Blame view

stim/envi/envi.h 75.4 KB
e8eb202f   David Mayerich   added a new ENVI ...
1
2
3
4
5
6
7
  #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"
9b2a5d71   David Mayerich   implemented finit...
8
  #include "../math/fd_coefficients.h"
9d34229e   David Mayerich   restructured the ...
9
  #include <stim/parser/filename.h>
91d472ac   David Mayerich   added file_size f...
10
  #include <stim/util/filesize.h>
bfe9c6db   heziqi   added feature_mat...
11
  #include <iostream>
48f356fa   David Mayerich   bug fixes for FFT...
12
  #include <fstream>
2ed641f0   David Mayerich   removed the depen...
13
  //#include "../image/image.h"
e8eb202f   David Mayerich   added a new ENVI ...
14
  
8a86bd56   David Mayerich   changed rts names...
15
  namespace stim{
e8eb202f   David Mayerich   added a new ENVI ...
16
  
cb455f98   David Mayerich   removed old ENVI ...
17
18
19
20
21
  /** 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.
  */
f92397d2   David Mayerich   fixed a Win32 bug...
22
  class envi{
e8eb202f   David Mayerich   added a new ENVI ...
23
24
  
  	void* file;		//void pointer to the relevant file reader (bip, bsq, or bil - with appropriate data type)
8057237a   David Mayerich   added an envi::op...
25
  	std::string fname;					//file name used for repeated opening and closing
e8eb202f   David Mayerich   added a new ENVI ...
26
  
735a2a24   David Mayerich   started testing o...
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
  	//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]);
  	}
08d1c3b9   David Mayerich   fixed casting war...
64
  	
e8eb202f   David Mayerich   added a new ENVI ...
65
  public:
08d1c3b9   David Mayerich   fixed casting war...
66
  	envi_header header;
e8eb202f   David Mayerich   added a new ENVI ...
67
  
08d1c3b9   David Mayerich   fixed casting war...
68
  	
edb975b0   David Mayerich   created a stim::e...
69
70
71
72
73
  	/// Default constructor
  	envi(){
  		file = NULL;				//set the file pointer to NULL
  	}
  
ec722ff9   David Mayerich   added spero mosai...
74
75
76
77
78
79
80
  	envi(std::string filename, std::string headername){
  		header.load(headername);
  
  		fname = filename;					//save the filename
  
  		allocate();
  	}
9d34229e   David Mayerich   restructured the ...
81
82
83
84
85
  	//used to test if the current ENVI file is valid
  	operator bool(){
  		if(file == NULL) return false;
  		return true;
  	}
ec722ff9   David Mayerich   added spero mosai...
86
  
9d34229e   David Mayerich   restructured the ...
87
88
  	//test to determine if the specified file is an ENVI file
  	static bool is_envi(std::string fname, std::string hname = ""){
9d34229e   David Mayerich   restructured the ...
89
90
91
92
93
94
95
96
97
98
99
100
  		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
91d472ac   David Mayerich   added file_size f...
101
  		size_t bytes = stim::file_size(fname);
9d34229e   David Mayerich   restructured the ...
102
103
  		if(bytes != targetBytes) return false;			//if the data doesn't match the header, return false
  		return true;									//otherwise everything looks fine
41e2f5ab   David Mayerich   fixed finite mask...
104
  
9d34229e   David Mayerich   restructured the ...
105
  	}
08d1c3b9   David Mayerich   fixed casting war...
106
  	
4a6f666c   heziqi   Added mask method
107
  
735a2a24   David Mayerich   started testing o...
108
109
110
111
112
113
114
115
  	void* malloc_spectrum(){
  		return alloc_array(header.bands);
  	}
  
  	void* malloc_band(){
  		return alloc_array(header.samples * header.lines);
  	}
  
c6251f8b   David Mayerich   allows user to de...
116
  	void set_buffer_frac(double memfrac = 0.5){
008ae990   David Mayerich   implemented Windo...
117
118
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
c6251f8b   David Mayerich   allows user to de...
119
  				((bsq<float>*)file)->set_buffer_frac(memfrac);
008ae990   David Mayerich   implemented Windo...
120
  			else if(header.data_type == envi_header::float64)
c6251f8b   David Mayerich   allows user to de...
121
  				((bsq<double>*)file)->set_buffer_frac(memfrac);
008ae990   David Mayerich   implemented Windo...
122
123
124
125
126
127
  			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)
c6251f8b   David Mayerich   allows user to de...
128
  				((bil<float>*)file)->set_buffer_frac(memfrac);
008ae990   David Mayerich   implemented Windo...
129
  			else if(header.data_type == envi_header::float64)
c6251f8b   David Mayerich   allows user to de...
130
  				((bil<double>*)file)->set_buffer_frac(memfrac);
008ae990   David Mayerich   implemented Windo...
131
132
133
134
135
136
  			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)
c6251f8b   David Mayerich   allows user to de...
137
  				((bip<float>*)file)->set_buffer_frac(memfrac);
008ae990   David Mayerich   implemented Windo...
138
  			else if(header.data_type == envi_header::float64)
c6251f8b   David Mayerich   allows user to de...
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
  				((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);
008ae990   David Mayerich   implemented Windo...
174
175
176
177
178
179
180
181
182
183
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  	}
  
f92397d2   David Mayerich   fixed a Win32 bug...
184
185
186
187
188
189
190
191
  	/// 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);
  	}
  
c6251f8b   David Mayerich   allows user to de...
192
193
194
195
196
197
198
199
200
201
  	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();
  	}
  
