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#ifndef STIM_ENVI_H
#define STIM_ENVI_H
#include "../envi/envi_header.h"
#include "../envi/bsq.h"
#include "../envi/bip.h"
#include "../envi/bil.h"
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#include <iostream>
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#include "../image/image.h"
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namespace stim{
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/** This class implements reading of ENVI hyperspectral files. These files can be stored in multiple orientations
(including BSQ, BIP, and BIL) in order to optimize streaming speed depending on applications. Basic ENVI
files are stored on disk as a large binary file with a corresponding header. Code for reading and processing
ENVI header files is in the envi_header class.
*/
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class envi{
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void* file; //void pointer to the relevant file reader (bip, bsq, or bil - with appropriate data type)
public:
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envi_header header;
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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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bool allocate(){
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)
return(file = new bsq<float>());
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else if(header.data_type == envi_header::float64)
return(file = new bsq<double>());
}
else if(header.interleave == envi_header::BIP){
if(header.data_type ==envi_header::float32)
return(file = new bip<float>());
else if(header.data_type == envi_header::float64)
return(file = new bip<double>());
}
else if(header.interleave == envi_header::BIL){
if(header.data_type ==envi_header::float32)
return(file = new bil<float>());
else if(header.data_type == envi_header::float64)
return(file = new bil<double>());
}
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exit(1); //if the function hasn't already returned, we don't handle this state
}
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/// Open an existing ENVI file given the file and header names.
/// @param filename is the name of the ENVI binary file
/// @param headername is the name of the ENVI header file
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bool open(std::string filename, std::string headername){
//allocate memory
allocate();
//load the header
header.load(headername);
//load the file
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if(header.interleave == envi_header::BSQ) { //if the infile is bsq file
if(header.data_type == envi_header::float32) {
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return ((bsq<float>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
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}
else if(header.data_type == envi_header::float64) {
return ((bsq<double>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
}
else
return false;
}
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else if(header.interleave == envi_header::BIL) { //if the infile is bil file
if(header.data_type == envi_header::float32) {
return ((bil<float>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
}
else if(header.data_type == envi_header::float64) {
return ((bil<double>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
}
else
return false;
}
else if(header.interleave == envi_header::BIP) { //if the infile is bip file
if(header.data_type == envi_header::float32) {
return ((bip<float>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
}
else if(header.data_type == envi_header::float64) {
return ((bip<double>*)file)->open(filename, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
}
else
return false;
}
else{
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std::cout<<"ERROR: unidentified type file "<<headername<<std::endl;
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exit(1);
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}
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}
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/// Normalize a hyperspectral ENVI file given a band number and threshold.
/// @param outfile is the name of the normalized file to be output
/// @param band is the band label to be output
/// @param threshold is a threshold value specified such that normalization will only be done to values in the band > threshold (preventing division by small numbers)
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bool normalize(std::string outfile, double band, double threshold = 0.0){
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if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
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if(header.data_type ==envi_header::float32)
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return ((bsq<float>*)file)->normalize(outfile, band, threshold);
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else if(header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->normalize(outfile,band, threshold);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
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else if(header.interleave == envi_header::BIL){ //if the infile is bil file
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->normalize(outfile, band);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->normalize(outfile,band);
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)->normalize(outfile, band);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->normalize(outfile,band);
else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
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return false;
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}
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/// Performs piecewise linear baseline correction of a hyperspectral file/
/// @param outfile is the file name for the baseline corrected output
/// @param w is a list of band labels to serve as baseline points (zero values)
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bool baseline(std::string outfile, std::vector<double> w){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->baseline(outfile, w);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->baseline(outfile,w);
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)
return ((bil<float>*)file)->baseline(outfile, w);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->baseline(outfile, w);
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->baseline(outfile, w);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->baseline(outfile, w);
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else{
std::cout<<"ERROR: unidentified file type"<<std::endl;
exit(1);
}
}
