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#ifndef STIM_ENVI_H
#define STIM_ENVI_H
#include "../envi/envi_header.h"
#include "../envi/bsq.h"
#include "../envi/bip.h"
#include "../envi/bil.h"
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#include <iostream>
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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 normalize(std::string outfile, double band, unsigned char* mask = NULL, bool PROGRESS = false){
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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)->normalize(outfile, band, mask, PROGRESS);
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else if(header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->normalize(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)->normalize(outfile, band, mask, PROGRESS);
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else if(header.data_type == envi_header::float64)
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return ((bil<double>*)file)->normalize(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)->normalize(outfile, band, mask, PROGRESS);
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else if(header.data_type == envi_header::float64)
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return ((bip<double>*)file)->normalize(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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/// 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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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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return ((bip<float>*)file)->baseline(outfile, w, mask, PROGRESS);
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return ((bip<double>*)file)->baseline(outfile, w, mask, PROGRESS);
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else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
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void project(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask, bool PROGRESS = false){
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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)
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((bip<float>*)file)->project(outfile, center, basis, M, mask, PROGRESS);
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else if(header.data_type == envi_header::float64)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
312
|
((bip<double>*)file)->project(outfile, center, basis, M, mask, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
313
314
315
316
317
318
319
320
|
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...
|
321
322
|
out_hdr.wavelength.clear();
out_hdr.band_names.clear();
|
63fc1df8
David Mayerich
added an inverse ...
|
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
|
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 ...
|
353
354
355
356
|
/// 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 ...
|
357
|
bool convert(std::string outfile, stim::envi_header::interleaveType interleave, bool PROGRESS = false){
|
6708cc25
heziqi
Ziqi added envi c...
|
358
359
360
361
362
363
364
365
366
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32){ //if the data type of infile is float
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL) //if the target file is bil file
|
63fc1df8
David Mayerich
added an inverse ...
|
367
368
369
370
371
372
|
return ((bsq<float>*)file)->bil(outfile, PROGRESS);
else if(interleave == envi_header::BIP){ //if the target file is bip file
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...
|
373
374
375
376
377
378
379
380
|
}
else if(header.data_type == envi_header::float64){ //if the data type is float
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL)
|
63fc1df8
David Mayerich
added an inverse ...
|
381
382
383
384
385
386
|
return ((bsq<double>*)file)->bil(outfile, PROGRESS);
else if(interleave == envi_header::BIP){ //if the target file is bip file
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...
|
387
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
388
|
|
6708cc25
heziqi
Ziqi added envi c...
|
389
390
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
391
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
392
393
394
395
396
397
398
399
400
401
402
|
}
}
else if(header.interleave == envi_header::BIL){
if(header.data_type ==envi_header::float32){ //if the data type of infile is float
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BSQ) //if the target file is bsq file
|
63fc1df8
David Mayerich
added an inverse ...
|
403
|
return ((bil<float>*)file)->bsq(outfile, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
404
|
else if(interleave == envi_header::BIP) //if the target file is bip file
|
63fc1df8
David Mayerich
added an inverse ...
|
405
|
return ((bil<float>*)file)->bip(outfile, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
406
407
408
409
410
411
412
413
|
}
else if(header.data_type == envi_header::float64){ //if the data type is float
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BSQ)
|
63fc1df8
David Mayerich
added an inverse ...
|
414
|
return ((bil<double>*)file)->bsq(outfile, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
415
|
else if(interleave == envi_header::BIP)
|
63fc1df8
David Mayerich
added an inverse ...
|
416
|
return ((bil<double>*)file)->bip(outfile, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
417
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
418
|
|
6708cc25
heziqi
Ziqi added envi c...
|
419
420
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
421
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
422
423
424
425
|
}
}
else if(header.interleave == envi_header::BIP){
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
426
|
|
6708cc25
heziqi
Ziqi added envi c...
|
427
428
429
430
431
432
|
if(header.data_type ==envi_header::float32){ //if the data type of infile is float
if(interleave == envi_header::BIP){
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL) //if the target file is bil file
|
63fc1df8
David Mayerich
added an inverse ...
|
433
434
435
436
437
438
|
return ((bip<float>*)file)->bil(outfile, PROGRESS);
else if(interleave == envi_header::BSQ){ //if the target file is bip file
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...
|
439
440
441
442
443
444
445
446
|
}
else if(header.data_type == envi_header::float64){ //if the data type is float
if(interleave == envi_header::BIP){
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL) //if the target file is bil file
|
63fc1df8
David Mayerich
added an inverse ...
