bsq.h
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#ifndef STIM_BSQ_H
#define STIM_BSQ_H
#include "../envi/envi_header.h"
#include "../envi/binary.h"
#include "../envi/bil.h"
#include <cstring>
#include <utility>
#include <vector>
namespace stim{
template <typename T>
class bsq: public binary<T> {
protected:
//envi_header header;
std::vector<double> w; //band wavelengths
unsigned int offset;
public:
using binary<T>::open;
using binary<T>::file;
using binary<T>::getSlice;
using binary<T>::R;
//open a file, given the file name and dimensions
bool open(std::string filename, unsigned int X, unsigned int Y, unsigned int B, unsigned int header_offset, std::vector<double> wavelengths){
//copy the wavelengths to the BSQ file structure
w = wavelengths;
//copy the wavelengths to the structure
offset = header_offset;
return open(filename, vec<unsigned int>(X, Y, B), header_offset);
}
//retrieve one band (specified by the band index)
bool band_index( T * p, unsigned int page){
if (page >= R[2]){ //make sure the bank number is right
std::cout<<"ERROR: page out of range"<<std::endl;
return false;
}
file.seekg(R[0] * R[1] * page * sizeof(T));
file.read((char *)p, sizeof(T) * R[0] * R[1]);
return true;
}
//retrieve one band (specified by the wavelength)
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 = R[0] * R[1]; //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 == R[2]) {
band_index(p, R[2]-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;
}
//save one pixel of the file into the memory, and return the pointer
bool spectrum(T * p, unsigned x, unsigned y){
unsigned int i;
if ( x >= R[0] || y >= R[1]){ //make sure the sample and line number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
file.seekg((x + y * R[0]) * sizeof(T), std::ios::beg); //point to the certain sample and line
for (i = 0; i < R[2]; i++)
{
file.read((char *)(p + i), sizeof(T));
file.seekg((R[1] * R[0] - 1) * sizeof(T), std::ios::cur); //go to the next band
}
return true;
}
//save one pixel into memory
bool pixel(T * p, unsigned n){
unsigned bandnum = R[0] * R[1]; //calculate numbers in one band
if ( n >= bandnum){ //make sure the pixel number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
file.seekg(n * sizeof(T), std::ios::beg); //point to the certain pixel
for (unsigned i = 0; i < R[2]; i++)
{
file.read((char *)(p + i), sizeof(T));
file.seekg((bandnum - 1) * sizeof(T), std::ios::cur); //go to the next band
}
return true;
}
//baseline correction and save it into file
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
unsigned int B = R[2]; //calculate the number of bands
unsigned int XY = R[0] * R[1]; //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 aii, bii; //stores the two baseline points number surrounding the current band
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<const char*>(c), S); //write the corrected data into destination
}
//header.save(headername); //save the new header file
free(a);
free(b);
free(c);
target.close();
return true;
}
// normalize the BSQ file
bool normalize(std::string outname, double w)
{
unsigned int B = R[2]; //calculate the number of bands
unsigned int XY = R[0] * R[1]; //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++)
{
c[i] = c[i] / b[i];
}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
}
//header.save(headername); //save the new header file
free(b);
free(c);
target.close();
return true;
}
//convert BSQ file to BIP file and save it
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<T> n;
if(n.open(temp, R[0], R[1], R[2], offset, w)==false){ //open infile
std::cout<<"ERROR: unable to open input file"<<std::endl;
exit(1);
}
//then convert bil file to bip file
n.bip(outname);
n.close();
remove(temp.c_str());
remove(headtemp.c_str());
return true;
}
//convert BSQ file to BIL file and save it
bool bil(std::string outname)
{
//simplify image resolution
unsigned int L = R[0] * R[2] * sizeof(T); //calculate the number of bytes of a ZX slice
unsigned int jump = (R[1] - 1) * R[0] * sizeof(T);
std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
T * p; //pointer to the current spectrum
