|
a43c4fe1
heziqi
Added crop in env...
|
1024
1025
1026
|
}
}
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1027
|
if(PROGRESS) progress = (double)(j+1) / xy * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1028
1029
|
}
//because correlation matrix is symmetric
|
2aa68315
David Mayerich
major bug fixes f...
|
1030
1031
|
for (unsigned long long i = 0; i < B; i++){
for (unsigned long long k = i + 1; k < B; k++){
|
a43c4fe1
heziqi
Added crop in env...
|
1032
1033
1034
1035
1036
|
co[k * B + i] = co[i * B + k];
}
}
free(temp);
|
a43c4fe1
heziqi
Added crop in env...
|
1037
1038
1039
|
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
1040
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1041
1042
1043
1044
1045
1046
1047
|
/// 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...
|
1048
1049
1050
1051
1052
|
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,
|
63fc1df8
David Mayerich
added an inverse ...
|
1053
1054
|
unsigned long long b1,
bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1055
|
|
3033b886
David Mayerich
implemented spect...
|
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
|
//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...
|
1069
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
3033b886
David Mayerich
implemented spect...
|
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
|
//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);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1080
|
for (unsigned long long x = 0; x < lines; x++)
|
a43c4fe1
heziqi
Added crop in env...
|
1081
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1082
|
for (unsigned long long z = b0; z < b1; z++)
|
a43c4fe1
heziqi
Added crop in env...
|
1083
|
{
|
3033b886
David Mayerich
implemented spect...
|
1084
|
file.read((char *)(temp + z * samples), sizeof(T) * samples);
|
a43c4fe1
heziqi
Added crop in env...
|
1085
|
file.seekg(jumpb, std::ios::cur); //go to the next band
|
3150c537
David Mayerich
added further pro...
|
1086
|
|
63fc1df8
David Mayerich
added an inverse ...
|
1087
|
if(PROGRESS) progress = (double)(x * Z() + z+1) / (lines * Z()) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1088
|
}
|
3033b886
David Mayerich
implemented spect...
|
1089
1090
1091
1092
1093
1094
|
//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...
|
1095
|
}
|
3033b886
David Mayerich
implemented spect...
|
1096
1097
|
//free the temporary frame
|
a43c4fe1
heziqi
Added crop in env...
|
1098
|
free(temp);
|
3150c537
David Mayerich
added further pro...
|
1099
|
|
a43c4fe1
heziqi
Added crop in env...
|
1100
1101
1102
|
return true;
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
|
/// Remove a list of bands from the ENVI file
/// @param outfile is the file name for the output hyperspectral image (with trimmed bands)
/// @param b is an array of bands to be eliminated
void trim(std::string outfile, std::vector<size_t> band_array, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
file.seekg(0, std::ios::beg); //move to the beginning of the input file
size_t Xb = X() * sizeof(T); //calculate the number of bytes in a line
T* line = (T*)malloc(Xb); //allocate space for a line
size_t i; //create an index into the band array
for(size_t y = 0; y < Y(); y++){ //for each Y plane
i = 0;
for(size_t b = 0; b < Z(); b++){ //for each band
if(b != band_array[i]){ //if this band isn't trimmed
file.read((char*)line, Xb); //read a line
out.write((char*)line, Xb); //write the line
}
else{
file.seekg(Xb, std::ios::cur); //if this band is trimmed, skip it
i++;
}
}
if(PROGRESS) progress = (double)(y+1) / (double)Y() * 100;
}
free(line);
}
|
2ce6954b
David Mayerich
added the ability...
|
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
|
/// Combine two BSQ images along the Y axis
/// @param outfile is the combined file to be output
/// @param infile is the input file stream for the image to combine with this one
/// @param Sx is the size of the second image along X
/// @param Sy is the size of the second image along Y
/// @param offset is a shift (negative or positive) in the combined image to the left or right
void combine(std::string outfile, bil<T>* C, long long xp, long long yp, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
file.seekg(0, std::ios::beg); //move to the beginning of both files
C->file.seekg(0, std::ios::beg);
size_t S[2]; //size of the output band image
size_t p0[2]; //position of the current image in the output
size_t p1[2]; //position of the source image in the output
hsi<T>::calc_combined_size(xp, yp, C->X(), C->Y(), S[0], S[1], p0[0], p0[1], p1[0], p1[1]); //calculate the image placement parameters
size_t line_bytes = X() * sizeof(T);
size_t band_bytes = X() * Y() * sizeof(T);
T* cur = (T*)malloc(line_bytes); //allocate space for a band of the current image
size_t line_src_bytes = C->X() * sizeof(T);
size_t band_src_bytes = C->X() * C->Y() * sizeof(T);
T* src = (T*)malloc(line_src_bytes); //allocate space for a band of the source image
size_t line_dst_bytes = S[0] * sizeof(T);
size_t band_dst_bytes = S[0] * S[1] * sizeof(T);
T* dst = (T*)malloc(line_dst_bytes); //allocate space for a band of the destination image
for(size_t y = 0; y < S[1]; y++){ //for each line in the destination file
memset(dst, 0, line_dst_bytes); //set all values to zero (0) in the destination image
for(size_t b = 0; b < Z(); b++){ //for each band in both images
if(y >= p0[1] && y < p0[1] + Y()){ //if the current image crosses this line
file.read((char*)cur, line_bytes); //read a line from the current image
memcpy(&dst[p0[0]], cur, line_bytes); //copy the current line to the correct spot in the destination line
}
if(y >= p1[1] && y < p1[1] + C->Y()){ //if the source image crosses this line
C->file.read((char*)src, line_src_bytes); //read a line from the source image
memcpy(&dst[p1[0]], src, line_src_bytes); //copy the source line into the correct spot in the destination line
}
out.write((char*)dst, line_dst_bytes);
if(PROGRESS) progress = (double)((y + 1)*Z() + b + 1) / (double) (Z() * S[1]) * 100;
}
}
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1179
|
/// Convolve the given band range with a kernel specified by a vector of coefficients.
