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#ifndef STIM_ENVI_H
#define STIM_ENVI_H
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#include <stim/envi/envi_header.h>
#include <stim/envi/bsq.h>
#include <stim/envi/bip.h>
#include <stim/envi/bil.h>
#include <stim/math/fd_coefficients.h>
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#include <stim/parser/filename.h>
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#include <stim/util/filesize.h>
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#include <iostream>
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#include <fstream>
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//#include "../image/image.h"
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namespace stim{
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/** This class implements reading of ENVI hyperspectral files. These files can be stored in multiple orientations
(including BSQ, BIP, and BIL) in order to optimize streaming speed depending on applications. Basic ENVI
files are stored on disk as a large binary file with a corresponding header. Code for reading and processing
ENVI header files is in the envi_header class.
*/
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class envi{
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void* file; //void pointer to the relevant file reader (bip, bsq, or bil - with appropriate data type)
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std::string fname; //file name used for repeated opening and closing
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//allocate sufficient space for a spectrum based on the data type and number of bands
void* alloc_array(size_t len){
switch(header.data_type){
case envi_header::int8:
return malloc(len);
case envi_header::int16:
case envi_header::uint16:
return malloc(2 * len);
case envi_header::int32:
case envi_header::uint32:
case envi_header::float32:
return malloc(4 * len);
case envi_header::int64:
case envi_header::uint64:
case envi_header::float64:
case envi_header::complex32:
return malloc(8 * len);
case envi_header::complex64:
return malloc(16 * len);
default:
std::cout<<"ERROR stim::envi data type not recognized for spectral allocation"<<std::endl;
exit(1);
}
}
//cast a value to DEST type from SRC type
template<typename DST, typename SRC>
inline void cast(DST* dst, SRC* src){
(*dst) = (DST)(*src);
}
//cast an array from type SRC to type DEST
template<typename DST, typename SRC>
inline void cast(DST* dst, SRC* src, size_t len){
for(size_t i = 0; i < len; i++)
cast(&dst[i], &src[i]);
}
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public:
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envi_header header;
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/// Default constructor
envi(){
file = NULL; //set the file pointer to NULL
}
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envi(std::string filename, std::string headername) : envi(){
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header.load(headername);
fname = filename; //save the filename
allocate();
}
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//used to test if the current ENVI file is valid
operator bool(){
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if (header.interleave == envi_header::BSQ) { //if the infile is bsq file
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->is_open();
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->is_open();
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else if (header.interleave == envi_header::BIL) { //if the infile is bil file
if (header.data_type == envi_header::float32)
return ((bil<float>*)file)->is_open();
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->is_open();
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else if (header.interleave == envi_header::BIP) { //if the infile is bip file
if (header.data_type == envi_header::float32)
return ((bip<float>*)file)->is_open();
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->is_open();
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else {
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
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return false;
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}
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//test to determine if the specified file is an ENVI file
static bool is_envi(std::string fname, std::string hname = ""){
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stim::filename data_file(fname);
stim::filename header_file;
if(hname == ""){ //if the header isn't provided
header_file = data_file; //assume that it's the same name as the data file, with a .hdr extension
header_file = header_file.extension("hdr");
}
else header_file = hname; //otherwise load the passed header
stim::envi_header H;
if(H.load(header_file) == false) //load the header file, if it doesn't load return false
return false;
size_t targetBytes = H.data_bytes(); //get the number of bytes that SHOULD be in the data file
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size_t bytes = stim::file_size(fname);
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if(bytes != targetBytes) return false; //if the data doesn't match the header, return false
return true; //otherwise everything looks fine
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}
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void* malloc_spectrum(){
return alloc_array(header.bands);
}
void* malloc_band(){
return alloc_array(header.samples * header.lines);
}
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void set_buffer_frac(double memfrac = 0.5){
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if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
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((bsq<float>*)file)->set_buffer_frac(memfrac);
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else if(header.data_type == envi_header::float64)
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((bsq<double>*)file)->set_buffer_frac(memfrac);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
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((bil<float>*)file)->set_buffer_frac(memfrac);
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else if(header.data_type == envi_header::float64)
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((bil<double>*)file)->set_buffer_frac(memfrac);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
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((bip<float>*)file)->set_buffer_frac(memfrac);
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((bip<double>*)file)->set_buffer_frac(memfrac);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
void set_buffer_raw(size_t bytes){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
((bsq<float>*)file)->set_buffer_raw(bytes);
else if(header.data_type == envi_header::float64)
((bsq<double>*)file)->set_buffer_raw(bytes);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
((bil<float>*)file)->set_buffer_raw(bytes);
else if(header.data_type == envi_header::float64)
((bil<double>*)file)->set_buffer_raw(bytes);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
((bip<float>*)file)->set_buffer_raw(bytes);
else if(header.data_type == envi_header::float64)
((bip<double>*)file)->set_buffer_raw(bytes);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
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/// Returns the size of the data type in bytes
unsigned int type_size(){
if(header.data_type == envi_header::float32) return 4;
if(header.data_type == envi_header::float64) return 8;
exit(1);
}
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size_t X(){ return header.samples; }
size_t Y(){ return header.lines; }
size_t Z(){ return header.bands; }
size_t B(){ return Z(); }
/// Return the size of the data set in bytes
size_t bytes(){
return X() * Y() * Z() * type_size();
}
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/// Returns the progress of the current processing operation as a percentage
void reset_progress(){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
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((bsq<float>*)file)->reset_progress();
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else if(header.data_type == envi_header::float64)
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((bsq<double>*)file)->reset_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
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((bil<float>*)file)->reset_progress();
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else if(header.data_type == envi_header::float64)
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((bil<double>*)file)->reset_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
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((bip<float>*)file)->reset_progress();
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else if(header.data_type == envi_header::float64)
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((bip<double>*)file)->reset_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
/// Returns the progress of the current processing operation as a percentage
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double progress(){
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if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
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return ((bsq<float>*)file)->get_progress();
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else if(header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->get_progress();
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
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return ((bil<float>*)file)->get_progress();
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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
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bool open(stim::iotype io = stim::io_in){
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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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David Mayerich
added an envi::op...
