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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 "../math/fd_coefficients.h"
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#include <iostream>
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//#include "../image/image.h"
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namespace stim{
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/** This class implements reading of ENVI hyperspectral files. These files can be stored in multiple orientations
(including BSQ, BIP, and BIL) in order to optimize streaming speed depending on applications. Basic ENVI
files are stored on disk as a large binary file with a corresponding header. Code for reading and processing
ENVI header files is in the envi_header class.
*/
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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)
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std::string fname; //file name used for repeated opening and closing
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public:
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envi_header header;
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/// Returns the size of the data type in bytes
unsigned int type_size(){
if(header.data_type == envi_header::float32) return 4;
if(header.data_type == envi_header::float64) return 8;
exit(1);
}
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/// Returns the progress of the current processing operation as a percentage
void reset_progress(){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
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((bsq<float>*)file)->reset_progress();
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else if(header.data_type == envi_header::float64)
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((bsq<double>*)file)->reset_progress();
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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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((bil<float>*)file)->reset_progress();
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else if(header.data_type == envi_header::float64)
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((bil<double>*)file)->reset_progress();
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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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((bip<float>*)file)->reset_progress();
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else if(header.data_type == envi_header::float64)
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((bip<double>*)file)->reset_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
/// Returns the progress of the current processing operation as a percentage
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double progress(){
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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)->get_progress();
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else if(header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->get_progress();
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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)->get_progress();
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else if(header.data_type == envi_header::float64)
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return ((bil<double>*)file)->get_progress();
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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)->get_progress();
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else if(header.data_type == envi_header::float64)
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return ((bip<double>*)file)->get_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
}
return 0;
}
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/// Allocate memory for a new ENVI file based on the current interleave format (BIP, BIL, BSQ) and data type.
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void allocate(){
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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)
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file = new bsq<float>();
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file = new bsq<double>();
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}
else if(header.interleave == envi_header::BIP){
if(header.data_type ==envi_header::float32)
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file = new bip<float>();
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else if(header.data_type == envi_header::float64)
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file = new bip<double>();
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}
else if(header.interleave == envi_header::BIL){
if(header.data_type ==envi_header::float32)
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file = new bil<float>();
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else if(header.data_type == envi_header::float64)
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file = new bil<double>();
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}
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}
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/// Open a previously opened ENVI file
bool open(){
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//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(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
else if(header.data_type == envi_header::float64) {
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return ((bsq<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
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) {
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return ((bil<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
else if(header.data_type == envi_header::float64) {
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return ((bil<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
else
return false;
}
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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)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
else if(header.data_type == envi_header::float64) {
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return ((bip<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
else
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return false;
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}
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return true;
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}
/// Open an existing ENVI file given the filename and a header structure
/// @param filename is the name of the ENVI binary file
/// @param header is an ENVI header structure
bool open(std::string filename, stim::envi_header h){
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header = h; //store the header
fname = filename; //save the filename
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allocate();
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return open(); //open the ENVI file;
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}
/// Open an existing ENVI file given the file and header names.
/// @param filename is the name of the ENVI binary file
/// @param headername is the name of the ENVI header file
bool open(std::string filename, std::string headername){
//allocate memory
//allocate();
stim::envi_header h;
h.load(headername);
//load the header
//header.load(headername);
return open(filename, h);
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}
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/// Normalize a hyperspectral ENVI file given a band number and threshold.
