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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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//allocate sufficient space for a spectrum based on the data type and number of bands
void* alloc_array(size_t len){
switch(header.data_type){
case envi_header::int8:
return malloc(len);
case envi_header::int16:
case envi_header::uint16:
return malloc(2 * len);
case envi_header::int32:
case envi_header::uint32:
case envi_header::float32:
return malloc(4 * len);
case envi_header::int64:
case envi_header::uint64:
case envi_header::float64:
case envi_header::complex32:
return malloc(8 * len);
case envi_header::complex64:
return malloc(16 * len);
default:
std::cout<<"ERROR stim::envi data type not recognized for spectral allocation"<<std::endl;
exit(1);
}
}
//cast a value to DEST type from SRC type
template<typename DST, typename SRC>
inline void cast(DST* dst, SRC* src){
(*dst) = (DST)(*src);
}
//cast an array from type SRC to type DEST
template<typename DST, typename SRC>
inline void cast(DST* dst, SRC* src, size_t len){
for(size_t i = 0; i < len; i++)
cast(&dst[i], &src[i]);
}
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public:
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/// Default constructor
envi(){
file = NULL; //set the file pointer to NULL
}
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envi_header header;
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void* malloc_spectrum(){
return alloc_array(header.bands);
}
void* malloc_band(){
return alloc_array(header.samples * header.lines);
}
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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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else if(header.data_type == envi_header::float64)
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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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}
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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
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)
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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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heziqi
Ziqi added envi c...
|
346
347
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
798cea97
David Mayerich
added progress ba...
|
348
|
return ((bsq<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
349
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
350
|
return ((bsq<double>*)file)->baseline(outfile,w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
351
352
353
354
355
356
357
358
|
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)
|
798cea97
David Mayerich
added progress ba...
|
359
|
return ((bil<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
360
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
361
|
return ((bil<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
362
363
364
365
366
367
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
368
|
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
|
6708cc25
heziqi
Ziqi added envi c...
|
369
|
if(header.data_type ==envi_header::float32)
|
798cea97
David Mayerich
added progress ba...
|
370
|
return ((bip<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
371
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
372
|
return ((bip<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
373
374
375
376
377
378
379
380
381
382
383
384
|
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...
|
385
|
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 ...
|
386
387
388
389
390
391
392
393
394
395
396
397
|
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...
|
398
|
((bip<float>*)file)->project(outfile, center, basis, M, mask, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
399
|
else if(header.data_type == envi_header::float64)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
400
|
((bip<double>*)file)->project(outfile, center, basis, M, mask, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
401
402
403
404
405
406
407
408
|
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...
|
409
410
|
out_hdr.wavelength.clear();
out_hdr.band_names.clear();
|
63fc1df8
David Mayerich
added an inverse ...
|
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
|
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 ...
|
441
442
443
444
|
/// 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 ...
|
445
|
bool convert(std::string outfile, stim::envi_header::interleaveType interleave, bool PROGRESS = false){
|
a2bf1d08
David Mayerich
general bug fixes...
|
446
|
|
6708cc25
heziqi
Ziqi added envi c...
|
447
448
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
a2bf1d08
David Mayerich
general bug fixes...
|
449
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
450
451
452
453
|
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
454
455
456
|
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 ...
|
457
458
459
460
|
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...
|
461
462
463
|
}
else if(header.data_type == envi_header::float64){ //if the data type is float
|
a2bf1d08
David Mayerich
general bug fixes...
|
464
|
if(interleave == envi_header::BSQ){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
465
466
467
|
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
468
469
470
|
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 ...
|
471
472
473
474
|
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...
|
475
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
476
|
|
6708cc25
heziqi
Ziqi added envi c...
|
477
478
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
479
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
480
481
482
483
484
|
}
}
else if(header.interleave == envi_header::BIL){
|
a2bf1d08
David Mayerich
general bug fixes...
|
485
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
486
487
488
489
|
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
490
491
492
493
|
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...
|
494
495
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
496
497
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIL){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
498
499
500
|
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
501
502
503
504
|
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...
|
505
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
506
|
|
6708cc25
heziqi
Ziqi added envi c...
|
507
508
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
509
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
510
511
512
513
|
}
}
else if(header.interleave == envi_header::BIP){
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
514
|
|
a2bf1d08
David Mayerich
general bug fixes...
