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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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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, Y, B), header_offset);
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}
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/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
/// @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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unsigned int L = R[0] * sizeof(T); //caculate the number of bytes in a sample line
unsigned int jump = R[0] * (R[2] - 1) * sizeof(T);
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if (page >= R[2]){ //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(R[0] * page * sizeof(T), std::ios::beg);
for (unsigned i = 0; i < R[1]; i++)
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{
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file.read((char *)(p + i * R[0]), 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 = R[0] * R[1]; //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 == R[2]) {
band_index(p, R[2]-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;
}
//get YZ line from the a Y slice, Y slice data should be already IN the MEMORY
bool getYZ(T* p, T* c, double wavelength)
{
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unsigned int X = R[0]; //calculate the number of pixels in a sample
unsigned int B = R[2];
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unsigned int L = X * sizeof(T);
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) {
memcpy(p, c + (B - 1) * X, L);
return true;
}
}
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if ( wavelength < w[page] )
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{
p1=(T*)malloc( L ); //memory allocation
p2=(T*)malloc( L );
memcpy(p1, c + (page - 1) * X, L);
memcpy(p2, c + page * X, L);
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
memcpy(p, c + page * X, L);
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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if ( x >= R[0] || y >= R[1]){ //make sure the sample and line number is right
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std::cout<<"ERROR: sample or line out of range"<<std::endl;
exit(1);
}
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unsigned jump = (R[0] - 1) * sizeof(T);
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file.seekg((y * R[0] * R[2] + x) * sizeof(T), std::ios::beg);
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for(unsigned i = 0; i < R[2]; i++)
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{
//point to the certain sample and line
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file.read((char *)(p + i), sizeof(T));
file.seekg(jump, std::ios::cur);
}
return true;
}
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/// Retrieve a single pixel and stores it in pre-allocated memory.
/// @param p is a pointer to pre-allocated memory at least sizeof(T) in size.
/// @param n is an integer index to the pixel using linear array indexing.
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bool pixel(T * p, unsigned n){
//calculate the corresponding x, y
unsigned int x = n % R[0];
unsigned int y = n / R[0];
//get the pixel
return spectrum(p, x, y);
}
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//given a Y ,return a XZ slice
bool getY(T * p, unsigned y)
{
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if ( y >= R[1]){ //make sure the line number is right
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std::cout<<"ERROR: line out of range"<<std::endl;
exit(1);
}
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file.seekg(y * R[2] * R[0] * sizeof(T), std::ios::beg);
file.read((char *)p, sizeof(T) * R[2] * R[0]);
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return true;
}
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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 = R[2] * R[0]; //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 = R[2];
unsigned int X = R[0];
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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;
a = (T*)malloc(X * sizeof(T));
b = (T*)malloc(X * sizeof(T));
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 < R[1]; k++)
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{
//get the current y slice
getY(c, k);
//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];
memset(a, (char)0, X * sizeof(T) );
}
//else get the low band
else{
control++;
getYZ(a, c, ai);
bi = wls[control];
}
//get the high band
getYZ(b, c, bi);
//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];
getYZ(b, c, bi);
}
//if the last BL point on the last band of the file?
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else if ( wls[control] < w[B - 1]) {
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std::swap(a, b); //swap the baseline band pointers
memset(b, (char)0, X * sizeof(T) ); //clear the high band
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;
//perform the baseline correction
for(unsigned i=0; i < X; i++)
{
double r = (double) (ci - ai) / (double) (bi - ai);
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c[i + jump] =(T) ( c[i + jump] - (b[i] - a[i]) * r - a[i] );
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}
}//loop for YZ line end
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target.write(reinterpret_cast<const char*>(c), L); //write the corrected data into destination
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}//loop for Y slice end
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free(a);
free(b);
free(c);
target.close();
return true;
}
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/// Normalize all spectra based on the value of a single band, storing the result in a new BSQ file.
/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
/// @param w is the label specifying the band that the hyperspectral image will be normalized to.
/// @param t is a threshold specified such that a spectrum with a value at w less than t is set to zero. Setting this threshold allows the user to limit division by extremely small numbers.
