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#ifndef STIM_ENVI_H
#define STIM_ENVI_H
#include "../envi/envi_header.h"
#include "../envi/bsq.h"
#include "../envi/bip.h"
#include "../envi/bil.h"
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#include <iostream>
#include "../../CImg/CImg.h"
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namespace stim{
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//container class for an ENVI binary file reader
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class envi{
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void* file; //void pointer to the relevant file reader (bip, bsq, or bil - with appropriate data type)
public:
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envi_header header;
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bool allocate(){
file = NULL; //set file to a NULL pointer
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if(header.interleave == envi_header::BSQ){
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if(header.data_type ==envi_header::float32)
return(file = new bsq<float>());
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else if(header.data_type == envi_header::float64)
return(file = new bsq<double>());
}
else if(header.interleave == envi_header::BIP){
if(header.data_type ==envi_header::float32)
return(file = new bip<float>());
else if(header.data_type == envi_header::float64)
return(file = new bip<double>());
}
else if(header.interleave == envi_header::BIL){
if(header.data_type ==envi_header::float32)
return(file = new bil<float>());
else if(header.data_type == envi_header::float64)
return(file = new bil<double>());
}
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exit(1); //if the function hasn't already returned, we don't handle this state
}
bool open(std::string filename, std::string headername){
//allocate memory
allocate();
//load the header
header.load(headername);
//load the file
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if(header.interleave == envi_header::BSQ) { //if the infile is bsq file
if(header.data_type == envi_header::float32) {
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return ((bsq<float>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
else if(header.data_type == envi_header::float64) {
return ((bsq<double>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
}
else
return false;
}
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else if(header.interleave == envi_header::BIL) { //if the infile is bil file
if(header.data_type == envi_header::float32) {
return ((bil<float>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
}
else if(header.data_type == envi_header::float64) {
return ((bil<double>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
}
else
return false;
}
else if(header.interleave == envi_header::BIP) { //if the infile is bip file
if(header.data_type == envi_header::float32) {
return ((bip<float>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
}
else if(header.data_type == envi_header::float64) {
return ((bip<double>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
}
else
return false;
}
else{
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std::cout<<"ERROR: unidentified type file "<<headername<<std::endl;
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exit(1);
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}
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}
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//perform normalization
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bool normalize(std::string outfile, double band){
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if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
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if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->normalize(outfile, band);
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else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->normalize(outfile,band);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
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else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->normalize(outfile, band);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->normalize(outfile,band);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->normalize(outfile, band);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->normalize(outfile,band);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
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return false;
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}
//perform baseline correction
bool baseline(std::string outfile, std::vector<double> w){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->baseline(outfile, w);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->baseline(outfile,w);
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->baseline(outfile, w);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->baseline(outfile, w);
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->baseline(outfile, w);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->baseline(outfile, w);
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
//perform conversion
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bool convert(std::string outfile, stim::envi_header::interleaveType interleave){
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if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32){ //if the data type of infile is float
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL) //if the target file is bil file
return ((bsq<float>*)file)->bil(outfile);
else if(interleave == envi_header::BIP) //if the target file is bip file
return ((bsq<float>*)file)->bip(outfile);
}
else if(header.data_type == envi_header::float64){ //if the data type is float
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL)
return ((bsq<double>*)file)->bil(outfile);
else if(interleave == envi_header::BIP)
return ((bsq<double>*)file)->bip(outfile);
}
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIL){
if(header.data_type ==envi_header::float32){ //if the data type of infile is float
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BSQ) //if the target file is bsq file
return ((bil<float>*)file)->bsq(outfile);
else if(interleave == envi_header::BIP) //if the target file is bip file
return ((bil<float>*)file)->bip(outfile);
}
else if(header.data_type == envi_header::float64){ //if the data type is float
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BSQ)
return ((bil<double>*)file)->bsq(outfile);
else if(interleave == envi_header::BIP)
return ((bil<double>*)file)->bip(outfile);
}
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIP){
if(header.data_type ==envi_header::float32){ //if the data type of infile is float
if(interleave == envi_header::BIP){
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL) //if the target file is bil file
return ((bip<float>*)file)->bil(outfile);
else if(interleave == envi_header::BSQ) //if the target file is bsq file
return ((bip<float>*)file)->bsq(outfile);
}
else if(header.data_type == envi_header::float64){ //if the data type is float
if(interleave == envi_header::BIP){
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL) //if the target file is bil file
return ((bip<double>*)file)->bil(outfile);
else if(interleave == envi_header::BSQ) //if the target file is bsq file
return ((bip<double>*)file)->bsq(outfile);