|
515
516
|
if(header.data_type ==envi_header::float32){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
517
518
519
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
520
521
522
|
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 ...
|
523
524
525
526
|
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...
|
527
528
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
529
530
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
531
532
533
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
534
535
536
|
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 ...
|
537
538
539
540
|
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...
|
541
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
542
|
|
6708cc25
heziqi
Ziqi added envi c...
|
543
544
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
545
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
546
547
|
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
548
|
|
6708cc25
heziqi
Ziqi added envi c...
|
549
550
551
552
|
else{
std::cout<<"ERROR: unidentified interleave type"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
553
554
555
556
557
|
stim::envi_header h = header;
h.interleave = interleave;
h.save(outfile + ".hdr");
return true;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
558
|
|
6708cc25
heziqi
Ziqi added envi c...
|
559
560
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
561
562
563
564
565
|
/// 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...
|
566
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false) {
|
4a6f666c
heziqi
Added mask method
|
567
568
569
|
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...
|
570
|
return ((bsq<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
571
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
572
|
return ((bsq<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
573
574
575
576
577
578
|
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...
|
579
|
return ((bil<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
580
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
581
|
return ((bil<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
582
583
584
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
cacc3cdc
heziqi
attempt to fix CImg
|
585
|
|
4a6f666c
heziqi
Added mask method
|
586
587
|
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...
|
588
|
return ((bip<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
589
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
590
|
return ((bip<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
591
592
593
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
bba4f4d9
David Mayerich
minor warning fixes
|
594
595
|
return false;
|
740f8cd2
heziqi
added apply_mask
|
596
597
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
|
/// 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 ...
|
628
629
630
631
|
/// 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...
|
632
|
void apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
740f8cd2
heziqi
added apply_mask
|
633
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
634
635
|
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...
|
636
|
((bsq<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
637
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
638
|
((bsq<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
639
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
640
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
641
642
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
643
644
|
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...
|
645
|
((bil<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
646
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
647
|
((bil<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
648
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
649
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
650
651
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
652
653
|
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...
|
654
|
((bip<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
655
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
656
|
((bip<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
657
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
658
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
659
|
}
|
4a6f666c
heziqi
Added mask method
|
660
661
|
else{
|
e843658b
Brad Deutsch
Previous push did...
|
662
663
664
|
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
665
|
header.save(outfile + ".hdr");
|
e843658b
Brad Deutsch
Previous push did...
|
666
667
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
668
669
670
|
/// 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...
|
671
672
|
/// @param matrix is the destination for the pixel data
/// @param p is the mask
|
814eb271
David Mayerich
fixed problems wi...
|
673
|
bool sift(void* matrix, unsigned char* p = NULL, bool PROGRESS = false){
|
43dec788
David Mayerich
added code for si...
|
674
675
676
|
if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
677
|
return ((bsq<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
43dec788
David Mayerich
added code for si...
|
678
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
679
|
return ((bsq<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
680
|
else{
|
43dec788
David Mayerich
added code for si...
|
681
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
682
683
|
exit(1);
}
|
43dec788
David Mayerich
added code for si...
|
684
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
685
686
|
if (header.interleave == envi_header::BIP){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
687
|
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
688
|
return ((bip<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
689
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
690
|
return ((bip<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
691
692
693
694
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
695
696
|
}
if (header.interleave == envi_header::BIL){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
697
|
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
698
|
return ((bil<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
699
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
700
|
return ((bil<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
701
702
703
704
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
705
|
}
|
43dec788
David Mayerich
added code for si...
|
706
707
708
709
|
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
710
|
/// Saves in an array only those spectra corresponding to nonzero values of the mask.
|
43dec788
David Mayerich
added code for si...
|
711
712
|
/// @param outfile is the name of the sifted output file
/// @param p is the mask
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
713
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
e843658b
Brad Deutsch
Previous push did...
|
714
715
|
{
|
2fcab4f0
David Mayerich
added unsifting f...
|
716
|
//calculate the number of non-zero values in the mask
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
717
718
719
|
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...
|
720
721
722
723
724
|
if( p[i] > 0 ) nnz++;
//create a new header
envi_header new_header = header;
|
f7e99517
David Mayerich
added sifting for...