/// @param outfile is the name of the normalized file to be output
/// @param band is the band label to be output
/// @param threshold is a threshold value specified such that normalization will only be done to values in the band > threshold (preventing division by small numbers)
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bool ratio(std::string outfile, double band, unsigned char* mask = NULL, bool PROGRESS = false){
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header.save(outfile + ".hdr");
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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)
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return ((bsq<float>*)file)->ratio(outfile, band, mask, PROGRESS);
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else if(header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->ratio(outfile,band, mask, PROGRESS);
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else
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}
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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)->ratio(outfile, band, mask, PROGRESS);
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else if(header.data_type == envi_header::float64)
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return ((bil<double>*)file)->ratio(outfile,band, mask, PROGRESS);
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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)->ratio(outfile, band, mask, PROGRESS);
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else if(header.data_type == envi_header::float64)
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return ((bip<double>*)file)->ratio(outfile,band, mask, PROGRESS);
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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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}
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/// Perform vector normalization on the ENVI image
void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){
header.save(outfile + ".hdr");
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
((bsq<float>*)file)->normalize(outfile, mask, PROGRESS);
else if(header.data_type == envi_header::float64)
((bsq<double>*)file)->normalize(outfile, mask, PROGRESS);
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)
((bil<float>*)file)->normalize(outfile, mask, PROGRESS);
else if(header.data_type == envi_header::float64)
((bil<double>*)file)->normalize(outfile, mask, PROGRESS);
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)
((bip<float>*)file)->normalize(outfile, mask, PROGRESS);
else if(header.data_type == envi_header::float64)
((bip<double>*)file)->normalize(outfile, mask, PROGRESS);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
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/// Performs piecewise linear baseline correction of a hyperspectral file/
/// @param outfile is the file name for the baseline corrected output
/// @param w is a list of band labels to serve as baseline points (zero values)
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bool baseline(std::string outfile, std::vector<double> w, unsigned char* mask = NULL, bool PROGRESS = false){
header.save(outfile + ".hdr");
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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)->baseline(outfile, w, mask, PROGRESS);
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else if(header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->baseline(outfile,w, mask, PROGRESS);
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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)
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return ((bil<float>*)file)->baseline(outfile, w, mask, PROGRESS);
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else if(header.data_type == envi_header::float64)
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return ((bil<double>*)file)->baseline(outfile, w, mask, PROGRESS);
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else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
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else if(header.interleave == envi_header::BIP){ //if the infile is bip file
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if(header.data_type ==envi_header::float32)
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798cea97
David Mayerich
added progress ba...
|
319
|
return ((bip<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
320
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
321
|
return ((bip<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
322
323
324
325
326
327
328
329
330
331
332
333
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
334
|
void project(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask, bool PROGRESS = false){
|
63fc1df8
David Mayerich
added an inverse ...
|
335
336
337
338
339
340
341
342
343
344
345
346
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
std::cout<<"ERROR: BSQ projection not supported"<<std::endl;
exit(1);
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
std::cout<<"ERROR: BIL projection not supported"<<std::endl;
exit(1);
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
347
|
((bip<float>*)file)->project(outfile, center, basis, M, mask, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
348
|
else if(header.data_type == envi_header::float64)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
349
|
((bip<double>*)file)->project(outfile, center, basis, M, mask, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
350
351
352
353
354
355
356
357
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
stim::envi_header out_hdr = header;
out_hdr.bands = M; //set the number of bands in the output header
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
358
359
|
out_hdr.wavelength.clear();
out_hdr.band_names.clear();
|
63fc1df8
David Mayerich
added an inverse ...
|
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
|
out_hdr.save(outfile + ".hdr"); //save the output header
}
void inverse(std::string outfile, double* center, double* basis, unsigned long long B, unsigned long long C = 0, bool PROGRESS = false){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
std::cout<<"ERROR: BSQ projection not supported"<<std::endl;
exit(1);
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
std::cout<<"ERROR: BIL projection not supported"<<std::endl;
exit(1);
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
((bip<float>*)file)->inverse(outfile, center, basis, B, C, PROGRESS);
else if(header.data_type == envi_header::float64)
((bip<double>*)file)->inverse(outfile, center, basis, B, C, PROGRESS);
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
stim::envi_header out_hdr = header;
out_hdr.bands = B; //set the number of bands in the output header
out_hdr.save(outfile + ".hdr"); //save the output header
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
390
391
392
393
|
/// Converts ENVI files between interleave types (BSQ, BIL, and BIP)
/// @param outfile is the file name for the converted output
/// @param interleave is the interleave format for the destination file
|
63fc1df8
David Mayerich
added an inverse ...
|
394
|
bool convert(std::string outfile, stim::envi_header::interleaveType interleave, bool PROGRESS = false){
|
a2bf1d08
David Mayerich
general bug fixes...
|
395
|
|
6708cc25
heziqi
Ziqi added envi c...
|
396
397
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
a2bf1d08
David Mayerich
general bug fixes...
|
398
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
399
400
401
402
|
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
403
404
405
|
else if(interleave == envi_header::BIL) //convert BSQ -> BIL
((bsq<float>*)file)->bil(outfile, PROGRESS);
else if(interleave == envi_header::BIP){ //ERROR
|
63fc1df8
David Mayerich
added an inverse ...