cbce396e   David Mayerich   added support for...
202
203
204
205
206
  	/// 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)
63fc1df8   David Mayerich   added an inverse ...
207
  				((bsq<float>*)file)->reset_progress();
cbce396e   David Mayerich   added support for...
208
  			else if(header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
209
  				((bsq<double>*)file)->reset_progress();
cbce396e   David Mayerich   added support for...
210
211
212
213
214
215
  			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)
63fc1df8   David Mayerich   added an inverse ...
216
  				((bil<float>*)file)->reset_progress();
cbce396e   David Mayerich   added support for...
217
  			else if(header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
218
  				((bil<double>*)file)->reset_progress();
cbce396e   David Mayerich   added support for...
219
220
221
222
223
224
  			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)
63fc1df8   David Mayerich   added an inverse ...
225
  				((bip<float>*)file)->reset_progress();
cbce396e   David Mayerich   added support for...
226
  			else if(header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
227
  				((bip<double>*)file)->reset_progress();
cbce396e   David Mayerich   added support for...
228
229
230
231
232
233
234
235
236
237
238
  			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
9d3ba0b1   David Mayerich   added stim::hsi a...
239
  	double progress(){
cbce396e   David Mayerich   added support for...
240
241
242
  
  		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 ...
243
  				return ((bsq<float>*)file)->get_progress();
cbce396e   David Mayerich   added support for...
244
  			else if(header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
245
  				return ((bsq<double>*)file)->get_progress();
cbce396e   David Mayerich   added support for...
246
247
248
249
250
251
  			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)
63fc1df8   David Mayerich   added an inverse ...
252
  				return ((bil<float>*)file)->get_progress();
cbce396e   David Mayerich   added support for...
253
  			else if(header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
254
  				return ((bil<double>*)file)->get_progress();
cbce396e   David Mayerich   added support for...
255
256
257
258
259
260
  			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)
63fc1df8   David Mayerich   added an inverse ...
261
  				return ((bip<float>*)file)->get_progress();
cbce396e   David Mayerich   added support for...
262
  			else if(header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
263
  				return ((bip<double>*)file)->get_progress();
cbce396e   David Mayerich   added support for...
264
265
266
267
268
269
270
271
272
273
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  		}
  		return 0;
  	}
  
c6251f8b   David Mayerich   allows user to de...
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
  	/// 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;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
310
  	/// Allocate memory for a new ENVI file based on the current interleave format (BIP, BIL, BSQ) and data type.
9d3ba0b1   David Mayerich   added stim::hsi a...
311
  	void allocate(){
e8eb202f   David Mayerich   added a new ENVI ...
312
313
314
  
  		file = NULL;	//set file to a NULL pointer
  
6708cc25   heziqi   Ziqi added envi c...
315
  		if(header.interleave == envi_header::BSQ){
e8eb202f   David Mayerich   added a new ENVI ...
316
  			if(header.data_type ==envi_header::float32)
9d3ba0b1   David Mayerich   added stim::hsi a...
317
  				file = new bsq<float>();
6708cc25   heziqi   Ziqi added envi c...
318
  			else if(header.data_type == envi_header::float64)
9d3ba0b1   David Mayerich   added stim::hsi a...
319
  				file = new bsq<double>();
6708cc25   heziqi   Ziqi added envi c...
320
321
322
  		}
  		else if(header.interleave == envi_header::BIP){
  			if(header.data_type ==envi_header::float32)
9d3ba0b1   David Mayerich   added stim::hsi a...
323
  				file = new bip<float>();
6708cc25   heziqi   Ziqi added envi c...
324
  			else if(header.data_type == envi_header::float64)
9d3ba0b1   David Mayerich   added stim::hsi a...
325
  				file = new bip<double>();
6708cc25   heziqi   Ziqi added envi c...
326
327
328
  		}
  		else if(header.interleave == envi_header::BIL){
  			if(header.data_type ==envi_header::float32)
9d3ba0b1   David Mayerich   added stim::hsi a...
329
  				file = new bil<float>();
6708cc25   heziqi   Ziqi added envi c...
330
  			else if(header.data_type == envi_header::float64)
9d3ba0b1   David Mayerich   added stim::hsi a...
331
  				file = new bil<double>();
6708cc25   heziqi   Ziqi added envi c...
332
  		}
e8eb202f   David Mayerich   added a new ENVI ...
333
  
e8eb202f   David Mayerich   added a new ENVI ...
334
335
  	}
  
8057237a   David Mayerich   added an envi::op...
336
337
  	/// Open a previously opened ENVI file
  	bool open(){
e8eb202f   David Mayerich   added a new ENVI ...
338
339
  
  		//load the file
6708cc25   heziqi   Ziqi added envi c...
340
341
  		if(header.interleave == envi_header::BSQ) {		//if the infile is bsq file
  			if(header.data_type == envi_header::float32) {
8057237a   David Mayerich   added an envi::op...
342
  				return ((bsq<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
343
344
  			}
  			else if(header.data_type == envi_header::float64) {
8057237a   David Mayerich   added an envi::op...
345
  				return ((bsq<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
346
347
348
349
  			}
  			else
  				return false;
  		}
e8eb202f   David Mayerich   added a new ENVI ...
350
  
6708cc25   heziqi   Ziqi added envi c...
351
352
  		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...
353
  				return ((bil<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
354
355
  			}
  			else if(header.data_type == envi_header::float64) {
8057237a   David Mayerich   added an envi::op...
356
  				return ((bil<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
357
358
359
360
  			}
  			else
  				return false;
  		}
f92397d2   David Mayerich   fixed a Win32 bug...
361
  
