#ifndef STIM_BSQ_H
#define STIM_BSQ_H
#include "../envi/envi_header.h"
#include "../envi/binary.h"
#include "../envi/bil.h"
#include
#include
#include
namespace stim{
/**
The BIP class represents a 3-dimensional binary file stored using band sequential (BSQ) image encoding. The binary file is stored
such that X-Y "frames" are stored sequentially to form an image stack along the z-axis. When accessing the data sequentially on disk,
the dimensions read, from fastest to slowest, are X, Y, Z.
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 bsq: public binary {
protected:
std::vector w; //band wavelengths
unsigned int offset;
using binary::R;
unsigned long X(){
return R[0];
}
unsigned long Y(){
return R[1];
}
unsigned long Z(){
return R[2];
}
using binary::thread_data;
public:
using binary::open;
using binary::file;
using binary::read_line_01;
using binary::read_plane_2;
//using binary::getSlice;
/// 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 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){
//copy the wavelengths to the BSQ file structure
w = wavelengths;
//copy the wavelengths to the structure
offset = header_offset;
return open(filename, vec(X, Y, B), 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 read_plane_2(p, page);
}
/// 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.
bool band( T * p, double wavelength){
//if there are no wavelengths in the BSQ file
if(w.size() == 0)
return band_index(p, (unsigned int)wavelength);
unsigned int XY = X() * Y(); //calculate the number of pixels in a band
unsigned page = 0;
//get the two neighboring bands (above and below 'wavelength')
//if wavelength is smaller than the first one in header file
if ( w[page] > wavelength ){
band_index(p, page);
return true;
}
while( w[page] < wavelength )
{
page++;
//if wavelength is larger than the last wavelength in the header file
// (the wavelength is out of bounds)
if (page == Z()) {
band_index(p, Z()-1); //return the last band
return true;
}
}
//when the page counter points to the first band above 'wavelength'
if ( wavelength < w[page] ){
//do the interpolation
T * p1;
T * p2;
p1=(T*)malloc( XY * sizeof(T)); //memory allocation
p2=(T*)malloc( XY * sizeof(T));
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);
}
//if the wavelength is equal to a wavelength in header file
else{
band_index(p, page); //return the band
}
return true;
}
/// Retrieve a single spectrum (Z-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 read_line_01(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){
unsigned bandnum = X() * Y(); //calculate numbers in one band
if ( n >= bandnum){ //make sure the pixel number is right
std::cout<<"ERROR: sample or line out of range"< 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 B = Z(); //calculate the number of bands
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
double ai, bi; //stores the two baseline points wavelength surrounding the current band
double ci; //stores the current band's wavelength
unsigned control=0;
T * a; //pointers to the high and low band images
T * b;
T * c; //pointer to the current image
a = (T*)malloc( S ); //memory allocation
b = (T*)malloc( S );
c = (T*)malloc( S );
if (a == NULL || b == NULL || c == NULL){
std::cout<<"ERROR: error allocating memory";
exit(1);
}
//initialize lownum, highnum, low, high
ai=w[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, S);
}
//else get the low band
else{
control += 1;
band(a, ai);
bi = wls[control];
}
//get the high band
band(b, bi);
//correct every band
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];
band(b, 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, S); //clear the high band
ai = bi;
bi = w[B - 1];
}
}
//get the current band
band_index(c, cii);
ci = w[cii];
//perform the baseline correction
for(unsigned i=0; i < XY; i++){
double r = (double) (ci - ai) / (double) (bi - ai);
c[i] =(T) ( c[i] - (b[i] - a[i]) * r - a[i] );
}
target.write(reinterpret_cast(c), S); //write the corrected data into destination
thread_data = (double)cii / B * 100;
}
//header.save(headername); //save the new header file
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 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
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
T * b; //pointers to the certain wavelength band
