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#ifndef STIM_ENVI_H
#define STIM_ENVI_H
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#include <stim/envi/envi_header.h>
#include <stim/envi/bsq.h>
#include <stim/envi/bip.h>
#include <stim/envi/bil.h>
#include <stim/math/fd_coefficients.h>
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#include <stim/parser/filename.h>
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#include <stim/util/filesize.h>
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#include <iostream>
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#include <fstream>
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//#include "../image/image.h"
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namespace stim{
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/** This class implements reading of ENVI hyperspectral files. These files can be stored in multiple orientations
(including BSQ, BIP, and BIL) in order to optimize streaming speed depending on applications. Basic ENVI
files are stored on disk as a large binary file with a corresponding header. Code for reading and processing
ENVI header files is in the envi_header class.
*/
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class envi{
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void* file; //void pointer to the relevant file reader (bip, bsq, or bil - with appropriate data type)
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std::string fname; //file name used for repeated opening and closing
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//allocate sufficient space for a spectrum based on the data type and number of bands
void* alloc_array(size_t len){
switch(header.data_type){
case envi_header::int8:
return malloc(len);
case envi_header::int16:
case envi_header::uint16:
return malloc(2 * len);
case envi_header::int32:
case envi_header::uint32:
case envi_header::float32:
return malloc(4 * len);
case envi_header::int64:
case envi_header::uint64:
case envi_header::float64:
case envi_header::complex32:
return malloc(8 * len);
case envi_header::complex64:
return malloc(16 * len);
default:
std::cout<<"ERROR stim::envi data type not recognized for spectral allocation"<<std::endl;
exit(1);
}
}
//cast a value to DEST type from SRC type
template<typename DST, typename SRC>
inline void cast(DST* dst, SRC* src){
(*dst) = (DST)(*src);
}
//cast an array from type SRC to type DEST
template<typename DST, typename SRC>
inline void cast(DST* dst, SRC* src, size_t len){
for(size_t i = 0; i < len; i++)
cast(&dst[i], &src[i]);
}
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public:
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envi_header header;
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/// Default constructor
envi(){
file = NULL; //set the file pointer to NULL
}
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envi(std::string filename, std::string headername) : envi(){
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header.load(headername);
fname = filename; //save the filename
allocate();
}
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//used to test if the current ENVI file is valid
operator bool(){
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if (header.interleave == envi_header::BSQ) { //if the infile is bsq file
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->is_open();
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->is_open();
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else if (header.interleave == envi_header::BIL) { //if the infile is bil file
if (header.data_type == envi_header::float32)
return ((bil<float>*)file)->is_open();
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->is_open();
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else if (header.interleave == envi_header::BIP) { //if the infile is bip file
if (header.data_type == envi_header::float32)
return ((bip<float>*)file)->is_open();
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->is_open();
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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//test to determine if the specified file is an ENVI file
static bool is_envi(std::string fname, std::string hname = ""){
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stim::filename data_file(fname);
stim::filename header_file;
if(hname == ""){ //if the header isn't provided
header_file = data_file; //assume that it's the same name as the data file, with a .hdr extension
header_file = header_file.extension("hdr");
}
else header_file = hname; //otherwise load the passed header
stim::envi_header H;
if(H.load(header_file) == false) //load the header file, if it doesn't load return false
return false;
size_t targetBytes = H.data_bytes(); //get the number of bytes that SHOULD be in the data file
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size_t bytes = stim::file_size(fname);
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if(bytes != targetBytes) return false; //if the data doesn't match the header, return false
return true; //otherwise everything looks fine
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}
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void* malloc_spectrum(){
return alloc_array(header.bands);
}
void* malloc_band(){
return alloc_array(header.samples * header.lines);
}
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void set_buffer_frac(double memfrac = 0.5){
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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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((bsq<float>*)file)->set_buffer_frac(memfrac);
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else if(header.data_type == envi_header::float64)
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((bsq<double>*)file)->set_buffer_frac(memfrac);
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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)->set_buffer_frac(memfrac);
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else if(header.data_type == envi_header::float64)
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((bil<double>*)file)->set_buffer_frac(memfrac);
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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)->set_buffer_frac(memfrac);
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((bip<double>*)file)->set_buffer_frac(memfrac);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
void set_buffer_raw(size_t bytes){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
((bsq<float>*)file)->set_buffer_raw(bytes);
else if(header.data_type == envi_header::float64)
((bsq<double>*)file)->set_buffer_raw(bytes);
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)->set_buffer_raw(bytes);
else if(header.data_type == envi_header::float64)
((bil<double>*)file)->set_buffer_raw(bytes);
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)->set_buffer_raw(bytes);
else if(header.data_type == envi_header::float64)
((bip<double>*)file)->set_buffer_raw(bytes);
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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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/// 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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size_t X(){ return header.samples; }
size_t Y(){ return header.lines; }
size_t Z(){ return header.bands; }
size_t B(){ return Z(); }
/// Return the size of the data set in bytes
size_t bytes(){
return X() * Y() * Z() * type_size();
}
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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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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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/// Returns the progress of the current processing operation as a percentage
size_t data_rate(){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->get_data_rate();
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->get_data_rate();
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->get_data_rate();
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->get_data_rate();
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->get_data_rate();
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->get_data_rate();
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
}
return 0;
}
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/// Allocate memory for a new ENVI file based on the current interleave format (BIP, BIL, BSQ) and data type.