6708cc25   heziqi   Ziqi added envi c...
362
363
  		else if(header.interleave == envi_header::BIP) {		//if the infile is bip file
  			if(header.data_type == envi_header::float32) {
8057237a   David Mayerich   added an envi::op...
364
  				return ((bip<float>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
365
366
  			}
  			else if(header.data_type == envi_header::float64) {
8057237a   David Mayerich   added an envi::op...
367
  				return ((bip<double>*)file)->open(fname, header.samples, header.lines, header.bands, header.header_offset, header.wavelength);
6708cc25   heziqi   Ziqi added envi c...
368
369
  			}
  			else
f92397d2   David Mayerich   fixed a Win32 bug...
370
  				return false;
6708cc25   heziqi   Ziqi added envi c...
371
372
  		}
  
f92397d2   David Mayerich   fixed a Win32 bug...
373
374
  		return true;
  
8057237a   David Mayerich   added an envi::op...
375
376
377
  
  	}
  
48f356fa   David Mayerich   bug fixes for FFT...
378
379
380
381
382
383
384
385
386
387
  	/// Open an Agilent binary file as an ENVI stream
  	bool open_agilent(std::string filename){
  		fname = filename;												//store the file name
  
  		//Open the file temporarily to get the header information
  		FILE* f = fopen(filename.c_str(), "r");							//open the binary file for reading
  		if(f == NULL) return false;										//return false if no file is opened
  
  		fseek(f, 9, SEEK_SET);											//seek to the number of bands
  		short b;														//allocate space for the number of bands
618dce30   David Mayerich   removed warnings ...
388
389
390
391
392
  		size_t nread = fread(&b, sizeof(short), 1, f);					//read the number of bands
  		if(nread != 1){
  			std::cout<<"Error reading band number from Agilent file."<<std::endl;
  			exit(1);
  		}
48f356fa   David Mayerich   bug fixes for FFT...
393
394
  		fseek(f, 13, SEEK_CUR);											//skip the the x and y dimensions
  		short x, y;
618dce30   David Mayerich   removed warnings ...
395
396
397
398
399
400
401
402
403
404
  		nread = fread(&x, sizeof(short), 1, f);									//read the image x and y size
  		if(nread != 1){
  			std::cout<<"Error reading X dimension from Agilent file."<<std::endl;
  			exit(1);
  		}
  		nread = fread(&y, sizeof(short), 1, f);
  		if(nread != 1){
  			std::cout<<"Error reading Y dimension from Agilent file."<<std::endl;
  			exit(1);
  		}
48f356fa   David Mayerich   bug fixes for FFT...
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
  		fclose(f);														//close the file
  
  		//store the information from the Agilent header in the ENVI header
  		header.bands = b;
  		header.samples = x;
  		header.lines = y;
  		header.data_type = envi_header::float32;						//all values are 32-bit floats
  		header.header_offset = 1020;									//number of bytes in an Agilent binary header
  		header.interleave = envi_header::BSQ;							//all Agilent binary files are BSQ
  
  		allocate();														//allocate the streaming file object
  		open();															//open the file for streaming
  
  		return true;
  	}
  
8057237a   David Mayerich   added an envi::op...
421
422
423
424
425
  	/// Open an existing ENVI file given the filename and a header structure
  
  	/// @param filename is the name of the ENVI binary file
  	/// @param header is an ENVI header structure
  	bool open(std::string filename, stim::envi_header h){
9d3ba0b1   David Mayerich   added stim::hsi a...
426
  		
8057237a   David Mayerich   added an envi::op...
427
428
429
430
  
  		header = h;							//store the header
  		fname = filename;					//save the filename
  
9d3ba0b1   David Mayerich   added stim::hsi a...
431
432
  		allocate();
  
8057237a   David Mayerich   added an envi::op...
433
434
435
  		return open();						//open the ENVI file;
  		
  
f92397d2   David Mayerich   fixed a Win32 bug...
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
  	}
  
  	/// Open an existing ENVI file given the file and header names.
  
  	/// @param filename is the name of the ENVI binary file
  	/// @param headername is the name of the ENVI header file
  	bool open(std::string filename, std::string headername){
  
  		//allocate memory
  		//allocate();
  
  		stim::envi_header h;
  		h.load(headername);
  
  		//load the header
  		//header.load(headername);
  
  		return open(filename, h);
e8eb202f   David Mayerich   added a new ENVI ...
454
455
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
456
457
458
459
460
  	/// Normalize a hyperspectral ENVI file given a band number and threshold.
  
  	/// @param outfile is the name of the normalized file to be output
  	/// @param band is the band label to be output
  	/// @param threshold is a threshold value specified such that normalization will only be done to values in the band > threshold (preventing division by small numbers)
c30dd3e6   David Mayerich   added vector norm...
461
  	bool ratio(std::string outfile, double band, unsigned char* mask = NULL, bool PROGRESS = false){
a2bf1d08   David Mayerich   general bug fixes...
462
  		header.save(outfile + ".hdr");
6708cc25   heziqi   Ziqi added envi c...
463
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
e8eb202f   David Mayerich   added a new ENVI ...
464
  			if(header.data_type ==envi_header::float32)
c30dd3e6   David Mayerich   added vector norm...
465
  				return ((bsq<float>*)file)->ratio(outfile, band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
466
  			else if(header.data_type == envi_header::float64)
c30dd3e6   David Mayerich   added vector norm...
467
  				return ((bsq<double>*)file)->ratio(outfile,band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
468
469
470
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
e8eb202f   David Mayerich   added a new ENVI ...
471
  