|
371
|
return ((bsq<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
372
373
|
}
else if(header.data_type == envi_header::float64) {
|
8057237a
David Mayerich
added an envi::op...
|
374
|
return ((bsq<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
375
376
|
}
else
|
9ef9bdfa
David Mayerich
generated an erro...
|
377
378
|
{
std::cout << "ERROR: The specified data format (" << header.data_type << ") is not supported" << std::endl;
|
6708cc25
heziqi
Ziqi added envi c...
|
379
|
return false;
|
9ef9bdfa
David Mayerich
generated an erro...
|
380
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
381
|
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
382
|
|
6708cc25
heziqi
Ziqi added envi c...
|
383
384
|
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...
|
385
|
return ((bil<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
386
387
|
}
else if(header.data_type == envi_header::float64) {
|
8057237a
David Mayerich
added an envi::op...
|
388
|
return ((bil<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
389
|
}
|
9ef9bdfa
David Mayerich
generated an erro...
|
390
391
|
{
std::cout << "ERROR: The specified data format (" << header.data_type << ") is not supported" << std::endl;
|
6708cc25
heziqi
Ziqi added envi c...
|
392
|
return false;
|
9ef9bdfa
David Mayerich
generated an erro...
|
393
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
394
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
395
|
|
6708cc25
heziqi
Ziqi added envi c...
|
396
397
|
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...
|
398
|
return ((bip<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
399
400
|
}
else if(header.data_type == envi_header::float64) {
|
8057237a
David Mayerich
added an envi::op...
|
401
|
return ((bip<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
|
6708cc25
heziqi
Ziqi added envi c...
|
402
|
}
|
9ef9bdfa
David Mayerich
generated an erro...
|
403
404
|
{
std::cout << "ERROR: The specified data format (" << header.data_type << ") is not supported" << std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
405
|
return false;
|
9ef9bdfa
David Mayerich
generated an erro...
|
406
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
407
408
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
409
410
|
return true;
|
8057237a
David Mayerich
added an envi::op...
|
411
412
413
|
}
|
48f356fa
David Mayerich
bug fixes for FFT...
|
414
415
416
417
418
419
420
421
422
423
|
/// 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 ...
|
424
425
426
427
428
|
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...
|
429
430
|
fseek(f, 13, SEEK_CUR); //skip the the x and y dimensions
short x, y;
|
618dce30
David Mayerich
removed warnings ...
|
431
432
433
434
435
436
437
438
439
440
|
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...
|
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
|
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...
|
457
458
459
460
|
/// 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
|
bb457896
David Mayerich
improved error me...
|
461
|
bool open(std::string filename, stim::envi_header h, stim::iotype io = stim::io_in){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
462
|
|
8057237a
David Mayerich
added an envi::op...
|
463
464
465
466
|
header = h; //store the header
fname = filename; //save the filename
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
467
468
|
allocate();
|
bb457896
David Mayerich
improved error me...
|
469
|
return open(io); //open the ENVI file;
|
8057237a
David Mayerich
added an envi::op...
|
470
471
|
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
472
473
474
475
476
477
|
}
/// 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
|
bb457896
David Mayerich
improved error me...
|
478
|
bool open(std::string filename, std::string headername, stim::iotype io = stim::io_in){
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
479
480
481
482
483
|
//allocate memory
//allocate();
stim::envi_header h;
|
bb457896
David Mayerich
improved error me...
|
484
485
486
487
|
if (!h.load(headername)) {
std::cout << "Error loading header file: " << headername << std::endl;
return false;
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
488
489
490
491
|
//load the header
//header.load(headername);
|
bb457896
David Mayerich
improved error me...
|
492
|
return open(filename, h, io);
|
e8eb202f
David Mayerich
added a new ENVI ...