T * c; //pointer to the current image
b = (T*)malloc( S ); //memory allocation
c = (T*)malloc( S );
band(b, w); //get the certain band into memory
for(unsigned j = 0; j < B; j++)
{
band_index(c, j); //get the current band into memory
for(unsigned i = 0; i < XY; i++)
{
if(b[i] < t)
c[i] = (T)0.0;
else
c[i] = c[i] / b[i];
}
target.write(reinterpret_cast(c), S); //write normalized data into destination
thread_data = (double)j / B * 100;
}
//header.save(headername); //save the new header file
free(b);
free(c);
target.close();
thread_data = 100; //make sure that the progress bar is full
return true;
}
/// Convert the current BSQ 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)
{
std::string temp = outname + "_temp";
std::string headtemp = temp + ".hdr";
//first creat a temporary bil file and convert bsq file to bil file
bil(temp);
stim::bil n;
if(n.open(temp, X(), Y(), Z(), offset, w)==false){ //open infile
std::cout<<"ERROR: unable to open input file"<(xz_slice), xz_bytes); //write the generated XZ slice to the target file
}
thread_data = 100;
free(xz_slice);
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 = NULL){
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);
unsigned XY = X() * Y(); //calculate number of a band
unsigned L = XY * sizeof(T);
T * temp = (T*)malloc(L);
for (unsigned i = 0; i < Z(); i++) //for each spectral bin
{
band_index(temp, i); //get the specified band (by index)
for ( unsigned j = 0; j < XY; j++) // for each pixel
{
if(p[j] == 0){ //if the mask is 0 at that pixel
temp[j] = 0; //set temp to zero
}
else{
continue;
}
}
target.write(reinterpret_cast(temp), L); //write the XY slice at that band to disk
}
target.close();
free(temp);
return true;
}
/// 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){
unsigned long long XY = X() * Y(); //Number of XY pixels
unsigned long long L = XY * sizeof(T); //size of XY plane (in bytes)
//calculate the number of pixels in the mask
unsigned long long P = 0;
if(mask == NULL) P = XY;
else{
for(unsigned long long xy = 0; xy < XY; xy++){
if(mask[xy] != 0) P++;
}
}
T* band_image = (T*) malloc( XY * sizeof(T)); //allocate space for a single band
unsigned long long i; //pixel index into the sifted array
for(unsigned long long b = 0; b < Z(); b++){ //for each band in the data set
band_index(band_image, b); //retrieve an image of that band
i = 0;
for(unsigned long long xy = 0; xy < XY; xy++){
if(mask == NULL || mask[xy] != 0){ //if the pixel is valid
matrix[i*Z() + b] = band_image[xy]; //copy it to the appropriate point in the values[] array
i++;
}
}
}
return true;
}
/// Saves only those spectra corresponding to mask value != 0 to pre-allocated memory
/// @param matrix is the destination for the sifted pixels
/// @param p is the mask file used for sifting
/*bool sift(T* matrix, unsigned char* p){
// open a band (XY plane)
unsigned long XY = X() * Y(); //Number of XY pixels
unsigned long L = XY * sizeof(T); //size of XY pixels
//count the number of masked pixels
unsigned long P = 0; //allocate space for the number of pixels
for(unsigned long xy = 0; xy < XY; xy++){ //count the number of pixels
if(p[xy] != 0) P++;
}
T* bandvals = (T*) malloc(sizeof(T) * P); //allocate a temporary array to store the pixels for a single band
memset(matrix, 0, sizeof(T) * P * Z());
for (unsigned long z = 0; z < Z(); z++){ //for each band
if(!sift_band(bandvals, z, p)){
std::cout<<"ERROR sifting band index "<(temp_vox), sizeof(T)); //write the XY slice at that band to disk
}
else{
continue;
}
thread_data = (double)(i * XY + j) / (XY * Z()) * 100;
}
}
target.close();
free(temp);
thread_data = 100;
return true;
}
/// Generates a spectral image from a matrix of spectral values in lexicographic order and a mask
bool unsift(std::string outfile, unsigned char* p, unsigned int samples, unsigned int lines){
//create a binary output stream
std::ofstream target(outfile.c_str(), std::ios::binary);
//make sure that there's only one line
if(Y() != 1){
std::cout<<"ERROR in stim::bsq::sift() - number of lines does not equal 1"<(unsifted), sizeof(T) * XY);
}
//std::cout<<"unsifted"<(temp), L); //write slice data into target file
file.seekg(jumpb, std::ios::cur);
}
free(temp);
thread_data = 100;
return true;
}
/// Close the file.
bool close(){
file.close();
return true;
}
};
}
#endif