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/// 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
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bool convert(std::string outfile, stim::envi_header::interleaveType interleave){
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if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32){ //if the data type of infile is float
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL) //if the target file is bil file
return ((bsq<float>*)file)->bil(outfile);
else if(interleave == envi_header::BIP) //if the target file is bip file
return ((bsq<float>*)file)->bip(outfile);
}
else if(header.data_type == envi_header::float64){ //if the data type is float
if(interleave == envi_header::BSQ){
std::cout<<"ERROR: is already BSQ file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL)
return ((bsq<double>*)file)->bil(outfile);
else if(interleave == envi_header::BIP)
return ((bsq<double>*)file)->bip(outfile);
}
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){ //if the data type of infile is float
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BSQ) //if the target file is bsq file
return ((bil<float>*)file)->bsq(outfile);
else if(interleave == envi_header::BIP) //if the target file is bip file
return ((bil<float>*)file)->bip(outfile);
}
else if(header.data_type == envi_header::float64){ //if the data type is float
if(interleave == envi_header::BIL){
std::cout<<"ERROR: is already BIL file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BSQ)
return ((bil<double>*)file)->bsq(outfile);
else if(interleave == envi_header::BIP)
return ((bil<double>*)file)->bip(outfile);
}
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){ //if the data type of infile is float
if(interleave == envi_header::BIP){
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL) //if the target file is bil file
return ((bip<float>*)file)->bil(outfile);
else if(interleave == envi_header::BSQ) //if the target file is bsq file
return ((bip<float>*)file)->bsq(outfile);
}
else if(header.data_type == envi_header::float64){ //if the data type is float
if(interleave == envi_header::BIP){
std::cout<<"ERROR: is already BIP file"<<std::endl;
exit(1);
}
else if(interleave == envi_header::BIL) //if the target file is bil file
return ((bip<double>*)file)->bil(outfile);
else if(interleave == envi_header::BSQ) //if the target file is bsq file
return ((bip<double>*)file)->bsq(outfile);
}
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else{
std::cout<<"ERROR: unidentified interleave type"<<std::endl;
exit(1);
}
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return false;
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}
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/// 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
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bool build_mask(double mask_band, double threshold, unsigned char* p = NULL) {
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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)->build_mask(mask_band, threshold, p);
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else if(header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->build_mask(mask_band, threshold, p);
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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)->build_mask(mask_band, threshold, p);
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else if(header.data_type == envi_header::float64)
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return ((bil<double>*)file)->build_mask(mask_band, threshold, p);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
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else if(header.interleave == envi_header::BIP){ //if the infile is bip file
if(header.data_type ==envi_header::float32)
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return ((bip<float>*)file)->build_mask(mask_band, threshold, p);
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else if(header.data_type == envi_header::float64)
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return ((bip<double>*)file)->build_mask(mask_band, threshold, p);
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else
std::cout<<"ERROR: unidentified data type"<<std::endl;
}
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return false;
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}
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/// 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)
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bool apply_mask(std::string outfile, unsigned char* p)
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{
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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)->apply_mask(outfile, p);
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else if (header.data_type == envi_header::float64)
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return ((bsq<double>*)file)->apply_mask(outfile, p);
else
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std::cout << "ERROR: unidentified data type" << std::endl;
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}
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else if (header.interleave == envi_header::BIL){ //if the infile is bil file
if (header.data_type == envi_header::float32)
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return ((bil<float>*)file)->apply_mask(outfile, p);
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else if (header.data_type == envi_header::float64)
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return ((bil<double>*)file)->apply_mask(outfile, p);
else
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std::cout << "ERROR: unidentified data type" << std::endl;
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}
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else if (header.interleave == envi_header::BIP){ //if the infile is bip file
if (header.data_type == envi_header::float32)
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return ((bip<float>*)file)->apply_mask(outfile, p);
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else if (header.data_type == envi_header::float64)
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return ((bip<double>*)file)->apply_mask(outfile, p);
else
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std::cout << "ERROR: unidentified data type" << std::endl;
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}
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else{
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std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
return false;
}
/// sift-mask saves in an array only those spectra corresponding to nonzero values of the mask.