|
493
494
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
495
496
497
498
499
|
/// 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...
|
500
|
bool ratio(std::string outfile, double band, unsigned char* mask = NULL, bool PROGRESS = false){
|
a2bf1d08
David Mayerich
general bug fixes...
|
501
|
header.save(outfile + ".hdr");
|
6708cc25
heziqi
Ziqi added envi c...
|
502
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
e8eb202f
David Mayerich
added a new ENVI ...
|
503
|
if(header.data_type ==envi_header::float32)
|
c30dd3e6
David Mayerich
added vector norm...
|
504
|
return ((bsq<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
505
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
506
|
return ((bsq<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
507
508
509
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
510
|
|
6708cc25
heziqi
Ziqi added envi c...
|
511
512
|
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...
|
513
|
return ((bil<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
514
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
515
|
return ((bil<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
516
517
518
519
520
521
|
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...
|
522
|
return ((bip<float>*)file)->ratio(outfile, band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
523
|
else if(header.data_type == envi_header::float64)
|
c30dd3e6
David Mayerich
added vector norm...
|
524
|
return ((bip<double>*)file)->ratio(outfile,band, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
525
526
527
528
529
530
531
532
|
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
|
533
|
return false;
|
6708cc25
heziqi
Ziqi added envi c...
|
534
535
|
}
|
c30dd3e6
David Mayerich
added vector norm...
|
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
|
/// 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);
}
}
|
b31c02eb
David Mayerich
added a --select ...
|
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
|
bool select(std::string outfile, std::vector<double> bandlist, unsigned char* MASK = NULL, bool PROGRESS = false) {
stim::envi_header new_header = header; //copy all of the data from the current header file to the new one
new_header.bands = bandlist.size(); //the number of bands in the new file is equal to the number of bands provided by the user
new_header.wavelength = bandlist; //the wavelength values in the output file are the same as those specified by the user
new_header.band_names.empty(); //no band names will be provided in the output file
new_header.save(outfile + ".hdr"); //save the output header file
if (header.interleave == envi_header::BSQ) { //if the infile is bip file
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->select(outfile, bandlist, MASK, PROGRESS);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->select(outfile, bandlist, MASK, PROGRESS);
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else if (header.interleave == envi_header::BIL) { //if the infile is bip file
if (header.data_type == envi_header::float32)
return ((bil<float>*)file)->select(outfile, bandlist, MASK, PROGRESS);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->select(outfile, bandlist, 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)
return ((bip<float>*)file)->select(outfile, bandlist, MASK, PROGRESS);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->select(outfile, bandlist, MASK, PROGRESS);
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
607
608
609
610
|
/// 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...
|
611
612
|
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...
|
613
614
|
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...
|
615
|
return ((bsq<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
616
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
617
|
return ((bsq<double>*)file)->baseline(outfile,w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
618
619
620
621
622
623
624
625
|
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...
|
626
|
return ((bil<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
627
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
628
|
return ((bil<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
629
630
631
632
633
634
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
635
|
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
|
6708cc25
heziqi
Ziqi added envi c...
|
636
|
if(header.data_type ==envi_header::float32)
|
798cea97
David Mayerich
added progress ba...
|
637
|
return ((bip<float>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
638
|
else if(header.data_type == envi_header::float64)
|
798cea97
David Mayerich
added progress ba...
|
639
|
return ((bip<double>*)file)->baseline(outfile, w, mask, PROGRESS);
|
6708cc25
heziqi
Ziqi added envi c...
|
640
641
642
643
644
645
646
647
648
649
650
651
|
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...
|
652
653
654
|
/// 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 ...
|
655
656
657
658
659
660
661
662
663
664
665
666
|
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...
|
667
|
((bip<float>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
668
|
else if(header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
669
|
((bip<double>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
|
63fc1df8
David Mayerich
added an inverse ...
|
670
671
672
673
674
675
676
677
|
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...
|
678
|
out_hdr.wavelength = bands;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
679
|
out_hdr.band_names.clear();
|
63fc1df8
David Mayerich
added an inverse ...
|
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
|
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 ...
|
710
711
712
713
|
/// 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...
|
714
|
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...
|
715
|
|
6708cc25
heziqi
Ziqi added envi c...
|
716
717
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
|
a2bf1d08
David Mayerich
general bug fixes...
|
718
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
719
720
721
722
|
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
723
|
else if(interleave == envi_header::BIL) //convert BSQ -> BIL
|
c6251f8b
David Mayerich
allows user to de...
|
724
|
((bsq<float>*)file)->bil(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
|
a2bf1d08
David Mayerich
general bug fixes...
|
725
|
else if(interleave == envi_header::BIP){ //ERROR
|
cf5b4c92
David Mayerich
simplified asynch...
|
726
|
//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
|
474c351a
David Mayerich
output timing dat...
|
727
|
((bsq<float>*)file)->bip(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
|
cf5b4c92
David Mayerich
simplified asynch...