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void allocate(){
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file = NULL; //set file to a NULL pointer
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if(header.interleave == envi_header::BSQ){
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if(header.data_type ==envi_header::float32)
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file = new bsq<float>();
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else if(header.data_type == envi_header::float64)
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file = new bsq<double>();
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}
else if(header.interleave == envi_header::BIP){
if(header.data_type ==envi_header::float32)
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file = new bip<float>();
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else if(header.data_type == envi_header::float64)
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file = new bip<double>();
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}
else if(header.interleave == envi_header::BIL){
if(header.data_type ==envi_header::float32)
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file = new bil<float>();
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else if(header.data_type == envi_header::float64)
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file = new bil<double>();
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}
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}
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/// Open a previously opened ENVI file
bool open(){
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//load the file
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if(header.interleave == envi_header::BSQ) { //if the infile is bsq file
if(header.data_type == envi_header::float32) {
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return ((bsq<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
372
373
|
}
else if(header.data_type == envi_header::float64) {
|
8057237a
David Mayerich
added an envi::op...
|
374
|
return ((bsq<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
375
376
377
378
|
}
else
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
379
|
|
6708cc25
heziqi
Ziqi added envi c...
|
380
381
|
else if(header.interleave == envi_header::BIL) { //if the infile is bil file
if(header.data_type == envi_header::float32) {
|
8057237a
David Mayerich
added an envi::op...
|
382
|
return ((bil<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
383
384
|
}
else if(header.data_type == envi_header::float64) {
|
8057237a
David Mayerich
added an envi::op...
|
385
|
return ((bil<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
386
387
388
389
|
}
else
return false;
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
390
|
|
6708cc25
heziqi
Ziqi added envi c...
|
391
392
|
else if(header.interleave == envi_header::BIP) { //if the infile is bip file
if(header.data_type == envi_header::float32) {
|
8057237a
David Mayerich
added an envi::op...
|
393
|
return ((bip<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
394
395
|
}
else if(header.data_type == envi_header::float64) {
|
8057237a
David Mayerich
added an envi::op...
|
396
|
return ((bip<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
397
398
|
}
else
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
399
|
return false;
|
6708cc25
heziqi
Ziqi added envi c...
|
400
401
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
402
403
|
return true;
|
8057237a
David Mayerich
added an envi::op...
|
404
405
406
|
}
|
48f356fa
David Mayerich
bug fixes for FFT...
|
407
408
409
410
411
412
413
414
415
416
|
/// Open an Agilent binary file as an ENVI stream
bool open_agilent(std::string filename){
fname = filename; //store the file name
//Open the file temporarily to get the header information
FILE* f = fopen(filename.c_str(), "r"); //open the binary file for reading
if(f == NULL) return false; //return false if no file is opened
fseek(f, 9, SEEK_SET); //seek to the number of bands
short b; //allocate space for the number of bands
|
618dce30
David Mayerich
removed warnings ...
|
417
418
419
420
421
|
size_t nread = fread(&b, sizeof(short), 1, f); //read the number of bands
if(nread != 1){
std::cout<<"Error reading band number from Agilent file."<<std::endl;
exit(1);
}
|
48f356fa
David Mayerich
bug fixes for FFT...
|
422
423
|
fseek(f, 13, SEEK_CUR); //skip the the x and y dimensions
short x, y;
|
618dce30
David Mayerich
removed warnings ...
|
424
425
426
427
428
429
430
431
432
433
|
nread = fread(&x, sizeof(short), 1, f); //read the image x and y size
if(nread != 1){
std::cout<<"Error reading X dimension from Agilent file."<<std::endl;
exit(1);
}
nread = fread(&y, sizeof(short), 1, f);
if(nread != 1){
std::cout<<"Error reading Y dimension from Agilent file."<<std::endl;
exit(1);
}
|
48f356fa
David Mayerich
bug fixes for FFT...
|
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
|
fclose(f); //close the file
//store the information from the Agilent header in the ENVI header
header.bands = b;
header.samples = x;
header.lines = y;
header.data_type = envi_header::float32; //all values are 32-bit floats
header.header_offset = 1020; //number of bytes in an Agilent binary header
header.interleave = envi_header::BSQ; //all Agilent binary files are BSQ
allocate(); //allocate the streaming file object
open(); //open the file for streaming
return true;
}
|
8057237a
David Mayerich
added an envi::op...
|
450
451
452
453
454
|
/// 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){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
455
|
|
8057237a
David Mayerich
added an envi::op...
|
456
457
458
459
|
header = h; //store the header
fname = filename; //save the filename
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
460
461
|
allocate();
|
8057237a
David Mayerich
added an envi::op...
|
462
463
464
|
return open(); //open the ENVI file;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
|
}
/// 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);
|
e8eb202f
David Mayerich
added a new ENVI ...
|
483
484
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
485
486
487
488
489
|
/// 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)
|
c30dd3e6
David Mayerich
added vector norm...
|
490
|
bool ratio(std::string outfile, double band, unsigned char* mask = NULL, bool PROGRESS = false){
|
a2bf1d08
David Mayerich
general bug fixes...
|
491
|
header.save(outfile + ".hdr");
|
6708cc25
heziqi
Ziqi added envi c...
|
492
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
e8eb202f
David Mayerich
added a new ENVI ...
|
493
|
if(header.data_type ==envi_header::float32)
|
c30dd3e6
David Mayerich
added vector norm...
|
494
|
return ((bsq<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
495
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
496
|
return ((bsq<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
497
498
499
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
500
|
|
6708cc25
heziqi
Ziqi added envi c...
|
501
502
|
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
|
c30dd3e6
David Mayerich
added vector norm...
|
503
|
return ((bil<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
504
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
505
|
return ((bil<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
506
507
508
509
510
511
|
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)
|
c30dd3e6
David Mayerich
added vector norm...
|
512
|
return ((bip<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
513
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
514
|
return ((bip<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
515
516
517
518
519
520
521
522
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
|
e933c14e
David Mayerich
cleaned up the code
|
523
|
return false;
|
6708cc25
heziqi
Ziqi added envi c...
|
524
525
|
}
|
c30dd3e6
David Mayerich
added vector norm...