|
725
726
|
//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...
|
727
|
new_header.interleave = envi_header::BIP;
|
f7e99517
David Mayerich
added sifting for...
|
728
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
729
730
731
732
733
|
//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...
|
734
735
|
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...
|
736
|
return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
737
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
738
|
return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
739
740
741
742
743
744
|
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...
|
745
|
return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
746
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
747
|
return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
748
749
750
751
752
753
|
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...
|
754
|
return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
755
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
756
|
return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
757
758
759
760
761
762
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
4a6f666c
heziqi
Added mask method
|
763
764
|
exit(1);
}
|
4a6f666c
heziqi
Added mask method
|
765
|
return false;
|
cacc3cdc
heziqi
attempt to fix CImg
|
766
767
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
768
|
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...
|
769
770
771
772
773
774
775
776
777
778
779
780
|
//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...
|
781
|
return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
782
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
783
|
return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
784
785
786
787
788
|
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...
|
789
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
790
791
792
793
|
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...
|
794
|
|
8550e94f
David Mayerich
added sifting and...
|
795
|
if (header.data_type == envi_header::float32)
|
a2bf1d08
David Mayerich
general bug fixes...
|
796
|
return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
797
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
798
|
return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
799
800
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
801
802
803
804
|
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
805
|
}
|
cbce396e
David Mayerich
added support for...
|
806
|
return 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
807
808
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
809
810
811
812
813
814
815
816
817
|
/// 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...
|
818
|
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...
|
819
820
|
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...
|
821
|
return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
822
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
823
|
return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
824
825
826
827
828
829
|
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...
|
830
|
return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
831
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
832
|
return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
833
834
835
836
837
838
|
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...
|
839
|
return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
840
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
841
|
return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
842
843
844
845
846
847
848
849
850
851
852
|
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 ...
|
853
854
855
856
857
858
859
860
861
|
/// 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...
|
862
|
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...
|
863
864
|
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...
|
865
|
return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
866
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
867
|
return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
868
869
870
871
872
873
|
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...
|
874
|
return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
875
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
876
|
return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
877
878
879
880
881
882
|
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...
|
883
|
return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
884
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
885
|
return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
886
887
888
889
890
891
892
893
894
895
896
|
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 ...
|
897
898
899
900
901
902
903
904
905
|
/// 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...
|
906
|
/// @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 ...
|
907
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
908
909
|
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...
|
910
911
|
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...
|
912
|
return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
913
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
914
|
return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
915
916
917
918
919
920
|
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...
|
921
|
return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
922
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
923
|
return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
924
925
926
927
928
929
|
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...
|
930
|
return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
931
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
932
|
return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
933
934
935
936
937
938
939
940
941
942
943
|
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 ...
|
944
945
946
947
948
949
950
|
/// 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...
|
951
|
bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
|
517876d6
heziqi
metrics finished ...
|
952
953
|
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...
|
954
|
return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
955
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
956
|
return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
957
958
959
960
961
962
|
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...
|
963
|
return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
964
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
965
|
return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
966
967
968
969
970
971
|
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...
|
972
|
return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
973
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
974
|
return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
975
976
977
978
979
980
981
982
983
984
985
|
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 ...
|
986
|
/// Closes the ENVI file.
|
edb975b0
David Mayerich
created a stim::e...
|
987
988
|
void close(){
if(file == NULL) return;
|
6708cc25
heziqi
Ziqi added envi c...
|
989
990
|
if(header.interleave == envi_header::BSQ){
if(header.data_type ==envi_header::float32)
|
edb975b0
David Mayerich
created a stim::e...
|
991
|
((bsq<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
992
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
993
|
((bsq<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
994
995
996
997
998
999
1000
1001
|
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)
|
edb975b0
David Mayerich
created a stim::e...
|
1002
|
((bil<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1003
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1004
|
((bil<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1005
1006
1007
1008
1009
1010
1011
1012
|
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)
|
edb975b0
David Mayerich
created a stim::e...
|
1013
|
((bip<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1014
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1015
|
((bip<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1016
1017
1018
1019
1020
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1021
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1022
1023
1024
1025
1026
|
/// 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...
|
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
|
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 ...
|
1060
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1061
|
/// Saves a header file describing the current ENVI file parameters.
