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#ifndef STIM_ENVI_H
#define STIM_ENVI_H
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#include <stim/envi/envi_header.h>
#include <stim/envi/bsq.h>
#include <stim/envi/bip.h>
#include <stim/envi/bil.h>
#include <stim/math/fd_coefficients.h>
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#include <stim/parser/filename.h>
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#include <stim/util/filesize.h>
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#include <iostream>
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#include <fstream>
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//#include "../image/image.h"
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namespace stim{
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/** This class implements reading of ENVI hyperspectral files. These files can be stored in multiple orientations
(including BSQ, BIP, and BIL) in order to optimize streaming speed depending on applications. Basic ENVI
files are stored on disk as a large binary file with a corresponding header. Code for reading and processing
ENVI header files is in the envi_header class.
*/
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class envi{
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void* file; //void pointer to the relevant file reader (bip, bsq, or bil - with appropriate data type)
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std::string fname; //file name used for repeated opening and closing
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//allocate sufficient space for a spectrum based on the data type and number of bands
void* alloc_array(size_t len){
switch(header.data_type){
case envi_header::int8:
return malloc(len);
case envi_header::int16:
case envi_header::uint16:
return malloc(2 * len);
case envi_header::int32:
case envi_header::uint32:
case envi_header::float32:
return malloc(4 * len);
case envi_header::int64:
case envi_header::uint64:
case envi_header::float64:
case envi_header::complex32:
return malloc(8 * len);
case envi_header::complex64:
return malloc(16 * len);
default:
std::cout<<"ERROR stim::envi data type not recognized for spectral allocation"<<std::endl;
exit(1);
}
}
//cast a value to DEST type from SRC type
template<typename DST, typename SRC>
inline void cast(DST* dst, SRC* src){
(*dst) = (DST)(*src);
}
//cast an array from type SRC to type DEST
template<typename DST, typename SRC>
inline void cast(DST* dst, SRC* src, size_t len){
for(size_t i = 0; i < len; i++)
cast(&dst[i], &src[i]);
}
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public:
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envi_header header;
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/// Default constructor
envi(){
file = NULL; //set the file pointer to NULL
}
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envi(std::string filename, std::string headername) : envi(){
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header.load(headername);
fname = filename; //save the filename
allocate();
}
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//used to test if the current ENVI file is valid
operator bool(){
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if (header.interleave == envi_header::BSQ) { //if the infile is bsq file
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->is_open();
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->is_open();
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else if (header.interleave == envi_header::BIL) { //if the infile is bil file
if (header.data_type == envi_header::float32)
return ((bil<float>*)file)->is_open();
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->is_open();
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else if (header.interleave == envi_header::BIP) { //if the infile is bip file
if (header.data_type == envi_header::float32)
return ((bip<float>*)file)->is_open();
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->is_open();
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else {
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
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}
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//test to determine if the specified file is an ENVI file
static bool is_envi(std::string fname, std::string hname = ""){
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stim::filename data_file(fname);
stim::filename header_file;
if(hname == ""){ //if the header isn't provided
header_file = data_file; //assume that it's the same name as the data file, with a .hdr extension
header_file = header_file.extension("hdr");
}
else header_file = hname; //otherwise load the passed header
stim::envi_header H;
if(H.load(header_file) == false) //load the header file, if it doesn't load return false
return false;
size_t targetBytes = H.data_bytes(); //get the number of bytes that SHOULD be in the data file
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size_t bytes = stim::file_size(fname);
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if(bytes != targetBytes) return false; //if the data doesn't match the header, return false
return true; //otherwise everything looks fine
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}
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void* malloc_spectrum(){
return alloc_array(header.bands);
}
void* malloc_band(){
return alloc_array(header.samples * header.lines);
}
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void set_buffer_frac(double memfrac = 0.5){
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if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
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((bsq<float>*)file)->set_buffer_frac(memfrac);
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else if(header.data_type == envi_header::float64)
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((bsq<double>*)file)->set_buffer_frac(memfrac);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
