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#include "../envi/envi.h"
#include "../envi/binary.h"
#include <cstring>
#include <utility>
namespace rts{
template <typename T>
class bip: public binary<T> {
protected:
envi header;
public:
using binary<T>::open;
using binary<T>::file;
using binary<T>::getSlice;
//open a file, given the file and its header's names
bool open(std::string filename, std::string headername){
if (header.load(headername)==false){
std::cout<<"ERROR: unable to load header file: "<<headername<<std::endl;
return false;
}
open(filename, vec<unsigned int>(header.samples, header.lines, header.bands), header.header_offset);
return true;
}
//save one band of the file into the memory, and return the pointer
bool band_index( T * p, unsigned int page){
if (page >= header.bands){ //make sure the bank number is right
std::cout<<"ERROR: page out of range"<<std::endl;
return false;
}
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//binary::getSlice(p, 0, page); //I met some problems when I called this function?????
file.seekg(page * sizeof(T), std::ios::beg);
for (unsigned i = 0; i < header.samples * header.lines; i++)
{
file.read((char *)(p + i), sizeof(T));
file.seekg( (header.bands - 1) * sizeof(T), std::ios::cur);
}
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return true;
}
bool getBand( T * p, double wavelength){
unsigned int XY = header.samples * header.lines; //calculate the number of pixels in a band
unsigned page=0; //bands 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 ( header.wavelength[page] > wavelength ){
band_index(p, page);
return true;
}
while( header.wavelength[page] < wavelength )
{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == header.bands) {
band_index(p, header.bands-1);
return true;
}
}
if ( wavelength < header.wavelength[page] )
{
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 - header.wavelength[page-1]) / (double) (header.wavelength[page] - header.wavelength[page-1]);
p[i] = (p2[i] - p1[i]) * r + p1[i];
}
}
else //if the wavelength is equal to a wavelength in header file
{
band_index(p, page);
}
free(p1);
free(p2);
return true;
}
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//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)
{
unsigned int X = header.samples; //calculate the number of pixels in a sample
unsigned int B = header.bands;
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 ( header.wavelength[page] > wavelength ){
for(unsigned j = 0; j < header.samples; j++)
{
p[j] = c[j * B];
}
return true;
}
while( header.wavelength[page] < wavelength )
{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == B) {
for(unsigned j = 0; j < header.samples; j++)
{
p[j] = c[(j + 1) * B - 1];
}
return true;
}
}
if ( wavelength < header.wavelength[page] )
{
p1=(T*)malloc( X * sizeof(T)); //memory allocation
p2=(T*)malloc( X * sizeof(T));
//band_index(p1, page - 1);
for(unsigned j = 0; j < X; j++)
{
p1[j] = c[j * B + page - 1];
}
//band_index(p2, page );
for(unsigned j = 0; j < X; j++)
{
p2[j] = c[j * B + page];
}
for(unsigned i=0; i < X; i++){
double r = (double) (wavelength - header.wavelength[page-1]) / (double) (header.wavelength[page] - header.wavelength[page-1]);
p[i] = (p2[i] - p1[i]) * r + p1[i];
}
}
else //if the wavelength is equal to a wavelength in header file
{
//band_index(p, page);
for(unsigned j = 0; j < X; j++)
{
p[j] = c[j * B + page];
}
}
return true;
}
//given a y and a wavelength, return the y-band data
//I do not use it right now, to accelerate the processing speed, I try to read a YZ whole slice into memory first, and then we can call "getYZ"
bool get_x_wavelength(T * p, unsigned y, double wavelength)
{
unsigned int X = header.samples; //calculate the number of pixels in a sample
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 ( header.wavelength[page] > wavelength ){
file.seekg( y * header.bands * header.samples * sizeof(T), std::ios::beg);
for(unsigned j = 0; j < header.samples; j++)
{
file.read((char *)(p + j), sizeof(T));
file.seekg((header.bands - 1) * sizeof(T), std::ios::cur);
}
return true;
}
while( header.wavelength[page] < wavelength )
{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == header.bands) {
file.seekg( (y * header.bands * header.samples + header.bands - 1)* sizeof(T), std::ios::beg);
for(unsigned j = 0; j < header.samples; j++)
{
file.read((char *)(p + j), sizeof(T));
file.seekg((header.bands - 1) * sizeof(T), std::ios::cur);
}
return true;
}
}
if ( wavelength < header.wavelength[page] )
{
p1=(T*)malloc( X * sizeof(T)); //memory allocation
p2=(T*)malloc( X * sizeof(T));
//band_index(p1, page - 1);
file.seekg( (y * header.bands * header.samples + page - 1)* sizeof(T), std::ios::beg);
for(unsigned j = 0; j < header.samples; j++)
{
file.read((char *)(p1 + j), sizeof(T));
file.seekg((header.bands - 1) * sizeof(T), std::ios::cur);
}
//band_index(p2, page );
file.seekg( (y * header.bands * header.samples + page)* sizeof(T), std::ios::beg);
for(unsigned j = 0; j < header.samples; j++)
{
file.read((char *)(p2 + j), sizeof(T));
file.seekg((header.bands - 1) * sizeof(T), std::ios::cur);
}
for(unsigned i=0; i < header.samples; i++){
double r = (double) (wavelength - header.wavelength[page-1]) / (double) (header.wavelength[page] - header.wavelength[page-1]);
p[i] = (p2[i] - p1[i]) * r + p1[i];
}
}
else //if the wavelength is equal to a wavelength in header file
{
//band_index(p, page);
file.seekg( (y * header.bands * header.samples + page) * sizeof(T), std::ios::beg);
for(unsigned j = 0; j < header.samples; j++)
{
file.read((char *)(p + j), sizeof(T));
file.seekg((header.bands - 1) * sizeof(T), std::ios::cur);
}
}
//free(p1);
//free(p2);
return true;
}
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//save one pixel of the BIP file into the memory, and return the pointer
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//I have not used it so far
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bool getSpectrum(T * p, unsigned x, unsigned y){
unsigned int i;
if ( x >= header.samples || y >= header.lines){ //make sure the sample and line number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
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exit(1);
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}