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bool sift(std::string outfile, unsigned char* p)
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{
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//calculate the number of non-zero values in the mask
unsigned int nnz = 0;
unsigned int npixels = header.lines * header.samples;
for(unsigned int i = 0; i < npixels; i++)
if( p[i] > 0 ) nnz++;
//create a new header
envi_header new_header = header;
//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");
std::cout<<"Saved: "<<outfile+".hdr"<<std::endl;
|
e843658b
Brad Deutsch
Previous push did...
|
395
396
|
if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
if (header.data_type == envi_header::float32)
|
2fcab4f0
David Mayerich
added unsifting f...
|
397
|
return ((bsq<float>*)file)->sift(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
398
|
else if (header.data_type == envi_header::float64)
|
2fcab4f0
David Mayerich
added unsifting f...
|
399
|
return ((bsq<double>*)file)->sift(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
400
401
402
403
404
405
|
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)
|
2fcab4f0
David Mayerich
added unsifting f...
|
406
|
return ((bil<float>*)file)->sift(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
407
|
else if (header.data_type == envi_header::float64)
|
2fcab4f0
David Mayerich
added unsifting f...
|
408
|
return ((bil<double>*)file)->sift(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
409
410
411
412
413
414
|
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)
|
2fcab4f0
David Mayerich
added unsifting f...
|
415
|
return ((bip<float>*)file)->sift(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
416
|
else if (header.data_type == envi_header::float64)
|
2fcab4f0
David Mayerich
added unsifting f...
|
417
|
return ((bip<double>*)file)->sift(outfile, p);
|
e843658b
Brad Deutsch
Previous push did...
|
418
419
420
421
422
423
|
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
|
4a6f666c
heziqi
Added mask method
|
424
425
|
exit(1);
}
|
2fcab4f0
David Mayerich
added unsifting f...
|
426
427
|
|
4a6f666c
heziqi
Added mask method
|
428
|
return false;
|
cacc3cdc
heziqi
attempt to fix CImg
|
429
430
|
}
|
2fcab4f0
David Mayerich
added unsifting f...
|
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
|
bool unsift(std::string outfile, unsigned char* mask, unsigned int samples, unsigned int lines){
//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)
return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines);
else
std::cout << "ERROR: unidentified data type" << std::endl;
}
else if (header.interleave == envi_header::BIL){ //if the infile is bil file
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
std::cout << "ERROR in stim::envi::unsift - BIP files aren't supported yet" << std::endl;
}
else{
std::cout << "ERROR: unidentified file type" << std::endl;
exit(1);
}
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
468
469
470
471
472
473
474
475
476
|
/// 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
|
70407ea9
heziqi
Ziqi completed he...
|
477
|
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, void * result){
|
20c212c0
heziqi
Ziqi added functi...
|
478
479
|
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
|
70407ea9
heziqi
Ziqi completed he...
|
480
|
return ((bsq<float>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (float*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
481
|
else if(header.data_type == envi_header::float64)
|
70407ea9
heziqi
Ziqi completed he...
|
482
|
return ((bsq<double>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (double*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
483
484
485
486
487
488
|
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)
|
70407ea9
heziqi
Ziqi completed he...
|
489
|
return ((bil<float>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (float*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
490
|
else if(header.data_type == envi_header::float64)
|
70407ea9
heziqi
Ziqi completed he...
|
491
|
return ((bil<double>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (double*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
492
493
494
495
496
497
|
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)
|
70407ea9
heziqi
Ziqi completed he...
|
498
|
return ((bip<float>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (float*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
499
|
else if(header.data_type == envi_header::float64)
|
70407ea9
heziqi
Ziqi completed he...
|
500
501
502
503
504
505
506
507
508
509
510
511
|
return ((bip<double>*)file)->ph_to_ph(lb1, rb1, pos1, lb2, rb2, pos2, (double*)result);
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 ...
|
512
513
514
515
516
517
518
519
520
|
/// 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
|
70407ea9
heziqi
Ziqi completed he...