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((bil<float>*)file)->set_buffer_frac(memfrac);
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else if(header.data_type == envi_header::float64)
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((bil<double>*)file)->set_buffer_frac(memfrac);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
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((bip<float>*)file)->set_buffer_frac(memfrac);
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((bip<double>*)file)->set_buffer_frac(memfrac);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
void set_buffer_raw(size_t bytes){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
((bsq<float>*)file)->set_buffer_raw(bytes);
else if(header.data_type == envi_header::float64)
((bsq<double>*)file)->set_buffer_raw(bytes);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
((bil<float>*)file)->set_buffer_raw(bytes);
else if(header.data_type == envi_header::float64)
((bil<double>*)file)->set_buffer_raw(bytes);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
((bip<float>*)file)->set_buffer_raw(bytes);
else if(header.data_type == envi_header::float64)
((bip<double>*)file)->set_buffer_raw(bytes);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
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/// Returns the size of the data type in bytes
unsigned int type_size(){
if(header.data_type == envi_header::float32) return 4;
if(header.data_type == envi_header::float64) return 8;
exit(1);
}
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size_t X(){ return header.samples; }
size_t Y(){ return header.lines; }
size_t Z(){ return header.bands; }
size_t B(){ return Z(); }
/// Return the size of the data set in bytes
size_t bytes(){
return X() * Y() * Z() * type_size();
}
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/// Returns the progress of the current processing operation as a percentage
void reset_progress(){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
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((bsq<float>*)file)->reset_progress();
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else if(header.data_type == envi_header::float64)
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((bsq<double>*)file)->reset_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
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((bil<float>*)file)->reset_progress();
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else if(header.data_type == envi_header::float64)
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((bil<double>*)file)->reset_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
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((bip<float>*)file)->reset_progress();
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else if(header.data_type == envi_header::float64)
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((bip<double>*)file)->reset_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
/// Returns the progress of the current processing operation as a percentage
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double progress(){
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if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
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return ((bsq<float>*)file)->get_progress();
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else if(header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->get_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
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return ((bil<float>*)file)->get_progress();
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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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Ziqi added envi c...
|
371
372
|
}
else if(header.data_type == envi_header::float64) {
|
8057237a
David Mayerich
added an envi::op...
|
373
|
return ((bsq<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
374
375
376
377
|
}
else
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
378
|
|
6708cc25
heziqi
Ziqi added envi c...
|
379
380
|
else if(header.interleave == envi_header::BIL) { //if the infile is bil file
if(header.data_type == envi_header::float32) {
|
8057237a
David Mayerich
added an envi::op...
|
381
|
return ((bil<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
382
383
|
}
else if(header.data_type == envi_header::float64) {
|
8057237a
David Mayerich
added an envi::op...
|
384
|
return ((bil<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
385
386
387
388
|
}
else
return false;
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
389
|
|
6708cc25
heziqi
Ziqi added envi c...
|
390
391
|
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...
|
392
|
return ((bip<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
393
394
|
}
else if(header.data_type == envi_header::float64) {
|
8057237a
David Mayerich
added an envi::op...
|
395
|
return ((bip<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
396
397
|
}
else
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
398
|
return false;
|
6708cc25
heziqi
Ziqi added envi c...
|
399
400
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
401
402
|
return true;
|
8057237a
David Mayerich
added an envi::op...
|
403
404
405
|
}
|
48f356fa
David Mayerich
bug fixes for FFT...
|
406
407
408
409
410
411
412
413
414
415
|
/// 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 ...
|
416
417
418
419
420
|
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...
|
421
422
|
fseek(f, 13, SEEK_CUR); //skip the the x and y dimensions
short x, y;
|
618dce30
David Mayerich
removed warnings ...
|
423
424
425
426
427
428
429
430
431
432
|
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...
|
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
|
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...
|
449
450
451
452
453
|
/// 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...