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1062
1063
1064
1065
1066
1067
1068
1069
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1070
1071
1072
1073
|
/// 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 ...
|
1074
|
bool band(void* ptr, double wavelength, bool PROGRESS = false){
|
d1d8ef91
David Mayerich
added band readin...
|
1075
1076
1077
|
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 ...
|
1078
|
return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1079
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1080
|
return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1081
1082
1083
1084
1085
1086
1087
|
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 ...
|
1088
|
return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1089
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1090
|
return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1091
1092
1093
1094
1095
1096
1097
|
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 ...
|
1098
|
return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1099
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1100
|
return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1101
1102
1103
1104
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
d1d8ef91
David Mayerich
added band readin...
|
1105
|
}
|
ee4dea28
David Mayerich
fixed errors in c...
|
1106
|
return false;
|
1582ce07
David Mayerich
added band_index(...
|
1107
1108
|
}
|
27b826a8
David Mayerich
added a spherical...
|
1109
1110
1111
1112
1113
|
/// 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
|
735a2a24
David Mayerich
started testing o...
|
1114
|
/*bool spectrum(void* ptr, unsigned long long x, unsigned long long y, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
1115
1116
1117
|
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 ...
|
1118
|
return ((bsq<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1119
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1120
|
return ((bsq<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1121
1122
1123
1124
1125
1126
1127
|
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 ...
|
1128
|
return ((bil<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1129
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1130
|
return ((bil<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1131
1132
1133
1134
1135
1136
1137
|
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 ...
|
1138
|
return ((bip<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1139
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1140
|
return ((bip<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1141
1142
1143
1144
1145
1146
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
|
735a2a24
David Mayerich
started testing o...
|
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
|
}*/
// Retrieve a spectrum at the specified 1D location
/// @param ptr is a pointer to pre-allocated memory of size B*sizeof(T)
/// @param x is the 1D coordinate of the spectrum
template<typename T>
void spectrum(T* ptr, size_t n, bool PROGRESS = false){
void* temp = alloc_array(header.bands); //allocate space for the output array
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32){
((bsq<float>*)file)->spectrum((float*)temp, n, PROGRESS);
cast<T, float>(ptr, (float*)temp, header.bands);
}
else if (header.data_type == envi_header::float64){
((bsq<double>*)file)->spectrum((double*)temp, n, PROGRESS);
cast<T, double>(ptr, (double*)temp, header.bands);
}
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)->spectrum((float*)temp, n, PROGRESS);
cast<T, float>(ptr, (float*)temp, header.bands);
}
else if (header.data_type == envi_header::float64){
((bil<double>*)file)->spectrum((double*)temp, n, PROGRESS);
cast<T, double>(ptr, (double*)temp, header.bands);
}
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)->spectrum((float*)temp, n, PROGRESS);
|
d4aa4cf7
David Mayerich
fixed the in-memo...
|
1189
|
float test = ((float*)temp)[0];
|
735a2a24
David Mayerich
started testing o...
|
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
|
cast<T, float>(ptr, (float*)temp, header.bands);
}
else if (header.data_type == envi_header::float64){
((bip<double>*)file)->spectrum((double*)temp, n, PROGRESS);
cast<T, double>(ptr, (double*)temp, header.bands);
}
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
}
/// Retrieve a spectrum from the specified (x, y) 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
template<typename T>
|
d0ef98e3
David Mayerich
fixed a Linux com...
|
1209
|
void spectrum(T* ptr, size_t x, size_t y, bool PROGRESS = false){
|
735a2a24
David Mayerich
started testing o...
|
1210
|
|
c4dd399a
David Mayerich
fixed a Linux com...
|
1211
|
spectrum<T>(ptr, y * header.samples + x, PROGRESS);
|
735a2a24
David Mayerich
started testing o...