|
728
|
//exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
729
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
730
731
732
|
}
else if(header.data_type == envi_header::float64){ //if the data type is float
|
a2bf1d08
David Mayerich
general bug fixes...
|
733
|
if(interleave == envi_header::BSQ){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
734
735
736
|
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
737
|
else if(interleave == envi_header::BIL) //convert BSQ -> BIL
|
c6251f8b
David Mayerich
allows user to de...
|
738
|
((bsq<double>*)file)->bil(outfile, PROGRESS, OPTIMIZATION);
|
a2bf1d08
David Mayerich
general bug fixes...
|
739
|
else if(interleave == envi_header::BIP){ //ERROR
|
cf5b4c92
David Mayerich
simplified asynch...
|
740
|
//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
|
f7cf19e4
David Mayerich
fixed warnings, t...
|
741
|
((bsq<double>*)file)->bip(outfile, PROGRESS, OPTIMIZATION);
|
cf5b4c92
David Mayerich
simplified asynch...
|
742
|
//exit(1);
|
63fc1df8
David Mayerich
added an inverse ...
|
743
|
}
|
6708cc25
heziqi
Ziqi added envi c...
|
744
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
745
|
|
6708cc25
heziqi
Ziqi added envi c...
|
746
747
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
748
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
749
750
751
752
753
|
}
}
else if(header.interleave == envi_header::BIL){
|
a2bf1d08
David Mayerich
general bug fixes...
|
754
|
if(header.data_type ==envi_header::float32){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
755
756
757
758
|
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
759
760
761
762
|
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...
|
763
764
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
765
766
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIL){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
767
768
769
|
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
770
771
772
773
|
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...
|
774
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
775
|
|
6708cc25
heziqi
Ziqi added envi c...
|
776
777
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
778
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
779
780
781
782
|
}
}
else if(header.interleave == envi_header::BIP){
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
783
|
|
a2bf1d08
David Mayerich
general bug fixes...
|
784
785
|
if(header.data_type ==envi_header::float32){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
786
787
788
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
789
790
791
|
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 ...
|
792
793
794
795
|
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...
|
796
797
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
798
799
|
else if(header.data_type == envi_header::float64){
if(interleave == envi_header::BIP){ //ERROR
|
6708cc25
heziqi
Ziqi added envi c...
|
800
801
802
|
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
803
804
805
|
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 ...
|
806
807
808
809
|
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...
|
810
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
811
|
|
6708cc25
heziqi
Ziqi added envi c...
|
812
813
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
814
|
exit(1);
|
6708cc25
heziqi
Ziqi added envi c...
|
815
816
|
}
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
817
|
|
6708cc25
heziqi
Ziqi added envi c...
|
818
819
820
821
|
else{
std::cout<<"ERROR: unidentified interleave type"<<std::endl;
exit(1);
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
822
823
824
825
826
|
stim::envi_header h = header;
h.interleave = interleave;
h.save(outfile + ".hdr");
return true;
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
827
|
|
6708cc25
heziqi
Ziqi added envi c...
|
828
829
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
830
831
832
833
834
|
/// 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...
|
835
|
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
|
836
837
838
|
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...
|
839
|
return ((bsq<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
840
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
841
|
return ((bsq<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
842
843
844
845
846
847
|
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...
|
848
|
return ((bil<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
849
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
850
|
return ((bil<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
851
852
853
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
cacc3cdc
heziqi
attempt to fix CImg
|
854
|
|
4a6f666c
heziqi
Added mask method
|
855
856
|
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...
|
857
|
return ((bip<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
858
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
859
|
return ((bip<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
860
861
862
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
|
bba4f4d9
David Mayerich
minor warning fixes
|
863
864
|
return false;
|
740f8cd2
heziqi
added apply_mask
|
865
866
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
867
|
/// Creates a mask with a true value for all pixels that contain finite values
|
e37ce7bf
David Mayerich
added the ability...
|
868
|
void mask_finite(unsigned char* out_mask, unsigned char* mask = NULL, bool PROGRESS = false){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
869
870
|
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...
|
871
|
((bsq<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
872
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
873
|
((bsq<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
874
875
876
877
878
879
|
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...
|
880
|
((bil<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
881
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
882
|
((bil<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
883
884
885
886
887
888
|
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...
|
889
|
((bip<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
890
|
else if(header.data_type == envi_header::float64)
|
e37ce7bf
David Mayerich
added the ability...
|
891
|
((bip<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
892
893
894
895
896
|
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
897
898
899
900
|
/// 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...
|
901
|
void apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
740f8cd2
heziqi
added apply_mask
|
902
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
903
904
|
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...
|
905
|
((bsq<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
906
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
907
|
((bsq<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
908
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
909
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
910
911
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
912
913
|
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...
|
914
|
((bil<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
915
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
916
|
((bil<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
917
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
918
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
919
920
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
921
922
|
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...
