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#ifndef STIM_BIP_H
#define STIM_BIP_H
#include "../envi/envi_header.h"
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#include "../envi/bil.h"
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#include "../envi/binary.h"
#include <cstring>
#include <utility>
namespace rts{
template <typename T>
class bip: public binary<T> {
protected:
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std::vector<double> w; //band wavelength
unsigned int offset; //header offset
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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 file, given the file and its header's names
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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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//copy the wavelengths to the BSQ file structure
w = wavelengths;
//copy the offset to the structure
offset = header_offset;
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return open(filename, vec<unsigned int>(X, Y, B), header_offset);
return false;
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}
//save one band of the file into the memory, and return the pointer
bool band_index( T * p, unsigned int page){
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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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//binary::getSlice(p, 0, page); //I met some problems when I called this function?????
file.seekg(page * sizeof(T), std::ios::beg);
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for (unsigned i = 0; i < R[0] * R[1]; i++)
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{
file.read((char *)(p + i), sizeof(T));
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file.seekg( (R[2] - 1) * sizeof(T), std::ios::cur);
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}
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return true;
}
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bool band( T * p, double 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 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
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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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{
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++){
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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
{
band_index(p, page);
}
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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)
{
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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 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 ){
for(unsigned j = 0; j < R[0]; j++)
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{
p[j] = c[j * B];
}
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) {
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for(unsigned j = 0; j < R[0]; j++)
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{
p[j] = c[(j + 1) * B - 1];
}
return true;
}
}
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if ( wavelength < w[page] )
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{
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++){
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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
{
//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)
{
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unsigned int X = R[0]; //calculate the number of pixels in a sample
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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 ){
file.seekg( y * R[2] * R[0] * sizeof(T), std::ios::beg);
for(unsigned j = 0; j < R[0]; j++)
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{
file.read((char *)(p + j), sizeof(T));
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file.seekg((R[2] - 1) * sizeof(T), std::ios::cur);
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}
return true;
}
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while( w[page] < wavelength )
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{
page++;
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if (page == R[2]) {
file.seekg( (y * R[2] * R[0] + R[2] - 1)* sizeof(T), std::ios::beg);
for(unsigned j = 0; j < R[0]; j++)
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{
file.read((char *)(p + j), sizeof(T));
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file.seekg((R[2] - 1) * sizeof(T), std::ios::cur);
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}
return true;
}
}
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if ( wavelength < w[page] )
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{
p1=(T*)malloc( X * sizeof(T)); //memory allocation
p2=(T*)malloc( X * sizeof(T));
//band_index(p1, page - 1);
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file.seekg( (y * R[2] * R[0] + page - 1)* sizeof(T), std::ios::beg);
for(unsigned j = 0; j < R[0]; j++)
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{
file.read((char *)(p1 + j), sizeof(T));
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file.seekg((R[2] - 1) * sizeof(T), std::ios::cur);
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}
//band_index(p2, page );
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file.seekg( (y * R[2] * R[0] + page)* sizeof(T), std::ios::beg);
for(unsigned j = 0; j < R[0]; j++)
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{
file.read((char *)(p2 + j), sizeof(T));
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file.seekg((R[2] - 1) * sizeof(T), std::ios::cur);
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}
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for(unsigned i=0; i < R[0]; i++){
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
{
//band_index(p, page);
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file.seekg( (y * R[2] * R[0] + page) * sizeof(T), std::ios::beg);
for(unsigned j = 0; j < R[0]; j++)
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{
file.read((char *)(p + j), sizeof(T));
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file.seekg((R[2] - 1) * sizeof(T), std::ios::cur);
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}
}
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return true;
}
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//save one pixel of the BIP file into the memory, and return the pointer
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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;
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exit(1);
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}
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file.seekg((x + y * R[0]) * R[2] * sizeof(T), std::ios::beg); //point to the certain sample and line
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file.read((char *)p, sizeof(T) * R[2]);
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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 >= 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;
}
//(BIP) baseline correction
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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 = 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
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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;
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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
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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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control=0;
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ai = w[0];
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//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] != 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++){
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//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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//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 * B + cii] =(T) ( c[i * B + cii] - (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
}//loop for Y slice end
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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 w)
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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);
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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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band(b, w); //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);
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unsigned jX = j * X; //to avoid calculating it many times
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for(unsigned i = 0; i < X; i++)
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{
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unsigned iB = i * B;
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for(unsigned m = 0; m < B; m++)
{
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c[m + iB] = c[m + iB] / b[i + jX]; //perform normalization
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}
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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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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)
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{
std::string temp = outname + "_temp";
std::string headtemp = temp + ".hdr";
//first creat a temporary bil file and convert bip file to bil file
bil(temp);
rts::bil<T> n;
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if(n.open(temp, R[0], R[1], R[2], offset, w)==false){ //open infile
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std::cout<<"ERROR: unable to open input file"<<std::endl;
exit(1);
}
//then convert bil file to bsq file
n.bsq(outname);
n.close();
remove(temp.c_str());
remove(headtemp.c_str());
return true;
}
//convert bip file to bil file and save it
bool bil(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";
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T * p; //pointer to the current ZX slice for bip file
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p = (T*)malloc(S);
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T * q; //pointer to the current XZ slice for bil file
q = (T*)malloc(S);
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for ( unsigned i = 0; i < R[1]; i++)
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{
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getY(p, i);
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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[ks + j] = p[k + j * R[2]];
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}
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
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}
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free(p);
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free(q);
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target.close();
return true;
}
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//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;
}
//untested
//providing the left and the right bound wavelength, return baseline-corrected band height
bool height(double lb, double rb, double bandwavelength){
T* lp;
T* rp;
T* result;
lp = (T*) malloc(sizeof(R[0] * R[1] * sizeof(T))); //memory allocation
rp = (T*) malloc(sizeof(R[0] * R[1] * sizeof(T)));
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result = (T*) malloc(sizeof(R[0] * R[1] * sizeof(T)));
|
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band(lp, lb); //get the data of the left bounbd and the right bound
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
return true;
}
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|
//calculate the area between two bound point(including baseline correction)
bool area(double lb, double rb){
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
T* result; //area result
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);
result = (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 (lb >= w[ai]){
ai++;
}
while (rb <= w[bi]){
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
baseline_band(lb, rb, lp, rp, w[bi], cur); //ending part
for(unsigned j = 0; j < XY; j++){
result[j] += (rb - w[bi]) * cur[j] / 2.0;
}
baseline_band(lb, rb, lp, rp, w[ai], cur); //beginnning part
for(unsigned j = 0; j < XY; j++){
result[j] += (w[ai] - lb) * cur[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
}
///////////////for testing use
std::ofstream text("area_result.txt",std::ios::out);
for (unsigned i = 0; i < 640; i++)
{
for (unsigned j = 0; j < 384; j++)
{
text<<result[i*384+j]<<", ";
}
text<<std::endl;
}
///////////////
return true;
}
|
4a6f666c
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Added mask method
|
595
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611
|
//create mask file
bool mask(unsigned char* p, double mask_band, double threshold){
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;
}
return true;
}
|
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|
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|
//close the file
bool close(){
file.close();
return true;
}
|
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|
618
|
};
|
6aa04ba2
David Mayerich
interleave types
|
619
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}
|
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added a new ENVI ...
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|
#endif
|