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bool normalize(std::string outname, double w, double t = 0.0)
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{
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unsigned int B = R[2]; //calculate the number of bands
unsigned int Y = R[1];
unsigned int X = R[0];
unsigned int ZX = R[2] * R[0];
unsigned int XY = R[0] * R[1]; //calculate the number of pixels in a band
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unsigned int S = XY * sizeof(T); //calculate the number of bytes in a band
unsigned int L = ZX * sizeof(T);
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 );
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band(b, w); //get the certain band into memory
|
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for(unsigned j = 0; j < Y; j++)
{
getY(c, j);
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for(unsigned i = 0; i < B; i++)
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{
|
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for(unsigned m = 0; m < X; m++)
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{
|
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David Mayerich
allowed masking d...
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if( b[m + j * X] < t )
c[m + i * X] = (T)0.0;
else
c[m + i * X] = c[m + i * X] / b[m + j * X];
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}
}
target.write(reinterpret_cast<const char*>(c), L); //write normalized data into destination
}
|
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free(b);
free(c);
target.close();
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
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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.
|
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bool bsq(std::string outname)
{
|
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|
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unsigned int S = R[0] * R[1] * sizeof(T); //calculate the number of bytes in a band
|
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std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
T * p; //pointer to the current band
p = (T*)malloc(S);
|
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|
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for ( unsigned i = 0; i < R[2]; i++)
|
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{
band_index(p, i);
target.write(reinterpret_cast<const char*>(p), S); //write a band data into target file
}
|
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|
411
|
|
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free(p);
target.close();
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
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/// 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.
|
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bool bip(std::string outname)
{
|
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|
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|
unsigned int S = R[0] * R[2] * sizeof(T); //calculate the number of bytes in a ZX slice
|
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std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
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);
|
6708cc25
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|
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|
for ( unsigned i = 0; i < R[1]; i++)
|
f6169dea
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|
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{
getY(p, i);
|
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|
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|
for ( unsigned k = 0; k < R[2]; k++)
|
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{
|
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|
unsigned ks = k * R[0];
for ( unsigned j = 0; j < R[0]; j++)
q[k + j * R[2]] = p[ks + j];
|
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}
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
}
|
6708cc25
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|
445
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|
free(p);
free(q);
target.close();
return true;
}
|
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|
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|
|
a23c4132
David Mayerich
Doxygen comments ...
|
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/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lp is a pointer to an array holding the band image for the left baseline point
/// @param rp is a pointer to an array holding the band image for the right baseline point
/// @param wavelength is the label value for the requested baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
|
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bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
unsigned XY = R[0] * R[1];
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 ...
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/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param bandwavelength is the label value for the desired baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
|
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heziqi
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|
480
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
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T* lp;
T* rp;
|
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|
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|
unsigned XY = R[0] * R[1];
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
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|
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|
489
|
band(lp, lb);
|
20c212c0
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|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
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|
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|
free(lp);
free(rp);
|
20c212c0
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|
return true;
}
|
70407ea9
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|
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|
|
a23c4132
David Mayerich
Doxygen comments ...
|
500
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|
/// Calculate the area under the spectrum between two specified points and stores the result in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label value for the left bound (start of the integration)
/// @param rab is the label value for the right bound (end of the integration)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
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|
508
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
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|
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|
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
|
20c212c0
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Ziqi added functi...
|
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|
unsigned XY = R[0] * R[1];
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
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Ziqi added functi...
|
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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...
|
544
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
545
546
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
547
|
while (rab <= w[bi]){
|
20c212c0
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Ziqi added functi...
|
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554
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
555
556
|
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
557
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
558
|
result[j] += (rab - w[bi]) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
559
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
560
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|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
562
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
563
|
result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
564
|
}
|
517876d6
heziqi
metrics finished ...
|
565
|
|
20c212c0
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|
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|
//calculate the area
ai++;
for(unsigned i = ai; i <= bi ;i++)
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
for(unsigned j = 0; j < XY; j++)
{
result[j] += (w[ai] - w[ai-1]) * (cur[j] + cur2[j]) / 2.0;
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
577
|
|
517876d6
heziqi
metrics finished ...
|
578
579
580
581
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
582
583
584
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
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|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param pos1 is the label value for the first peak (numerator) position
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param pos2 is the label value for the second peak (denominator) position
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
594
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604
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607
608
|
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
T* p1 = (T*)malloc(R[0] * R[1] * sizeof(T));
T* p2 = (T*)malloc(R[0] * R[1] * sizeof(T));
//get the two peak band
height(lb1, rb1, pos1, p1);
height(lb2, rb2, pos2, p2);
//calculate the ratio in result
for(unsigned i = 0; i < R[0] * R[1]; i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
609
610
611
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
612
613
614
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
615
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618
619
620
621
622
623
|
/// 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...
