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#ifndef STIM_ENVI_H
#define STIM_ENVI_H
#include "../envi/envi_header.h"
#include "../envi/bsq.h"
#include "../envi/bip.h"
#include "../envi/bil.h"
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#include "../math/fd_coefficients.h"
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#include <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){
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(){
if(file == NULL) return false;
return true;
}
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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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return ((bsq<double>*)file)->get_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
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return ((bil<float>*)file)->get_progress();
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else if(header.data_type == envi_header::float64)
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return ((bil<double>*)file)->get_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
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return ((bip<float>*)file)->get_progress();
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else if(header.data_type == envi_header::float64)
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return ((bip<double>*)file)->get_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
}
return 0;
}
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/// 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);
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}
else if(header.data_type == envi_header::float64) {
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return ((bsq<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
else
return false;
}
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else if(header.interleave == envi_header::BIL) { //if the infile is bil file
if(header.data_type == envi_header::float32) {
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return ((bil<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
else if(header.data_type == envi_header::float64) {
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return ((bil<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
else
return false;
}
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David Mayerich
fixed a Win32 bug...
|
361
|
|
6708cc25
heziqi
Ziqi added envi c...
|
362
363
|
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...
|
364
|
return ((bip<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
365
366
|
}
else if(header.data_type == envi_header::float64) {
|
8057237a
David Mayerich
added an envi::op...
|
367
|
return ((bip<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
368
369
|
}
else
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
370
|
return false;
|
6708cc25
heziqi
Ziqi added envi c...
|
371
372
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
373
374
|
return true;
|
8057237a
David Mayerich
added an envi::op...
|
375
376
377
|
}
|
48f356fa
David Mayerich
bug fixes for FFT...
|
378
379
380
381
382
383
384
385
386
387
|
/// 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 ...
|
388
389
390
391
392
|
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...
|
393
394
|
fseek(f, 13, SEEK_CUR); //skip the the x and y dimensions
short x, y;
|
618dce30
David Mayerich
removed warnings ...
|
395
396
397
398
399
400
401
402
403
404
|
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...
|
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
|
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...
|
421
422
423
424
425
|
/// 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...
|
426
|
|
8057237a
David Mayerich
added an envi::op...
|
427
428
429
430
|
header = h; //store the header
fname = filename; //save the filename
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
431
432
|
allocate();
|
8057237a
David Mayerich
added an envi::op...
|
433
434
435
|
return open(); //open the ENVI file;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
|
}
/// 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 ...
|
454
455
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
456
457
458
459
460
|
/// 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...
|
461
|
bool ratio(std::string outfile, double band, unsigned char* mask = NULL, bool PROGRESS = false){
|
a2bf1d08
David Mayerich
general bug fixes...
|
462
|
header.save(outfile + ".hdr");
|
6708cc25
heziqi
Ziqi added envi c...
|
463
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
e8eb202f
David Mayerich
added a new ENVI ...
|
464
|
if(header.data_type ==envi_header::float32)
|
c30dd3e6
David Mayerich
added vector norm...
|
465
|
return ((bsq<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
466
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
467
|
return ((bsq<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
468
469
470
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
471
|
|
6708cc25
heziqi
Ziqi added envi c...
|
472
473
|
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...
|
474
|
return ((bil<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
475
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
476
|
return ((bil<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
477
478
479
480
481
482
|
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...
|
483
|
return ((bip<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
484
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
485
|
return ((bip<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
486
487
488
489
490
491
492
493
|
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
|
494
|
return false;
|
6708cc25
heziqi
Ziqi added envi c...
|
495
496
|
}
|
c30dd3e6
David Mayerich
added vector norm...
|
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
|
/// 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 ...
|
533
534
535
536
|
/// 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...
|
537
538
|
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...
|
539
540
|
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...
|
541
|
return ((bsq<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
542
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
543
|
return ((bsq<double>*)file)->baseline(outfile,w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
544
545
546
547
548
549
550
551
|
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...