p = (T*)malloc(L);
for ( unsigned i = 0; i < R[1]; i++)
{
file.seekg(R[0] * i * sizeof(T), std::ios::beg);
for ( unsigned j = 0; j < R[2]; j++ )
{
file.read((char *)(p + j * R[0]), sizeof(T) * R[0]);
file.seekg(jump, std::ios::cur); //go to the next band
}
target.write(reinterpret_cast<const char*>(p), L); //write XZ slice data into target file
}
//header.interleave = rts::envi_header::BIL; //change the type of file in header file
//header.save(headername);
free(p);
target.close();
return true;
}
//providing the left and the right bound data, return baseline-corrected band height
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;
}
//providing the left and the right bound wavelength, return baseline-corrected band height
bool height(double lb, double rb, double bandwavelength, T* result){
T* lp;
T* rp;
unsigned XY = R[0] * R[1];
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 between two bound point(including baseline correction)
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 = 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]) * (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;
}
//peak height ratio
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];
}
free(p1);
free(p2);
return true;
}
//peak are to peak height ratio
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];
}
free(p1);
free(p2);
return true;
}
//peak area to peak area ratio
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];
}
free(p1);
free(p2);
return true;
}
//x * f(x)
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;
}
//centroid point
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;
}
//create mask file
bool build_mask(double mask_band, double threshold, unsigned char* p = NULL){
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;
}
free(temp);
return true;
}
//apply mask
bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
unsigned XY = R[0] * R[1]; //calculate number of a band
unsigned L = XY * sizeof(T);
T * temp = (T*)malloc(L);
for (unsigned i = 0; i < R[2]; i++)
{
band_index(temp, i);
for ( unsigned j = 0; j < XY; j++)
{
if(p[j] == 0){
temp[j] = 0;
}
else{
continue;
}
}
target.write(reinterpret_cast<const char*>(temp), L); //write a band data into target file
}
target.close();
free(temp);
return true;
}
//calculate the average band
bool band_avg(T* p){
unsigned long long XY = R[0] * R[1];
T* temp = (T*)malloc(sizeof(T) * XY);
//initialize p
band_index(p, 0);
for (unsigned j = 0; j < XY; j++){
p[j] /= (T)R[2];
}
//get every band and add them all
for (unsigned i = 1; i < R[2]; i++){
band_index(temp, i);
for (unsigned j = 0; j < XY; j++){
p[j] += temp[j]/(T)R[2];
}
}
free(temp);
return true;
}
//calculate the average number of every band
bool avg_band(T*p, unsigned char* mask){
unsigned long long XY = R[0] * R[1];
unsigned count = 0; //number of vaild pixel in a band
T* temp = (T*)malloc(sizeof(T) * XY);
//calculate valid pixel number
for (unsigned j = 0; j < XY; j++){
if (mask[j] != 0){
count++;
}
}
//calculate average of a band
for (unsigned i = 0; i < R[2]; i++){
p[i] = 0;
band_index(temp, i);
for (unsigned j = 0; j < XY; j++){
if (mask[j] != 0){
p[i] += temp[j] / (T)count;
}
}
}
free(temp);
return true;
}
//calculate correlated matrix
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* bandi = (T*)malloc(sizeof(T) * xy);
T* bandj = (T*)malloc(sizeof(T) * xy);
//count vaild pixels in a band
unsigned count = 0;
for (unsigned j = 0; j < xy; j++){
if (mask[j] != 0){
count++;
}
}
//calculate correlation coefficient matrix
for (unsigned i = 0; i < B; i++)
{
band_index(bandi, i);
for (unsigned j = i; j < B; j++){
band_index(bandj, j);
T numerator = 0; //to calculate element in correlation coefficient matrix, numerator part
//calculate the R(i,j) in correlation coeffient matrix
for (unsigned k = 0; k < xy; k++){
if (mask[k] != 0){
numerator += (bandi[k] - avg[i]) * (bandj[k] - avg[j]) / count;
}
}
co[i*B + j] = numerator;
co[j*B + i] = numerator; //because correlated matrix is a symmetric matrix
}
}
free(bandi);
free(bandj);
return true;
}
//close the file
bool close(){
file.close();
return true;
}
};
}
#endif