#ifndef STIM_BIL_H
#define STIM_BIL_H
#include "../envi/envi_header.h"
#include "../envi/binary.h"
#include
#include
namespace stim{
/**
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.
*/
template
class bil: public binary {
protected:
std::vector w; //band wavelength
unsigned long X(){
return R[0];
}
unsigned long Y(){
return R[2];
}
unsigned long Z(){
return R[1];
}
using binary::thread_data;
public:
using binary::open;
using binary::file;
using binary::R;
/// 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
bool open(std::string filename, unsigned int X, unsigned int Y, unsigned int B, unsigned int header_offset, std::vector wavelengths){
w = wavelengths;
return open(filename, vec(X, B, Y), header_offset);
}
/// 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.
bool band_index( T * p, unsigned int page){
//return binary::read_plane_1(p, page);
unsigned int L = X() * sizeof(T); //caculate the number of bytes in a sample line
unsigned int jump = X() * (Z() - 1) * sizeof(T);
if (page >= Z()){ //make sure the bank number is right
std::cout<<"ERROR: page out of range"< wavelength ){
band_index(p, page);
return true;
}
while( w[page] < wavelength )
{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == Z()) {
band_index(p, Z()-1);
return true;
}
}
if ( wavelength < w[page] )
{
T * p1;
T * p2;
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++){
double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
p[i] = (p2[i] - p1[i]) * r + p1[i];
}
free(p1);
free(p2);
}
else //if the wavelength is equal to a wavelength in header file
{
band_index(p, page);
}
return true;
}
/// 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)
{
unsigned int B = Z();
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
if ( w[page] > wavelength ){
memcpy(p, c, L);
return true;
}
while( w[page] < wavelength )
{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == B) {
memcpy(p, c + (B - 1) * X(), L);
return true;
}
}
if ( wavelength < w[page] )
{
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++){
double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
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;
}
/// 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.
bool spectrum(T * p, unsigned x, unsigned y){
return binary::read_line_02(p, x, y);
}
/// 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.
bool pixel(T * p, unsigned n){
//calculate the corresponding x, y
unsigned int x = n % X();
unsigned int y = n / X();
//get the pixel
return spectrum(p, x, y);
}
//given a Y ,return a XZ slice
bool read_plane_y(T * p, unsigned y){
return binary::read_plane_2(p, y);
}
/// 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.
bool baseline(std::string outname, std::vector 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
unsigned int ZX = Z() * X(); //calculate the number of points in a Y slice
unsigned int L = ZX * sizeof(T); //calculate the number of bytes of a Y slice
unsigned int B = Z();
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
unsigned control;
if (a == NULL || b == NULL || c == NULL){
std::cout<<"ERROR: error allocating memory";
exit(1);
}
// loop start correct every y slice
for (unsigned k =0; k < Y(); k++)
{
//get the current y slice
read_plane_y(c, k);
//initialize lownum, highnum, low, high
ai = w[0];
control=0;
//if no baseline point is specified at band 0,
//set the baseline point at band 0 to 0
if(wls[0] != w[0]){
bi = wls[control];
memset(a, (char)0, X() * sizeof(T) );
}
//else get the low band
else{
control++;
read_x_from_xz(a, c, ai);
bi = wls[control];
}
//get the high band
read_x_from_xz(b, c, bi);
//correct every YZ line
for(unsigned cii = 0; cii < B; cii++){
//update baseline points, if necessary
if( w[cii] >= bi && cii != B - 1) {
//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];
read_x_from_xz(b, c, bi);
}
//if the last BL point on the last band of the file?
else if ( wls[control] < w[B - 1]) {
std::swap(a, b); //swap the baseline band pointers
memset(b, (char)0, X() * sizeof(T) ); //clear the high band
ai = bi;
bi = w[B - 1];
}
}
ci = w[cii];
unsigned jump = cii * X();
//perform the baseline correction
for(unsigned i=0; i < X(); i++)
{
double r = (double) (ci - ai) / (double) (bi - ai);
c[i + jump] =(T) ( c[i + jump] - (b[i] - a[i]) * r - a[i] );
}
}//loop for YZ line end
target.write(reinterpret_cast(c), L); //write the corrected data into destination
thread_data = (double)k / Y() * 100;
}//loop for Y slice end
free(a);
free(b);
free(c);
target.close();
thread_data = 100;
return true;
}
/// 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.