|
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
|
/// Perform vector normalization on the ENVI image
void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){
header.save(outfile + ".hdr");
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
((bsq<float>*)file)->normalize(outfile, mask, PROGRESS);
else if(header.data_type == envi_header::float64)
((bsq<double>*)file)->normalize(outfile, mask, PROGRESS);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
((bil<float>*)file)->normalize(outfile, mask, PROGRESS);
else if(header.data_type == envi_header::float64)
((bil<double>*)file)->normalize(outfile, mask, PROGRESS);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
((bip<float>*)file)->normalize(outfile, mask, PROGRESS);
else if(header.data_type == envi_header::float64)
((bip<double>*)file)->normalize(outfile, mask, PROGRESS);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
562
563
564
565
|
/// 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)
|
798cea97
David Mayerich
added progress ba...
|
566
567
|
bool baseline(std::string outfile, std::vector<double> w, unsigned char* mask = NULL, bool PROGRESS = false){
header.save(outfile + ".hdr");
|
6708cc25
heziqi
Ziqi added envi c...
|
568
569
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
798cea97
David Mayerich
added progress ba...
|
570
|
return ((bsq<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
571
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
572
|
return ((bsq<double>*)file)->baseline(outfile,w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
573
574
575
576
577
578
579
580
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
|
798cea97
David Mayerich
added progress ba...
|
581
|
return ((bil<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
582
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
583
|
return ((bil<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
584
585
586
587
588
589
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
590
|
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
|
6708cc25
heziqi
Ziqi added envi c...
|
591
|
if(header.data_type ==envi_header::float32)
|
798cea97
David Mayerich
added progress ba...
|
592
|
return ((bip<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
593
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
594
|
return ((bip<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
595
596
597
598
599
600
601
602
603
604
605
606
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
|
dd5aab2f
David Mayerich
fixed errors in s...
|
607
608
609
|
/// Project an array of coefficients onto a basis matrix
void project(std::string outfile, double* center, double* basis, size_t M, std::vector<double> bands, unsigned char* mask, int cuda_device = 0, bool PROGRESS = false) {
|
63fc1df8
David Mayerich
added an inverse ...
|
610
611
612
613
614
615
616
617
618
619
620
621
|
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)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
622
|
((bip<float>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
623
|
else if(header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
624
|
((bip<double>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
625
626
627
628
629
630
631
632
|
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
|
dd5aab2f
David Mayerich
fixed errors in s...
|
633
|
out_hdr.wavelength = bands;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
634
|
out_hdr.band_names.clear();
|
63fc1df8
David Mayerich
added an inverse ...
|
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
|
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 ...
|
665
666
667
668
|
/// 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
|
c6251f8b
David Mayerich
allows user to de...
|
669
|
bool convert(std::string outfile, stim::envi_header::interleaveType interleave, bool PROGRESS = false, bool VERBOSE = false, bool OPTIMIZATION = true){
|
a2bf1d08
David Mayerich
general bug fixes...
|
670
|
|
6708cc25
heziqi
Ziqi added envi c...
|
671
672
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
a2bf1d08
David Mayerich
general bug fixes...
|
673
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
674
675
676
677
|
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
678
|
else if(interleave == envi_header::BIL) //convert BSQ -> BIL
|
c6251f8b
David Mayerich
allows user to de...
|
679
|
((bsq<float>*)file)->bil(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
|
a2bf1d08
David Mayerich
general bug fixes...
|
680
|
else if(interleave == envi_header::BIP){ //ERROR
|
cf5b4c92
David Mayerich
simplified asynch...
|
681
|
//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
|
474c351a
David Mayerich
output timing dat...
|
682
|
((bsq<float>*)file)->bip(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
|
cf5b4c92
David Mayerich
simplified asynch...
|
683
|
//exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
684
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
685
686
687
|
}
else if(header.data_type == envi_header::float64){ //if the data type is float
|
a2bf1d08
David Mayerich
general bug fixes...
|
688
|
if(interleave == envi_header::BSQ){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
689
690
691
|
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
692
|
else if(interleave == envi_header::BIL) //convert BSQ -> BIL
|
c6251f8b
David Mayerich
allows user to de...
|
693
|
((bsq<double>*)file)->bil(outfile, PROGRESS, OPTIMIZATION);
|
a2bf1d08
David Mayerich
general bug fixes...
|
694
|
else if(interleave == envi_header::BIP){ //ERROR
|
cf5b4c92
David Mayerich
simplified asynch...
|
695
|
//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
|
f7cf19e4
David Mayerich
fixed warnings, t...
|
696
|
((bsq<double>*)file)->bip(outfile, PROGRESS, OPTIMIZATION);
|
cf5b4c92
David Mayerich
simplified asynch...
|
697
|
//exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
698
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
699
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
700
|
|
6708cc25
heziqi
Ziqi added envi c...
|
701
702
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
703
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
704
705
706
707
708
|
}
}
else if(header.interleave == envi_header::BIL){
|
a2bf1d08
David Mayerich
general bug fixes...
|
709
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
710
711
712
713
|
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
714
715
716
717
|
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...
|
718
719
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
720
721
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIL){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
722
723
724
|
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
725
726
727
728
|
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...
|
729
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
730
|
|
6708cc25
heziqi
Ziqi added envi c...
|
731
732
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
733
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
734
735
736
737
|
}
}
else if(header.interleave == envi_header::BIP){
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
738
|
|
a2bf1d08
David Mayerich
general bug fixes...
|
739
740
|
if(header.data_type ==envi_header::float32){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
741
742
743
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
744
745
746
|
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 ...
|
747
748
749
750
|
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...
|
751
752
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
753
754
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
755
756
757
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
758
759
760
|
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 ...
|
761
762
763
764
|
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...
|
765
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
766
|
|
6708cc25
heziqi
Ziqi added envi c...
|
767
768
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
769
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
770
771
|
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
772
|
|
6708cc25
heziqi
Ziqi added envi c...
|
773
774
775
776
|
else{
std::cout<<"ERROR: unidentified interleave type"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
777
778
779
780
781
|
stim::envi_header h = header;
h.interleave = interleave;
h.save(outfile + ".hdr");
return true;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
782
|
|
6708cc25
heziqi
Ziqi added envi c...