|
454
|
|
8057237a
David Mayerich
added an envi::op...
|
455
456
457
458
|
header = h; //store the header
fname = filename; //save the filename
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
459
460
|
allocate();
|
8057237a
David Mayerich
added an envi::op...
|
461
462
463
|
return open(); //open the ENVI file;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
|
}
/// 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 ...
|
482
483
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
484
485
486
487
488
|
/// 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...
|
489
|
bool ratio(std::string outfile, double band, unsigned char* mask = NULL, bool PROGRESS = false){
|
a2bf1d08
David Mayerich
general bug fixes...
|
490
|
header.save(outfile + ".hdr");
|
6708cc25
heziqi
Ziqi added envi c...
|
491
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
e8eb202f
David Mayerich
added a new ENVI ...
|
492
|
if(header.data_type ==envi_header::float32)
|
c30dd3e6
David Mayerich
added vector norm...
|
493
|
return ((bsq<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
494
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
495
|
return ((bsq<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
496
497
498
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
499
|
|
6708cc25
heziqi
Ziqi added envi c...
|
500
501
|
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...
|
502
|
return ((bil<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
503
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
504
|
return ((bil<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
505
506
507
508
509
510
|
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...
|
511
|
return ((bip<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
512
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
513
|
return ((bip<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
514
515
516
517
518
519
520
521
|
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
|
522
|
return false;
|
6708cc25
heziqi
Ziqi added envi c...
|
523
524
|
}
|
c30dd3e6
David Mayerich
added vector norm...
|
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
|
/// 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 ...
|
561
562
563
564
|
/// 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...
|
565
566
|
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...
|
567
568
|
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...
|
569
|
return ((bsq<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
570
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
571
|
return ((bsq<double>*)file)->baseline(outfile,w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
572
573
574
575
576
577
578
579
|
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...
|
580
|
return ((bil<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
581
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
582
|
return ((bil<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
583
584
585
586
587
588
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
589
|
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
|
6708cc25
heziqi
Ziqi added envi c...
|
590
|
if(header.data_type ==envi_header::float32)
|
798cea97
David Mayerich
added progress ba...
|
591
|
return ((bip<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
592
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
593
|
return ((bip<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
594
595
596
597
598
599
600
601
602
603
604
605
|
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...
|
606
607
608
|
/// 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 ...
|
609
610
611
612
613
614
615
616
617
618
619
620
|
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...
|
621
|
((bip<float>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
622
|
else if(header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
623
|
((bip<double>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
624
625
626
627
628
629
630
631
|
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...
|
632
|
out_hdr.wavelength = bands;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
633
|
out_hdr.band_names.clear();
|
63fc1df8
David Mayerich
added an inverse ...
|
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
|
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 ...
|
664
665
666
667
|
/// 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...
|
668
|
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...
|
669
|
|
6708cc25
heziqi
Ziqi added envi c...
|
670
671
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
a2bf1d08
David Mayerich
general bug fixes...
|
672
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
673
674
675
676
|
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
677
|
else if(interleave == envi_header::BIL) //convert BSQ -> BIL
|
c6251f8b
David Mayerich
allows user to de...
|
678
|
((bsq<float>*)file)->bil(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
|
a2bf1d08
David Mayerich
general bug fixes...
|
679
|
else if(interleave == envi_header::BIP){ //ERROR
|
cf5b4c92
David Mayerich
simplified asynch...
|
680
|
//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
|
474c351a
David Mayerich
output timing dat...
|
681
|
((bsq<float>*)file)->bip(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
|
cf5b4c92
David Mayerich
simplified asynch...
|
682
|
//exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
683
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
684
685
686
|
}
else if(header.data_type == envi_header::float64){ //if the data type is float
|
a2bf1d08
David Mayerich
general bug fixes...
|
687
|
if(interleave == envi_header::BSQ){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
688
689
690
|
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
691
|
else if(interleave == envi_header::BIL) //convert BSQ -> BIL
|
c6251f8b
David Mayerich
allows user to de...