|
406
407
408
409
|
std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
//return ((bsq<float>*)file)->bip(outfile, PROGRESS);
exit(1);
}
|
6708cc25
heziqi
Ziqi added envi c...
|
410
411
412
|
}
else if(header.data_type == envi_header::float64){ //if the data type is float
|
a2bf1d08
David Mayerich
general bug fixes...
|
413
|
if(interleave == envi_header::BSQ){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
414
415
416
|
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
417
418
419
|
else if(interleave == envi_header::BIL) //convert BSQ -> BIL
((bsq<double>*)file)->bil(outfile, PROGRESS);
else if(interleave == envi_header::BIP){ //ERROR
|
63fc1df8
David Mayerich
added an inverse ...
|
420
421
422
423
|
std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
//return ((bsq<float>*)file)->bip(outfile, PROGRESS);
exit(1);
}
|
6708cc25
heziqi
Ziqi added envi c...
|
424
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
425
|
|
6708cc25
heziqi
Ziqi added envi c...
|
426
427
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
428
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
429
430
431
432
433
|
}
}
else if(header.interleave == envi_header::BIL){
|
a2bf1d08
David Mayerich
general bug fixes...
|
434
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
435
436
437
438
|
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
439
440
441
442
|
else if(interleave == envi_header::BSQ) //BIL -> BSQ
((bil<float>*)file)->bsq(outfile, PROGRESS);
else if(interleave == envi_header::BIP) //BIL -> BIP
((bil<float>*)file)->bip(outfile, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
443
444
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
445
446
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIL){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
447
448
449
|
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
450
451
452
453
|
else if(interleave == envi_header::BSQ) //BIL -> BSQ
((bil<double>*)file)->bsq(outfile, PROGRESS);
else if(interleave == envi_header::BIP) //BIL -> BIP
((bil<double>*)file)->bip(outfile, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
454
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
455
|
|
6708cc25
heziqi
Ziqi added envi c...
|
456
457
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
458
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
459
460
461
462
|
}
}
else if(header.interleave == envi_header::BIP){
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
463
|
|
a2bf1d08
David Mayerich
general bug fixes...
|
464
465
|
if(header.data_type ==envi_header::float32){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
466
467
468
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
469
470
471
|
else if(interleave == envi_header::BIL) //BIP -> BIL
((bip<float>*)file)->bil(outfile, PROGRESS);
else if(interleave == envi_header::BSQ){ //ERROR
|
63fc1df8
David Mayerich
added an inverse ...
|
472
473
474
475
|
std::cout<<"ERROR: conversion from BIP to BSQ isn't practical; use BIP->BIL->BSQ instead"<<std::endl;
//return ((bsq<float>*)file)->bip(outfile, PROGRESS);
exit(1);
}
|
6708cc25
heziqi
Ziqi added envi c...
|
476
477
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
478
479
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
480
481
482
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
483
484
485
|
else if(interleave == envi_header::BIL) //BIP -> BIL
((bip<double>*)file)->bil(outfile, PROGRESS);
else if(interleave == envi_header::BSQ){ //ERROR
|
63fc1df8
David Mayerich
added an inverse ...
|
486
487
488
489
|
std::cout<<"ERROR: conversion from BIP to BSQ isn't practical; use BIP->BIL->BSQ instead"<<std::endl;
//return ((bsq<float>*)file)->bip(outfile, PROGRESS);
exit(1);
}
|
6708cc25
heziqi
Ziqi added envi c...
|
490
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
491
|
|
6708cc25
heziqi
Ziqi added envi c...
|
492
493
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
494
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
495
496
|
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
497
|
|
6708cc25
heziqi
Ziqi added envi c...
|
498
499
500
501
|
else{
std::cout<<"ERROR: unidentified interleave type"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
502
503
504
505
506
|
stim::envi_header h = header;
h.interleave = interleave;
h.save(outfile + ".hdr");
return true;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
507
|
|
6708cc25
heziqi
Ziqi added envi c...
|
508
509
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
510
511
512
513
514
|
/// Builds a mask from a band image and threshold value
/// @param mask_band is the label for the band that will be used to build the mask
/// @param threshold is a value selected such that all band values greater than threshold will have a mask value of 'true'
/// @param p is memory of size X*Y that will store the resulting mask
|
ba51ae6a
David Mayerich
fixed metric calc...