|
783
784
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
785
786
787
788
789
|
/// 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
|
e37ce7bf
David Mayerich
added the ability...
|
790
|
bool build_mask(unsigned char* out_mask, double mask_band, double lower, double upper, unsigned char* mask = NULL, bool PROGRESS = false) {
|
4a6f666c
heziqi
Added mask method
|
791
792
793
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
e37ce7bf
David Mayerich
added the ability...
|
794
|
return ((bsq<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
795
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
796
|
return ((bsq<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
797
798
799
800
801
802
|
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)
|
e37ce7bf
David Mayerich
added the ability...
|
803
|
return ((bil<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
804
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
805
|
return ((bil<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
806
807
808
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
cacc3cdc
heziqi
attempt to fix CImg
|
809
|
|
4a6f666c
heziqi
Added mask method
|
810
811
|
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
|
e37ce7bf
David Mayerich
added the ability...
|
812
|
return ((bip<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
813
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
814
|
return ((bip<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
815
816
817
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
bba4f4d9
David Mayerich
minor warning fixes
|
818
819
|
return false;
|
740f8cd2
heziqi
added apply_mask
|
820
821
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
822
|
/// Creates a mask with a true value for all pixels that contain finite values
|
e37ce7bf
David Mayerich
added the ability...
|
823
|
void mask_finite(unsigned char* out_mask, unsigned char* mask = NULL, bool PROGRESS = false){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
824
825
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
e37ce7bf
David Mayerich
added the ability...
|
826
|
((bsq<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
827
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
828
|
((bsq<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
829
830
831
832
833
834
|
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)
|
e37ce7bf
David Mayerich
added the ability...
|
835
|
((bil<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
836
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
837
|
((bil<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
838
839
840
841
842
843
|
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)
|
e37ce7bf
David Mayerich
added the ability...
|
844
|
((bip<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
845
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
846
|
((bip<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
847
848
849
850
851
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
852
853
854
855
|
/// 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...
|
856
|
void apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
740f8cd2
heziqi
added apply_mask
|
857
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
858
859
|
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...
|
860
|
((bsq<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
861
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
862
|
((bsq<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
863
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
864
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
865
866
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
867
868
|
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...
|
869
|
((bil<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
870
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
871
|
((bil<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
872
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
873
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
874
875
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
876
877
|
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...
|
878
|
((bip<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
879
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
880
|
((bip<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
881
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
882
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
883
|
}
|
4a6f666c
heziqi
Added mask method
|
884
885
|
else{
|
e843658b
Brad Deutsch
Previous push did...
|
886
887
888
|
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
889
|
header.save(outfile + ".hdr");
|
e843658b
Brad Deutsch
Previous push did...
|
890
891
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
892
893
894
|
/// 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...
|
895
896
|
/// @param matrix is the destination for the pixel data
/// @param p is the mask
|
814eb271
David Mayerich
fixed problems wi...
|
897
|
bool sift(void* matrix, unsigned char* p = NULL, bool PROGRESS = false){
|
43dec788
David Mayerich
added code for si...
|
898
899
900
|
if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
901
|
return ((bsq<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
43dec788
David Mayerich
added code for si...
|
902
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
903
|
return ((bsq<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
904
|
else{
|
43dec788
David Mayerich
added code for si...
|
905
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
906
907
|
exit(1);
}
|
43dec788
David Mayerich
added code for si...
|
908
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
909
910
|
if (header.interleave == envi_header::BIP){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
911
|
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
912
|
return ((bip<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
913
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
914
|
return ((bip<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
915
916
917
918
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
919
920
|
}
if (header.interleave == envi_header::BIL){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
921
|
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
922
|
return ((bil<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
923
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
924
|
return ((bil<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
925
926
927
928
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
929
|
}
|
43dec788
David Mayerich
added code for si...
|
930
931
932
933
|
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
934
|
/// Saves in an array only those spectra corresponding to nonzero values of the mask.
|
43dec788
David Mayerich
added code for si...
|
935
936
|
/// @param outfile is the name of the sifted output file
/// @param p is the mask
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
937
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
e843658b
Brad Deutsch
Previous push did...
|
938
939
|
{
|
2fcab4f0
David Mayerich
added unsifting f...
|
940
|
//calculate the number of non-zero values in the mask
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
941
942
943
|
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...
|
944
945
946
947
948
|
if( p[i] > 0 ) nnz++;
//create a new header
envi_header new_header = header;
|
f7e99517
David Mayerich
added sifting for...
|
949
950
|
//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...
|
951
|
new_header.interleave = envi_header::BIP;
|
f7e99517
David Mayerich
added sifting for...
|
952
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
953
954
955
956
957
|
//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...
|
958
959
|
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...
|
960
|
return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
961
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
962
|
return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
963
964
965
966
967
968
|
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...
|
969
|
return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
970
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
971
|
return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
972
973
974
975
976
977
|
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...
|
978
|
return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
979
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
980
|
return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
981
982
983
984
985
986
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
4a6f666c
heziqi
Added mask method
|
987
988
|
exit(1);
}
|
4a6f666c
heziqi
Added mask method
|
989
|
return false;
|
cacc3cdc
heziqi
attempt to fix CImg
|
990
991
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
992
|
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...
|
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
|
//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...
|
1005
|
return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
1006
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
1007
|
return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
1008
1009
1010
1011
1012
|
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...
|
1013
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
1014
1015
1016
1017
|
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...
|
1018
|
|
8550e94f
David Mayerich
added sifting and...
|
1019
|
if (header.data_type == envi_header::float32)
|
a2bf1d08
David Mayerich
general bug fixes...
|
1020
|
return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
1021
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
1022
|
return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
1023
1024
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1025
1026
1027
1028
|
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1029
|
}
|
cbce396e
David Mayerich
added support for...
|
1030
|
return 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1031
1032
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1033
1034
1035
1036
1037
1038
1039
1040
1041
|
/// 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...