bool normalize(std::string outname, double w, double t = 0.0)
{
unsigned int B = Z(); //calculate the number of bands
unsigned int ZX = Z() * X();
unsigned int XY = X() * Y(); //calculate the number of pixels in a band
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 );
band(b, w); //get the certain band into memory
for(unsigned j = 0; j < Y(); j++)
{
read_plane_y(c, j);
for(unsigned i = 0; i < B; i++)
{
for(unsigned m = 0; m < X(); m++)
{
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()];
}
}
target.write(reinterpret_cast(c), L); //write normalized data into destination
thread_data = (double)j / Y() * 100;
}
free(b);
free(c);
target.close();
thread_data = 100;
return true;
}
/// 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.
bool bsq(std::string outname)
{
unsigned int S = X() * Y() * sizeof(T); //calculate the number of bytes in a band
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);
for ( unsigned i = 0; i < Z(); i++)
{
band_index(p, i);
target.write(reinterpret_cast(p), S); //write a band data into target file
thread_data = (double)i / Z() * 100; //store the progress for the current operation
}
thread_data = 100; //set the current progress to 100%
free(p);
target.close();
return true;
}
/// 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.
bool bip(std::string outname)
{
unsigned int S = X() * Z() * sizeof(T); //calculate the number of bytes in a ZX slice
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);
for ( unsigned i = 0; i < Y(); i++)
{
read_plane_y(p, i);
for ( unsigned k = 0; k < Z(); k++)
{
unsigned ks = k * X();
for ( unsigned j = 0; j < X(); j++)
q[k + j * Z()] = p[ks + j];
thread_data = (double)(i * Z() + k) / (Z() * Y()) * 100; //store the progress for the current operation
}
target.write(reinterpret_cast(q), S); //write a band data into target file
}
thread_data = 100;
free(p);
free(q);
target.close();
return true;
}
/// 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.
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
unsigned XY = X() * Y();
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;
}
/// 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.
bool height(double lb, double rb, double bandwavelength, T* result){
T* lp;
T* rp;
unsigned XY = X() * Y();
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
band(lp, lb);
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
free(lp);
free(rp);
return true;
}
/// 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
bool 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 = X() * Y();
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"< rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<= 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]) * (cur[j] + cur2[j]) / 2.0;
}
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) * (cur[j] + cur2[j]) / 2.0;
}
//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
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
/// 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
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * 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 < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// 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
bool pa_to_ph(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, T* result){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * 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 < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// 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
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(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * 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 < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// 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
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 = X() * Y();
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"< rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<= 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;
}
/// 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
bool cpoint(double lb, double rb, double lab, double rab, T* result){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * 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 < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// 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
bool build_mask(double mask_band, double threshold, unsigned char* p){
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
band(temp, mask_band);
for (unsigned int i = 0; i < X() * Y(); i++) {
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
}
free(temp);
return true;
}
/// 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.
bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
//I THINK THIS IS WRONG
unsigned XZ = X() * Z(); //calculate the number of values in a 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 (unsigned i = 0; i < Y(); i++) //for each value in Y() (BIP should be X)
{
read_plane_y(temp, i); //retrieve an ZX slice, stored in temp
for ( unsigned j = 0; j < Z(); j++) //for each Z() (Y)
{
for (unsigned k = 0; k < X(); k++) //for each band
{
if(p[i * X() + k] == 0)
temp[j * X() + k] = 0;
else
continue;
}
}
target.write(reinterpret_cast(temp), L); //write a band data into target file
}
target.close();
free(temp);
return true;
}
/// 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
bool sift(std::string outfile, unsigned char* p){
// Assume X() = X, Y() = Y, Z() = Z.