|
447
448
449
450
451
452
|
return ((bip<double>*)file)->bil(outfile, PROGRESS);
else if(interleave == envi_header::BSQ){ //if the target file is bip file
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...
|
453
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
454
|
|
6708cc25
heziqi
Ziqi added envi c...
|
455
456
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
457
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
458
459
|
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
460
|
|
6708cc25
heziqi
Ziqi added envi c...
|
461
462
463
464
|
else{
std::cout<<"ERROR: unidentified interleave type"<<std::endl;
exit(1);
}
|
e933c14e
David Mayerich
cleaned up the code
|
465
|
return false;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
466
|
|
6708cc25
heziqi
Ziqi added envi c...
|
467
468
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
469
470
471
472
473
|
/// 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
|
798cea97
David Mayerich
added progress ba...
|
474
|
bool build_mask(double mask_band, double threshold, unsigned char* p = NULL, bool PROGRESS = false) {
|
4a6f666c
heziqi
Added mask method
|
475
476
477
|
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...
|
478
|
return ((bsq<float>*)file)->build_mask(mask_band, threshold, p, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
479
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
480
|
return ((bsq<double>*)file)->build_mask(mask_band, threshold, p, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
481
482
483
484
485
486
|
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)
|
798cea97
David Mayerich
added progress ba...
|
487
|
return ((bil<float>*)file)->build_mask(mask_band, threshold, p, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
488
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
489
|
return ((bil<double>*)file)->build_mask(mask_band, threshold, p, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
490
491
492
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
cacc3cdc
heziqi
attempt to fix CImg
|
493
|
|
4a6f666c
heziqi
Added mask method
|
494
495
|
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
|
798cea97
David Mayerich
added progress ba...
|
496
|
return ((bip<float>*)file)->build_mask(mask_band, threshold, p, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
497
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
498
|
return ((bip<double>*)file)->build_mask(mask_band, threshold, p, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
499
500
501
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
bba4f4d9
David Mayerich
minor warning fixes
|
502
503
|
return false;
|
740f8cd2
heziqi
added apply_mask
|
504
505
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
506
507
508
509
|
/// 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)
|
e843658b
Brad Deutsch
Previous push did...
|
510
|
bool apply_mask(std::string outfile, unsigned char* p)
|
740f8cd2
heziqi
added apply_mask
|
511
512
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
513
514
|
if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
if (header.data_type == envi_header::float32)
|
740f8cd2
heziqi
added apply_mask
|
515
|
return ((bsq<float>*)file)->apply_mask(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
516
|
else if (header.data_type == envi_header::float64)
|
740f8cd2
heziqi
added apply_mask
|
517
518
|
return ((bsq<double>*)file)->apply_mask(outfile, p);
else
|
e843658b
Brad Deutsch
Previous push did...
|
519
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
520
521
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
522
523
|
else if (header.interleave == envi_header::BIL){ //if the infile is bil file
if (header.data_type == envi_header::float32)
|
740f8cd2
heziqi
added apply_mask
|
524
|
return ((bil<float>*)file)->apply_mask(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
525
|
else if (header.data_type == envi_header::float64)
|
740f8cd2
heziqi
added apply_mask
|
526
527
|
return ((bil<double>*)file)->apply_mask(outfile, p);
else
|
e843658b
Brad Deutsch
Previous push did...
|
528
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
529
530
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
531
532
|
else if (header.interleave == envi_header::BIP){ //if the infile is bip file
if (header.data_type == envi_header::float32)
|
740f8cd2
heziqi
added apply_mask
|
533
|
return ((bip<float>*)file)->apply_mask(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
534
|
else if (header.data_type == envi_header::float64)
|
740f8cd2
heziqi
added apply_mask
|
535
536
|
return ((bip<double>*)file)->apply_mask(outfile, p);
else
|
e843658b
Brad Deutsch
Previous push did...
|
537
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
538
|
}
|
4a6f666c
heziqi
Added mask method
|
539
540
|
else{
|
e843658b
Brad Deutsch
Previous push did...
|
541
542
543
544
545
546
|
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
547
548
549
|
/// 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...
|
550
551
552
553
554
555
556
557
558
559
560
561
|
/// @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);
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
562
563
564
565
566
567
568
569
570
|
if (header.interleave == envi_header::BIP){
std::cout<<"Memory sifting not supported for BIP files"<<std::endl;
exit(1);
}
if (header.interleave == envi_header::BIL){
std::cout<<"Memory sifting not supported for BIL files"<<std::endl;
exit(1);
}
|
43dec788
David Mayerich
added code for si...
