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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)
|
e843658b
Brad Deutsch
Previous push did...
|
544
|
bool apply_mask(std::string outfile, unsigned char* p)
|
740f8cd2
heziqi
added apply_mask
|
545
|
{
|
a2bf1d08
David Mayerich
general bug fixes...
|
546
|
header.save(outfile + ".hdr");
|
e843658b
Brad Deutsch
Previous push did...
|
547
548
|
if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
if (header.data_type == envi_header::float32)
|
740f8cd2
heziqi
added apply_mask
|
549
|
return ((bsq<float>*)file)->apply_mask(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
550
|
else if (header.data_type == envi_header::float64)
|
740f8cd2
heziqi
added apply_mask
|
551
552
|
return ((bsq<double>*)file)->apply_mask(outfile, p);
else
|
e843658b
Brad Deutsch
Previous push did...
|
553
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
554
555
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
556
557
|
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
|
558
|
return ((bil<float>*)file)->apply_mask(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
559
|
else if (header.data_type == envi_header::float64)
|
740f8cd2
heziqi
added apply_mask
|
560
561
|
return ((bil<double>*)file)->apply_mask(outfile, p);
else
|
e843658b
Brad Deutsch
Previous push did...
|
562
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
563
564
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
565
566
|
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
|
567
|
return ((bip<float>*)file)->apply_mask(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
568
|
else if (header.data_type == envi_header::float64)
|
740f8cd2
heziqi
added apply_mask
|
569
570
|
return ((bip<double>*)file)->apply_mask(outfile, p);
else
|
e843658b
Brad Deutsch
Previous push did...
|
571
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
572
|
}
|
4a6f666c
heziqi
Added mask method
|
573
574
|
else{
|
e843658b
Brad Deutsch
Previous push did...
|
575
576
577
578
579
580
|
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
581
582
583
|
/// 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...
|
584
585
586
587
588
589
590
591
592
|
/// @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...
|
593
|
else{
|
43dec788
David Mayerich
added code for si...
|
594
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
595
596
|
exit(1);
}
|
43dec788
David Mayerich
added code for si...
|
597
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
598
599
|
if (header.interleave == envi_header::BIP){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
600
601
602
603
604
605
606
607
|
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...
|
608
609
|
}
if (header.interleave == envi_header::BIL){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
610
611
612
613
614
615
616
617
|
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...
|
618
|
}
|
43dec788
David Mayerich
added code for si...
|
619
620
621
622
|
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
623
|
/// Saves in an array only those spectra corresponding to nonzero values of the mask.
|
43dec788
David Mayerich
added code for si...
|
624
625
|
/// @param outfile is the name of the sifted output file
/// @param p is the mask
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
626
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
e843658b
Brad Deutsch
Previous push did...
|
627
628
|
{
|
2fcab4f0
David Mayerich
added unsifting f...
|
629
|
//calculate the number of non-zero values in the mask
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
630
631
632
|
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...
|
633
634
635
636
637
|
if( p[i] > 0 ) nnz++;
//create a new header
envi_header new_header = header;
|
f7e99517
David Mayerich
added sifting for...
|
638
639
|
//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...
|
640
|
new_header.interleave = envi_header::BIP;
|
f7e99517
David Mayerich
added sifting for...
|
641
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
642
643
644
645
646
|
//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...
|
647
648
|
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...
|
649
|
return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
650
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
651
|
return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
652
653
654
655
656
657
|
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...
|
658
|
return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
659
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
660
|
return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
661
662
663
664
665
666
|
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...
|
667
|
return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
668
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
669
|
return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
670
671
672
673
674
675
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
4a6f666c
heziqi
Added mask method
|
676
677
|
exit(1);
}
|
4a6f666c
heziqi
Added mask method
|
678
|
return false;
|
cacc3cdc
heziqi
attempt to fix CImg
|
679
680
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
681
|
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...
|
682
683
684
685
686
687
688
689
690
691
692
693
|
//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...
|
694
|
return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
695
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
696
|
return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
697
698
699
700
701
|
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...
|
702
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
703
704
705
706
|
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...
|
707
|
|
8550e94f
David Mayerich
added sifting and...
|
708
|
if (header.data_type == envi_header::float32)
|
a2bf1d08
David Mayerich
general bug fixes...
|
709
|
return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
710
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
711
|
return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
712
713
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
714
715
716
717
|
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
718
|
}
|
cbce396e
David Mayerich
added support for...
|
719
|
return 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
720
721
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
722
723
724
725
726
727
728
729
730
|
/// 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...
|
731
|
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...
|
732
733
|
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...
|
734
|
return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
735
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
736
|
return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
737
738
739
740
741
742
|
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...
|
743
|
return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
744
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
745
|
return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
746
747
748
749
750
751
|
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...
|
752
|
return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
753
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
754
|
return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
755
756
757
758
759
760
761
762
763
764
765
|
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 ...
|
766
767
768
769
770
771
772
773
774
|
/// 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...
|
775
|
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...
|
776
777
|
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...
|
778
|
return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
779
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
780
|
return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
781
782
783
784
785
786
|
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...
|
787
|
return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
788
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
789
|
return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
790
791
792
793
794
795
|
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...
|
796
|
return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
797
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
798
|
return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
799
800
801
802
803
804
805
806
807
808
809
|
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 ...
|
810
811
812
813
814
815
816
817
818
|
/// 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...
|
819
|
/// @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 ...