|
923
|
((bip<float>*)file)->apply_mask(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
924
|
else if (header.data_type == envi_header::float64)
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
925
|
((bip<double>*)file)->apply_mask(outfile, p, PROGRESS);
|
740f8cd2
heziqi
added apply_mask
|
926
|
else
|
e843658b
Brad Deutsch
Previous push did...
|
927
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
740f8cd2
heziqi
added apply_mask
|
928
|
}
|
4a6f666c
heziqi
Added mask method
|
929
930
|
else{
|
e843658b
Brad Deutsch
Previous push did...
|
931
932
933
|
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
934
|
header.save(outfile + ".hdr");
|
e843658b
Brad Deutsch
Previous push did...
|
935
936
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
937
938
939
|
/// 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...
|
940
941
|
/// @param matrix is the destination for the pixel data
/// @param p is the mask
|
814eb271
David Mayerich
fixed problems wi...
|
942
|
bool sift(void* matrix, unsigned char* p = NULL, bool PROGRESS = false){
|
43dec788
David Mayerich
added code for si...
|
943
944
945
|
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...
|
946
|
return ((bsq<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
43dec788
David Mayerich
added code for si...
|
947
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
948
|
return ((bsq<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
949
|
else{
|
43dec788
David Mayerich
added code for si...
|
950
|
std::cout << "ERROR: unidentified data type" << std::endl;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
951
952
|
exit(1);
}
|
43dec788
David Mayerich
added code for si...
|
953
|
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
954
955
|
if (header.interleave == envi_header::BIP){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
956
|
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
957
|
return ((bip<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
958
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
959
|
return ((bip<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
960
961
962
963
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
964
965
|
}
if (header.interleave == envi_header::BIL){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
966
|
if (header.data_type == envi_header::float32)
|
814eb271
David Mayerich
fixed problems wi...
|
967
|
return ((bil<float>*)file)->sift((float*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
968
|
else if (header.data_type == envi_header::float64)
|
814eb271
David Mayerich
fixed problems wi...
|
969
|
return ((bil<double>*)file)->sift((double*)matrix, p, PROGRESS);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
970
971
972
973
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
974
|
}
|
43dec788
David Mayerich
added code for si...
|
975
976
977
978
|
return false;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
979
|
/// Saves in an array only those spectra corresponding to nonzero values of the mask.
|
43dec788
David Mayerich
added code for si...
|
980
981
|
/// @param outfile is the name of the sifted output file
/// @param p is the mask
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
982
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
|
e843658b
Brad Deutsch
Previous push did...
|
983
984
|
{
|
2fcab4f0
David Mayerich
added unsifting f...
|
985
|
//calculate the number of non-zero values in the mask
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
986
987
988
|
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...
|
989
990
991
992
993
|
if( p[i] > 0 ) nnz++;
//create a new header
envi_header new_header = header;
|
f7e99517
David Mayerich
added sifting for...
|
994
995
|
//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...
|
996
|
new_header.interleave = envi_header::BIP;
|
f7e99517
David Mayerich
added sifting for...
|
997
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
998
999
1000
1001
1002
|
//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...
|
1003
1004
|
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...
|
1005
|
return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
1006
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
1007
|
return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
1008
1009
1010
1011
1012
1013
|
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...
|
1014
|
return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
1015
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
1016
|
return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
1017
1018
1019
1020
1021
1022
|
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...
|
1023
|
return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
1024
|
else if (header.data_type == envi_header::float64)
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
1025
|
return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
|
e843658b
Brad Deutsch
Previous push did...
|
1026
1027
1028
1029
1030
1031
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
4a6f666c
heziqi
Added mask method
|
1032
1033
|
exit(1);
}
|
4a6f666c
heziqi
Added mask method
|
1034
|
return false;
|
cacc3cdc
heziqi
attempt to fix CImg
|
1035
1036
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
1037
|
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...
|
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
|
//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...
|
1050
|
return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
1051
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
1052
|
return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
2fcab4f0
David Mayerich
added unsifting f...
|
1053
1054
1055
1056
1057
|
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...
|
1058
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
1059
1060
1061
1062
|
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...
|
1063
|
|
8550e94f
David Mayerich
added sifting and...
|
1064
|
if (header.data_type == envi_header::float32)
|
a2bf1d08
David Mayerich
general bug fixes...
|
1065
|
return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
1066
|
else if (header.data_type == envi_header::float64)
|
a2bf1d08
David Mayerich
general bug fixes...
|
1067
|
return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
|
8550e94f
David Mayerich
added sifting and...
|
1068
1069
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1070
1071
1072
1073
|
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1074
|
}
|
cbce396e
David Mayerich
added support for...
|
1075
|
return 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
1076
1077
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1078
1079
1080
1081
1082
1083
1084
1085
1086
|
/// 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...
|
1087
|
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...
|
1088
1089
|
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...
|
1090
|
return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1091
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1092
|
return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1093
|
else
|
11ff9d7e
David Mayerich
improved user out...