|
571
572
573
574
|
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
575
|
/// Saves in an array only those spectra corresponding to nonzero values of the mask.
|
43dec788
David Mayerich
added code for si...
|
576
577
|
/// @param outfile is the name of the sifted output file
/// @param p is the mask
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
578
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
e843658b
Brad Deutsch
Previous push did...
|
579
580
|
{
|
2fcab4f0
David Mayerich
added unsifting f...
|
581
|
//calculate the number of non-zero values in the mask
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
582
583
584
|
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...
|
585
586
587
588
589
|
if( p[i] > 0 ) nnz++;
//create a new header
envi_header new_header = header;
|
f7e99517
David Mayerich
added sifting for...
|
590
591
|
//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...
|
592
|
new_header.interleave = envi_header::BIP;
|
f7e99517
David Mayerich
added sifting for...
|
593
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
594
595
596
597
598
|
//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...
|
599
600
|
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...
|
601
|
return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
602
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
603
|
return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
604
605
606
607
608
609
|
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...
|
610
|
return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
611
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
612
|
return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
613
614
615
616
617
618
|
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...
|
619
|
return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
620
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
621
|
return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
622
623
624
625
626
627
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
4a6f666c
heziqi
Added mask method
|
628
629
|
exit(1);
}
|
4a6f666c
heziqi
Added mask method
|
630
|
return false;
|
cacc3cdc
heziqi
attempt to fix CImg
|
631
632
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
633
|
bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines){
|
2fcab4f0
David Mayerich
added unsifting f...
|
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
|
//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)
return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines);
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...
|
654
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
655
656
657
658
|
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...
|
659
|
|
8550e94f
David Mayerich
added sifting and...
|
660
661
662
663
664
665
|
if (header.data_type == envi_header::float32)
return ((bip<float>*)file)->unsift(outfile, mask, samples, lines);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->unsift(outfile, mask, samples, lines);
else
std::cout << "ERROR: unidentified data type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
666
667
668
669
|
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
670
|
}
|
cbce396e
David Mayerich
added support for...
|
671
|
return 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
672
673
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
674
675
676
677
678
679
680
681
682
|
/// 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
|
70407ea9
heziqi
Ziqi completed he...
|
683
|
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, void * result){
|
20c212c0
heziqi
Ziqi added functi...
|
684
685
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
70407ea9
heziqi
Ziqi completed he...
|
686
|
return ((bsq<float>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (float*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
687
|
else if(header.data_type == envi_header::float64)
|
70407ea9
heziqi
Ziqi completed he...
|
688
|
return ((bsq<double>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (double*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
689
690
691
692
693
694
|
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)
|
70407ea9
heziqi
Ziqi completed he...
|
695
|
return ((bil<float>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (float*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
696
|
else if(header.data_type == envi_header::float64)
|
70407ea9
heziqi
Ziqi completed he...
|
697
|
return ((bil<double>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (double*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
698
699
700
701
702
703
|
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)
|
70407ea9
heziqi
Ziqi completed he...
|
704
|
return ((bip<float>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (float*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
705
|
else if(header.data_type == envi_header::float64)
|
70407ea9
heziqi
Ziqi completed he...
|
706
707
708
709
710
711
712
713
714
715
716
717
|
return ((bip<double>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
718
719
720
721
722
723
724
725
726
|
/// 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
|
70407ea9
heziqi
Ziqi completed he...
|
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
|
bool pa_to_ph(double lb1, double rb1, double lab1, double rab1, double lb2, double rb2, double pos, void * result){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
762
763
764
765
766
767
768
769
770
|
/// 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...
|
771
|
/// @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 ...
|
772
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
|
bool pa_to_pa(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, void* result){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (double*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
798
799
800
801
802
803
804
805
806
807
808
|
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 ...
|
809
810
811
812
813
814
815
|
/// 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
|
517876d6
heziqi
metrics finished ...
|
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
|
bool cpoint(double lb1, double rb1, double lab1, double rab1, void* result){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->cpoint(lb1, rb1, lab1, rab1, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->cpoint(lb1, rb1, lab1, rab1, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->cpoint(lb1, rb1, lab1, rab1, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->cpoint(lb1, rb1, lab1, rab1, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->cpoint(lb1, rb1, lab1, rab1,(float*)result);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->cpoint(lb1, rb1, lab1, rab1, (double*)result);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
851
|
/// Closes the ENVI file.