}
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else{
std::cout<<"ERROR: unidentified interleave type"<<std::endl;
exit(1);
}
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return false;
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}
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//create a mask based on a band and threshold, save it to p (if p is not NULL)
bool build_mask(double mask_band, double threshold, unsigned char* p = NULL) {
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if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
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return ((bsq<float>*)file)->build_mask(mask_band, threshold, p);
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else if(header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->build_mask(mask_band, threshold, p);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
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return ((bil<float>*)file)->build_mask(mask_band, threshold, p);
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else if(header.data_type == envi_header::float64)
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return ((bil<double>*)file)->build_mask(mask_band, threshold, p);
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else
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}
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else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
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return ((bip<float>*)file)->build_mask(mask_band, threshold, p);
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else if(header.data_type == envi_header::float64)
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return ((bip<double>*)file)->build_mask(mask_band, threshold, p);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
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return false;
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}
//apply mask
bool apply_mask(std::string outfile, unsigned char* p)
{
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->apply_mask(outfile, p);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->apply_mask(outfile, p);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->apply_mask(outfile, p);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->apply_mask(outfile, p);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->apply_mask(outfile, p);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->apply_mask(outfile, p);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
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else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
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}
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//peak height to peak height ratio
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, void * result){
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if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
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return ((bsq<float>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (float*)result);
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else if(header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (double*)result);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
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return ((bil<float>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (float*)result);
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else if(header.data_type == envi_header::float64)
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return ((bil<double>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (double*)result);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
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return ((bip<float>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (float*)result);
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else if(header.data_type == envi_header::float64)
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return ((bip<double>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
//peak area to peak height ratio
bool pa_to_ph(double lb1, double rb1, double lab1, double rab1, double lb2, double rb2, double pos, void * result){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
//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, void* result){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (double*)result);
|
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20c212c0
heziqi
Ziqi added functi...
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
|
|
517876d6
heziqi
metrics finished ...
|
458
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//center of gravity
bool cpoint(double lb1, double rb1, double lab1, double rab1, void* result){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->cpoint(lb1, rb1, lab1, rab1, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->cpoint(lb1, rb1, lab1, rab1, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->cpoint(lb1, rb1, lab1, rab1, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->cpoint(lb1, rb1, lab1, rab1, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->cpoint(lb1, rb1, lab1, rab1,(float*)result);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->cpoint(lb1, rb1, lab1, rab1, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
|
|
6708cc25
heziqi
Ziqi added envi c...
|
494
495
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bool close(){
if(header.interleave == envi_header::BSQ){
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->close();
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->close();
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIL){
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->close();
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->close();
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIP){
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->close();
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->close();
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
|
e933c14e
David Mayerich
cleaned up the code
|
527
|
return false;
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
528
|
}
|
|
bfe9c6db
heziqi
added feature_mat...
|
529
530
531
532
533
534
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541
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559
560
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562
|
//get one pixel from binary file
bool pixel(void * p, unsigned n){
if(header.interleave == envi_header::BSQ){
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->pixel((float*)p, n);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->pixel((double*)p, n);
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIL){
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->pixel((float*)p, n);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->pixel((double*)p, n);
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIP){
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->pixel((float*)p, n);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->pixel((double*)p, n);
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
return false;
}
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
563
564
565
566
567
568
569
570
571
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
|
d1d8ef91
David Mayerich
added band readin...