|
692
|
((bsq<double>*)file)->bil(outfile, PROGRESS, OPTIMIZATION);
|
a2bf1d08
David Mayerich
general bug fixes...
|
693
|
else if(interleave == envi_header::BIP){ //ERROR
|
cf5b4c92
David Mayerich
simplified asynch...
|
694
|
//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
|
f7cf19e4
David Mayerich
fixed warnings, t...
|
695
|
((bsq<double>*)file)->bip(outfile, PROGRESS, OPTIMIZATION);
|
cf5b4c92
David Mayerich
simplified asynch...
|
696
|
//exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
697
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
698
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
699
|
|
6708cc25
heziqi
Ziqi added envi c...
|
700
701
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
702
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
703
704
705
706
707
|
}
}
else if(header.interleave == envi_header::BIL){
|
a2bf1d08
David Mayerich
general bug fixes...
|
708
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
709
710
711
712
|
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
713
714
715
716
|
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...
|
717
718
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
719
720
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIL){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
721
722
723
|
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
724
725
726
727
|
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...
|
728
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
729
|
|
6708cc25
heziqi
Ziqi added envi c...
|
730
731
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
732
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
733
734
735
736
|
}
}
else if(header.interleave == envi_header::BIP){
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
737
|
|
a2bf1d08
David Mayerich
general bug fixes...
|
738
739
|
if(header.data_type ==envi_header::float32){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
740
741
742
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
743
744
745
|
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 ...
|
746
747
748
749
|
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...
|
750
751
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
752
753
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
754
755
756
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
757
758
759
|
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 ...
|
760
761
762
763
|
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...
|
764
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
765
|
|
6708cc25
heziqi
Ziqi added envi c...
|
766
767
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
768
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
769
770
|
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
771
|
|
6708cc25
heziqi
Ziqi added envi c...
|
772
773
774
775
|
else{
std::cout<<"ERROR: unidentified interleave type"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
776
777
778
779
780
|
stim::envi_header h = header;
h.interleave = interleave;
h.save(outfile + ".hdr");
return true;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
781
|
|
6708cc25
heziqi
Ziqi added envi c...
|
782
783
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
784
785
786
787
788
|
/// 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...
|
789
|
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
|
790
791
792
|
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...
|
793
|
return ((bsq<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
794
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
795
|
return ((bsq<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
796
797
798
799
800
801
|
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...
|
802
|
return ((bil<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
803
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
804
|
return ((bil<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
805
806
807
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
cacc3cdc
heziqi
attempt to fix CImg
|
808
|
|
4a6f666c
heziqi
Added mask method
|
809
810
|
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...
|
811
|
return ((bip<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
812
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
813
|
return ((bip<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
814
815
816
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
bba4f4d9
David Mayerich
minor warning fixes
|
817
818
|
return false;
|
740f8cd2
heziqi
added apply_mask
|
819
820
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
821
|
/// Creates a mask with a true value for all pixels that contain finite values
|
e37ce7bf
David Mayerich
added the ability...
|
822
|
void mask_finite(unsigned char* out_mask, unsigned char* mask = NULL, bool PROGRESS = false){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
823
824
|
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...
|
825
|
((bsq<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
826
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
827
|
((bsq<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
828
829
830
831
832
833
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
|
e37ce7bf
David Mayerich
added the ability...
|
834
|
((bil<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
835
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
836
|
((bil<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
837
838
839
840
841
842
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
|
e37ce7bf
David Mayerich
added the ability...
|
843
|
((bip<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
844
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
845
|
((bip<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
846
847
848
849
850
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
851
852
853
854
|
/// 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...
|
855
|
void apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
740f8cd2
heziqi
added apply_mask
|
856
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
857
858
|
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...
|
859
|
((bsq<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
860
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
861
|
((bsq<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
862
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
863
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
864
865
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
866
867
|
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...