|
1094
|
std::cout<<"envi::ph_to_ph ERROR - unidentified data type"<<std::endl;
|
20c212c0
heziqi
Ziqi added functi...
|
1095
1096
1097
1098
|
}
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...
|
1099
|
return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1100
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1101
|
return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1102
|
else
|
11ff9d7e
David Mayerich
improved user out...
|
1103
|
std::cout<<"envi::ph_to_ph ERROR - unidentified data type"<<std::endl;
|
20c212c0
heziqi
Ziqi added functi...
|
1104
1105
1106
1107
|
}
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...
|
1108
|
return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1109
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1110
|
return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1111
|
else
|
11ff9d7e
David Mayerich
improved user out...
|
1112
|
std::cout<<"envi::ph_to_ph ERROR - unidentified data type"<<std::endl;
|
70407ea9
heziqi
Ziqi completed he...
|
1113
1114
1115
|
}
else{
|
11ff9d7e
David Mayerich
improved user out...
|
1116
|
std::cout<<"envi::ph_to_ph ERROR - unidentified file type"<<std::endl;
|
70407ea9
heziqi
Ziqi completed he...
|
1117
1118
1119
1120
1121
|
exit(1);
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1122
1123
1124
1125
1126
1127
1128
1129
1130
|
/// 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...
|
1131
|
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...
|
1132
1133
|
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...
|
1134
|
return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1135
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1136
|
return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1137
1138
1139
1140
1141
1142
|
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...
|
1143
|
return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1144
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1145
|
return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1146
1147
1148
1149
1150
1151
|
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...
|
1152
|
return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1153
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1154
|
return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
|
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 ...
|
1166
1167
1168
1169
1170
1171
1172
1173
1174
|
/// 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...
|
1175
|
/// @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 ...
|
1176
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1177
1178
|
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...
|
1179
1180
|
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...
|
1181
|
return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1182
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1183
|
return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1184
1185
1186
1187
1188
1189
|
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...
|
1190
|
return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1191
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1192
|
return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1193
1194
1195
1196
1197
1198
|
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...
|
1199
|
return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
70407ea9
heziqi
Ziqi completed he...
|
1200
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1201
|
return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
|
20c212c0
heziqi
Ziqi added functi...
|
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
|
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 ...
|
1213
1214
1215
1216
1217
1218
1219
|
/// 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...
|
1220
|
bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
|
517876d6
heziqi
metrics finished ...
|
1221
1222
|
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...
|
1223
|
return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1224
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1225
|
return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1226
1227
1228
1229
1230
1231
|
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...
|
1232
|
return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1233
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1234
|
return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1235
1236
1237
1238
1239
1240
|
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...
|
1241
|
return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1242
|
else if(header.data_type == envi_header::float64)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
1243
|
return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
|
517876d6
heziqi
metrics finished ...
|
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
|
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 ...
|
1255
|
/// Closes the ENVI file.
|
edb975b0
David Mayerich
created a stim::e...
|
1256
1257
|
void close(){
if(file == NULL) return;
|
6708cc25
heziqi
Ziqi added envi c...
|
1258
1259
|
if(header.interleave == envi_header::BSQ){
if(header.data_type ==envi_header::float32)
|
edb975b0
David Mayerich
created a stim::e...
|
1260
|
((bsq<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1261
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1262
|
((bsq<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1263
1264
1265
1266
1267
1268
1269
1270
|
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...
|
1271
|
((bil<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1272
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1273
|
((bil<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1274
1275
1276
1277
1278
1279
1280
1281
|
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...
|
1282
|
((bip<float>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1283
|
else if(header.data_type == envi_header::float64)
|
edb975b0
David Mayerich
created a stim::e...
|
1284
|
((bip<double>*)file)->close();
|
6708cc25
heziqi
Ziqi added envi c...
|
1285
1286
1287
1288
1289
|
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1290
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1291
1292
1293
1294
1295
|
/// 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...
|
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
|
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 ...
|
1329
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1330
|
/// Saves a header file describing the current ENVI file parameters.
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1331
1332
1333
1334
1335
1336
1337
1338
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1339
1340
1341
1342
|
/// 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 ...
|
1343
|
bool band(void* ptr, double wavelength, bool PROGRESS = false){
|
d1d8ef91
David Mayerich
added band readin...
|
1344
1345
1346
|
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 ...
|
1347
|
return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1348
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1349
|
return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1350
1351
1352
1353
1354
1355
1356
|
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 ...
|
1357
|
return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1358
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1359
|
return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1360
1361
1362
1363
1364
1365
1366
|
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 ...
|
1367
|
return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1368
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1369
|
return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
|
081f2c9f
heziqi
made bip bil file...
|
1370
1371
1372
1373
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
d1d8ef91
David Mayerich
added band readin...
|
1374
|
}
|
ee4dea28
David Mayerich
fixed errors in c...
|
1375
|
return false;
|
1582ce07
David Mayerich
added band_index(...
|
1376
1377
|
}
|
f4069d3f
David Mayerich
fixed the crop fu...