|
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
|
bool pa_to_ph(double lb1, double rb1, double lab1, double rab1, double lb2, double rb2, double pos, void * result){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (double*)result);
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)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (double*)result);
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)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->pa_to_ph(lb1, rb1, lab1, rab1, lb2, rb2, pos, (double*)result);
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 ...
|
556
557
558
559
560
561
562
563
564
565
566
|
/// 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)
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
|
bool pa_to_pa(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, void* result){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (double*)result);
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)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (double*)result);
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)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->pa_to_pa(lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, (double*)result);
|
20c212c0
heziqi
Ziqi added functi...
|
592
593
594
595
596
597
598
599
600
601
602
|
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 ...
|
603
604
605
606
607
608
609
|
/// 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
|
517876d6
heziqi
metrics finished ...
|
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
|
bool cpoint(double lb1, double rb1, double lab1, double rab1, void* result){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->cpoint(lb1, rb1, lab1, rab1, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->cpoint(lb1, rb1, lab1, rab1, (double*)result);
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)->cpoint(lb1, rb1, lab1, rab1, (float*)result);
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->cpoint(lb1, rb1, lab1, rab1, (double*)result);
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)->cpoint(lb1, rb1, lab1, rab1,(float*)result);
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->cpoint(lb1, rb1, lab1, rab1, (double*)result);
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 ...
|
645
|
/// Closes the ENVI file.
|
6708cc25
heziqi
Ziqi added envi c...
|
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
|
bool close(){
if(header.interleave == envi_header::BSQ){
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->close();
else if(header.data_type == envi_header::float64)
return ((bsq<double>*)file)->close();
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIL){
if(header.data_type ==envi_header::float32)
return ((bil<float>*)file)->close();
else if(header.data_type == envi_header::float64)
return ((bil<double>*)file)->close();
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
else if(header.interleave == envi_header::BIP){
if(header.data_type ==envi_header::float32)
return ((bip<float>*)file)->close();
else if(header.data_type == envi_header::float64)
return ((bip<double>*)file)->close();
else{
std::cout<<"ERROR: unidentified data type"<<std::endl;
exit(1);
}
}
|
e933c14e
David Mayerich
cleaned up the code
|
679
|
return false;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
680
|
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
681
682
683
684
685
|
/// 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...
|
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
|
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 ...
|
719
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
720
|
/// Saves a header file describing the current ENVI file parameters.
|
e8eb202f
David Mayerich
added a new ENVI ...
|
721
722
723
724
725
726
727
728
|
bool save_header(std::string filename){
//save the header file here
header.save(filename);
return true;
}
|
cb455f98
David Mayerich
removed old ENVI ...
|
729
730
731
732
|
/// 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.
|
d1d8ef91
David Mayerich
added band readin...
|
733
734
735
736
737
|
bool band(void* ptr, double wavelength){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->band((float*)ptr, wavelength);
|
081f2c9f
heziqi
made bip bil file...
|
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
|
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->band((double*)ptr, wavelength);
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((float*)ptr, wavelength);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->band((double*)ptr, wavelength);
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((float*)ptr, wavelength);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->band((double*)ptr, wavelength);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
|
d1d8ef91
David Mayerich
added band readin...
|
764
|
}
|
ee4dea28
David Mayerich
fixed errors in c...
|
765
|
return false;
|
1582ce07
David Mayerich
added band_index(...
|
766
767
|
}
|
27b826a8
David Mayerich
added a spherical...
|
768
769
770
771
772
|
/// Retrieve a spectrum from the specified location
/// @param ptr is a pointer to pre-allocated memory of size B*sizeof(T)
/// @param x is the x-coordinate of the spectrum
/// @param y is the y-coordinate of the spectrum
|
724ec347
David Mayerich
simplified the EN...
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bool spectrum(void* ptr, unsigned int x, unsigned int y){
if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
if(header.data_type ==envi_header::float32)
return ((bsq<float>*)file)->spectrum((float*)ptr, x, y);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->spectrum((double*)ptr, x, y);
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)->spectrum((float*)ptr, x, y);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->spectrum((double*)ptr, x, y);
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)->spectrum((float*)ptr, x, y);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->spectrum((double*)ptr, x, y);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
cb455f98
David Mayerich
removed old ENVI ...