|
624
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626
627
628
629
630
631
632
633
634
635
636
637
638
639
|
bool pa_to_ph(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, T* result){
T* p1 = (T*)malloc(R[0] * R[1] * sizeof(T));
T* p2 = (T*)malloc(R[0] * R[1] * sizeof(T));
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
height(lb2, rb2, pos, p2);
//calculate the ratio in result
for(unsigned i = 0; i < R[0] * R[1]; i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
640
641
642
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
643
644
645
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
646
647
648
649
650
651
652
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655
656
|
/// 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...
|
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
|
bool pa_to_pa(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, T* result){
T* p1 = (T*)malloc(R[0] * R[1] * sizeof(T));
T* p2 = (T*)malloc(R[0] * R[1] * sizeof(T));
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
area(lb2, rb2, lab2, rab2, p2);
//calculate the ratio in result
for(unsigned i = 0; i < R[0] * R[1]; i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
673
674
675
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
676
677
678
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
679
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681
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683
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685
|
/// 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 ...
|
686
687
688
689
690
691
692
693
694
695
696
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703
704
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706
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|
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
unsigned XY = R[0] * R[1];
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 ...
|
760
761
762
763
764
765
766
|
/// 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 ...
|
767
768
769
770
771
772
773
774
775
776
777
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780
781
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783
784
785
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|
bool cpoint(double lb, double rb, double lab, double rab, T* result){
T* p1 = (T*)malloc(R[0] * R[1] * sizeof(T));
T* p2 = (T*)malloc(R[0] * R[1] * sizeof(T));
//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
for(unsigned i = 0; i < R[0] * R[1]; i++){
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 ...
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787
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/// 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
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f4c5d71b
David Mayerich
started working w...
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794
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bool build_mask(double mask_band, double threshold, unsigned char* p){
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heziqi
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T* temp = (T*)malloc(R[0] * R[1] * sizeof(T)); //allocate memory for the certain band
band(temp, mask_band);
for (unsigned int i = 0; i < R[0] * R[1]; i++) {
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
}
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heziqi
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free(temp);
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4a6f666c
heziqi
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return true;
}
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a23c4132
David Mayerich
Doxygen comments ...
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/// 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.
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740f8cd2
heziqi
added apply_mask
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bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
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1a55a328
David Mayerich
Added comments fo...
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//I THINK THIS IS WRONG
unsigned XZ = R[0] * R[2]; //calculate the number of values in a page on disk
unsigned L = XZ * sizeof(T); //calculate the size of the page (in bytes)
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heziqi
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1a55a328
David Mayerich
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T * temp = (T*)malloc(L); //allocate memory for a temporary page
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740f8cd2
heziqi
added apply_mask
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1a55a328
David Mayerich
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for (unsigned i = 0; i < R[1]; i++) //for each value in R[1] (BIP should be X)
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740f8cd2
heziqi
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{
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1a55a328
David Mayerich
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getY(temp, i); //retrieve an ZX slice, stored in temp
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e843658b
Brad Deutsch
Previous push did...
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for ( unsigned j = 0; j < R[2]; j++) //for each R[2] (Y)
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heziqi
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{
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e843658b
Brad Deutsch
Previous push did...
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for (unsigned k = 0; k < R[0]; k++) //for each band
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heziqi
added apply_mask
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{
if(p[i * R[0] + k] == 0)
temp[j * R[0] + k] = 0;
else
continue;
}
}
target.write(reinterpret_cast<const char*>(temp), L); //write a band data into target file
}
target.close();
free(temp);
return true;
}
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e843658b
Brad Deutsch
Previous push did...
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///Saves to disk only those spectra corresponding to mask values != 0
bool sift_mask(std::string outfile, unsigned char* p){
// Assume R[0] = X, R[1] = Y, R[2] = Z.