6708cc25   heziqi   Ziqi added envi c...
472
473
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
c30dd3e6   David Mayerich   added vector norm...
474
  				return ((bil<float>*)file)->ratio(outfile, band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
475
  			else if(header.data_type == envi_header::float64)
c30dd3e6   David Mayerich   added vector norm...
476
  				return ((bil<double>*)file)->ratio(outfile,band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
477
478
479
480
481
482
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
c30dd3e6   David Mayerich   added vector norm...
483
  				return ((bip<float>*)file)->ratio(outfile, band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
484
  			else if(header.data_type == envi_header::float64)
c30dd3e6   David Mayerich   added vector norm...
485
  				return ((bip<double>*)file)->ratio(outfile,band, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
486
487
488
489
490
491
492
493
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
e933c14e   David Mayerich   cleaned up the code
494
  		return false;
6708cc25   heziqi   Ziqi added envi c...
495
496
  	}
  
c30dd3e6   David Mayerich   added vector norm...
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
  	/// Perform vector normalization on the ENVI image
  	void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){
  		header.save(outfile + ".hdr");
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
  				((bsq<float>*)file)->normalize(outfile, mask, PROGRESS);
  			else if(header.data_type == envi_header::float64)
  				((bsq<double>*)file)->normalize(outfile, mask, PROGRESS);
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
  				((bil<float>*)file)->normalize(outfile, mask, PROGRESS);
  			else if(header.data_type == envi_header::float64)
  				((bil<double>*)file)->normalize(outfile, mask, PROGRESS);
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
  				((bip<float>*)file)->normalize(outfile, mask, PROGRESS);
  			else if(header.data_type == envi_header::float64)
  				((bip<double>*)file)->normalize(outfile, mask, PROGRESS);
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
533
534
535
536
  	/// Performs piecewise linear baseline correction of a hyperspectral file/
  
  	/// @param outfile is the file name for the baseline corrected output
  	/// @param w is a list of band labels to serve as baseline points (zero values)
798cea97   David Mayerich   added progress ba...
537
538
  	bool baseline(std::string outfile, std::vector<double> w, unsigned char* mask = NULL, bool PROGRESS = false){
  		header.save(outfile + ".hdr");
6708cc25   heziqi   Ziqi added envi c...
539
540
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
798cea97   David Mayerich   added progress ba...
541
  				return ((bsq<float>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
542
  			else if(header.data_type == envi_header::float64)
798cea97   David Mayerich   added progress ba...
543
  				return ((bsq<double>*)file)->baseline(outfile,w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
544
545
546
547
548
549
550
551
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
798cea97   David Mayerich   added progress ba...
552
  				return ((bil<float>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
553
  			else if(header.data_type == envi_header::float64)
798cea97   David Mayerich   added progress ba...
554
  				return ((bil<double>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
555
556
557
558
559
560
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
f92397d2   David Mayerich   fixed a Win32 bug...
561
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
6708cc25   heziqi   Ziqi added envi c...
562
  			if(header.data_type ==envi_header::float32)
798cea97   David Mayerich   added progress ba...
563
  				return ((bip<float>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
564
  			else if(header.data_type == envi_header::float64)
798cea97   David Mayerich   added progress ba...
565
  				return ((bip<double>*)file)->baseline(outfile, w, mask, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
566
567
568
569
570
571
572
573
574
575
576
577
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  	}
  
dd5aab2f   David Mayerich   fixed errors in s...
578
579
580
  	/// Project an array of coefficients onto a basis matrix
  
  	void project(std::string outfile, double* center, double* basis, size_t M, std::vector<double> bands, unsigned char* mask, int cuda_device = 0, bool PROGRESS = false) {
63fc1df8   David Mayerich   added an inverse ...
581
582
583
584
585
586
587
588
589
590
591
592
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			std::cout<<"ERROR: BSQ projection not supported"<<std::endl;
  			exit(1);
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			std::cout<<"ERROR: BIL projection not supported"<<std::endl;
  			exit(1);
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
dd5aab2f   David Mayerich   fixed errors in s...
593
  				((bip<float>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
63fc1df8   David Mayerich   added an inverse ...
594
  			else if(header.data_type == envi_header::float64)
dd5aab2f   David Mayerich   fixed errors in s...
595
  				((bip<double>*)file)->project(outfile, center, basis, M, mask, cuda_device, PROGRESS);
63fc1df8   David Mayerich   added an inverse ...
596
597
598
599
600
601
602
603
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		stim::envi_header out_hdr = header;							
  		out_hdr.bands = M;											//set the number of bands in the output header
dd5aab2f   David Mayerich   fixed errors in s...
604
  		out_hdr.wavelength = bands;
9d3ba0b1   David Mayerich   added stim::hsi a...
605
  		out_hdr.band_names.clear();
63fc1df8   David Mayerich   added an inverse ...
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
  		out_hdr.save(outfile + ".hdr");								//save the output header
  	}
  
  	void inverse(std::string outfile, double* center, double* basis, unsigned long long B, unsigned long long C = 0, bool PROGRESS = false){
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			std::cout<<"ERROR: BSQ projection not supported"<<std::endl;
  			exit(1);
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			std::cout<<"ERROR: BIL projection not supported"<<std::endl;
  			exit(1);
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
  				((bip<float>*)file)->inverse(outfile, center, basis, B, C, PROGRESS);
  			else if(header.data_type == envi_header::float64)
  				((bip<double>*)file)->inverse(outfile, center, basis, B, C, PROGRESS);
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		stim::envi_header out_hdr = header;							
  		out_hdr.bands = B;											//set the number of bands in the output header
  		out_hdr.save(outfile + ".hdr");								//save the output header
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
636
637
638
639
  	/// Converts ENVI files between interleave types (BSQ, BIL, and BIP)
  
  	/// @param outfile is the file name for the converted output
  	/// @param interleave is the interleave format for the destination file
c6251f8b   David Mayerich   allows user to de...
640
  	bool convert(std::string outfile, stim::envi_header::interleaveType interleave, bool PROGRESS = false, bool VERBOSE = false, bool OPTIMIZATION = true){
a2bf1d08   David Mayerich   general bug fixes...
641
  		