|
572
573
574
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576
577
578
|
bool band(void* ptr, double wavelength){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->band((float*)ptr, wavelength);
}
|
|
ee4dea28
David Mayerich
fixed errors in c...
|
579
|
return false;
|
|
1582ce07
David Mayerich
added band_index(...
|
580
581
582
583
584
585
|
}
bool band_index(void* ptr, unsigned int b){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
|
d1d8ef91
David Mayerich
added band readin...
|
586
|
|
|
1582ce07
David Mayerich
added band_index(...
|
587
588
|
}
return false;
|
|
d1d8ef91
David Mayerich
added band readin...
|
589
|
}
|
|
9f489bb3
heziqi
Added load_mask a...
|
590
|
|
|
bfe9c6db
heziqi
added feature_mat...
|
591
592
593
|
//load mask from maskfile and save it into memory
bool load_mask(unsigned char * mask, std::string maskname){
//open the mask file
|
|
9f489bb3
heziqi
Added load_mask a...
|
594
|
cimg_library::CImg<unsigned char> mask_image(maskname.c_str());
|
|
bfe9c6db
heziqi
added feature_mat...
|
595
|
//save mask file into memory
|
|
9f489bb3
heziqi
Added load_mask a...
|
596
|
memcpy(mask, mask_image.data(), mask_image.size());
|
|
bfe9c6db
heziqi
added feature_mat...
|
597
598
|
mask_image.clear();
return true;
|
|
9f489bb3
heziqi
Added load_mask a...
|
599
|
}
|
|
d1d8ef91
David Mayerich
added band readin...
|
600
|
|
|
bfe9c6db
heziqi
added feature_mat...
|
601
|
//p:start positon; N: number of pixels saved in X;
|
|
9f489bb3
heziqi
Added load_mask a...
|
602
|
bool feature_matrix(void * X, unsigned char * mask, unsigned start, unsigned N)
|
|
bfe9c6db
heziqi
added feature_mat...
|
603
|
{
|
|
4b37859f
heziqi
added predict
|
604
605
|
//save pixels in X as floating numbers: float * p
float * p = (float*)malloc(header.bands * sizeof(float)); //save pixel information
|
|
c9fd97f0
David Mayerich
edits for classif...
|
606
|
unsigned pixels = header.samples * header.lines; //calculate pixel numbers in a band
|
|
bfe9c6db
heziqi
added feature_mat...
|
607
608
609
|
unsigned count = 0; //for counting use
unsigned j = 0; //memory the pointer location in X
|
|
c9fd97f0
David Mayerich
edits for classif...
|
610
611
612
613
614
615
616
617
618
619
620
|
//create two indices into the mask (mask index and pixel index)
unsigned mi = 0; //valid pixel index
unsigned pi = 0; //actual pixel in the mask
//find the actual pixel index for the mask index "start"
while(mi < start){
if(mask[pi])
mi++;
pi++;
}
|
|
c9fd97f0
David Mayerich
edits for classif...
|
621
622
|
for(unsigned i = pi; i < pixels; i++){
|
|
bfe9c6db
heziqi
added feature_mat...
|
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
|
if(mask[i] != 0){
pixel(p, i);
//copy p to X
for(unsigned k = 0; k < header.bands; k++){
((float *)X)[j] = p[k];
j++;
}
count++;
if(count == N)
break;
}
else
continue;
}
if(count < N){
std::cout << "number of valid pixels in the mask : " << count <<"is less than N: "<< N;
exit(1);
}
|
|
b0fee590
heziqi
convert long int ...
|
641
|
free(p);
|
|
bfe9c6db
heziqi
added feature_mat...
|
642
643
|
return true;
}
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
644
645
646
647
648
649
650
651
|
};
} //end namespace rts
#endif
|