|
820
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
821
822
|
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...
|
823
824
|
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...
|
825
|
return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
826
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
827
|
return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
828
829
830
831
832
833
|
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...
|
834
|
return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
835
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
836
|
return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
837
838
839
840
841
842
|
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...
|
843
|
return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
844
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
845
|
return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
846
847
848
849
850
851
852
853
854
855
856
|
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 ...
|
857
858
859
860
861
862
863
|
/// 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...
|
864
|
bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
|
517876d6
heziqi
metrics finished ...
|
865
866
|
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...
|
867
|
return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
868
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
869
|
return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
870
871
872
873
874
875
|
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...
|
876
|
return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
877
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
878
|
return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
879
880
881
882
883
884
|
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...
|
885
|
return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
886
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
887
|
return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
888
889
890
891
892
893
894
895
896
897
898
|
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 ...
|
899
|
/// Closes the ENVI file.
|
6708cc25
heziqi
Ziqi added envi c...
|
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
932
|
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
|
933
|
return false;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
934
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
935
936
937
938
939
|
/// 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...
|
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
972
|
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 ...
|
973
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
974
|
/// Saves a header file describing the current ENVI file parameters.
|
e8eb202f
David Mayerich
added a new ENVI ...
|
975
976
977
978
979
980
981
982
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
983
984
985
986
|
/// 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 ...
|
987
|
bool band(void* ptr, double wavelength, bool PROGRESS = false){
|
d1d8ef91
David Mayerich
added band readin...
|
988
989
990
|
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 ...
|
991
|
return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
992
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
993
|
return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
994
995
996
997
998
999
1000
|
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 ...
|
1001
|
return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1002
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1003
|
return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1004
1005
1006
1007
1008
1009
1010
|
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 ...
|
1011
|
return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1012
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1013
|
return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1014
1015
1016
1017
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
d1d8ef91
David Mayerich
added band readin...
|
1018
|
}
|
ee4dea28
David Mayerich
fixed errors in c...
|
1019
|
return false;
|
1582ce07
David Mayerich
added band_index(...
|
1020
1021
|
}
|
27b826a8
David Mayerich
added a spherical...
|
1022
1023
1024
1025
1026
|
/// 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...
|
1027
|
bool spectrum(void* ptr, unsigned long long x, unsigned long long y, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
1028
1029
1030
|
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 ...
|
1031
|
return ((bsq<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1032
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1033
|
return ((bsq<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1034
1035
1036
1037
1038
1039
1040
|
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 ...
|
1041
|
return ((bil<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1042
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1043
|
return ((bil<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1044
1045
1046
1047
1048
1049
1050
|
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 ...
|
1051
|
return ((bip<float>*)file)->spectrum((float*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1052
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1053
|
return ((bip<double>*)file)->spectrum((double*)ptr, x, y, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1054
1055
1056
1057
1058
1059
1060
1061
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1062
1063
1064
1065
|
/// 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...
|
1066
|
bool band_index(void* ptr, unsigned long long b){
|
081f2c9f
heziqi
made bip bil file...
|
1067
1068
|
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(...
|
1069
|
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
081f2c9f
heziqi
made bip bil file...
|
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
1095
|
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(...
|
1096
1097
|
}
return false;
|
d1d8ef91
David Mayerich
added band readin...
|
1098
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
1099
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1100
1101
1102
1103
|
/// 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 ...
|
1104
|
bool avg_band(double * p, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1105
1106
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1107
|
return ((bsq<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1108
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1109
|
return ((bsq<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1110
1111
1112
1113
1114
1115
1116
|
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 ...
|
1117
|
return ((bil<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1118
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1119
|
return ((bil<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1120
1121
1122
1123
1124
1125
1126
|
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 ...
|
1127
|
return ((bip<float>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1128
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1129
|
return ((bip<double>*)file)->avg_band(p, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1130
1131
1132
1133
1134
1135
1136
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1137
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1138
1139
1140
1141
1142
|
/// 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 ...
|
1143
|
bool co_matrix(double* co, double* avg, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1144
|
if (header.interleave == envi_header::BSQ){
|
63fc1df8
David Mayerich
added an inverse ...
|
1145
1146
1147
1148
|
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...
|
1149
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1150
|
return ((bsq<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1151
1152
1153
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
1154
|
}*/
|
a43c4fe1
heziqi
Added crop in env...
|
1155
1156
1157
|
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1158
|
return ((bil<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1159
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1160
|
return ((bil<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1161
1162
1163
1164
1165
1166
1167
|
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 ...
|
1168
|
return ((bip<float>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1169
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1170
|
return ((bip<double>*)file)->co_matrix(co, avg, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1171
1172
1173
1174
1175
1176
1177
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1178
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1179
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1180
1181
1182
1183
1184
1185
1186
|
/// 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...
|
1187
1188
1189
1190
1191
1192
1193
1194
|
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...
|
1195
|
|
177c7863
David Mayerich
updated the ENVI ...
|
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
|
//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...
|
1206
1207
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1208
|
return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1209
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1210
|
return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1211
1212
1213
1214
1215
1216
1217
|
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 ...
|
1218
|
return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1219
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1220
|
return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1221
1222
1223
1224
1225
1226
1227
|
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 ...
|
1228
|
return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1229
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1230
|
return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1231
1232
1233
1234
1235
1236
1237
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1238
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1239
1240
1241
1242
1243
|
};
} //end namespace rts
#endif
|