6708cc25   heziqi   Ziqi added envi c...
642
643
  		if(header.interleave == envi_header::BSQ){			//if the infile is bsq file
  
a2bf1d08   David Mayerich   general bug fixes...
644
  			if(header.data_type ==envi_header::float32){		//ERROR
6708cc25   heziqi   Ziqi added envi c...
645
646
647
648
  				if(interleave == envi_header::BSQ){
  					std::cout<<"ERROR:  is already BSQ file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
649
  				else if(interleave == envi_header::BIL)			//convert BSQ -> BIL
c6251f8b   David Mayerich   allows user to de...
650
  					((bsq<float>*)file)->bil(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
a2bf1d08   David Mayerich   general bug fixes...
651
  				else if(interleave == envi_header::BIP){			//ERROR
cf5b4c92   David Mayerich   simplified asynch...
652
  					//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
474c351a   David Mayerich   output timing dat...
653
  					((bsq<float>*)file)->bip(outfile, PROGRESS, VERBOSE, OPTIMIZATION);
cf5b4c92   David Mayerich   simplified asynch...
654
  					//exit(1);
63fc1df8   David Mayerich   added an inverse ...
655
  				}
6708cc25   heziqi   Ziqi added envi c...
656
657
658
  			}
  
  			else if(header.data_type == envi_header::float64){		//if the data type is float
a2bf1d08   David Mayerich   general bug fixes...
659
  				if(interleave == envi_header::BSQ){							//ERROR
6708cc25   heziqi   Ziqi added envi c...
660
661
662
  					std::cout<<"ERROR:  is already BSQ file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
663
  				else if(interleave == envi_header::BIL)					//convert BSQ -> BIL
c6251f8b   David Mayerich   allows user to de...
664
  					((bsq<double>*)file)->bil(outfile, PROGRESS, OPTIMIZATION);
a2bf1d08   David Mayerich   general bug fixes...
665
  				else if(interleave == envi_header::BIP){					//ERROR
cf5b4c92   David Mayerich   simplified asynch...
666
  					//std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
f7cf19e4   David Mayerich   fixed warnings, t...
667
  					((bsq<double>*)file)->bip(outfile, PROGRESS, OPTIMIZATION);
cf5b4c92   David Mayerich   simplified asynch...
668
  					//exit(1);
63fc1df8   David Mayerich   added an inverse ...
669
  				}
6708cc25   heziqi   Ziqi added envi c...
670
  			}
f92397d2   David Mayerich   fixed a Win32 bug...
671
  
6708cc25   heziqi   Ziqi added envi c...
672
673
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
f92397d2   David Mayerich   fixed a Win32 bug...
674
  				exit(1);
6708cc25   heziqi   Ziqi added envi c...
675
676
677
678
679
  			}
  		}
  
  		else if(header.interleave == envi_header::BIL){
  
a2bf1d08   David Mayerich   general bug fixes...
680
  			if(header.data_type ==envi_header::float32){						//ERROR
6708cc25   heziqi   Ziqi added envi c...
681
682
683
684
  				if(interleave == envi_header::BIL){
  					std::cout<<"ERROR:  is already BIL file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
685
686
687
688
  				else if(interleave == envi_header::BSQ)							//BIL -> BSQ
  					((bil<float>*)file)->bsq(outfile, PROGRESS);
  				else if(interleave == envi_header::BIP)							//BIL -> BIP
  					((bil<float>*)file)->bip(outfile, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
689
690
  			}
  
a2bf1d08   David Mayerich   general bug fixes...
691
692
  			else if(header.data_type == envi_header::float64){
  				if(interleave == envi_header::BIL){								//ERROR
6708cc25   heziqi   Ziqi added envi c...
693
694
695
  					std::cout<<"ERROR:  is already BIL file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
696
697
698
699
  				else if(interleave == envi_header::BSQ)							//BIL -> BSQ
  					((bil<double>*)file)->bsq(outfile, PROGRESS);
  				else if(interleave == envi_header::BIP)							//BIL -> BIP
  					((bil<double>*)file)->bip(outfile, PROGRESS);
6708cc25   heziqi   Ziqi added envi c...
700
  			}
f92397d2   David Mayerich   fixed a Win32 bug...
701
  
6708cc25   heziqi   Ziqi added envi c...
702
703
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
f92397d2   David Mayerich   fixed a Win32 bug...
704
  				exit(1);
6708cc25   heziqi   Ziqi added envi c...
705
706
707
708
  			}
  		}
  
  		else if(header.interleave == envi_header::BIP){
f92397d2   David Mayerich   fixed a Win32 bug...
709
  
a2bf1d08   David Mayerich   general bug fixes...
710
711
  			if(header.data_type ==envi_header::float32){
  				if(interleave == envi_header::BIP){								//ERROR
6708cc25   heziqi   Ziqi added envi c...
712
713
714
  					std::cout<<"ERROR:  is already BIP file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
715
716
717
  				else if(interleave == envi_header::BIL)							//BIP -> BIL
  					((bip<float>*)file)->bil(outfile, PROGRESS);
  				else if(interleave == envi_header::BSQ){						//ERROR
63fc1df8   David Mayerich   added an inverse ...
718
719
720
721
  					std::cout<<"ERROR: conversion from BIP to BSQ isn't practical; use BIP->BIL->BSQ instead"<<std::endl;
  					//return ((bsq<float>*)file)->bip(outfile, PROGRESS);
  					exit(1);
  				}
6708cc25   heziqi   Ziqi added envi c...
722
723
  			}
  
a2bf1d08   David Mayerich   general bug fixes...
724
725
  			else if(header.data_type == envi_header::float64){
  				if(interleave == envi_header::BIP){								//ERROR
6708cc25   heziqi   Ziqi added envi c...
726
727
728
  					std::cout<<"ERROR:  is already BIP file"<<std::endl;
  					exit(1);
  				}
a2bf1d08   David Mayerich   general bug fixes...
729
730
731
  				else if(interleave == envi_header::BIL)							//BIP -> BIL
  					((bip<double>*)file)->bil(outfile, PROGRESS);
  				else if(interleave == envi_header::BSQ){						//ERROR
63fc1df8   David Mayerich   added an inverse ...
732
733
734
735
  					std::cout<<"ERROR: conversion from BIP to BSQ isn't practical; use BIP->BIL->BSQ instead"<<std::endl;
  					//return ((bsq<float>*)file)->bip(outfile, PROGRESS);
  					exit(1);
  				}
6708cc25   heziqi   Ziqi added envi c...
736
  			}
f92397d2   David Mayerich   fixed a Win32 bug...
737
  