|
1042
|
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...
|
1043
1044
|
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...
|
1045
|
return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1046
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1047
|
return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1048
1049
1050
1051
1052
1053
|
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...
|
1054
|
return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1055
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1056
|
return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1057
1058
1059
1060
1061
1062
|
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...
|
1063
|
return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1064
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1065
|
return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
|
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 ...
|
1077
1078
1079
1080
1081
1082
1083
1084
1085
|
/// 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...
|
1086
|
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...
|
1087
1088
|
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...
|
1089
|
return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1090
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1091
|
return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1092
1093
1094
1095
1096
1097
|
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...
|
1098
|
return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1099
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1100
|
return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1101
1102
1103
1104
1105
1106
|
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...
|
1107
|
return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1108
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1109
|
return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
|
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 ...
|
1121
1122
1123
1124
1125
1126
1127
1128
1129
|
/// 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...
|
1130
|
/// @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 ...
|
1131
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1132
1133
|
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...
|
1134
1135
|
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...
|
1136
|
return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1137
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1138
|
return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1139
1140
1141
1142
1143
1144
|
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...
|
1145
|
return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1146
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1147
|
return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1148
1149
1150
1151
1152
1153
|
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...
|
1154
|
return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1155
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1156
|
return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
|
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 ...
|
1168
1169
1170
1171
1172
1173
1174
|
/// 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...
|
1175
|
bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
|
517876d6
heziqi
metrics finished ...
|
1176
1177
|
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...
|
1178
|
return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1179
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1180
|
return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1181
1182
1183
1184
1185
1186
|
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...
|
1187
|
return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1188
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1189
|
return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1190
1191
1192
1193
1194
1195
|
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...
|
1196
|
return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1197
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1198
|
return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
|
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 ...
|
1210
|
/// Closes the ENVI file.
|
edb975b0
David Mayerich
created a stim::e...
|
1211
1212
|
void close(){
if(file == NULL) return;
|
6708cc25
heziqi
Ziqi added envi c...
|
1213
1214
|
if(header.interleave == envi_header::BSQ){
if(header.data_type ==envi_header::float32)
|
edb975b0
David Mayerich
created a stim::e...
|
1215
|
((bsq<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1216
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1217
|
((bsq<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1218
1219
1220
1221
1222
1223
1224
1225
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIL){
if(header.data_type ==envi_header::float32)
|
edb975b0
David Mayerich
created a stim::e...
|
1226
|
((bil<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1227
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1228
|
((bil<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1229
1230
1231
1232
1233
1234
1235
1236
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIP){
if(header.data_type ==envi_header::float32)
|
edb975b0
David Mayerich
created a stim::e...
|
1237
|
((bip<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1238
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1239
|
((bip<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1240
1241
1242
1243
1244
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1245
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1246
1247
1248
1249
1250
|
/// 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...
|
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
|
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 ...
|
1284
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1285
|
/// Saves a header file describing the current ENVI file parameters.
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1286
1287
1288
1289
1290
1291
1292
1293
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1294
1295
1296
1297
|
/// 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 ...
|
1298
|
bool band(void* ptr, double wavelength, bool PROGRESS = false){
|
d1d8ef91
David Mayerich
added band readin...
|
1299
1300
1301
|
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 ...
|
1302
|
return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1303
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1304
|
return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1305
1306
1307
1308
1309
1310
1311
|
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 ...
|
1312
|
return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1313
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1314
|
return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1315
1316
1317
1318
1319
1320
1321
|
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 ...
|
1322
|
return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1323
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1324
|
return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1325
1326
1327
1328
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
d1d8ef91
David Mayerich
added band readin...
|
1329
|
}
|
ee4dea28
David Mayerich
fixed errors in c...
|
1330
|
return false;
|
1582ce07
David Mayerich
added band_index(...
|
1331
1332
|
}
|
735a2a24
David Mayerich
started testing o...
|
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
|
// Retrieve a spectrum at the specified 1D location
/// @param ptr is a pointer to pre-allocated memory of size B*sizeof(T)
/// @param x is the 1D coordinate of the spectrum
template<typename T>
void spectrum(T* ptr, size_t n, bool PROGRESS = false){
void* temp = alloc_array(header.bands); //allocate space for the output array
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32){
((bsq<float>*)file)->spectrum((float*)temp, n, PROGRESS);
cast<T, float>(ptr, (float*)temp, header.bands);
}
else if (header.data_type == envi_header::float64){
((bsq<double>*)file)->spectrum((double*)temp, n, PROGRESS);
cast<T, double>(ptr, (double*)temp, header.bands);
}
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32){
((bil<float>*)file)->spectrum((float*)temp, n, PROGRESS);
cast<T, float>(ptr, (float*)temp, header.bands);
}
else if (header.data_type == envi_header::float64){
((bil<double>*)file)->spectrum((double*)temp, n, PROGRESS);
cast<T, double>(ptr, (double*)temp, header.bands);
}
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32){
((bip<float>*)file)->spectrum((float*)temp, n, PROGRESS);
|
d4aa4cf7
David Mayerich
fixed the in-memo...
|
1373
|
float test = ((float*)temp)[0];
|
735a2a24
David Mayerich
started testing o...
|
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
|
cast<T, float>(ptr, (float*)temp, header.bands);
}
else if (header.data_type == envi_header::float64){
((bip<double>*)file)->spectrum((double*)temp, n, PROGRESS);
cast<T, double>(ptr, (double*)temp, header.bands);
}
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
}
/// Retrieve a spectrum from the specified (x, y) location
/// @param ptr is a pointer to pre-allocated memory of size B*sizeof(T)
/// @param x is the x-coordinate of the spectrum
/// @param y is the y-coordinate of the spectrum
template<typename T>
|
d0ef98e3
David Mayerich
fixed a Linux com...
|
1393
|
void spectrum(T* ptr, size_t x, size_t y, bool PROGRESS = false){
|
735a2a24
David Mayerich
started testing o...
