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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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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)->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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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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else if(header.data_type == envi_header::float64)
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return ((bil<double>*)file)->baseline(outfile, w, mask, PROGRESS);
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else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
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else if(header.interleave == envi_header::BIP){ //if the infile is bip file
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if(header.data_type ==envi_header::float32)
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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){
|
a2bf1d08
David Mayerich
general bug fixes...
|
358
|
|
6708cc25
heziqi
Ziqi added envi c...
|
359
360
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
a2bf1d08
David Mayerich
general bug fixes...
|
361
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
362
363
364
365
|
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
366
367
368
|
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 ...
|
369
370
371
372
|
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
|
}
else if(header.data_type == envi_header::float64){ //if the data type is float
|
a2bf1d08
David Mayerich
general bug fixes...
|
376
|
if(interleave == envi_header::BSQ){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
377
378
379
|
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
380
381
382
|
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 ...
|
383
384
385
386
|
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
|
}
}
else if(header.interleave == envi_header::BIL){
|
a2bf1d08
David Mayerich
general bug fixes...
|
397
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
398
399
400
401
|
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
402
403
404
405
|
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...
|
406
407
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
408
409
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIL){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
410
411
412
|
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
413
414
415
416
|
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...
|
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
|
|
a2bf1d08
David Mayerich
general bug fixes...
|
427
428
|
if(header.data_type ==envi_header::float32){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
429
430
431
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
432
433
434
|
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 ...
|
435
436
437
438
|
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
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
441
442
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
443
444
445
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
446
447
448
|
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 ...
|
449
450
451
452
|
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);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
465
466
467
468
469
|
stim::envi_header h = header;
h.interleave = interleave;
h.save(outfile + ".hdr");
return true;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
470
|
|
6708cc25
heziqi
Ziqi added envi c...
|
471
472
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
473
474
475
476
477
|
/// 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...
|
478
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false) {
|
4a6f666c
heziqi
Added mask method
|
479
480
481
|
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...
|
482
|
return ((bsq<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
483
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
484
|
return ((bsq<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
485
486
487
488
489
490
|
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...
|
491
|
return ((bil<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
492
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
493
|
return ((bil<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
494
495
496
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
cacc3cdc
heziqi
attempt to fix CImg
|
497
|
|
4a6f666c
heziqi
Added mask method
|
498
499
|
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...
|
500
|
return ((bip<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
501
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
502
|
return ((bip<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
503
504
505
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
bba4f4d9
David Mayerich
minor warning fixes
|
506
507
|
return false;
|
740f8cd2
heziqi
added apply_mask
|
508
509
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
|
/// 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 ...
|
540
541
542
543
|
/// 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...
|
544
|
void apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
740f8cd2
heziqi
added apply_mask
|
545
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
546
547
|
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...
|
548
|
((bsq<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
549
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
550
|
((bsq<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
551
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
552
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
553
554
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
555
556
|
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...
|
557
|
((bil<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
558
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
559
|
((bil<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
560
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
561
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
562
563
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
564
565
|
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...
|
566
|
((bip<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
567
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
568
|
((bip<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
569
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
570
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
571
|
}
|
4a6f666c
heziqi
Added mask method
|
572
573
|
else{
|
e843658b
Brad Deutsch
Previous push did...
|
574
575
576
|
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
577
|
header.save(outfile + ".hdr");
|
e843658b
Brad Deutsch
Previous push did...
|
578
579
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
580
581
582
|
/// 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...
|
583
584
585
586
587
588
589
590
591
|
/// @param matrix is the destination for the pixel data
/// @param p is the mask
bool sift(void* matrix, unsigned char* p){
if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->sift((float*)matrix, p);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->sift((double*)matrix, p);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
592
|
else{
|
43dec788
David Mayerich
added code for si...
|
593
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
594
595
|
exit(1);
}
|
43dec788
David Mayerich
added code for si...
|
596
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
597
598
|
if (header.interleave == envi_header::BIP){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
599
600
601
602
603
604
605
606
|
if (header.data_type == envi_header::float32)
return ((bip<float>*)file)->sift((float*)matrix, p);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->sift((double*)matrix, p);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
607
608
|
}
if (header.interleave == envi_header::BIL){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
609
610
611
612
613
614
615
616
|
if (header.data_type == envi_header::float32)
return ((bil<float>*)file)->sift((float*)matrix, p);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->sift((double*)matrix, p);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
617
|
}
|
43dec788
David Mayerich
added code for si...