6708cc25   heziqi   Ziqi added envi c...
738
739
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
f92397d2   David Mayerich   fixed a Win32 bug...
740
  				exit(1);
6708cc25   heziqi   Ziqi added envi c...
741
742
  			}
  		}
f92397d2   David Mayerich   fixed a Win32 bug...
743
  
6708cc25   heziqi   Ziqi added envi c...
744
745
746
747
  		else{
  			std::cout<<"ERROR: unidentified interleave type"<<std::endl;
  			exit(1);
  		}
a2bf1d08   David Mayerich   general bug fixes...
748
749
750
751
752
  		stim::envi_header h = header;
  		h.interleave = interleave;
  		h.save(outfile + ".hdr");
  
  		return true;
f92397d2   David Mayerich   fixed a Win32 bug...
753
  
6708cc25   heziqi   Ziqi added envi c...
754
755
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
756
757
758
759
760
  	/// Builds a mask from a band image and threshold value
  
  	/// @param mask_band is the label for the band that will be used to build the mask
  	/// @param threshold is a value selected such that all band values greater than threshold will have a mask value of 'true'
  	/// @param p is memory of size X*Y that will store the resulting mask
e37ce7bf   David Mayerich   added the ability...
761
  	bool build_mask(unsigned char* out_mask, double mask_band, double lower, double upper, unsigned char* mask = NULL, bool PROGRESS = false)	{
4a6f666c   heziqi   Added mask method
762
763
764
  
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
765
  				return ((bsq<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
766
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
767
  				return ((bsq<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
768
769
770
771
772
773
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
774
  				return ((bil<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
775
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
776
  				return ((bil<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
777
778
779
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
cacc3cdc   heziqi   attempt to fix CImg
780
  
4a6f666c   heziqi   Added mask method
781
782
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
783
  				return ((bip<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
784
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
785
  				return ((bip<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
4a6f666c   heziqi   Added mask method
786
787
788
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
bba4f4d9   David Mayerich   minor warning fixes
789
790
  
  		return false;
740f8cd2   heziqi   added apply_mask
791
792
  	}
  
ba51ae6a   David Mayerich   fixed metric calc...
793
  	/// Creates a mask with a true value for all pixels that contain finite values
e37ce7bf   David Mayerich   added the ability...
794
  	void mask_finite(unsigned char* out_mask, unsigned char* mask = NULL, bool PROGRESS = false){
ba51ae6a   David Mayerich   fixed metric calc...
795
796
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
797
  				((bsq<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
798
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
799
  				((bsq<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
800
801
802
803
804
805
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
806
  				((bil<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
807
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
808
  				((bil<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
809
810
811
812
813
814
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
e37ce7bf   David Mayerich   added the ability...
815
  				((bip<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
816
  			else if(header.data_type == envi_header::float64)
e37ce7bf   David Mayerich   added the ability...
817
  				((bip<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
818
819
820
821
822
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
823
824
825
826
  	/// Applies a mask to the ENVI file.
  
  	/// @param outfile is the name of the resulting masked output file
  	/// @param p is memory of size X*Y containing the mask (0 = false, all other values are true)
6a46c8ff   David Mayerich   fixed bugs in app...
827
  	void apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false)
740f8cd2   heziqi   added apply_mask
828
  	{
e843658b   Brad Deutsch   Previous push did...
829
830
  		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
6a46c8ff   David Mayerich   fixed bugs in app...
831
  				((bsq<float>*)file)->apply_mask(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
832
  			else if (header.data_type == envi_header::float64)
6a46c8ff   David Mayerich   fixed bugs in app...
833
  				((bsq<double>*)file)->apply_mask(outfile, p, PROGRESS);
740f8cd2   heziqi   added apply_mask
834
  			else
e843658b   Brad Deutsch   Previous push did...
835
  				std::cout << "ERROR: unidentified data type" << std::endl;
740f8cd2   heziqi   added apply_mask
836
837
  		}
  
e843658b   Brad Deutsch   Previous push did...
838
839
  		else if (header.interleave == envi_header::BIL){		//if the infile is bil file
  			if (header.data_type == envi_header::float32)
6a46c8ff   David Mayerich   fixed bugs in app...
840
  				((bil<float>*)file)->apply_mask(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
841
  			else if (header.data_type == envi_header::float64)
6a46c8ff   David Mayerich   fixed bugs in app...
842
  				((bil<double>*)file)->apply_mask(outfile, p, PROGRESS);
740f8cd2   heziqi   added apply_mask
843
  			else
e843658b   Brad Deutsch   Previous push did...
844
  				std::cout << "ERROR: unidentified data type" << std::endl;
740f8cd2   heziqi   added apply_mask
845
846
  		}
  
e843658b   Brad Deutsch   Previous push did...
847
848
  		else if (header.interleave == envi_header::BIP){		//if the infile is bip file
  			if (header.data_type == envi_header::float32)
6a46c8ff   David Mayerich   fixed bugs in app...
849
  				((bip<float>*)file)->apply_mask(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
850
  			else if (header.data_type == envi_header::float64)
6a46c8ff   David Mayerich   fixed bugs in app...
851
  				((bip<double>*)file)->apply_mask(outfile, p, PROGRESS);
740f8cd2   heziqi   added apply_mask
852
  			else
e843658b   Brad Deutsch   Previous push did...
853
  				std::cout << "ERROR: unidentified data type" << std::endl;
740f8cd2   heziqi   added apply_mask
854
  		}
4a6f666c   heziqi   Added mask method
855
856
  
  		else{
e843658b   Brad Deutsch   Previous push did...
857
858
859
  			std::cout << "ERROR: unidentified file type" << std::endl;
  			exit(1);
  		}
6a46c8ff   David Mayerich   fixed bugs in app...
860
  		header.save(outfile + ".hdr");
e843658b   Brad Deutsch   Previous push did...
861
862
  	}
  