|
1394
|
|
c4dd399a
David Mayerich
fixed a Linux com...
|
1395
|
spectrum<T>(ptr, y * header.samples + x, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1396
1397
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1398
1399
1400
1401
|
/// 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...
|
1402
|
bool band_index(void* ptr, unsigned long long b){
|
081f2c9f
heziqi
made bip bil file...
|
1403
1404
|
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(...
|
1405
|
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
081f2c9f
heziqi
made bip bil file...
|
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
|
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(...
|
1432
1433
|
}
return false;
|
d1d8ef91
David Mayerich
added band readin...
|
1434
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
1435
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1436
1437
1438
1439
|
/// 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
|
35a7195f
David Mayerich
added median spec...
|
1440
|
bool mean_spectrum(double * p, double* std, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1441
1442
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
35a7195f
David Mayerich
added median spec...
|
1443
|
return ((bsq<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1444
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1445
|
return ((bsq<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1446
1447
1448
1449
1450
1451
1452
|
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)
|
35a7195f
David Mayerich
added median spec...
|
1453
|
return ((bil<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1454
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1455
|
return ((bil<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1456
1457
1458
1459
1460
1461
1462
|
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)
|
35a7195f
David Mayerich
added median spec...
|
1463
|
return ((bip<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1464
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1465
|
return ((bip<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1466
1467
1468
1469
1470
1471
1472
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1473
|
|
35a7195f
David Mayerich
added median spec...
|
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
|
/// 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
bool median_spectrum(double* m, unsigned char* mask, bool PROGRESS = false){
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->median_spectrum(m, mask, PROGRESS);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->median_spectrum(m, mask, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else{
std::cout<<"ERROR: median calculation is only supported for BSQ interleave types. Convert to process."<<std::endl;
exit(1);
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1496
1497
1498
1499
1500
|
/// 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
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1501
|
bool co_matrix(double* co, double* avg, unsigned char* mask, int cuda_device, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1502
|
if (header.interleave == envi_header::BSQ){
|
63fc1df8
David Mayerich
added an inverse ...
|
1503
1504
|
std::cout<<"ERROR: calculating the covariance matrix for a BSQ file is impractical; convert to BIL or BIP first"<<std::endl;
exit(1);
|
a43c4fe1
heziqi
Added crop in env...
|
1505
1506
1507
|
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1508
|
return ((bil<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1509
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1510
|
return ((bil<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1511
1512
1513
1514
1515
1516
1517
|
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)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1518
|
return ((bip<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1519
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1520
|
return ((bip<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1521
1522
1523
1524
1525
1526
1527
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1528
|
|
334547d8
sam
changes for mnf: ...
|
1529
1530
1531
1532
1533
|
/// Calculate the covariance of noise 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
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1534
|
bool coNoise_matrix(double* coN, double* avg, unsigned char* mask, int cuda_device = 0, bool PROGRESS = false){
|
334547d8
sam
changes for mnf: ...
|
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
|
if (header.interleave == envi_header::BSQ){
std::cout<<"ERROR: calculating the covariance matrix of noise for a BSQ file is impractical; convert to BIP first"<<std::endl;
exit(1);
}
else if (header.interleave == envi_header::BIL){
std::cout<<"ERROR: calculating the covariance matrix of noise for a BIL file is impractical; convert to BIP first"<<std::endl;
exit(1);
}
else if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1548
|
return ((bip<float>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
|
334547d8
sam
changes for mnf: ...
|
1549
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1550
|
return ((bip<double>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
|
334547d8
sam
changes for mnf: ...
|
1551
1552
1553
1554
1555
1556
1557
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1558
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1559
1560
1561
1562
1563
1564
1565
|
/// 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...
|
1566
1567
1568
1569
1570
1571
1572
1573
|
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...
|
1574
|
|
177c7863
David Mayerich
updated the ENVI ...
|
1575
1576
|
//save the header for the cropped file
stim::envi_header new_header = header;
|
f78ceb64
David Mayerich
fixed BIP croppin...
|
1577
1578
1579
|
new_header.samples = x1 - x0 + 1;
new_header.lines = y1 - y0 + 1;
new_header.bands = b1 - b0 + 1;
|
177c7863
David Mayerich
updated the ENVI ...
|
1580
|
std::vector<double>::const_iterator first = new_header.wavelength.begin() + b0;
|
f78ceb64
David Mayerich
fixed BIP croppin...
|
1581
|
std::vector<double>::const_iterator last = new_header.wavelength.begin() + b1 + 1;
|
177c7863
David Mayerich
updated the ENVI ...
|
1582
1583
1584
|
new_header.wavelength = std::vector<double>(first, last);
new_header.save(outfile + ".hdr");
|
a43c4fe1
heziqi
Added crop in env...
|
1585
1586
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1587
|
return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1588
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1589
|
return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1590
1591
1592
1593
1594
1595
1596
|
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 ...
|
1597
|
return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1598
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1599
|
return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1600
1601
1602
1603
1604
1605
1606
|
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 ...
|
1607
|
return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1608
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1609
|
return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1610
1611
1612
1613
1614
1615
1616
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1617
|
|
bb61cb18
David Mayerich
added subimage fu...