|
515
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false) {
|
4a6f666c
heziqi
Added mask method
|
516
517
518
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
519
|
return ((bsq<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
520
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
521
|
return ((bsq<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
522
523
524
525
526
527
|
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)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
528
|
return ((bil<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
529
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
530
|
return ((bil<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
531
532
533
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
cacc3cdc
heziqi
attempt to fix CImg
|
534
|
|
4a6f666c
heziqi
Added mask method
|
535
536
|
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
537
|
return ((bip<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
538
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
539
|
return ((bip<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
540
541
542
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
bba4f4d9
David Mayerich
minor warning fixes
|
543
544
|
return false;
|
740f8cd2
heziqi
added apply_mask
|
545
546
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
|
/// Creates a mask with a true value for all pixels that contain finite values
void mask_finite(unsigned char* mask, bool PROGRESS = false){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
((bsq<float>*)file)->mask_finite(mask, PROGRESS);
else if(header.data_type == envi_header::float64)
((bsq<double>*)file)->mask_finite(mask, PROGRESS);
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)
((bil<float>*)file)->mask_finite(mask, PROGRESS);
else if(header.data_type == envi_header::float64)
((bil<double>*)file)->mask_finite(mask, PROGRESS);
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)
((bip<float>*)file)->mask_finite(mask, PROGRESS);
else if(header.data_type == envi_header::float64)
((bip<double>*)file)->mask_finite(mask, PROGRESS);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
577
578
579
580
|
/// Applies a mask to the ENVI file.
/// @param outfile is the name of the resulting masked output file
/// @param p is memory of size X*Y containing the mask (0 = false, all other values are true)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
581
|
void apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
740f8cd2
heziqi
added apply_mask
|
582
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
583
584
|
if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
if (header.data_type == envi_header::float32)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
585
|
((bsq<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
586
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
587
|
((bsq<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
588
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
589
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
590
591
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
592
593
|
else if (header.interleave == envi_header::BIL){ //if the infile is bil file
if (header.data_type == envi_header::float32)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
594
|
((bil<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
595
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
596
|
((bil<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
597
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
598
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
599
600
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
601
602
|
else if (header.interleave == envi_header::BIP){ //if the infile is bip file
if (header.data_type == envi_header::float32)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
603
|
((bip<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
604
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
605
|
((bip<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
606
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
607
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
608
|
}
|
4a6f666c
heziqi
Added mask method
|
609
610
|
else{
|
e843658b
Brad Deutsch
Previous push did...
|
611
612
613
|
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
614
|
header.save(outfile + ".hdr");
|
e843658b
Brad Deutsch
Previous push did...
|
615
616
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
617
618
619
|
/// Copies all spectra corresponding to nonzero values of a mask into a pre-allocated matrix of size (P x B)
/// where P is the number of masked pixels and B is the number of bands. The allocated memory can be accessed
/// using the following indexing: i = b*P + p
|
43dec788
David Mayerich
added code for si...
|
620
621
622
623
624
625
626
627
628
|
/// @param matrix is the destination for the pixel data
/// @param p is the mask
bool sift(void* matrix, 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)->sift((float*)matrix, p);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->sift((double*)matrix, p);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
629
|
else{
|
43dec788
David Mayerich
added code for si...
|
630
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
631
632
|
exit(1);
}
|
43dec788
David Mayerich
added code for si...
|
633
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
634
635
|
if (header.interleave == envi_header::BIP){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
636
637
638
639
640
641
642
643
|
if (header.data_type == envi_header::float32)
return ((bip<float>*)file)->sift((float*)matrix, p);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->sift((double*)matrix, p);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
644
645
|
}
if (header.interleave == envi_header::BIL){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
646
647
648
649
650
651
652
653
|
if (header.data_type == envi_header::float32)
return ((bil<float>*)file)->sift((float*)matrix, p);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->sift((double*)matrix, p);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
654
|
}
|
43dec788
David Mayerich
added code for si...
|
655
656
657
658
|
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
659
|
/// Saves in an array only those spectra corresponding to nonzero values of the mask.
|
43dec788
David Mayerich
added code for si...
|
660
661
|
/// @param outfile is the name of the sifted output file
/// @param p is the mask
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
662
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
e843658b
Brad Deutsch
Previous push did...
|
663
664
|
{
|
2fcab4f0
David Mayerich
added unsifting f...