|
552
|
return ((bil<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
553
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
554
|
return ((bil<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
555
556
557
558
559
560
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
561
|
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
|
6708cc25
heziqi
Ziqi added envi c...
|
562
|
if(header.data_type ==envi_header::float32)
|
798cea97
David Mayerich
added progress ba...
|
563
|
return ((bip<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
564
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
565
|
return ((bip<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
566
567
568
569
570
571
572
573
574
575
576
577
|
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...
|
578
579
580
|
/// 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 ...
|
581
582
583
584
585
586
587
588
589
590
591
592
|
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...
|
593
|
((bip<float>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
594
|
else if(header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
595
|
((bip<double>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
596
597
598
599
600
601
602
603
|
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...
|
604
|
out_hdr.wavelength = bands;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
605
|
out_hdr.band_names.clear();
|
63fc1df8
David Mayerich
added an inverse ...
|
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
|
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 ...
|
636
637
638
639
|
/// 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...
|
640
|
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...
|
641
|
|
6708cc25
heziqi
Ziqi added envi c...
|
642
643
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
a2bf1d08
David Mayerich
general bug fixes...
|
644
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
645
646
647
648
|
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
649
|
else if(interleave == envi_header::BIL) //convert BSQ -> BIL
|
c6251f8b
David Mayerich
allows user to de...
|
650
|
((bsq<float>*)file)->bil(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
|
a2bf1d08
David Mayerich
general bug fixes...
|
651
|
else if(interleave == envi_header::BIP){ //ERROR
|
cf5b4c92
David Mayerich
simplified asynch...
|
652
|
//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
|
474c351a
David Mayerich
output timing dat...
|
653
|
((bsq<float>*)file)->bip(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
|
cf5b4c92
David Mayerich
simplified asynch...
|
654
|
//exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
655
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
656
657
658
|
}
else if(header.data_type == envi_header::float64){ //if the data type is float
|
a2bf1d08
David Mayerich
general bug fixes...
|
659
|
if(interleave == envi_header::BSQ){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
660
661
662
|
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
663
|
else if(interleave == envi_header::BIL) //convert BSQ -> BIL
|
c6251f8b
David Mayerich
allows user to de...
|
664
|
((bsq<double>*)file)->bil(outfile, PROGRESS, OPTIMIZATION);
|
a2bf1d08
David Mayerich
general bug fixes...
|
665
|
else if(interleave == envi_header::BIP){ //ERROR
|
cf5b4c92
David Mayerich
simplified asynch...
|
666
|
//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
|
f7cf19e4
David Mayerich
fixed warnings, t...
|
667
|
((bsq<double>*)file)->bip(outfile, PROGRESS, OPTIMIZATION);
|
cf5b4c92
David Mayerich
simplified asynch...
|
668
|
//exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
669
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
670
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
671
|
|
6708cc25
heziqi
Ziqi added envi c...
|
672
673
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
674
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
675
676
677
678
679
|
}
}
else if(header.interleave == envi_header::BIL){
|
a2bf1d08
David Mayerich
general bug fixes...
|
680
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
681
682
683
684
|
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
685
686
687
688
|
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...
|
689
690
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
691
692
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIL){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
693
694
695
|
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
696
697
698
699
|
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...
|
700
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
701
|
|
6708cc25
heziqi
Ziqi added envi c...
|
702
703
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
704
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
705
706
707
708
|
}
}
else if(header.interleave == envi_header::BIP){
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
709
|
|
a2bf1d08
David Mayerich
general bug fixes...
|
710
711
|
if(header.data_type ==envi_header::float32){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
712
713
714
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
715
716
717
|
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 ...
|
718
719
720
721
|
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...
|
722
723
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
724
725
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
726
727
728
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
729
730
731
|
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 ...
|
732
733
734
735
|
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...
|
736
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
737
|
|
6708cc25
heziqi
Ziqi added envi c...
|
738
739
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
740
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
741
742
|
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
743
|
|
6708cc25
heziqi
Ziqi added envi c...