file.seekg((x + y * header.samples) * header.bands * sizeof(T), std::ios::beg); //point to the certain sample and line
file.read((char *)p, sizeof(T) * header.bands);
return true;
}
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//given a Y ,return a ZX slice
bool getY(T * p, unsigned y)
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{
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if ( y >= header.lines){ //make sure the line number is right
std::cout<<"ERROR: line out of range"<<std::endl;
exit(1);
}
file.seekg(y * header.bands * header.samples * sizeof(T), std::ios::beg);
file.read((char *)p, sizeof(T) * header.bands * header.samples);
return true;
}
//(BIP) baseline correction
//processing speed is too slow
bool baseline(std::string outname, std::vector<double> wls){
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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 = header.bands * header.samples; //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 = header.bands;
unsigned int X = header.samples;
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T* c; //pointer to the current Y slice
c = (T*)malloc(L); //memory allocation
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T* a; //pointer to the two YZ lines surrounding the current YZ line
T* b;
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a = (T*)malloc(X * sizeof(T));
b = (T*)malloc(X * sizeof(T));
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double ai, bi; //stores the two baseline points wavelength surrounding the current band
double ci; //stores the current band's wavelength
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unsigned control=0;
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if (a == NULL || b == NULL || c == NULL){
std::cout<<"ERROR: error allocating memory";
exit(1);
}
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// loop start correct every y slice
for (unsigned k =0; k < header.lines; k++)
{
//get the current y slice
getY(c, k);
//initialize lownum, highnum, low, high
ai = header.wavelength[0];
//if no baseline point is specified at band 0,
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//set the baseline point at band 0 to 0
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if(wls[0] != header.wavelength[0]){
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++){
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//update baseline points, if necessary
if( header.wavelength[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];
getYZ(b, c, bi);
}
//if the last BL point on the last band of the file?
else if ( wls[control] < header.wavelength[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 = header.wavelength[B - 1];
}
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}
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//get the current YZ line
//band_index(c, cii);
file.seekg( (k * header.bands * X + cii)* sizeof(T), std::ios::beg);
for(unsigned j = 0; j < X; j++)
{
file.read((char *)(c + j), sizeof(T));
file.seekg((B - 1) * sizeof(T), std::ios::cur);
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}
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ci = header.wavelength[cii];
//perform the baseline correction
for(unsigned i=0; i < X; i++)
{
double r = (double) (ci - ai) / (double) (bi - ai);
c[i * B + cii] =(float) ( c[i * B + cii] - (b[i] - a[i]) * r - a[i] );
}
}//loop for YZ line end
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target.write(reinterpret_cast<const char*>(c), L); //write the corrected data into destination
}//loop for Y slice end
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header.save(headername); //save the new header file
free(a);
free(b);
free(c);
target.close();
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return true;
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}
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// normalize the BIP file
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bool normalize(std::string outname, double band)
{
unsigned int B = header.bands; //calculate the number of bands
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unsigned int Y = header.lines;
unsigned int X = header.samples;
unsigned int ZX = header.bands * header.samples;
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unsigned int XY = header.samples * header.lines; //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);
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std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
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T * c; //pointer to the current ZX slice
T * b; //pointer to the standard band
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b = (T*)malloc( S ); //memory allocation
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c = (T*)malloc( L );
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getBand(b, band); //get the certain band into memory
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for(unsigned j = 0; j < Y; j++)
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{
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getY(c, j);
for(unsigned i = 0; i < X; i++)
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for(unsigned m = 0; m < B; m++)
{
c[m + i * B] = c[m + i * B] / b[i + j * X];
}
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}
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target.write(reinterpret_cast<const char*>(c), L); //write normalized data into destination
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}
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header.save(headername); //save the new header file
free(b);
free(c);
target.close();
return true;
}
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//convert BIP file to BSQ file and save it
bool bsq(std::string outname)
{
unsigned int S = header.samples * header.lines * 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 < header.bands; i++)
{
band_index(p, i);
target.write(reinterpret_cast<const char*>(p), S); //write a band data into target file
}
header.interleave = rts::envi::interleaveType::BSQ; //change the type of file in header file
header.save(headername);
free(p);
target.close();
return true;
}
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};
}
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