|
6708cc25
heziqi
Ziqi added envi c...
|
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
|
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
|
885
|
return false;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
886
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
887
888
889
890
891
|
/// 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...
|
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
|
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 ...
|
925
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
926
|
/// Saves a header file describing the current ENVI file parameters.
|
e8eb202f
David Mayerich
added a new ENVI ...
|
927
928
929
930
931
932
933
934
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
935
936
937
938
|
/// 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 ...
|
939
|
bool band(void* ptr, double wavelength, bool PROGRESS = false){
|
d1d8ef91
David Mayerich
added band readin...
|
940
941
942
|
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 ...
|
943
|
return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
944
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
945
|
return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
946
947
948
949
950
951
952
|
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 ...
|
953
|
return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
954
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
955
|
return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
956
957
958
959
960
961
962
|
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 ...
|
963
|
return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
964
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
965
|
return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
966
967
968
969
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
d1d8ef91
David Mayerich
added band readin...
|
970
|
}
|
ee4dea28
David Mayerich
fixed errors in c...
|
971
|
return false;
|
1582ce07
David Mayerich
added band_index(...
|
972
973
|
}
|
27b826a8
David Mayerich
added a spherical...
|
974
975
976
977
978
|
/// 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...
|
979
|
bool spectrum(void* ptr, unsigned long long x, unsigned long long y, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
980
981
982
|
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 ...
|
983
|
return ((bsq<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
984
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
985
|
return ((bsq<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
986
987
988
989
990
991
992
|
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 ...
|
993
|
return ((bil<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
994
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
995
|
return ((bil<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
996
997
998
999
1000
1001
1002
|
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 ...
|
1003
|
return ((bip<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1004
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1005
|
return ((bip<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1006
1007
1008
1009
1010
1011
1012
1013
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1014
1015
1016
1017
|
/// 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...
|
1018
|
bool band_index(void* ptr, unsigned long long b){
|
081f2c9f
heziqi
made bip bil file...
|
1019
1020
|
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(...
|
1021
|
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
081f2c9f
heziqi
made bip bil file...
|
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
|
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(...
|
1048
1049
|
}
return false;
|
d1d8ef91
David Mayerich
added band readin...
|
1050
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
1051
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1052
1053
1054
1055
|
/// 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 ...
|
1056
|
bool avg_band(double * p, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1057
1058
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1059
|
return ((bsq<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1060
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1061
|
return ((bsq<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1062
1063
1064
1065
1066
1067
1068
|
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 ...
|
1069
|
return ((bil<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1070
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1071
|
return ((bil<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1072
1073
1074
1075
1076
1077
1078
|
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 ...
|
1079
|
return ((bip<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1080
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1081
|
return ((bip<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1082
1083
1084
1085
1086
1087
1088
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1089
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1090
1091
1092
1093
1094
|
/// 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 ...
|
1095
|
bool co_matrix(double* co, double* avg, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1096
|
if (header.interleave == envi_header::BSQ){
|
63fc1df8
David Mayerich
added an inverse ...
|
1097
1098
1099
1100
|
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...
|
1101
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1102
|
return ((bsq<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1103
1104
1105
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
1106
|
}*/
|
a43c4fe1
heziqi
Added crop in env...
|
1107
1108
1109
|
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1110
|
return ((bil<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1111
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1112
|
return ((bil<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1113
1114
1115
1116
1117
1118
1119
|
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 ...
|
1120
|
return ((bip<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1121
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1122
|
return ((bip<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1123
1124
1125
1126
1127
1128
1129
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1130
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1131
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1132
1133
1134
1135
1136
1137
1138
|
/// 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...
|
1139
1140
1141
1142
1143
1144
1145
1146
|
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...
|
1147
|
|
177c7863
David Mayerich
updated the ENVI ...
|
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
|
//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...
|
1158
1159
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1160
|
return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1161
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1162
|
return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1163
1164
1165
1166
1167
1168
1169
|
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 ...
|
1170
|
return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1171
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1172
|
return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1173
1174
1175
1176
1177
1178
1179
|
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 ...
|
1180
|
return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1181
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1182
|
return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1183
1184
1185
1186
1187
1188
1189
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1190
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1191
1192
1193
1194
1195
|
};
} //end namespace rts
#endif
|