|
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
|
/*void* temp = alloc_array<T>(header.bands); //allocate space for the output array
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32){
((bsq<float>*)file)->spectrum((float*)temp, x, y, PROGRESS);
cast<T, float>(ptr, temp, header.bands);
}
else if (header.data_type == envi_header::float64){
((bsq<double>*)file)->spectrum((double*)temp, x, y, PROGRESS);
cast<T, double>(ptr, temp, header.bands);
}
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)->spectrum((float*)temp, x, y, PROGRESS);
cast<T, float>(ptr, temp, header.bands);
}
else if (header.data_type == envi_header::float64){
((bil<double>*)file)->spectrum((double*)temp, x, y, PROGRESS);
cast<T, double>(ptr, temp, header.bands);
}
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)->spectrum((float*)temp, x, y, PROGRESS);
cast<T, float>(ptr, temp, header.bands);
}
else if (header.data_type == envi_header::float64){
((bip<double>*)file)->spectrum((double*)temp, x, y, PROGRESS);
cast<T, double>(ptr, temp, header.bands);
}
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}*/
|
724ec347
David Mayerich
simplified the EN...
|
1256
1257
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1258
1259
1260
1261
|
/// 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...
|
1262
|
bool band_index(void* ptr, unsigned long long b){
|
081f2c9f
heziqi
made bip bil file...
|
1263
1264
|
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(...
|
1265
|
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
081f2c9f
heziqi
made bip bil file...
|
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
|
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(...
|
1292
1293
|
}
return false;
|
d1d8ef91
David Mayerich
added band readin...
|
1294
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
1295
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1296
1297
1298
1299
|
/// 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 ...
|
1300
|
bool avg_band(double * p, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1301
1302
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1303
|
return ((bsq<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1304
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1305
|
return ((bsq<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1306
1307
1308
1309
1310
1311
1312
|
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 ...
|
1313
|
return ((bil<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1314
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1315
|
return ((bil<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1316
1317
1318
1319
1320
1321
1322
|
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 ...
|
1323
|
return ((bip<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1324
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1325
|
return ((bip<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1326
1327
1328
1329
1330
1331
1332
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1333
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1334
1335
1336
1337
1338
|
/// 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 ...
|
1339
|
bool co_matrix(double* co, double* avg, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1340
|
if (header.interleave == envi_header::BSQ){
|
63fc1df8
David Mayerich
added an inverse ...
|
1341
1342
1343
1344
|
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...
|
1345
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1346
|
return ((bsq<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1347
1348
1349
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
1350
|
}*/
|
a43c4fe1
heziqi
Added crop in env...
|
1351
1352
1353
|
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1354
|
return ((bil<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1355
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1356
|
return ((bil<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1357
1358
1359
1360
1361
1362
1363
|
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 ...
|
1364
|
return ((bip<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1365
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1366
|
return ((bip<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1367
1368
1369
1370
1371
1372
1373
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1374
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1375
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1376
1377
1378
1379
1380
1381
1382
|
/// 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...
|
1383
1384
1385
1386
1387
1388
1389
1390
|
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...
|
1391
|
|
177c7863
David Mayerich
updated the ENVI ...
|
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
|
//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...
|
1402
1403
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1404
|
return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1405
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1406
|
return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1407
1408
1409
1410
1411
1412
1413
|
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 ...
|
1414
|
return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1415
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1416
|
return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1417
1418
1419
1420
1421
1422
1423
|
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 ...
|
1424
|
return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1425
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1426
|
return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1427
1428
1429
1430
1431
1432
1433
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1434
|
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
|
/// 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...
|
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
|
/// 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...
|
1541
1542
1543
1544
1545
1546
1547
1548
|
/// 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...
|
1549
|
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...
|
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
|
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...
|
1567
|
((bsq<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1568
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1569
|
((bsq<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1570
1571
1572
1573
1574
1575
1576
|
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...
|
1577
|
((bil<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1578
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1579
|
((bil<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1580
1581
1582
1583
1584
1585
1586
|
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...
|
1587
|
((bip<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1588
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1589
|
((bip<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
|
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...
|
1602
|
void deriv(std::string outfile, size_t d, size_t order, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1603
1604
1605
|
header.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1606
|
((bsq<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1607
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1608
|
((bsq<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1609
1610
1611
1612
1613
1614
1615
1616
|
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...
|
1617
|
((bil<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1618
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1619
|
((bil<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1620
1621
1622
1623
1624
1625
1626
1627
|
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...
|
1628
|
((bip<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1629
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1630
|
((bip<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1631
1632
1633
1634
1635
1636
1637
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
exit(1);
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1638
1639
1640
1641
1642
|
};
} //end namespace rts
#endif
|