std::ofstream target(outfile.c_str(), std::ios::binary);
//for loading pages:
unsigned XZ = R[0] * R[2]; //calculate the number of values in an XZ page on disk
unsigned L = XZ * sizeof(T); //calculate the size of the page (in bytes)
T * temp = (T*)malloc(L); //allocate memory for a temporary page
//for saving spectra:
unsigned Z = R[2]; //calculate the number of values in a spectrum
unsigned LZ = Z * sizeof(T); //calculate the size of the spectrum (in bytes)
T * tempZ = (T*)malloc(LZ); //allocate memory for a temporary spectrum
spectrum(tempZ, R[0] - 1, R[1] - 1); //creates a dummy spectrum by taking the last spectrum in the image
for (unsigned i = 0; i < R[1]; i++) //Select a page by choosing Y coordinate, R[1]
{
getY(temp, i); //retrieve an ZX page, store in "temp"
for (unsigned j = 0; j < R[0]; j++) //Select a pixel by choosing X coordinate in the page, R[0]
{
if (p[j * R[0] + i] != 0) //if the mask != 0 at that XY pixel
{
for (unsigned k = 0; k < R[2]; k++) //Select a voxel by choosing Z coordinate at the pixel
{
tempZ[k] = temp[k*R[0] + i]; //Pass the correct spectral value from XZ page into the spectrum to be saved.
}
target.write(reinterpret_cast<const char*>(tempZ), LZ); //write that spectrum to disk. Size is L2.
}
else
continue;
}
}
target.close();
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
882
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/// 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.
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a43c4fe1
heziqi
Added crop in env...
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bool band_avg(T* p){
unsigned long long XZ = R[0] * R[2];
T* temp = (T*)malloc(sizeof(T) * XZ);
T* line = (T*)malloc(sizeof(T) * R[0]);
for (unsigned i = 0; i < R[1]; i++){
getY(temp, i);
//initialize x-line
for (unsigned j = 0; j < R[0]; j++){
line[j] = 0;
}
unsigned c = 0;
for (unsigned j = 0; j < R[2]; j++){
for (unsigned k = 0; k < R[0]; k++){
line[k] += temp[c] / (T)R[2];
c++;
}
}
for (unsigned j = 0; j < R[0]; j++){
p[j + i * R[0]] = line[j];
}
}
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
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/// 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...
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bool avg_band(T*p, unsigned char* mask){
unsigned long long XZ = R[0] * R[2];
unsigned long long XY = R[0] * R[1];
T* temp = (T*)malloc(sizeof(T) * XZ);
for (unsigned j = 0; j < R[2]; j++){
p[j] = 0;
}
//calculate vaild number in a band
unsigned count = 0;
for (unsigned j = 0; j < XY; j++){
if (mask[j] != 0){
count++;
}
}
for (unsigned k = 0; k < R[1]; k++){
getY(temp, k);
unsigned kx = k * R[0];
for (unsigned i = 0; i < R[0]; i++){
if (mask[kx + i] != 0){
for (unsigned j = 0; j < R[2]; j++){
p[j] += temp[j * R[0] + i] / (T)count;
}
}
}
}
free(temp);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
944
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/// 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...
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bool co_matrix(T* co, T* avg, unsigned char *mask){
//memory allocation
unsigned long long xy = R[0] * R[1];
unsigned int B = R[2];
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
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989
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a23c4132
David Mayerich
Doxygen comments ...
|
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/// Crop a region of the image and save it to a new file.
/// @param outfile is the file name for the new cropped image
/// @param x0 is the lower-left x pixel coordinate to be included in the cropped image
/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
|
a43c4fe1
heziqi
Added crop in env...
|
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bool crop(std::string outfile, unsigned x0, unsigned y0, unsigned x1, unsigned y1){
//calculate the new number of samples and lines
unsigned long long sam = x1 - x0; //samples
unsigned long long lin = y1 - y0; //lines
unsigned long long L = sam * R[2] * sizeof(T);
//get specified band and save
T* temp = (T*)malloc(L);
std::ofstream out(outfile.c_str(), std::ios::binary);
unsigned long long jumpb = (R[0] - sam) * sizeof(T); //jump pointer to the next band
//get start
file.seekg((y0 * R[0] * R[2] + x0) * sizeof(T), std::ios::beg);
for (unsigned i = 0; i < lin; i++)
{
for (unsigned j = 0; j < R[2]; j++)
{
file.read((char *)(temp + j * sam), sizeof(T) * sam);
file.seekg(jumpb, std::ios::cur); //go to the next band
}
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
}
free(temp);
return true;
}
|
0df38ff3
heziqi
fixed head detached
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|
a23c4132
David Mayerich
Doxygen comments ...
|
1023
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
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bool close(){
file.close();
return true;
}
|
c25e7d0d
heziqi
speed of bip.base...
|
1029
|
};
|
cac62fd3
David Mayerich
modified to work ...
|
1030
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}
|
6aa04ba2
David Mayerich
interleave types
|
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#endif
|