|
868
|
((bil<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
869
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
870
|
((bil<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
871
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
872
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
873
874
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
875
876
|
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...
|
877
|
((bip<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
878
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
879
|
((bip<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
880
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
881
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
882
|
}
|
4a6f666c
heziqi
Added mask method
|
883
884
|
else{
|
e843658b
Brad Deutsch
Previous push did...
|
885
886
887
|
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
888
|
header.save(outfile + ".hdr");
|
e843658b
Brad Deutsch
Previous push did...
|
889
890
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
891
892
893
|
/// 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...
|
894
895
|
/// @param matrix is the destination for the pixel data
/// @param p is the mask
|
814eb271
David Mayerich
fixed problems wi...
|
896
|
bool sift(void* matrix, unsigned char* p = NULL, bool PROGRESS = false){
|
43dec788
David Mayerich
added code for si...
|
897
898
899
|
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...
|
900
|
return ((bsq<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
43dec788
David Mayerich
added code for si...
|
901
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
902
|
return ((bsq<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
903
|
else{
|
43dec788
David Mayerich
added code for si...
|
904
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
905
906
|
exit(1);
}
|
43dec788
David Mayerich
added code for si...
|
907
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
908
909
|
if (header.interleave == envi_header::BIP){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
910
|
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
911
|
return ((bip<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
912
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
913
|
return ((bip<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
914
915
916
917
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
918
919
|
}
if (header.interleave == envi_header::BIL){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
920
|
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
921
|
return ((bil<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
922
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
923
|
return ((bil<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
924
925
926
927
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
928
|
}
|
43dec788
David Mayerich
added code for si...
|
929
930
931
932
|
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
933
|
/// Saves in an array only those spectra corresponding to nonzero values of the mask.
|
43dec788
David Mayerich
added code for si...
|
934
935
|
/// @param outfile is the name of the sifted output file
/// @param p is the mask
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
936
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
e843658b
Brad Deutsch
Previous push did...
|
937
938
|
{
|
2fcab4f0
David Mayerich
added unsifting f...
|
939
|
//calculate the number of non-zero values in the mask
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
940
941
942
|
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...
|
943
944
945
946
947
|
if( p[i] > 0 ) nnz++;
//create a new header
envi_header new_header = header;
|
f7e99517
David Mayerich
added sifting for...
|
948
949
|
//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...
|
950
|
new_header.interleave = envi_header::BIP;
|
f7e99517
David Mayerich
added sifting for...
|
951
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
952
953
954
955
956
|
//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...
|
957
958
|
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...
|
959
|
return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
960
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
961
|
return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
962
963
964
965
966
967
|
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...
|
968
|
return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
969
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
970
|
return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
971
972
973
974
975
976
|
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...
|
977
|
return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
978
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
979
|
return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
980
981
982
983
984
985
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
4a6f666c
heziqi
Added mask method
|
986
987
|
exit(1);
}
|
4a6f666c
heziqi
Added mask method
|
988
|
return false;
|
cacc3cdc
heziqi
attempt to fix CImg
|
989
990
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
991
|
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...
|
992
993
994
995
996
997
998
999
1000
1001
1002
1003
|
//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...
|
1004
|
return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
1005
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
1006
|
return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
1007
1008
1009
1010
1011
|
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...
|
1012
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
1013
1014
1015
1016
|
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...
|
1017
|
|
8550e94f
David Mayerich
added sifting and...
|
1018
|
if (header.data_type == envi_header::float32)
|
a2bf1d08
David Mayerich
general bug fixes...
|
1019
|
return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
1020
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
1021
|
return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
1022
1023
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1024
1025
1026
1027
|
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1028
|
}
|
cbce396e
David Mayerich
added support for...
|
1029
|
return 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1030
1031
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1032
1033
1034
1035
1036
1037
1038
1039
1040
|
/// 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...
|
1041
|
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...
|
1042
1043
|
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...