|
744
745
746
747
|
else{
std::cout<<"ERROR: unidentified interleave type"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
748
749
750
751
752
|
stim::envi_header h = header;
h.interleave = interleave;
h.save(outfile + ".hdr");
return true;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
753
|
|
6708cc25
heziqi
Ziqi added envi c...
|
754
755
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
756
757
758
759
760
|
/// 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...
|
761
|
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
|
762
763
764
|
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...
|
765
|
return ((bsq<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
766
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
767
|
return ((bsq<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
768
769
770
771
772
773
|
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...
|
774
|
return ((bil<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
775
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
776
|
return ((bil<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
777
778
779
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
cacc3cdc
heziqi
attempt to fix CImg
|
780
|
|
4a6f666c
heziqi
Added mask method
|
781
782
|
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...
|
783
|
return ((bip<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
784
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
785
|
return ((bip<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
786
787
788
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
bba4f4d9
David Mayerich
minor warning fixes
|
789
790
|
return false;
|
740f8cd2
heziqi
added apply_mask
|
791
792
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
793
|
/// Creates a mask with a true value for all pixels that contain finite values
|
e37ce7bf
David Mayerich
added the ability...
|
794
|
void mask_finite(unsigned char* out_mask, unsigned char* mask = NULL, bool PROGRESS = false){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
795
796
|
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...
|
797
|
((bsq<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
798
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
799
|
((bsq<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
800
801
802
803
804
805
|
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...
|
806
|
((bil<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
807
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
808
|
((bil<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
809
810
811
812
813
814
|
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...
|
815
|
((bip<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
816
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
817
|
((bip<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
818
819
820
821
822
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
823
824
825
826
|
/// 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...
|
827
|
void apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
740f8cd2
heziqi
added apply_mask
|
828
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
829
830
|
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...
|
831
|
((bsq<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
832
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
833
|
((bsq<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
834
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
835
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
836
837
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
838
839
|
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...
|
840
|
((bil<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
841
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
842
|
((bil<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
843
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
844
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
845
846
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
847
848
|
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...
|
849
|
((bip<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
850
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
851
|
((bip<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
852
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
853
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
854
|
}
|
4a6f666c
heziqi
Added mask method
|
855
856
|
else{
|
e843658b
Brad Deutsch
Previous push did...
|
857
858
859
|
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
860
|
header.save(outfile + ".hdr");
|
e843658b
Brad Deutsch
Previous push did...
|
861
862
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
863
864
865
|
/// 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...
|
866
867
|
/// @param matrix is the destination for the pixel data
/// @param p is the mask
|
814eb271
David Mayerich
fixed problems wi...
|
868
|
bool sift(void* matrix, unsigned char* p = NULL, bool PROGRESS = false){
|
43dec788
David Mayerich
added code for si...
|
869
870
871
|
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...
|
872
|
return ((bsq<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
43dec788
David Mayerich
added code for si...
|
873
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
874
|
return ((bsq<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
875
|
else{
|
43dec788
David Mayerich
added code for si...
|
876
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
877
878
|
exit(1);
}
|
43dec788
David Mayerich
added code for si...
|
879
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
880
881
|
if (header.interleave == envi_header::BIP){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
882
|
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
883
|
return ((bip<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
884
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
885
|
return ((bip<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
886
887
888
889
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
890
891
|
}
if (header.interleave == envi_header::BIL){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
892
|
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
893
|
return ((bil<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
894
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
895
|
return ((bil<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
896
897
898
899
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
900
|
}
|
43dec788
David Mayerich
added code for si...
|
901
902
903
904
|
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
905
|
/// Saves in an array only those spectra corresponding to nonzero values of the mask.
|
43dec788
David Mayerich
added code for si...
|
906
907
|
/// @param outfile is the name of the sifted output file
/// @param p is the mask
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
908
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
e843658b
Brad Deutsch
Previous push did...
|
909
910
|
{
|
2fcab4f0
David Mayerich
added unsifting f...
|
911
|
//calculate the number of non-zero values in the mask
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
912
913
914
|
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...