|
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
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1652
|
void subimages(std::string outfile, size_t nx, size_t ny, unsigned char* mask, bool PROGRESS = false){
size_t nnz = 0; //initialize the number of subimages to zero
for(size_t i = 0; i < header.lines * header.samples; i++) //for each pixel in the mask
if(mask[i]) nnz++; //if the pixel is valid, add a subimage
//save the header for the cropped file
stim::envi_header new_header = header;
new_header.samples = nx; //calculate the width of the output image (concatenated subimages)
new_header.lines = nnz * ny; //calculate the height of the output image (height of subimages)
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
((bsq<float>*)file)->subimages(outfile, nx, ny, mask, PROGRESS);
else if (header.data_type == envi_header::float64)
((bsq<double>*)file)->subimages(outfile, nx, ny, mask, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIL){
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
else if (header.interleave == envi_header::BIP){
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
new_header.save(outfile + ".hdr"); //save the header for the output file
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1653
1654
1655
1656
1657
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1659
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1709
1710
|
/// Remove a list of bands from the ENVI file
/// @param outfile is the file name for the output hyperspectral image (with trimmed bands)
/// @param b is an array of bands to be eliminated
void trim(std::string outfile, std::vector<size_t> trimmed, bool PROGRESS = false){
envi_header h = header;
h.bands = header.bands - trimmed.size(); //calculate the new number of bands
if(header.wavelength.size() != 0)
h.wavelength.resize(h.bands);
if(header.band_names.size() != 0)
h.band_names.resize(h.bands);
size_t it = 0; //allocate an index into the trimmed bands array
size_t i = 0;
for(size_t b = 0; b < header.bands; b++){ //for each band
if(b != trimmed[it]){
if(h.wavelength.size()) h.wavelength[i] = header.wavelength[b];
if(h.band_names.size()) h.band_names[i] = header.band_names[i];
i++;
}
else it++;
}
h.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->trim(outfile, trimmed, PROGRESS);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->trim(outfile, trimmed, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
return ((bil<float>*)file)->trim(outfile, trimmed, PROGRESS);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->trim(outfile, trimmed, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
return ((bip<float>*)file)->trim(outfile, trimmed, PROGRESS);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->trim(outfile, trimmed, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
}
|
2ce6954b
David Mayerich
added the ability...
|
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
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1734
1735
1736
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1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
1756
1757
1758
|
/// Combine two ENVI images along the Y axis
/// @param outfile is the combined file to be output
/// @param C is the ENVI object for the image to be combined
void combine(std::string outfile, envi C, long long x, long long y, bool PROGRESS = false){
envi_header h = header;
long long left = std::min<long long>(0, x); //calculate the left edge of the final image
long long right = std::max<long long>((long long)header.samples, C.header.samples + x); //calculate the right edge of the final image
long long top = std::min<long long>(0, y); //calculate the top edge of the final image
long long bottom = std::max<long long>((long long)header.lines, C.header.lines + y); //calculate the bottom edge of the final image
h.samples = right - left;
h.lines = bottom - top;
h.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
((bsq<float>*)file)->combine(outfile, (bsq<float>*)C.file, x, y, PROGRESS);
else if (header.data_type == envi_header::float64)
((bsq<double>*)file)->combine(outfile, (bsq<double>*)C.file, x, y, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
((bil<float>*)file)->combine(outfile, (bil<float>*)C.file, x, y, PROGRESS);
else if (header.data_type == envi_header::float64)
((bil<double>*)file)->combine(outfile, (bil<double>*)C.file, x, y, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
((bip<float>*)file)->combine(outfile, (bip<float>*)C.file, x, y, PROGRESS);
else if (header.data_type == envi_header::float64)
((bip<double>*)file)->combine(outfile, (bip<double>*)C.file, x, y, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1759
|
|
82a7c08c
David Mayerich
added an append c...
|
1760
1761
1762
1763
1764
1765
1766
1767
1768
1769
1770
1771
1772
1773
1774
1775
1776
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
1787
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1800
1801
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1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
|
void append(std::string outfile, envi C, bool PROGRESS = false) {
if (C.header.samples != header.samples || //verify that the images are the same size
C.header.lines != header.lines) {
std::cout << "ERROR - appended images must be the same size: input = [" << header.samples << " x " << header.lines << "], output = [" << C.header.samples << " x " << C.header.lines << "]" << std::endl;
exit(1);
}
if (C.header.interleave != header.interleave) {
std::cout << "ERROR - appended images must have the same interleave format" << std::endl;
exit(1);
}
stim::envi_header new_header = header; //create a header for the output image
new_header.bands = header.bands + C.header.bands; //calculate the number of bands in the new image
if (header.wavelength.size() != 0 && C.header.wavelength.size() != 0) { //if both files contain wavelength information
for (size_t b = 0; b < C.header.wavelength.size(); b++)
new_header.wavelength.push_back(C.header.wavelength[b]); //append the wavelength labels to the new header array
}
else new_header.wavelength.clear();
if (header.band_names.size() != 0 && C.header.band_names.size() != 0) { //if both files contain band name information
for (size_t b = 0; b < C.header.band_names.size(); b++)
new_header.band_names.push_back(C.header.band_names[b]); //append the wavelength labels to the new header array
}
else new_header.wavelength.clear();
new_header.save(outfile + ".hdr"); //save the output
if (header.interleave == envi_header::BSQ) {
if (header.data_type == envi_header::float32)
((bsq<float>*)file)->append(outfile, (bsq<float>*)C.file, PROGRESS);
else if (header.data_type == envi_header::float64)
((bsq<double>*)file)->append(outfile, (bsq<double>*)C.file, PROGRESS);
else {
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIL) {
if (header.data_type == envi_header::float32)
((bil<float>*)file)->append(outfile, (bil<float>*)C.file, PROGRESS);
else if (header.data_type == envi_header::float64)
((bil<double>*)file)->append(outfile, (bil<double>*)C.file, PROGRESS);
else {
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIP) {
if (header.data_type == envi_header::float32)
((bip<float>*)file)->append(outfile, (bip<float>*)C.file, PROGRESS);
else if (header.data_type == envi_header::float64)
((bip<double>*)file)->append(outfile, (bip<double>*)C.file, PROGRESS);
else {
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1821
1822
1823
1824
1825
1826
1827
|
/// Convolve the given band range with a kernel specified by a vector of coefficients.