3d0b6243   David Mayerich   fixed hsiproc bug...
863
864
865
  	/// Copies all spectra corresponding to nonzero values of a mask into a pre-allocated matrix of size (P x B)
  	///		where P is the number of masked pixels and B is the number of bands. The allocated memory can be accessed
  	///		using the following indexing: i = b*P + p
43dec788   David Mayerich   added code for si...
866
867
  	/// @param matrix is the destination for the pixel data
  	/// @param p is the mask
814eb271   David Mayerich   fixed problems wi...
868
  	bool sift(void* matrix, unsigned char* p = NULL, bool PROGRESS = false){
43dec788   David Mayerich   added code for si...
869
870
871
  
  		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
814eb271   David Mayerich   fixed problems wi...
872
  				return ((bsq<float>*)file)->sift((float*)matrix, p, PROGRESS);
43dec788   David Mayerich   added code for si...
873
  			else if (header.data_type == envi_header::float64)
814eb271   David Mayerich   fixed problems wi...
874
  				return ((bsq<double>*)file)->sift((double*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
875
  			else{
43dec788   David Mayerich   added code for si...
876
  				std::cout << "ERROR: unidentified data type" << std::endl;
ba51ae6a   David Mayerich   fixed metric calc...
877
878
  				exit(1);
  			}
43dec788   David Mayerich   added code for si...
879
  		}
3d0b6243   David Mayerich   fixed hsiproc bug...
880
881
  
  		if (header.interleave == envi_header::BIP){
ba51ae6a   David Mayerich   fixed metric calc...
882
  			if (header.data_type == envi_header::float32)
814eb271   David Mayerich   fixed problems wi...
883
  				return ((bip<float>*)file)->sift((float*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
884
  			else if (header.data_type == envi_header::float64)
814eb271   David Mayerich   fixed problems wi...
885
  				return ((bip<double>*)file)->sift((double*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
886
887
888
889
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
3d0b6243   David Mayerich   fixed hsiproc bug...
890
891
  		}
  		if (header.interleave == envi_header::BIL){
ba51ae6a   David Mayerich   fixed metric calc...
892
  			if (header.data_type == envi_header::float32)
814eb271   David Mayerich   fixed problems wi...
893
  				return ((bil<float>*)file)->sift((float*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
894
  			else if (header.data_type == envi_header::float64)
814eb271   David Mayerich   fixed problems wi...
895
  				return ((bil<double>*)file)->sift((double*)matrix, p, PROGRESS);
ba51ae6a   David Mayerich   fixed metric calc...
896
897
898
899
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
3d0b6243   David Mayerich   fixed hsiproc bug...
900
  		}
43dec788   David Mayerich   added code for si...
901
902
903
904
  		return false;
  
  	}
  
3d0b6243   David Mayerich   fixed hsiproc bug...
905
  	/// Saves in an array only those spectra corresponding to nonzero values of the mask.
43dec788   David Mayerich   added code for si...
906
907
  	/// @param outfile is the name of the sifted output file
  	/// @param p is the mask
c1078e19   David Mayerich   HSIproc bug fixes...
908
  	bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false)
e843658b   Brad Deutsch   Previous push did...
909
910
  	{
  
2fcab4f0   David Mayerich   added unsifting f...
911
  		//calculate the number of non-zero values in the mask
9d3ba0b1   David Mayerich   added stim::hsi a...
912
913
914
  		unsigned long long nnz = 0;
  		unsigned long long npixels = header.lines * header.samples;
  		for(unsigned long long i = 0; i < npixels; i++)
2fcab4f0   David Mayerich   added unsifting f...
915
916
917
918
919
  			if( p[i] > 0 ) nnz++;
  
  		//create a new header
  		envi_header new_header = header;
  
f7e99517   David Mayerich   added sifting for...
920
921
  		//if a BIL file is sifted, it's saved as a BIP
  		if(header.interleave == envi_header::BIL)
f92397d2   David Mayerich   fixed a Win32 bug...
922
  			new_header.interleave = envi_header::BIP;
f7e99517   David Mayerich   added sifting for...
923
  
2fcab4f0   David Mayerich   added unsifting f...
924
925
926
927
928
  		//set the number of lines to 1 (this is a matrix with 1 line and N samples)
  		new_header.lines = 1;
  		new_header.samples = nnz;
  		new_header.save(outfile + ".hdr");
  