|
1044
|
return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1045
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1046
|
return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1047
1048
1049
1050
1051
1052
|
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...
|
1053
|
return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1054
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1055
|
return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1056
1057
1058
1059
1060
1061
|
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...
|
1062
|
return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1063
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1064
|
return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
|
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 ...
|
1076
1077
1078
1079
1080
1081
1082
1083
1084
|
/// 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...
|
1085
|
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...
|
1086
1087
|
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...
|
1088
|
return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1089
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1090
|
return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1091
1092
1093
1094
1095
1096
|
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...
|
1097
|
return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1098
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1099
|
return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1100
1101
1102
1103
1104
1105
|
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...
|
1106
|
return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1107
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1108
|
return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
|
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 ...
|
1120
1121
1122
1123
1124
1125
1126
1127
1128
|
/// 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...
|
1129
|
/// @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 ...
|
1130
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1131
1132
|
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...
|
1133
1134
|
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...
|
1135
|
return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1136
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1137
|
return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1138
1139
1140
1141
1142
1143
|
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...
|
1144
|
return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1145
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1146
|
return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1147
1148
1149
1150
1151
1152
|
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...
|
1153
|
return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1154
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1155
|
return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
|
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 ...
|
1167
1168
1169
1170
1171
1172
1173
|
/// 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...
|
1174
|
bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
|
517876d6
heziqi
metrics finished ...
|
1175
1176
|
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...
|
1177
|
return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1178
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1179
|
return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1180
1181
1182
1183
1184
1185
|
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...
|
1186
|
return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1187
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1188
|
return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1189
1190
1191
1192
1193
1194
|
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...
|
1195
|
return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1196
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1197
|
return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
|
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 ...
|
1209
|
/// Closes the ENVI file.
|
edb975b0
David Mayerich
created a stim::e...
|
1210
1211
|
void close(){
if(file == NULL) return;
|
6708cc25
heziqi
Ziqi added envi c...
|
1212
1213
|
if(header.interleave == envi_header::BSQ){
if(header.data_type ==envi_header::float32)
|
edb975b0
David Mayerich
created a stim::e...
|
1214
|
((bsq<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1215
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1216
|
((bsq<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1217
1218
1219
1220
1221
1222
1223
1224
|
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...
|
1225
|
((bil<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1226
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1227
|
((bil<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1228
1229
1230
1231
1232
1233
1234
1235
|
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...
|
1236
|
((bip<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1237
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1238
|
((bip<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1239
1240
1241
1242
1243
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1244
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1245
1246
1247
1248
1249
|
/// 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...
|
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
|
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 ...
|
1283
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1284
|
/// Saves a header file describing the current ENVI file parameters.
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1285
1286
1287
1288
1289
1290
1291
1292
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1293
1294
1295
1296
|
/// 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 ...
|
1297
|
bool band(void* ptr, double wavelength, bool PROGRESS = false){
|
d1d8ef91
David Mayerich
added band readin...
|
1298
1299
1300
|
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 ...
|
1301
|
return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1302
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1303
|
return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1304
1305
1306
1307
1308
1309
1310
|
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 ...
|
1311
|
return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1312
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1313
|
return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1314
1315
1316
1317
1318
1319
1320
|
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 ...
|
1321
|
return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1322
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1323
|
return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1324
1325
1326
1327
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
d1d8ef91
David Mayerich
added band readin...
|
1328
|
}
|
ee4dea28
David Mayerich
fixed errors in c...
|
1329
|
return false;
|
1582ce07
David Mayerich
added band_index(...
|
1330
1331
|
}
|
735a2a24
David Mayerich
started testing o...
|
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
|
// 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...
|
1372
|
float test = ((float*)temp)[0];
|
735a2a24
David Mayerich
started testing o...
|
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
|
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...
|
1392
|
void spectrum(T* ptr, size_t x, size_t y, bool PROGRESS = false){
|
735a2a24
David Mayerich
started testing o...