|
665
|
//calculate the number of non-zero values in the mask
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
666
667
668
|
unsigned long long nnz = 0;
unsigned long long npixels = header.lines * header.samples;
for(unsigned long long i = 0; i < npixels; i++)
|
2fcab4f0
David Mayerich
added unsifting f...
|
669
670
671
672
673
|
if( p[i] > 0 ) nnz++;
//create a new header
envi_header new_header = header;
|
f7e99517
David Mayerich
added sifting for...
|
674
675
|
//if a BIL file is sifted, it's saved as a BIP
if(header.interleave == envi_header::BIL)
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
676
|
new_header.interleave = envi_header::BIP;
|
f7e99517
David Mayerich
added sifting for...
|
677
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
678
679
680
681
682
|
//set the number of lines to 1 (this is a matrix with 1 line and N samples)
new_header.lines = 1;
new_header.samples = nnz;
new_header.save(outfile + ".hdr");
|
e843658b
Brad Deutsch
Previous push did...
|
683
684
|
if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
if (header.data_type == envi_header::float32)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
685
|
return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
686
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
687
|
return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
688
689
690
691
692
693
|
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)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
694
|
return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
695
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
696
|
return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
697
698
699
700
701
702
|
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)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
703
|
return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
704
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
705
|
return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
706
707
708
709
710
711
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
4a6f666c
heziqi
Added mask method
|
712
713
|
exit(1);
}
|
4a6f666c
heziqi
Added mask method
|
714
|
return false;
|
cacc3cdc
heziqi
attempt to fix CImg
|
715
716
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
717
|
bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
|
2fcab4f0
David Mayerich
added unsifting f...
|
718
719
720
721
722
723
724
725
726
727
728
729
|
//create a new header
envi_header new_header = header;
//set the number of lines and samples in the output file (that's all that changes)
new_header.lines = lines;
new_header.samples = samples;
new_header.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
if (header.data_type == envi_header::float32)
|
a2bf1d08
David Mayerich
general bug fixes...
|
730
|
return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
731
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
732
|
return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
733
734
735
736
737
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else if (header.interleave == envi_header::BIL){ //if the infile is bil file
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
738
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
739
740
741
742
|
std::cout << "ERROR in stim::envi::unsift - BIL files aren't supported yet" << std::endl;
}
else if (header.interleave == envi_header::BIP){ //if the infile is bip file
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
743
|
|
8550e94f
David Mayerich
added sifting and...
|
744
|
if (header.data_type == envi_header::float32)
|
a2bf1d08
David Mayerich
general bug fixes...
|
745
|
return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
746
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
747
|
return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
748
749
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
750
751
752
753
|
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
754
|
}
|
cbce396e
David Mayerich
added support for...
|
755
|
return 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
756
757
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
758
759
760
761
762
763
764
765
766
|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param pos1 is the label value for the first peak (numerator) position
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param pos2 is the label value for the second peak (denominator) position
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
767
|
bool ph_to_ph(void * result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask){
|
20c212c0
heziqi
Ziqi added functi...
|
768
769
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
770
|
return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
771
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
772
|
return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
773
774
775
776
777
778
|
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)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
779
|
return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
780
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
781
|
return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
782
783
784
785
786
787
|
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)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
788
|
return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
789
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
790
|
return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
791
792
793
794
795
796
797
798
799
800
801
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
802
803
804
805
806
807
808
809
810
|
/// Compute the ratio between a peak area and peak height.
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param pos1 is the label value for the first peak (numerator) position
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param pos2 is the label value for the second peak (denominator) position
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
811
|
bool pa_to_ph(void* result, double lb1, double rb1, double lab1, double rab1, double lb2, double rb2, double pos, unsigned char* mask = NULL){
|
70407ea9
heziqi
Ziqi completed he...
|
812
813
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
814
|
return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
815
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
816
|
return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
817
818
819
820
821
822
|
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)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
823
|
return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
824
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
825
|
return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
826
827
828
829
830
831
|
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)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
832
|
return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
833
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
834
|
return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
835
836
837
838
839
840
841
842
843
844
845
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
846
847
848
849
850
851
852
853
854
|
/// Compute the ratio between two peak areas.