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808
809
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811
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/// 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.
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1582ce07
David Mayerich
added band_index(...
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812
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bool band_index(void* ptr, unsigned int b){
|
081f2c9f
heziqi
made bip bil file...
|
813
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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(...
|
815
|
return ((bsq<float>*)file)->band_index((float*)ptr, b);
|
081f2c9f
heziqi
made bip bil file...
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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(...
|
842
843
|
}
return false;
|
d1d8ef91
David Mayerich
added band readin...
|
844
|
}
|
9f489bb3
heziqi
Added load_mask a...
|
845
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
846
847
848
849
|
/// Helper function that loads a mask into memory given a filename.
/// @param mask is a pointer to pre-allocated memory of size X*Y
/// @param maskname is the file name for the image that will serve as the mask
|
bfe9c6db
heziqi
added feature_mat...
|
850
851
|
bool load_mask(unsigned char * mask, std::string maskname){
//open the mask file
|
7b3948ab
David Mayerich
added support for...
|
852
|
stim::image<unsigned char> mask_image(maskname);
|
32504c2c
David Mayerich
fixed some functi...
|
853
|
mask_image.data_noninterleaved(mask);
|
bfe9c6db
heziqi
added feature_mat...
|
854
|
//save mask file into memory
|
32504c2c
David Mayerich
fixed some functi...
|
855
|
//memcpy(mask, mask_image.data_noninterleaved(), mask_image.size());
|
7b3948ab
David Mayerich
added support for...
|
856
|
//mask_image.clear();
|
bfe9c6db
heziqi
added feature_mat...
|
857
|
return true;
|
9f489bb3
heziqi
Added load_mask a...
|
858
|
}
|
d1d8ef91
David Mayerich
added band readin...
|
859
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
860
861
862
863
|
/// 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
|
a43c4fe1
heziqi
Added crop in env...
|
864
865
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|
bool avg_band(void * p, unsigned char* mask){
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->avg_band((float*)p, mask);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->avg_band((double*)p, mask);
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)->avg_band((float*)p, mask);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->avg_band((double*)p, mask);
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)->avg_band((float*)p, mask);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->avg_band((double*)p, mask);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
897
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
898
899
900
901
902
|
/// 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
|
a43c4fe1
heziqi
Added crop in env...
|
903
904
905
906
907
908
909
910
911
912
913
914
915
916
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918
919
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929
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931
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933
934
935
|
bool co_matrix(void* co, void* avg, unsigned char* mask){
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->co_matrix((float*)co, (float*)avg, mask);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->co_matrix((double*)co, (double*)avg, mask);
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)->co_matrix((float*)co, (float*)avg, mask);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->co_matrix((double*)co, (double*)avg, mask);
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)->co_matrix((float*)co, (float*)avg, mask);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->co_matrix((double*)co, (double*)avg, mask);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
936
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
937
|
|
cb455f98
David Mayerich
removed old ENVI ...
|
938
939
940
941
942
943
944
|
/// 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
|
a43c4fe1
heziqi
Added crop in env...
|
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
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970
971
972
973
974
975
976
977
978
|
bool crop(std::string outfile,unsigned x0, unsigned y0, unsigned x1, unsigned y1){
if (header.interleave == envi_header::BSQ){
if (header.data_type == envi_header::float32)
return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1);
else if (header.data_type == envi_header::float64)
return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1);
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)->crop(outfile, x0, y0, x1, y1);
else if (header.data_type == envi_header::float64)
return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1);
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)->crop(outfile, x0, y0, x1, y1);
else if (header.data_type == envi_header::float64)
return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1);
else{
std::cout << "ERROR: unidentified data type" << std::endl;
exit(1);
}
}
return false;
}
|
0df38ff3
heziqi
fixed head detached
|
979
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
980
981
982
983
984
|
};
} //end namespace rts
#endif
|