|
1393
|
|
c4dd399a
David Mayerich
fixed a Linux com...
|
1394
|
spectrum<T>(ptr, y * header.samples + x, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1395
1396
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1397
1398
1399
1400
|
/// 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...
|
1401
|
bool band_index(void* ptr, unsigned long long b){
|
081f2c9f
heziqi
made bip bil file...
|
1402
1403
|
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(...
|
1404
|
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
081f2c9f
heziqi
made bip bil file...
|
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
|
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(...
|
1431
1432
|
}
return false;
|
d1d8ef91
David Mayerich
added band readin...
|
1433
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
1434
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1435
1436
1437
1438
|
/// 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...
|
1439
|
bool mean_spectrum(double * p, double* std, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1440
1441
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
35a7195f
David Mayerich
added median spec...
|
1442
|
return ((bsq<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1443
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1444
|
return ((bsq<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1445
1446
1447
1448
1449
1450
1451
|
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...
|
1452
|
return ((bil<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1453
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1454
|
return ((bil<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1455
1456
1457
1458
1459
1460
1461
|
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...
|
1462
|
return ((bip<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1463
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1464
|
return ((bip<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1465
1466
1467
1468
1469
1470
1471
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1472
|
|
35a7195f
David Mayerich
added median spec...
|
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
|
/// 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 ...
|
1495
1496
1497
1498
1499
|
/// 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...
|
1500
|
bool co_matrix(double* co, double* avg, unsigned char* mask, int cuda_device, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1501
|
if (header.interleave == envi_header::BSQ){
|
63fc1df8
David Mayerich
added an inverse ...
|
1502
1503
|
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...
|
1504
1505
1506
|
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1507
|
return ((bil<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1508
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1509
|
return ((bil<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1510
1511
1512
1513
1514
1515
1516
|
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...
|
1517
|
return ((bip<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1518
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1519
|
return ((bip<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1520
1521
1522
1523
1524
1525
1526
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1527
|
|
334547d8
sam
changes for mnf: ...
|
1528
1529
1530
1531
1532
|
/// 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...
|
1533
|
bool coNoise_matrix(double* coN, double* avg, unsigned char* mask, int cuda_device = 0, bool PROGRESS = false){
|
334547d8
sam
changes for mnf: ...
|
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
|
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...
|
1547
|
return ((bip<float>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
|
334547d8
sam
changes for mnf: ...
|
1548
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1549
|
return ((bip<double>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
|
334547d8
sam
changes for mnf: ...
|
1550
1551
1552
1553
1554
1555
1556
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1557
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1558
1559
1560
1561
1562
1563
1564
|
/// 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...
|
1565
1566
1567
1568
1569
1570
1571
1572
|
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...
|
1573
|
|
177c7863
David Mayerich
updated the ENVI ...
|
1574
1575
|
//save the header for the cropped file
stim::envi_header new_header = header;
|
f78ceb64
David Mayerich
fixed BIP croppin...
|
1576
1577
1578
|
new_header.samples = x1 - x0 + 1;
new_header.lines = y1 - y0 + 1;
new_header.bands = b1 - b0 + 1;
|
177c7863
David Mayerich
updated the ENVI ...
|
1579
|
std::vector<double>::const_iterator first = new_header.wavelength.begin() + b0;
|
f78ceb64
David Mayerich
fixed BIP croppin...
|
1580
|
std::vector<double>::const_iterator last = new_header.wavelength.begin() + b1 + 1;
|
177c7863
David Mayerich
updated the ENVI ...
|
1581
1582
1583
|
new_header.wavelength = std::vector<double>(first, last);
new_header.save(outfile + ".hdr");
|
a43c4fe1
heziqi
Added crop in env...
|
1584
1585
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1586
|
return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1587
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1588
|
return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1589
1590
1591
1592
1593
1594
1595
|
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 ...
|
1596
|
return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1597
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1598
|
return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1599
1600
1601
1602
1603
1604
1605
|
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 ...