|
915
916
917
918
919
|
if( p[i] > 0 ) nnz++;
//create a new header
envi_header new_header = header;
|
f7e99517
David Mayerich
added sifting for...
|
920
921
|
//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...
|
922
|
new_header.interleave = envi_header::BIP;
|
f7e99517
David Mayerich
added sifting for...
|
923
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
924
925
926
927
928
|
//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...
|
929
930
|
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...
|
931
|
return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
932
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
933
|
return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
934
935
936
937
938
939
|
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...
|
940
|
return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
941
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
942
|
return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
943
944
945
946
947
948
|
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...
|
949
|
return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
950
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
951
|
return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
952
953
954
955
956
957
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
4a6f666c
heziqi
Added mask method
|
958
959
|
exit(1);
}
|
4a6f666c
heziqi
Added mask method
|
960
|
return false;
|
cacc3cdc
heziqi
attempt to fix CImg
|
961
962
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
963
|
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...
|
964
965
966
967
968
969
970
971
972
973
974
975
|
//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...
|
976
|
return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
977
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
978
|
return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
979
980
981
982
983
|
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...
|
984
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
985
986
987
988
|
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...
|
989
|
|
8550e94f
David Mayerich
added sifting and...
|
990
|
if (header.data_type == envi_header::float32)
|
a2bf1d08
David Mayerich
general bug fixes...
|
991
|
return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
992
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
993
|
return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
994
995
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
996
997
998
999
|
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1000
|
}
|
cbce396e
David Mayerich
added support for...
|
1001
|
return 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1002
1003
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1004
1005
1006
1007
1008
1009
1010
1011
1012
|
/// 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...
|
1013
|
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...
|
1014
1015
|
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...
|
1016
|
return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1017
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1018
|
return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1019
1020
1021
1022
1023
1024
|
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...
|
1025
|
return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1026
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1027
|
return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1028
1029
1030
1031
1032
1033
|
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...
|
1034
|
return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1035
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1036
|
return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
|
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 ...
|
1048
1049
1050
1051
1052
1053
1054
1055
1056
|
/// 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...
|
1057
|
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...
|
1058
1059
|
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...
|
1060
|
return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1061
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1062
|
return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1063
1064
1065
1066
1067
1068
|
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...
|
1069
|
return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1070
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1071
|
return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1072
1073
1074
1075
1076
1077
|
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...
|
1078
|
return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1079
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1080
|
return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
|
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 ...
|
1092
1093
1094
1095
1096
1097
1098
1099
1100
|
/// 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...
|
1101
|
/// @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 ...
|
1102
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1103
1104
|
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...
|
1105
1106
|
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...
|
1107
|
return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1108
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1109
|
return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1110
1111
1112
1113
1114
1115
|
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...
|
1116
|
return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1117
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1118
|
return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1119
1120
1121
1122
1123
1124
|
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...
|
1125
|
return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1126
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1127
|
return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
|
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 ...
|
1139
1140
1141
1142
1143
1144
1145
|
/// 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...
|
1146
|
bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
|
517876d6
heziqi
metrics finished ...
|
1147
1148
|
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...
|
1149
|
return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1150
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1151
|
return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1152
1153
1154
1155
1156
1157
|
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...
|
1158
|
return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1159
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1160
|
return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1161
1162
1163
1164
1165
1166
|
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...
|
1167
|
return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1168
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1169
|
return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
|
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 ...
|
1181
|
/// Closes the ENVI file.
|
edb975b0
David Mayerich
created a stim::e...
|
1182
1183
|
void close(){
if(file == NULL) return;
|
6708cc25
heziqi
Ziqi added envi c...
|
1184
1185
|
if(header.interleave == envi_header::BSQ){
if(header.data_type ==envi_header::float32)
|
edb975b0
David Mayerich
created a stim::e...
|
1186
|
((bsq<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1187
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1188
|
((bsq<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1189
1190
1191
1192
1193
1194
1195
1196
|
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...
|
1197
|
((bil<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1198
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1199
|
((bil<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1200
1201
1202
1203
1204
1205
1206
1207
|
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...
|
1208
|
((bip<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1209
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1210
|
((bip<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1211
1212
1213
1214
1215
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1216
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1217
1218
1219
1220
1221
|
/// 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...
|
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
|
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 ...
|
1255
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1256
|
/// Saves a header file describing the current ENVI file parameters.