/// @param outfile is the combined file to be output
/// @param c is an array of coefficients
/// @param start is the band to start processing (the first coefficient starts here)
/// @param nbands is the number of bands to process
/// @param center is the index for the center coefficient for the kernel (used to set the wavelengths in the output file)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1828
|
void convolve(std::string outfile, std::vector<double> C, size_t start, size_t end, size_t center = 0, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1829
1830
1831
1832
1833
1834
1835
1836
1837
1838
1839
1840
1841
1842
1843
1844
1845
|
size_t nbands = end - start + 1;
envi_header h = header; //copy the current header
h.bands = nbands; //set the number of new bands
if(header.wavelength.size() != 0){
h.wavelength.resize(nbands); //set the number of wavelengths to the number of bands
for(size_t b = 0; b < nbands; b++)
h.wavelength[b] = header.wavelength[b+center];
}
if(header.band_names.size() != 0){
h.band_names.resize(nbands);
for(size_t b = 0; b < nbands; b++)
h.band_names[b] = header.band_names[b+center];
}
h.save(outfile + ".hdr"); //save the new header
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1846
|
((bsq<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1847
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1848
|
((bsq<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1849
1850
1851
1852
1853
1854
1855
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1856
|
((bil<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1857
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1858
|
((bil<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1859
1860
1861
1862
1863
1864
1865
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1866
|
((bip<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1867
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1868
|
((bip<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1869
1870
1871
1872
1873
1874
1875
1876
1877
1878
1879
1880
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
}
/// Approximates the nth derivative of the spectra to the specified order
/// @param outfile is the file where the derivative approximation will be saved
/// @n is the derivative to be calculated
/// @order is the order of the error (must be even)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1881
|
void deriv(std::string outfile, size_t d, size_t order, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1882
1883
1884
|
header.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1885
|
((bsq<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1886
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1887
|
((bsq<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1888
1889
1890
1891
1892
1893
1894
1895
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1896
|
((bil<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1897
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1898
|
((bil<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1899
1900
1901
1902
1903
1904
1905
1906
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1907
|
((bip<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1908
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1909
|
((bip<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1910
1911
1912
1913
1914
1915
1916
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
exit(1);
}
|
278c622b
David Mayerich
finished Windows ...
|
1917
1918
1919
1920
1921
1922
1923
1924
1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
1936
1937
1938
1939
1940
1941
1942
1943
1944
1945
1946
1947
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1971
1972
1973
1974
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1976
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1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
|
void multiply(std::string outfile, double v, unsigned char* mask = NULL, bool PROGRESS = false){
header.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
((bsq<float>*)file)->multiply(outfile, v, mask, PROGRESS);
else if (header.data_type == envi_header::float64)
((bsq<double>*)file)->multiply(outfile, v, mask, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
((bil<float>*)file)->multiply(outfile, v, mask, PROGRESS);
else if (header.data_type == envi_header::float64)
((bil<double>*)file)->multiply(outfile, v, mask, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
((bip<float>*)file)->multiply(outfile, v, mask, PROGRESS);
else if (header.data_type == envi_header::float64)
((bip<double>*)file)->multiply(outfile, v, mask, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
exit(1);
}
void add(std::string outfile, double v, unsigned char* mask = NULL, bool PROGRESS = false){
header.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
((bsq<float>*)file)->add(outfile, v, mask, PROGRESS);
else if (header.data_type == envi_header::float64)
((bsq<double>*)file)->add(outfile, v, mask, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
((bil<float>*)file)->add(outfile, v, mask, PROGRESS);
else if (header.data_type == envi_header::float64)
((bil<double>*)file)->add(outfile, v, mask, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
((bip<float>*)file)->add(outfile, v, mask, PROGRESS);
else if (header.data_type == envi_header::float64)
((bip<double>*)file)->add(outfile, v, mask, PROGRESS);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
exit(1);
}
|
9d34229e
David Mayerich
restructured the ...
|
1991
1992
1993
1994
1995
|
void fft(std::string outfile, double band_min, double band_max, size_t samples = 0, void* ratio = NULL, size_t rx = 0, size_t ry = 0, bool PROGRESS = false, int cuda_device = 0){
|
6e9cf1ac
David Mayerich
fixed image bug i...
|
1996
|
if(samples == 0) samples = header.bands;
|
f1365506
David Mayerich
modifications to ...
|
1997
|
//double B = (double)header.bands;
|
9d34229e
David Mayerich
restructured the ...
|
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
|
double delta = header.wavelength[1] - header.wavelength[0]; //calculate spacing in the current domain
double span = samples * delta; //calculate the span in the current domain
double fft_delta = 1.0 / span; //calculate the span in the FFT domain
double fft_max = fft_delta * samples/2; //calculate the maximum range of the FFT
if(band_max > fft_max) band_max = fft_max; //the user gave a band outside of the FFT range, reset the band to the maximum available
size_t start_i = (size_t)std::ceil(band_min / fft_delta); //calculate the first band to store
size_t size_i = (size_t)std::floor(band_max / fft_delta) - start_i + 1; //calculate the number of bands to store
size_t end_i = start_i + size_i - 1; //last band number
envi_header new_header = header;
new_header.bands = size_i;
new_header.set_wavelengths(start_i * fft_delta, fft_delta);
|
6e9cf1ac
David Mayerich
fixed image bug i...
|
2011
|
new_header.wavelength_units = "inv_" + header.wavelength_units;
|
9d34229e
David Mayerich
restructured the ...
|
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2022
2023
2024
2025
2026
2027
2028
|
new_header.save(outfile + ".hdr");
if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
((bip<float>*)file)->fft(outfile, start_i, end_i, samples, (float*)ratio, rx, ry, PROGRESS, cuda_device);
else if (header.data_type == envi_header::float64)
((bip<double>*)file)->fft(outfile, start_i, end_i, samples, (double*)ratio, rx, ry, PROGRESS, cuda_device);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else{
std::cout<<"ERROR: only BIP files supported for FFT"<<std::endl;
exit(1);
}
}
|
278c622b
David Mayerich
finished Windows ...
|
2029
|
}; //end ENVI
|
e8eb202f
David Mayerich
added a new ENVI ...
|
2030
2031
2032
2033
|
} //end namespace rts
#endif
|