|
618
619
620
621
|
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
622
|
/// Saves in an array only those spectra corresponding to nonzero values of the mask.
|
43dec788
David Mayerich
added code for si...
|
623
624
|
/// @param outfile is the name of the sifted output file
/// @param p is the mask
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
625
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
e843658b
Brad Deutsch
Previous push did...
|
626
627
|
{
|
2fcab4f0
David Mayerich
added unsifting f...
|
628
|
//calculate the number of non-zero values in the mask
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
629
630
631
|
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...
|
632
633
634
635
636
|
if( p[i] > 0 ) nnz++;
//create a new header
envi_header new_header = header;
|
f7e99517
David Mayerich
added sifting for...
|
637
638
|
//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...
|
639
|
new_header.interleave = envi_header::BIP;
|
f7e99517
David Mayerich
added sifting for...
|
640
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
641
642
643
644
645
|
//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...
|
646
647
|
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...
|
648
|
return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
649
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
650
|
return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
651
652
653
654
655
656
|
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...
|
657
|
return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
658
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
659
|
return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
660
661
662
663
664
665
|
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...
|
666
|
return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
667
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
668
|
return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
669
670
671
672
673
674
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
4a6f666c
heziqi
Added mask method
|
675
676
|
exit(1);
}
|
4a6f666c
heziqi
Added mask method
|
677
|
return false;
|
cacc3cdc
heziqi
attempt to fix CImg
|
678
679
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
680
|
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...
|
681
682
683
684
685
686
687
688
689
690
691
692
|
//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...
|
693
|
return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
694
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
695
|
return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
696
697
698
699
700
|
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...
|
701
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
702
703
704
705
|
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...
|
706
|
|
8550e94f
David Mayerich
added sifting and...
|
707
|
if (header.data_type == envi_header::float32)
|
a2bf1d08
David Mayerich
general bug fixes...
|
708
|
return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
709
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
710
|
return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
711
712
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
713
714
715
716
|
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
717
|
}
|
cbce396e
David Mayerich
added support for...
|
718
|
return 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
719
720
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
721
722
723
724
725
726
727
728
729
|
/// 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...
|
730
|
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...
|
731
732
|
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...
|
733
|
return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
734
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
735
|
return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
736
737
738
739
740
741
|
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...
|
742
|
return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
743
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
744
|
return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
745
746
747
748
749
750
|
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...
|
751
|
return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
752
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
753
|
return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
754
755
756
757
758
759
760
761
762
763
764
|
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 ...
|
765
766
767
768
769
770
771
772
773
|
/// 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...
|
774
|
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...
|
775
776
|
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...
|
777
|
return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
778
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
779
|
return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
780
781
782
783
784
785
|
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...
|
786
|
return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
787
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
788
|
return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
789
790
791
792
793
794
|
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...
|
795
|
return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
796
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
797
|
return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
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
816
817
|
/// 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...
|
818
|
/// @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 ...
|
819
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
820
821
|
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...
|
822
823
|
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...
|
824
|
return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
825
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
826
|
return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
827
828
829
830
831
832
|
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...
|
833
|
return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
834
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
835
|
return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
836
837
838
839
840
841
|
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...
|
842
|
return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
843
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
844
|
return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
845
846
847
848
849
850
851
852
853
854
855
|
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 ...
|
856
857
858
859
860
861
862
|
/// 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...
|
863
|
bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
|
517876d6
heziqi
metrics finished ...
|
864
865
|
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...
|
866
|
return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
867
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
868
|
return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
869
870
871
872
873
874
|
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...
|
875
|
return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
876
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
877
|
return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
878
879
880
881
882
883
|
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...
|
884
|
return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
885
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
886
|
return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
887
888
889
890
891
892
893
894
895
896
897
|
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 ...
|
898
|
/// Closes the ENVI file.
|
6708cc25
heziqi
Ziqi added envi c...
|
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
925
926
927
928
929
930
931
|
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
|
932
|
return false;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
933
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
934
935
936
937
938
|
/// 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...