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param lab1 is the label value for the left bound (start of the integration) of the first peak (numerator)
/// @param rab1 is the label value for the right bound (end of the integration) of the first peak (numerator)
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param lab2 is the label value for the left bound (start of the integration) of the second peak (denominator)
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
855
|
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
|
cb455f98
David Mayerich
removed old ENVI ...
|
856
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
857
858
|
bool pa_to_pa(void* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, unsigned char* mask = NULL){
|
70407ea9
heziqi
Ziqi completed he...
|
859
860
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
861
|
return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
862
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
863
|
return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
864
865
866
867
868
869
|
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)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
870
|
return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
871
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
872
|
return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
873
874
875
876
877
878
|
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)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
879
|
return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
880
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
881
|
return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
882
883
884
885
886
887
888
889
890
891
892
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
893
894
895
896
897
898
899
|
/// Compute the centroid of a baseline corrected peak.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label for the start of the peak
/// @param rab is the label for the end of the peak
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
900
|
bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
|
517876d6
heziqi
metrics finished ...
|
901
902
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
903
|
return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
904
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
905
|
return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
906
907
908
909
910
911
|
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)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
912
|
return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
913
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
914
|
return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
915
916
917
918
919
920
|
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)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
921
|
return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
922
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
923
|
return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
924
925
926
927
928
929
930
931
932
933
934
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
935
|
/// Closes the ENVI file.
|
6708cc25
heziqi
Ziqi added envi c...
|
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
|
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
|
969
|
return false;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
970
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
971
972
973
974
975
|
/// Retrieve a single pixel and stores it in pre-allocated memory.
/// @param p is a pointer to pre-allocated memory at least sizeof(T) in size.
/// @param n is an integer index to the pixel using linear array indexing.
|
bfe9c6db
heziqi
added feature_mat...
|
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
|
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 ...
|
1009
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1010
|
/// Saves a header file describing the current ENVI file parameters.
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1011
1012
1013
1014
1015
1016
1017
1018
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1019
1020
1021
1022
|
/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
/// @param wavelength is a floating point value (usually a wavelength in spectral data) used as a label for the band to be copied.
|
63fc1df8
David Mayerich
added an inverse ...
|
1023
|
bool band(void* ptr, double wavelength, bool PROGRESS = false){
|
d1d8ef91
David Mayerich
added band readin...
|
1024
1025
1026
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1027
|
return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1028
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1029
|
return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1030
1031
1032
1033
1034
1035
1036
|
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)
|
63fc1df8
David Mayerich
added an inverse ...
|
1037
|
return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1038
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1039
|
return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1040
1041
1042
1043
1044
1045
1046
|
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)
|
63fc1df8
David Mayerich
added an inverse ...
|
1047
|
return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1048
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1049
|
return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1050
1051
1052
1053
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
d1d8ef91
David Mayerich
added band readin...
|
1054
|
}
|
ee4dea28
David Mayerich
fixed errors in c...
|
1055
|
return false;
|
1582ce07
David Mayerich
added band_index(...
|
1056
1057
|
}
|
27b826a8
David Mayerich
added a spherical...
|
1058
1059
1060
1061
1062
|
/// Retrieve a spectrum from the specified location
/// @param ptr is a pointer to pre-allocated memory of size B*sizeof(T)
/// @param x is the x-coordinate of the spectrum
/// @param y is the y-coordinate of the spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1063
|
bool spectrum(void* ptr, unsigned long long x, unsigned long long y, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
1064
1065
1066
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1067
|
return ((bsq<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1068
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1069
|
return ((bsq<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1070
1071
1072
1073
1074
1075
1076
|
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)
|
63fc1df8
David Mayerich
added an inverse ...
|
1077
|
return ((bil<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1078
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1079
|
return ((bil<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1080
1081
1082
1083
1084
1085
1086
|
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)
|
63fc1df8
David Mayerich
added an inverse ...
|
1087
|
return ((bip<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1088
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1089
|
return ((bip<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1090
1091
1092
1093
1094
1095
1096
1097
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1098
1099
1100
1101
|
/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
/// @param page <= B is the integer number of the band to be copied.