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1257
1258
1259
1260
1261
1262
1263
1264
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1265
1266
1267
1268
|
/// 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 ...
|
1269
|
bool band(void* ptr, double wavelength, bool PROGRESS = false){
|
d1d8ef91
David Mayerich
added band readin...
|
1270
1271
1272
|
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 ...
|
1273
|
return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1274
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1275
|
return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1276
1277
1278
1279
1280
1281
1282
|
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 ...
|
1283
|
return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1284
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1285
|
return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1286
1287
1288
1289
1290
1291
1292
|
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 ...
|
1293
|
return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1294
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1295
|
return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1296
1297
1298
1299
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
d1d8ef91
David Mayerich
added band readin...
|
1300
|
}
|
ee4dea28
David Mayerich
fixed errors in c...
|
1301
|
return false;
|
1582ce07
David Mayerich
added band_index(...
|
1302
1303
|
}
|
735a2a24
David Mayerich
started testing o...
|
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
|
// 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...
|
1344
|
float test = ((float*)temp)[0];
|
735a2a24
David Mayerich
started testing o...
|
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
|
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...
|
1364
|
void spectrum(T* ptr, size_t x, size_t y, bool PROGRESS = false){
|
735a2a24
David Mayerich
started testing o...
|
1365
|
|
c4dd399a
David Mayerich
fixed a Linux com...
|
1366
|
spectrum<T>(ptr, y * header.samples + x, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1367
1368
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1369
1370
1371
1372
|
/// 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...
|
1373
|
bool band_index(void* ptr, unsigned long long b){
|
081f2c9f
heziqi
made bip bil file...
|
1374
1375
|
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(...
|
1376
|
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
081f2c9f
heziqi
made bip bil file...
|
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
|
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(...
|
1403
1404
|
}
return false;
|
d1d8ef91
David Mayerich
added band readin...
|
1405
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
1406
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1407
1408
1409
1410
|
/// 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...
|
1411
|
bool mean_spectrum(double * p, double* std, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1412
1413
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
35a7195f
David Mayerich
added median spec...
|
1414
|
return ((bsq<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1415
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1416
|
return ((bsq<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1417
1418
1419
1420
1421
1422
1423
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
35a7195f
David Mayerich
added median spec...
|
1424
|
return ((bil<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1425
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1426
|
return ((bil<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1427
1428
1429
1430
1431
1432
1433
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
|
35a7195f
David Mayerich
added median spec...
|
1434
|
return ((bip<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1435
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1436
|
return ((bip<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1437
1438
1439
1440
1441
1442
1443
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1444
|
|
35a7195f
David Mayerich
added median spec...
|
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
|
/// 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 ...
|
1467
1468
1469
1470
1471
|
/// 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...
|
1472
|
bool co_matrix(double* co, double* avg, unsigned char* mask, int cuda_device, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1473
|
if (header.interleave == envi_header::BSQ){
|
63fc1df8
David Mayerich
added an inverse ...
|
1474
1475
|
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...
|
1476
1477
1478
|
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1479
|
return ((bil<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1480
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1481
|
return ((bil<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1482
1483
1484
1485
1486
1487
1488
|
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...
|
1489
|
return ((bip<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1490
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1491
|
return ((bip<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1492
1493
1494
1495
1496
1497
1498
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1499
|
|
334547d8
sam
changes for mnf: ...
|
1500
1501
1502
1503
1504
|
/// 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...
|
1505
|
bool coNoise_matrix(double* coN, double* avg, unsigned char* mask, int cuda_device = 0, bool PROGRESS = false){
|
334547d8
sam
changes for mnf: ...
|
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
|
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...
