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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>
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namespace stim{
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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);
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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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//if there are no wavelengths in the BSQ file
if(w.size() == 0)
return band_index(p, (unsigned int)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
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//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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{
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T * p1;
T * p2;
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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];
}
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free(p1);
free(p2);
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}
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
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//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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{
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T * p1;
T * p2;
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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];
}
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free(p1);
free(p2);
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}
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;
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//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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337
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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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|
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|
//update baseline points, if necessary
|
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|
if( w[cii] >= bi && cii != B - 1) {
|
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350
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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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|
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|
else if ( wls[control] < w[B - 1]) {
|
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|
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359
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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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}
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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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386
|
return true;
|
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|
}
|
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|
// normalize the BIP file
|
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cleaned up the code
|
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|
bool normalize(std::string outname, double w)
|
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|
{
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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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|
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c = (T*)malloc( L );
|
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|
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|
|
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David Mayerich
cleaned up the code
|
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band(b, w); //get the certain band into memory
|
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|
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|
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for(unsigned j = 0; j < Y; j++)
|
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|
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|
{
|
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|
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|
getY(c, j);
|
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|
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|
unsigned jX = j * X; //to avoid calculating it many times
|
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|
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|
for(unsigned i = 0; i < X; i++)
|
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|
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|
{
|
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|
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|
unsigned iB = i * B;
|
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|
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419
|
for(unsigned m = 0; m < B; m++)
{
|
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|
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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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|
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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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|
}
|
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|
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|
|
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|
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430
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|
free(b);
free(c);
target.close();
return true;
}
|
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|
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434
|
//convert BIP file to BSQ file and save it
bool bsq(std::string outname)
|
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|
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436
437
438
439
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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);
|
8a86bd56
David Mayerich
changed rts names...
|
441
|
stim::bil<T> n;
|
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David Mayerich
cleaned up the code
|
442
|
if(n.open(temp, R[0], R[1], R[2], offset, w)==false){ //open infile
|
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|
443
444
445
446
447
448
449
450
451
452
453
454
455
|
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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|
456
|
{
|
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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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Ziqi added functi...
|
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459
460
461
|
std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
|
f6169dea
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|
462
|
T * p; //pointer to the current ZX slice for bip file
|
11f177d5
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Ziqi added functi...
|
463
|
p = (T*)malloc(S);
|
f6169dea
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|
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465
|
T * q; //pointer to the current XZ slice for bil file
q = (T*)malloc(S);
|
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Ziqi added functi...
|
466
|
|
6708cc25
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|
467
|
for ( unsigned i = 0; i < R[1]; i++)
|
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|
468
|
{
|
f6169dea
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|
469
|
getY(p, i);
|
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|
470
|
for ( unsigned k = 0; k < R[2]; k++)
|
f6169dea
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Ziqi completed bi...
|
471
|
{
|
6708cc25
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|
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473
474
|
unsigned ks = k * R[0];
for ( unsigned j = 0; j < R[0]; j++)
q[ks + j] = p[k + j * R[2]];
|
f6169dea
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Ziqi completed bi...
|
475
476
|
}
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
|
11f177d5
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Ziqi added functi...
|
477
|
}
|
f6169dea
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Ziqi completed bi...
|
478
|
|
11f177d5
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Ziqi added functi...
|
479
480
|
free(p);
|
f6169dea
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Ziqi completed bi...
|
481
|
free(q);
|
11f177d5
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Ziqi added functi...
|
482
483
484
|
target.close();
return true;
}
|
88c3e636
heziqi
Ziqi added big.h
|
485
|
|
20c212c0
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Ziqi added functi...
|
486
487
488
489
490
491
492
493
494
495
496
497
498
|
//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;
}
|
517876d6
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metrics finished ...
|
499
|
|
70407ea9
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Ziqi completed he...
|
500
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
501
502
503
|
T* lp;
T* rp;
|
70407ea9
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Ziqi completed he...
|
504
505
506
507
|
unsigned XY = R[0] * R[1];
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
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Ziqi added functi...
|
508
|
|
70407ea9
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Ziqi completed he...
|
509
|
band(lp, lb);
|
20c212c0
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Ziqi added functi...
|
510
511
512
513
|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
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metrics finished ...
|
514
515
|
free(lp);
free(rp);
|
20c212c0
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|
516
517
518
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
519
|
|
20c212c0
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Ziqi added functi...
|
520
|
//calculate the area between two bound point(including baseline correction)
|
70407ea9
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|
521
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
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Ziqi added functi...
|
522
523
524
525
526
|
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
|
20c212c0
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Ziqi added functi...
|
527
528
529
530
531
532
533
534
|
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);
|
20c212c0
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Ziqi added functi...
|
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
|
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
|
70407ea9
heziqi
Ziqi completed he...
|
557
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
558
559
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
560
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
561
562
563
564
565
566
567
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
568
569
|
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
570
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
571
|
result[j] += (rab - w[bi]) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
572
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
573
574
|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
575
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
576
|
result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
577
|
}
|
517876d6
heziqi
metrics finished ...
|
578
|
|
20c212c0
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Ziqi added functi...
|
579
580
581
582
583
584
585
586
587
588
589
|
//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
}
|
70407ea9
heziqi
Ziqi completed he...
|
590
|
|
517876d6
heziqi
metrics finished ...
|
591
592
593
594
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
595
596
597
|
return true;
}
|
70407ea9
heziqi
Ziqi completed he...
|
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
|
//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];
}
|
517876d6
heziqi
metrics finished ...
|
614
615
616
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
|
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];
}
|
517876d6
heziqi
metrics finished ...
|
637
638
639
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
|
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];
}
|
517876d6
heziqi
metrics finished ...
|
660
661
662
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
663
664
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
|
//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;
}
|
4a6f666c
heziqi
Added mask method
|
762
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//create mask file
|
f4c5d71b
David Mayerich
started working w...
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763
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bool build_mask(double mask_band, double threshold, unsigned char* p){
|
4a6f666c
heziqi
Added mask method
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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;
}
|
517876d6
heziqi
metrics finished ...
|
775
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
776
777
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|
return true;
}
|
740f8cd2
heziqi
added apply_mask
|
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//apply mask
bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
unsigned ZX = R[2] * R[0]; //calculate number of a band
unsigned L = ZX * sizeof(T);
T * temp = (T*)malloc(L);
for (unsigned i = 0; i < R[1]; i++)
{
getY(temp, i);
for ( unsigned j = 0; j < R[0]; j++)
{
for (unsigned k = 0; k < R[2]; k++)
{
if(p[i * R[0] + k] == 0)
temp[j * R[2] + k] = 0;
else
continue;
}
}
target.write(reinterpret_cast<const char*>(temp), L); //write a band data into target file
}
target.close();
free(temp);
return true;
}
|
f6169dea
heziqi
Ziqi completed bi...
|
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811
812
813
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815
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//close the file
bool close(){
file.close();
return true;
}
|
88c3e636
heziqi
Ziqi added big.h
|
816
|
};
|
6aa04ba2
David Mayerich
interleave types
|
817
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}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
818
819
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#endif
|