std::ofstream target(outfile.c_str(), std::ios::binary);
//for loading pages:
unsigned long XZ = X() * Z(); //calculate the number of values in an XZ page on disk
unsigned long B = Z(); //calculate the number of bands
unsigned long L = XZ * sizeof(T); //calculate the size of the page (in bytes)
//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));
//for each slice along the y axis
for (unsigned long y = 0; y < Y(); y++) //Select a page by choosing Y coordinate, Y()
{
read_plane_y(slice, y); //retrieve an ZX page, store in "slice"
//for each sample along X
for (unsigned long x = 0; x < X(); x++) //Select a pixel by choosing X coordinate in the page, X()
{
//if the mask != 0 at that xy pixel
if (p[y * X() + x] != 0) //if the mask != 0 at that XY pixel
{
//for each band at that pixel
for (unsigned long b = 0; b < B; b++) //Select a voxel by choosing Z coordinate at the pixel
{
spec[b] = slice[b*X() + x]; //Pass the correct spectral value from XZ page into the spectrum to be saved.
}
target.write((char*)spec, B * sizeof(T)); //write that spectrum to disk. Size is L2.
}
thread_data = (double) (y * X() + x) / (Y() * X()) * 100;
}
}
target.close();
free(slice);
free(spec);
thread_data = 100;
return true;
}
/// 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.
bool band_avg(T* p){
unsigned long long XZ = X() * Z();
T* temp = (T*)malloc(sizeof(T) * XZ);
T* line = (T*)malloc(sizeof(T) * X());
for (unsigned i = 0; i < Y(); i++){
getY(temp, i);
//initialize x-line
for (unsigned j = 0; j < X(); j++){
line[j] = 0;
}
unsigned c = 0;
for (unsigned j = 0; j < Z(); j++){
for (unsigned k = 0; k < X(); k++){
line[k] += temp[c] / (T)Z();
c++;
}
}
for (unsigned j = 0; j < X(); j++){
p[j + i * X()] = line[j];
}
}
free(temp);
return true;
}
/// 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
bool avg_band(T*p, unsigned char* mask){
unsigned long long XZ = X() * Z();
unsigned long long XY = X() * Y();
T* temp = (T*)malloc(sizeof(T) * XZ);
for (unsigned j = 0; j < Z(); 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 < Y(); k++){
read_plane_y(temp, k);
unsigned kx = k * X();
for (unsigned i = 0; i < X(); i++){
if (mask[kx + i] != 0){
for (unsigned j = 0; j < Z(); j++){
p[j] += temp[j * X() + i] / (T)count;
}
}
}
}
free(temp);
return true;
}
/// 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
bool co_matrix(T* co, T* avg, unsigned char *mask){
//memory allocation
unsigned long long xy = X() * Y();
unsigned int B = Z();
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;
}
/// 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
bool crop(std::string outfile, unsigned long long x0,
unsigned long long y0,
unsigned long long x1,
unsigned long long y1,
unsigned long long b0,
unsigned long long b1){
//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
std::ofstream out(outfile.c_str(), std::ios::binary);
//calculate the distance between bands
unsigned long long jumpb = (X() - samples) * sizeof(T);
//distance needed to jump from the previous line of the last band to the next line of the first band
unsigned long long longjump = ((Z() - b1) * X() + b0 * X()) * sizeof(T);
//set the start position for the cropped region
file.seekg((y0 * X() * Z() + b0 * X() + x0) * sizeof(T), std::ios::beg);
for (unsigned x = 0; x < lines; x++)
{
for (unsigned z = b0; z < b1; z++)
{
file.read((char *)(temp + z * samples), sizeof(T) * samples);
file.seekg(jumpb, std::ios::cur); //go to the next band
thread_data = (double)(x * Z() + z) / (lines * Z()) * 100;
}
//write slice data into target file
out.write(reinterpret_cast(temp), bands * L);
//seek to the beginning of the next X-Z slice
file.seekg(longjump, std::ios::cur);
}
//free the temporary frame
free(temp);
thread_data = 100;
return true;
}
/// Close the file.
bool close(){
file.close();
return true;
}
};
}
#endif