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1102
|
bool band_index(void* ptr, unsigned long long b){
|
081f2c9f
heziqi
made bip bil file...
|
1103
1104
|
if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
if (header.data_type == envi_header::float32)
|
1582ce07
David Mayerich
added band_index(...
|
1105
|
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
081f2c9f
heziqi
made bip bil file...
|
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
|
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->band_index((double*)ptr, b);
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)->band_index((float*)ptr, b);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->band_index((double*)ptr, b);
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)->band_index((float*)ptr, b);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->band_index((double*)ptr, b);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
1582ce07
David Mayerich
added band_index(...
|
1132
1133
|
}
return false;
|
d1d8ef91
David Mayerich
added band readin...
|
1134
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
1135
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1136
1137
1138
1139
|
/// Calculate the mean value for all masked (or valid) pixels in a band and returns the average spectrum
/// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
|
63fc1df8
David Mayerich
added an inverse ...
|
1140
|
bool avg_band(double * p, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1141
1142
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1143
|
return ((bsq<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1144
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1145
|
return ((bsq<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1146
1147
1148
1149
1150
1151
1152
|
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)
|
63fc1df8
David Mayerich
added an inverse ...
|
1153
|
return ((bil<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1154
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1155
|
return ((bil<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1156
1157
1158
1159
1160
1161
1162
|
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)
|
63fc1df8
David Mayerich
added an inverse ...
|
1163
|
return ((bip<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1164
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1165
|
return ((bip<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1166
1167
1168
1169
1170
1171
1172
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1173
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1174
1175
1176
1177
1178
|
/// Calculate the covariance matrix for all masked pixels in the image.
/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
/// @param avg is a pointer to memory of size B that stores the average spectrum
/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
|
63fc1df8
David Mayerich
added an inverse ...
|
1179
|
bool co_matrix(double* co, double* avg, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1180
|
if (header.interleave == envi_header::BSQ){
|
63fc1df8
David Mayerich
added an inverse ...
|
1181
1182
1183
1184
|
std::cout<<"ERROR: calculating the covariance matrix for a BSQ file is impractical; convert to BIL or BIP first"<<std::endl;
exit(1);
/*if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1185
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1186
|
return ((bsq<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1187
1188
1189
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
1190
|
}*/
|
a43c4fe1
heziqi
Added crop in env...
|
1191
1192
1193
|
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1194
|
return ((bil<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1195
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1196
|
return ((bil<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1197
1198
1199
1200
1201
1202
1203
|
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)
|
63fc1df8
David Mayerich
added an inverse ...
|
1204
|
return ((bip<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1205
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1206
|
return ((bip<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1207
1208
1209
1210
1211
1212
1213
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1214
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1215
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1216
1217
1218
1219
1220
1221
1222
|
/// Crop a region of the image and save it to a new file.
/// @param outfile is the file name for the new cropped image
/// @param x0 is the lower-left x pixel coordinate to be included in the cropped image
/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
|
c8c976a9
David Mayerich
replaced CImg wit...
|
1223
1224
1225
1226
1227
1228
1229
1230
|
bool crop(std::string outfile,
unsigned long long x0,
unsigned long long y0,
unsigned long long x1,
unsigned long long y1,
unsigned long long b0,
unsigned long long b1,
bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1231
|
|
177c7863
David Mayerich
updated the ENVI ...
|
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
|
//save the header for the cropped file
stim::envi_header new_header = header;
new_header.samples = x1 - x0;
new_header.lines = y1 - y0;
new_header.bands = b1 - b0;
std::vector<double>::const_iterator first = new_header.wavelength.begin() + b0;
std::vector<double>::const_iterator last = new_header.wavelength.begin() + b1;
new_header.wavelength = std::vector<double>(first, last);
new_header.save(outfile + ".hdr");
|
a43c4fe1
heziqi
Added crop in env...
|
1242
1243
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1244
|
return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1245
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1246
|
return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1247
1248
1249
1250
1251
1252
1253
|
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)
|
63fc1df8
David Mayerich
added an inverse ...
|
1254
|
return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1255
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1256
|
return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1257
1258
1259
1260
1261
1262
1263
|
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)
|
63fc1df8
David Mayerich
added an inverse ...
|
1264
|
return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1265
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1266
|
return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1267
1268
1269
1270
1271
1272
1273
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1274
|
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
|
/// Remove a list of bands from the ENVI file
/// @param outfile is the file name for the output hyperspectral image (with trimmed bands)
/// @param b is an array of bands to be eliminated
void trim(std::string outfile, std::vector<size_t> trimmed, bool PROGRESS = false){
envi_header h = header;
h.bands = header.bands - trimmed.size(); //calculate the new number of bands
if(header.wavelength.size() != 0)
h.wavelength.resize(h.bands);
if(header.band_names.size() != 0)
h.band_names.resize(h.bands);
size_t it = 0; //allocate an index into the trimmed bands array
size_t i = 0;
for(size_t b = 0; b < header.bands; b++){ //for each band
if(b != trimmed[it]){
if(h.wavelength.size()) h.wavelength[i] = header.wavelength[b];
if(h.band_names.size()) h.band_names[i] = header.band_names[i];
i++;
}
else it++;
}
h.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->trim(outfile, trimmed, PROGRESS);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->trim(outfile, trimmed, PROGRESS);
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)->trim(outfile, trimmed, PROGRESS);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->trim(outfile, trimmed, PROGRESS);
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)->trim(outfile, trimmed, PROGRESS);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->trim(outfile, trimmed, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
}
|
2ce6954b
David Mayerich
added the ability...