|
1519
|
return ((bip<float>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
|
334547d8
sam
changes for mnf: ...
|
1520
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1521
|
return ((bip<double>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
|
334547d8
sam
changes for mnf: ...
|
1522
1523
1524
1525
1526
1527
1528
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1529
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1530
1531
1532
1533
1534
1535
1536
|
/// 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...
|
1537
1538
1539
1540
1541
1542
1543
1544
|
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...
|
1545
|
|
177c7863
David Mayerich
updated the ENVI ...
|
1546
1547
|
//save the header for the cropped file
stim::envi_header new_header = header;
|
f78ceb64
David Mayerich
fixed BIP croppin...
|
1548
1549
1550
|
new_header.samples = x1 - x0 + 1;
new_header.lines = y1 - y0 + 1;
new_header.bands = b1 - b0 + 1;
|
177c7863
David Mayerich
updated the ENVI ...
|
1551
|
std::vector<double>::const_iterator first = new_header.wavelength.begin() + b0;
|
f78ceb64
David Mayerich
fixed BIP croppin...
|
1552
|
std::vector<double>::const_iterator last = new_header.wavelength.begin() + b1 + 1;
|
177c7863
David Mayerich
updated the ENVI ...
|
1553
1554
1555
|
new_header.wavelength = std::vector<double>(first, last);
new_header.save(outfile + ".hdr");
|
a43c4fe1
heziqi
Added crop in env...
|
1556
1557
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1558
|
return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1559
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1560
|
return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1561
1562
1563
1564
1565
1566
1567
|
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 ...
|
1568
|
return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1569
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1570
|
return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
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1572
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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 ...
|
1578
|
return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1579
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1580
|
return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1581
1582
1583
1584
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1587
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1588
|
|
bb61cb18
David Mayerich
added subimage fu...
|
1589
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|
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...
|
1624
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|
/// 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...
|
1682
1683
1684
1685
1686
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1726
1727
1728
1729
|
/// 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...
|
1730
|
|
82a7c08c
David Mayerich
added an append c...
|
1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
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1788
1789
1790
1791
|
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...
|
1792
1793
1794
1795
1796
1797
1798
|
/// 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...
|
1799
|
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...
|
1800
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
|
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...
|
1817
|
((bsq<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1818
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1819
|
((bsq<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1820
1821
1822
1823
1824
1825
1826
|
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...
|
1827
|
((bil<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1828
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1829
|
((bil<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1830
1831
1832
1833
1834
1835
1836
|
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...
|
1837
|
((bip<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1838
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1839
|
((bip<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1840
1841
1842
1843
1844
1845
1846
1847
1848
1849
1850
1851
|
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...
|
1852
|
void deriv(std::string outfile, size_t d, size_t order, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1853
1854
1855
|
header.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1856
|
((bsq<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1857
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1858
|
((bsq<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1859
1860
1861
1862
1863
1864
1865
1866
|
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...
|
1867
|
((bil<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1868
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1869
|
((bil<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1870
1871
1872
1873
1874
1875
1876
1877
|
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...
|
1878
|
((bip<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1879
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1880
|
((bip<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1881
1882
1883
1884
1885
1886
1887
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
exit(1);
}
|
278c622b
David Mayerich
finished Windows ...
|
1888
1889
1890
1891
1892
1893
1894
1895
1896
1897
1898
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1900
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|
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 ...
|
1962
1963
1964
1965
1966
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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){
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6e9cf1ac
David Mayerich
fixed image bug i...
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1967
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if(samples == 0) samples = header.bands;
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9d34229e
David Mayerich
restructured the ...
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double B = (double)header.bands;
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);
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6e9cf1ac
David Mayerich
fixed image bug i...
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1982
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new_header.wavelength_units = "inv_" + header.wavelength_units;
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9d34229e
David Mayerich
restructured the ...
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1983
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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);
}
}
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278c622b
David Mayerich
finished Windows ...
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2000
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}; //end ENVI
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e8eb202f
David Mayerich
added a new ENVI ...
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2001
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} //end namespace rts
#endif
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