|
2ce6954b
David Mayerich
added the ability...
|
1180
|
|
9b2a5d71
David Mayerich
implemented finit...
|
1181
1182
1183
1184
1185
1186
|
/// @param outfile is an already open stream to the output file
/// @param C is an array of coefficients
/// @param start is the band to start processing (the first coefficient starts here)
/// @param nbands is the number of bands to process
/// @param center is the index for the center coefficient for the kernel (used to set the wavelengths in the output file)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1187
|
void convolve(std::string outfile, std::vector<double> C, size_t start, size_t end, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
size_t B = end - start + 1;
size_t Xb = X() * sizeof(T); //calculate the size of a band (frame) in bytes
size_t XBb = Xb * Z();
size_t N = C.size(); //get the number of bands that the kernel spans
std::deque<T*> frame(N, NULL); //create an array to store pointers to each frame
for(size_t f = 0; f < N; f++)
frame[f] = (T*)malloc(Xb); //allocate space for the frame
T* outline = (T*)malloc(Xb); //allocate space for the output band
//Implementation: In order to minimize reads from secondary storage, each band is only loaded once into the 'frame' deque.
// When a new band is loaded, the last band is popped, a new frame is copied to the pointer, and it is
// re-inserted into the deque.
for(size_t y = 0; y < Y(); y++){
file.seekg(y * XBb + start * Xb, std::ios::beg); //move to the beginning of the 'start' band
for(size_t f = 0; f < N; f++) //for each frame
file.read((char*)frame[f], Xb); //load the frame
for(size_t b = 0; b < B; b++){ //for each band
memset(outline, 0, Xb); //set the output band to zero (0)
for(size_t c = 0; c < N; c++){ //for each frame (corresponding to each coefficient)
for(size_t x = 0; x < X(); x++){ //for each pixel
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1211
1212
1213
|
if(mask == NULL || mask[y * X() + x]){
outline[x] += (T)(C[c] * frame[c][x]); //calculate the contribution of the current frame (scaled by the corresponding coefficient)
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
|
}
}
out.write((char*)outline, Xb); //output the band
file.read((char*)frame[0], Xb); //read the next band
frame.push_back(frame.front()); //put the first element in the back
frame.pop_front(); //pop the first element
}
if(PROGRESS) progress = (double)(y+1) / (double)Y() * 100;
}
}
/// Approximate the spectral derivative of the image
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1226
|
void deriv(std::string outfile, size_t d, size_t order, const std::vector<double> w = std::vector<double>(), unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
size_t Xb = X() * sizeof(T); //calculate the size of a line (frame) in bytes
size_t XBb = Xb * Z();
size_t B = Z();
file.seekg(0, std::ios::beg); //seek to the beginning of the file
size_t N = order + d; //approximating a derivative requires order + d samples
std::deque<T*> frame(N, NULL); //create an array to store pointers to each frame
for(size_t f = 0; f < N; f++) //for each frame
frame[f] = (T*)malloc(Xb); //allocate space for the frame
T* outline = (T*)malloc(Xb); //allocate space for the output band
//Implementation: In order to minimize reads from secondary storage, each band is only loaded once into the 'frame' deque.
// When a new band is loaded, the last band is popped, a new frame is copied to the pointer, and it is
// re-inserted into the deque.
size_t mid = (size_t)(N / 2); //calculate the mid point of the kernel
size_t iw; //index to the first wavelength used to evaluate the derivative at this band
for(size_t y = 0; y < Y(); y++){
//file.seekg(y * XBb, std::ios::beg); //seek to the beginning of the current Y plane
for(size_t f = 0; f < N; f++) //for each frame
file.read((char*)frame[f], Xb); //load a line
for(size_t b = 0; b < B; b++){ //for each band
if(b < mid) //calculate the first wavelength used to evaluate the derivative at this band
iw = 0;
else if(b > B - (N - mid + 1))
iw = B - N;
else{
iw = b - mid;
file.read((char*)frame[0], Xb); //read the next band
frame.push_back(frame.front()); //put the first element in the back
frame.pop_front(); //pop the first element
}
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + N); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
memset(outline, 0, Xb); //set the output band to zero (0)
for(size_t c = 0; c < N; c++){ //for each frame (corresponding to each coefficient)
for(size_t x = 0; x < X(); x++){ //for each pixel
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1270
1271
1272
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if(mask == NULL || mask[y * X() + x]){
outline[x] += (T)(C[c] * frame[c][x]); //calculate the contribution of the current frame (scaled by the corresponding coefficient)
}
|
9b2a5d71
David Mayerich
implemented finit...
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1273
1274
1275
1276
1277
1278
1279
1280
1281
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}
}
out.write((char*)outline, Xb); //output the band
}
if(PROGRESS) progress = (double)(y+1) / (double)Y() * 100;
}
}
|
0df38ff3
heziqi
fixed head detached
|
1282
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1283
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
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1284
1285
1286
1287
1288
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bool close(){
file.close();
return true;
}
|
c25e7d0d
heziqi
speed of bip.base...
|
1289
|
};
|
cac62fd3
David Mayerich
modified to work ...
|
1290
|
}
|
6aa04ba2
David Mayerich
interleave types
|
1291
1292
|
#endif
|