|
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
|
/// Combine two ENVI images along the Y axis
/// @param outfile is the combined file to be output
/// @param C is the ENVI object for the image to be combined
void combine(std::string outfile, envi C, long long x, long long y, bool PROGRESS = false){
envi_header h = header;
long long left = std::min<long long>(0, x); //calculate the left edge of the final image
long long right = std::max<long long>((long long)header.samples, C.header.samples + x); //calculate the right edge of the final image
long long top = std::min<long long>(0, y); //calculate the top edge of the final image
long long bottom = std::max<long long>((long long)header.lines, C.header.lines + y); //calculate the bottom edge of the final image
h.samples = right - left;
h.lines = bottom - top;
h.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
((bsq<float>*)file)->combine(outfile, (bsq<float>*)C.file, x, y, PROGRESS);
else if (header.data_type == envi_header::float64)
((bsq<double>*)file)->combine(outfile, (bsq<double>*)C.file, x, y, PROGRESS);
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)
((bil<float>*)file)->combine(outfile, (bil<float>*)C.file, x, y, PROGRESS);
else if (header.data_type == envi_header::float64)
((bil<double>*)file)->combine(outfile, (bil<double>*)C.file, x, y, PROGRESS);
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)
((bip<float>*)file)->combine(outfile, (bip<float>*)C.file, x, y, PROGRESS);
else if (header.data_type == envi_header::float64)
((bip<double>*)file)->combine(outfile, (bip<double>*)C.file, x, y, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1381
1382
1383
1384
1385
1386
1387
1388
|
/// Convolve the given band range with a kernel specified by a vector of coefficients.
/// @param outfile is the combined file to be output
/// @param c is an array of coefficients
/// @param start is the band to start processing (the first coefficient starts here)
/// @param nbands is the number of bands to process
/// @param center is the index for the center coefficient for the kernel (used to set the wavelengths in the output file)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1389
|
void convolve(std::string outfile, std::vector<double> C, size_t start, size_t end, size_t center = 0, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
|
size_t nbands = end - start + 1;
envi_header h = header; //copy the current header
h.bands = nbands; //set the number of new bands
if(header.wavelength.size() != 0){
h.wavelength.resize(nbands); //set the number of wavelengths to the number of bands
for(size_t b = 0; b < nbands; b++)
h.wavelength[b] = header.wavelength[b+center];
}
if(header.band_names.size() != 0){
h.band_names.resize(nbands);
for(size_t b = 0; b < nbands; b++)
h.band_names[b] = header.band_names[b+center];
}
h.save(outfile + ".hdr"); //save the new header
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1407
|
((bsq<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1408
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1409
|
((bsq<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1410
1411
1412
1413
1414
1415
1416
|
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)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1417
|
((bil<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1418
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1419
|
((bil<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1420
1421
1422
1423
1424
1425
1426
|
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)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1427
|
((bip<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1428
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1429
|
((bip<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
}
/// Approximates the nth derivative of the spectra to the specified order
/// @param outfile is the file where the derivative approximation will be saved
/// @n is the derivative to be calculated
/// @order is the order of the error (must be even)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1442
|
void deriv(std::string outfile, size_t d, size_t order, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1443
1444
1445
|
header.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1446
|
((bsq<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1447
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1448
|
((bsq<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1449
1450
1451
1452
1453
1454
1455
1456
|
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)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1457
|
((bil<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1458
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1459
|
((bil<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1460
1461
1462
1463
1464
1465
1466
1467
|
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)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1468
|
((bip<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1469
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1470
|
((bip<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1471
1472
1473
1474
1475
1476
1477
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
exit(1);
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1478
1479
1480
1481
1482
|
};
} //end namespace rts
#endif
|