|
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
|
void band_bounds(double wavelength, size_t& low, size_t& high) {
if (header.interleave == envi_header::BSQ) { //if the infile is bsq file
if (header.data_type == envi_header::float32)
((bsq<float>*)file)->band_bounds(wavelength, low, high);
else if (header.data_type == envi_header::float64)
((bsq<double>*)file)->band_bounds(wavelength, low, high);
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)->band_bounds(wavelength, low, high);
else if (header.data_type == envi_header::float64)
((bil<double>*)file)->band_bounds(wavelength, low, high);
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)->band_bounds(wavelength, low, high);
else if (header.data_type == envi_header::float64)
((bip<double>*)file)->band_bounds(wavelength, low, high);
else {
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
}
|
735a2a24
David Mayerich
started testing o...
|
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
|
// 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...
|
1451
|
float test = ((float*)temp)[0];
|
735a2a24
David Mayerich
started testing o...
|
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
|
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);
}
}
|
889c89dd
David Mayerich
fixed memory leak...
|
1463
|
free(temp);
|
735a2a24
David Mayerich
started testing o...
|
1464
1465
1466
1467
1468
1469
1470
1471
|
}
/// 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...
|
1472
|
void spectrum(T* ptr, size_t x, size_t y, bool PROGRESS = false){
|
735a2a24
David Mayerich
started testing o...
|
1473
|
|
c4dd399a
David Mayerich
fixed a Linux com...
|
1474
|
spectrum<T>(ptr, y * header.samples + x, PROGRESS);
|
724ec347
David Mayerich
simplified the EN...
|
1475
1476
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
1477
1478
1479
1480
|
/// 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...
|
1481
|
bool band_index(void* ptr, unsigned long long b){
|
081f2c9f
heziqi
made bip bil file...
|
1482
1483
|
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(...
|
1484
|
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
081f2c9f
heziqi
made bip bil file...
|
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
|
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(...
|
1511
1512
|
}
return false;
|
d1d8ef91
David Mayerich
added band readin...
|
1513
|
}
|
f92397d2
David Mayerich
fixed a Win32 bug...
|
1514
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1515
1516
1517
1518
|
/// 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...
|
1519
|
bool mean_spectrum(double * p, double* std, unsigned char* mask, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1520
1521
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
35a7195f
David Mayerich
added median spec...
|
1522
|
return ((bsq<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1523
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1524
|
return ((bsq<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1525
1526
1527
1528
1529
1530
1531
|
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...
|
1532
|
return ((bil<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1533
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1534
|
return ((bil<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1535
1536
1537
1538
1539
1540
1541
|
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...
|
1542
|
return ((bip<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1543
|
else if (header.data_type == envi_header::float64)
|
35a7195f
David Mayerich
added median spec...
|
1544
|
return ((bip<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1545
1546
1547
1548
1549
1550
1551
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1552
|
|
35a7195f
David Mayerich
added median spec...
|
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
|
/// 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 ...
|
1575
1576
1577
1578
1579
|
/// 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...
|
1580
|
bool co_matrix(double* co, double* avg, unsigned char* mask, int cuda_device, bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1581
|
if (header.interleave == envi_header::BSQ){
|
63fc1df8
David Mayerich
added an inverse ...
|
1582
1583
|
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...
|
1584
1585
1586
|
}
else if (header.interleave == envi_header::BIL){
if (header.data_type == envi_header::float32)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1587
|
return ((bil<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1588
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1589
|
return ((bil<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1590
1591
1592
1593
1594
1595
1596
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
else if (header.interleave == envi_header::BIP){
if (header.data_type == envi_header::float32)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1597
|
return ((bip<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1598
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1599
|
return ((bip<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1600
1601
1602
1603
1604
1605
1606
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1607
|
|
334547d8
sam
changes for mnf: ...
|
1608
1609
1610
1611
1612
|
/// 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...
|
1613
|
bool coNoise_matrix(double* coN, double* avg, unsigned char* mask, int cuda_device = 0, bool PROGRESS = false){
|
334547d8
sam
changes for mnf: ...
|
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
|
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...
|
1627
|
return ((bip<float>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
|
334547d8
sam
changes for mnf: ...
|
1628
|
else if (header.data_type == envi_header::float64)
|
dd5aab2f
David Mayerich
fixed errors in s...
|
1629
|
return ((bip<double>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
|
334547d8
sam
changes for mnf: ...
|
1630
1631
1632
1633
1634
1635
1636
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1637
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
1638
1639
1640
1641
1642
1643
1644
|
/// 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...
|
1645
1646
1647
1648
1649
1650
1651
1652
|
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...
|
1653
|
|
177c7863
David Mayerich
updated the ENVI ...
|
1654
1655
|
//save the header for the cropped file
stim::envi_header new_header = header;
|
f78ceb64
David Mayerich
fixed BIP croppin...