|
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
|
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 ...
|
972
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
973
|
/// Saves a header file describing the current ENVI file parameters.
|
e8eb202f
David Mayerich
added a new ENVI ...
|
974
975
976
977
978
979
980
981
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
982
983
984
985
|
/// 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 ...
|
986
|
bool band(void* ptr, double wavelength, bool PROGRESS = false){
|
d1d8ef91
David Mayerich
added band readin...
|
987
988
989
|
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 ...
|
990
|
return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
991
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
992
|
return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
993
994
995
996
997
998
999
|
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 ...
|
1000
|
return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1001
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1002
|
return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1003
1004
1005
1006
1007
1008
1009
|
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 ...
|
1010
|
return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1011
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1012
|
return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1013
1014
1015
1016
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
d1d8ef91
David Mayerich
added band readin...
|
1017
|
}
|
ee4dea28
David Mayerich
fixed errors in c...
|
1018
|
return false;
|
1582ce07
David Mayerich
added band_index(...
|
1019
1020
|
}
|
27b826a8
David Mayerich
added a spherical...
|
1021
1022
1023
1024
1025
|
/// 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...
|
1026
|
bool spectrum(void* ptr, unsigned long long x, unsigned long long y, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
1027
1028
1029
|
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 ...
|
1030
|
return ((bsq<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1031
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1032
|
return ((bsq<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1033
1034
1035
1036
1037
1038
1039
|
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 ...
|
1040
|
return ((bil<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1041
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1042
|
return ((bil<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1043
1044
1045
1046
1047
1048
1049
|
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 ...
|
1050
|
return ((bip<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1051
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1052
|
return ((bip<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1053
1054
1055
1056
1057
1058
1059
1060
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1061
1062
1063
1064
|
/// 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...
|
1065
|
bool band_index(void* ptr, unsigned long long b){
|
081f2c9f
heziqi
made bip bil file...
|
1066
1067
|
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(...
|
1068
|
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
081f2c9f
heziqi
made bip bil file...
|
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
|
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(...
|
1095
1096
|
}
return false;
|
d1d8ef91
David Mayerich
added band readin...
|
1097
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
1098
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1099
1100
1101
1102
|
/// 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 ...
|
1103
|
bool avg_band(double * p, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1104
1105
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1106
|
return ((bsq<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1107
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1108
|
return ((bsq<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1109
1110
1111
1112
1113
1114
1115
|
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 ...
|
1116
|
return ((bil<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1117
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1118
|
return ((bil<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1119
1120
1121
1122
1123
1124
1125
|
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 ...
|
1126
|
return ((bip<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1127
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1128
|
return ((bip<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1129
1130
1131
1132
1133
1134
1135
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1136
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1137
1138
1139
1140
1141
|
/// 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 ...
|
1142
|
bool co_matrix(double* co, double* avg, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1143
|
if (header.interleave == envi_header::BSQ){
|
63fc1df8
David Mayerich
added an inverse ...
|
1144
1145
1146
1147
|
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...
|
1148
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1149
|
return ((bsq<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1150
1151
1152
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
1153
|
}*/
|
a43c4fe1
heziqi
Added crop in env...
|
1154
1155
1156
|
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1157
|
return ((bil<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1158
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1159
|
return ((bil<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1160
1161
1162
1163
1164
1165
1166
|
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 ...
|
1167
|
return ((bip<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1168
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1169
|
return ((bip<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1170
1171
1172
1173
1174
1175
1176
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1177
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1178
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1179
1180
1181
1182
1183
1184
1185
|
/// 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...
|
1186
1187
1188
1189
1190
1191
1192
1193
|
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...
|
1194
|
|
177c7863
David Mayerich
updated the ENVI ...
|
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
|
//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...
|
1205
1206
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1207
|
return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1208
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1209
|
return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1210
1211
1212
1213
1214
1215
1216
|
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 ...
|
1217
|
return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1218
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1219
|
return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1220
1221
1222
1223
1224
1225
1226
|
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 ...
|
1227
|
return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1228
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1229
|
return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1230
1231
1232
1233
1234
1235
1236
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1237
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1238
1239
1240
1241
1242
|
};
} //end namespace rts
#endif
|