|
1606
|
return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1607
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1608
|
return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1609
1610
1611
1612
1613
1614
1615
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1616
|
|
bb61cb18
David Mayerich
added subimage fu...
|
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
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1635
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1637
1638
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1642
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1647
1648
1649
1650
1651
|
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...
|
1652
1653
1654
1655
1656
1657
1658
1659
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1661
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1663
1664
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1700
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1707
1708
1709
|
/// 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...
|
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
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1730
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1733
1734
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1737
1738
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1740
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1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
1756
1757
|
/// 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...
|
1758
|
|
82a7c08c
David Mayerich
added an append c...
|
1759
1760
1761
1762
1763
1764
1765
1766
1767
1768
1769
1770
1771
1772
1773
1774
1775
1776
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
1787
1788
1789
1790
1791
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1794
1795
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1797
1798
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1800
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
|
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...
|
1820
1821
1822
1823
1824
1825
1826
|
/// 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...
|
1827
|
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...
|
1828
1829
1830
1831
1832
1833
1834
1835
1836
1837
1838
1839
1840
1841
1842
1843
1844
|
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...
|
1845
|
((bsq<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1846
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1847
|
((bsq<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1848
1849
1850
1851
1852
1853
1854
|
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...
|
1855
|
((bil<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1856
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1857
|
((bil<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1858
1859
1860
1861
1862
1863
1864
|
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...
|
1865
|
((bip<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1866
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1867
|
((bip<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1868
1869
1870
1871
1872
1873
1874
1875
1876
1877
1878
1879
|
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...
|
1880
|
void deriv(std::string outfile, size_t d, size_t order, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1881
1882
1883
|
header.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1884
|
((bsq<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1885
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1886
|
((bsq<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1887
1888
1889
1890
1891
1892
1893
1894
|
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...
|
1895
|
((bil<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1896
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1897
|
((bil<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1898
1899
1900
1901
1902
1903
1904
1905
|
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...
|
1906
|
((bip<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1907
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1908
|
((bip<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1909
1910
1911
1912
1913
1914
1915
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
exit(1);
}
|
278c622b
David Mayerich
finished Windows ...
|
1916
1917
1918
1919
1920
1921
1922
1923
1924
1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
1936
1937
1938
1939
1940
1941
1942
1943
1944
1945
1946
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1949
1950
1951
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1953
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1969
1970
1971
1972
1973
1974
1975
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
|
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 ...
|
1990
1991
1992
1993
1994
|
void fft(std::string outfile, double band_min, double band_max, size_t samples = 0, void* ratio = NULL, size_t rx = 0, size_t ry = 0, bool PROGRESS = false, int cuda_device = 0){
|
6e9cf1ac
David Mayerich
fixed image bug i...
|
1995
|
if(samples == 0) samples = header.bands;
|
9d34229e
David Mayerich
restructured the ...
|
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
|
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);
|
6e9cf1ac
David Mayerich
fixed image bug i...
|
2010
|
new_header.wavelength_units = "inv_" + header.wavelength_units;
|
9d34229e
David Mayerich
restructured the ...
|
2011
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2022
2023
2024
2025
2026
2027
|
new_header.save(outfile + ".hdr");
if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
((bip<float>*)file)->fft(outfile, start_i, end_i, samples, (float*)ratio, rx, ry, PROGRESS, cuda_device);
else if (header.data_type == envi_header::float64)
((bip<double>*)file)->fft(outfile, start_i, end_i, samples, (double*)ratio, rx, ry, PROGRESS, cuda_device);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else{
std::cout<<"ERROR: only BIP files supported for FFT"<<std::endl;
exit(1);
}
}
|
278c622b
David Mayerich
finished Windows ...
|
2028
|
}; //end ENVI
|
e8eb202f
David Mayerich
added a new ENVI ...
|
2029
2030
2031
2032
|
} //end namespace rts
#endif
|