|
1656
1657
1658
|
new_header.samples = x1 - x0 + 1;
new_header.lines = y1 - y0 + 1;
new_header.bands = b1 - b0 + 1;
|
177c7863
David Mayerich
updated the ENVI ...
|
1659
|
std::vector<double>::const_iterator first = new_header.wavelength.begin() + b0;
|
f78ceb64
David Mayerich
fixed BIP croppin...
|
1660
|
std::vector<double>::const_iterator last = new_header.wavelength.begin() + b1 + 1;
|
177c7863
David Mayerich
updated the ENVI ...
|
1661
1662
1663
|
new_header.wavelength = std::vector<double>(first, last);
new_header.save(outfile + ".hdr");
|
a43c4fe1
heziqi
Added crop in env...
|
1664
1665
|
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
63fc1df8
David Mayerich
added an inverse ...
|
1666
|
return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1667
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1668
|
return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1669
1670
1671
1672
1673
1674
1675
|
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 ...
|
1676
|
return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1677
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1678
|
return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1679
1680
1681
1682
1683
1684
1685
|
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 ...
|
1686
|
return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1687
|
else if (header.data_type == envi_header::float64)
|
63fc1df8
David Mayerich
added an inverse ...
|
1688
|
return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
|
a43c4fe1
heziqi
Added crop in env...
|
1689
1690
1691
1692
1693
1694
1695
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
1696
|
|
bb61cb18
David Mayerich
added subimage fu...
|
1697
1698
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
1728
1729
1730
1731
|
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...
|
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
1756
1757
1758
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
|
/// 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...
|
1790
1791
1792
1793
1794
1795
1796
1797
1798
1799
1800
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
1821
1822
1823
1824
1825
1826
1827
1828
1829
1830
1831
1832
1833
1834
1835
1836
1837
|
/// 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...
|
1838
|
|
82a7c08c
David Mayerich
added an append c...
|
1839
1840
1841
1842
1843
1844
1845
1846
1847
1848
1849
1850
1851
1852
1853
1854
1855
1856
1857
1858
1859
1860
1861
1862
1863
1864
1865
1866
1867
1868
1869
1870
1871
1872
1873
1874
1875
1876
1877
1878
1879
1880
1881
1882
1883
1884
1885
1886
1887
1888
1889
1890
1891
1892
1893
1894
1895
1896
1897
1898
1899
|
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...
|
1900
1901
1902
1903
1904
1905
1906
|
/// 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...
|
1907
|
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...
|
1908
1909
1910
1911
1912
1913
1914
1915
1916
1917
1918
1919
1920
1921
1922
1923
1924
|
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...
|
1925
|
((bsq<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1926
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1927
|
((bsq<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1928
1929
1930
1931
1932
1933
1934
|
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...
|
1935
|
((bil<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1936
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1937
|
((bil<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1938
1939
1940
1941
1942
1943
1944
|
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...
|
1945
|
((bip<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1946
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1947
|
((bip<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1948
1949
1950
1951
1952
1953
1954
1955
1956
1957
1958
1959
|
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...
|
1960
|
void deriv(std::string outfile, size_t d, size_t order, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1961
1962
1963
|
header.save(outfile + ".hdr");
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1964
|
((bsq<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1965
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1966
|
((bsq<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1967
1968
1969
1970
1971
1972
1973
1974
|
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...
|
1975
|
((bil<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1976
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1977
|
((bil<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1978
1979
1980
1981
1982
1983
1984
1985
|
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...
|
1986
|
((bip<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1987
|
else if (header.data_type == envi_header::float64)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1988
|
((bip<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
|
9b2a5d71
David Mayerich
implemented finit...
|
1989
1990
1991
1992
1993
1994
1995
|
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
exit(1);
}
|
278c622b
David Mayerich
finished Windows ...
|
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2022
2023
2024
2025
2026
2027
2028
2029
2030
2031
2032
2033
2034
2035
2036
2037
2038
2039
2040
2041
2042
2043
2044
2045
2046
2047
2048
2049
2050
2051
2052
2053
2054
2055
2056
2057
2058
2059
2060
2061
2062
2063
2064
2065
2066
2067
2068
2069
|
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 ...
|
2070
2071
2072
2073
2074
|
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...
|
2075
|
if(samples == 0) samples = header.bands;
|
f1365506
David Mayerich
modifications to ...
|
2076
|
//double B = (double)header.bands;
|
9d34229e
David Mayerich
restructured the ...
|
2077
2078
2079
2080
2081
2082
2083
2084
2085
2086
2087
2088
2089
|
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...
|
2090
|
new_header.wavelength_units = "inv_" + header.wavelength_units;
|
9d34229e
David Mayerich
restructured the ...
|
2091
2092
2093
2094
2095
2096
2097
2098
2099
2100
2101
2102
2103
2104
2105
2106
2107
|
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 ...
|
2108
|
}; //end ENVI
|
e8eb202f
David Mayerich
added a new ENVI ...
|
2109
2110
2111
2112
|
} //end namespace rts
#endif
|