e843658b   Brad Deutsch   Previous push did...
929
930
  		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
c1078e19   David Mayerich   HSIproc bug fixes...
931
  				return ((bsq<float>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
932
  			else if (header.data_type == envi_header::float64)
c1078e19   David Mayerich   HSIproc bug fixes...
933
  				return ((bsq<double>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
934
935
936
937
938
939
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  
  		else if (header.interleave == envi_header::BIL){		//if the infile is bil file
  			if (header.data_type == envi_header::float32)
c1078e19   David Mayerich   HSIproc bug fixes...
940
  				return ((bil<float>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
941
  			else if (header.data_type == envi_header::float64)
c1078e19   David Mayerich   HSIproc bug fixes...
942
  				return ((bil<double>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
943
944
945
946
947
948
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  
  		else if (header.interleave == envi_header::BIP){		//if the infile is bip file
  			if (header.data_type == envi_header::float32)
c1078e19   David Mayerich   HSIproc bug fixes...
949
  				return ((bip<float>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
950
  			else if (header.data_type == envi_header::float64)
c1078e19   David Mayerich   HSIproc bug fixes...
951
  				return ((bip<double>*)file)->sift(outfile, p, PROGRESS);
e843658b   Brad Deutsch   Previous push did...
952
953
954
955
956
957
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  
  		else{
  			std::cout << "ERROR: unidentified file type" << std::endl;
4a6f666c   heziqi   Added mask method
958
959
  			exit(1);
  		}
4a6f666c   heziqi   Added mask method
960
  		return false;
cacc3cdc   heziqi   attempt to fix CImg
961
962
  	}
  
a2bf1d08   David Mayerich   general bug fixes...
963
  	bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
2fcab4f0   David Mayerich   added unsifting f...
964
965
966
967
968
969
970
971
972
973
974
975
  
  		//create a new header
  		envi_header new_header = header;
  
  		//set the number of lines and samples in the output file (that's all that changes)
  		new_header.lines = lines;
  		new_header.samples = samples;
  		new_header.save(outfile + ".hdr");
  
  
  		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
a2bf1d08   David Mayerich   general bug fixes...
976
  				return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
2fcab4f0   David Mayerich   added unsifting f...
977
  			else if (header.data_type == envi_header::float64)
a2bf1d08   David Mayerich   general bug fixes...
978
  				return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
2fcab4f0   David Mayerich   added unsifting f...
979
980
981
982
983
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
  		}
  
  		else if (header.interleave == envi_header::BIL){		//if the infile is bil file
f92397d2   David Mayerich   fixed a Win32 bug...
984
  
2fcab4f0   David Mayerich   added unsifting f...
985
986
987
988
  				std::cout << "ERROR in stim::envi::unsift - BIL files aren't supported yet" << std::endl;
  		}
  
  		else if (header.interleave == envi_header::BIP){		//if the infile is bip file
f92397d2   David Mayerich   fixed a Win32 bug...
989
  
8550e94f   David Mayerich   added sifting and...
990
  			if (header.data_type == envi_header::float32)
a2bf1d08   David Mayerich   general bug fixes...
991
  				return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
8550e94f   David Mayerich   added sifting and...
992
  			else if (header.data_type == envi_header::float64)
a2bf1d08   David Mayerich   general bug fixes...
993
  				return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
8550e94f   David Mayerich   added sifting and...
994
995
  			else
  				std::cout << "ERROR: unidentified data type" << std::endl;
2fcab4f0   David Mayerich   added unsifting f...
996
997
998
999
  		}
  
  		else{
  			std::cout << "ERROR: unidentified file type" << std::endl;
2fcab4f0   David Mayerich   added unsifting f...
1000
  		}
cbce396e   David Mayerich   added support for...
1001
  		return 0;
2fcab4f0   David Mayerich   added unsifting f...
1002
1003
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1004
1005
1006
1007
1008
1009
1010
1011
1012
  	/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
  
  	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
  	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
  	/// @param pos1 is the label value for the first peak (numerator) position
  	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
  	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
  	/// @param pos2 is the label value for the second peak (denominator) position
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
ba51ae6a   David Mayerich   fixed metric calc...
1013
  	bool ph_to_ph(void * result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask){
20c212c0   heziqi   Ziqi added functi...
1014
1015
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1016
  				return ((bsq<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
1017
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1018
  				return ((bsq<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
1019
1020
1021
1022
1023
1024
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1025
  				return ((bil<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
1026
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1027
  				return ((bil<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
1028
1029
1030
1031
1032
1033
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1034
  				return ((bip<float>*)file)->ph_to_ph((float*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
20c212c0   heziqi   Ziqi added functi...
1035
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1036
  				return ((bip<double>*)file)->ph_to_ph((double*)result, lb1, rb1, pos1, lb2, rb2, pos2, mask);
70407ea9   heziqi   Ziqi completed he...
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1048
1049
1050
1051
1052
1053
1054
1055
1056
  	/// Compute the ratio between a peak area and peak height.
  
  	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
  	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
  	/// @param pos1 is the label value for the first peak (numerator) position
  	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
  	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
  	/// @param pos2 is the label value for the second peak (denominator) position
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
ba51ae6a   David Mayerich   fixed metric calc...
1057
  	bool pa_to_ph(void* result, double lb1, double rb1, double lab1, double rab1, double lb2, double rb2, double pos, unsigned char* mask = NULL){
70407ea9   heziqi   Ziqi completed he...
1058
1059
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1060
  				return ((bsq<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1061
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1062
  				return ((bsq<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1063
1064
1065
1066
1067
1068
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1069
  				return ((bil<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1070
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1071
  				return ((bil<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1072
1073
1074
1075
1076
1077
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1078
  				return ((bip<float>*)file)->pa_to_ph((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1079
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1080
  				return ((bip<double>*)file)->pa_to_ph((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, pos, mask);
70407ea9   heziqi   Ziqi completed he...
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1092
1093
1094
1095
1096
1097
1098
1099
1100
  	/// Compute the ratio between two peak areas.
  
  	/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
  	/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
  	/// @param lab1 is the label value for the left bound (start of the integration) of the first peak (numerator)
  	/// @param rab1 is the label value for the right bound (end of the integration) of the first peak (numerator)
  	/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
  	/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
  	/// @param lab2 is the label value for the left bound (start of the integration) of the second peak (denominator)
f92397d2   David Mayerich   fixed a Win32 bug...
1101
  	/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
cb455f98   David Mayerich   removed old ENVI ...
1102
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
ba51ae6a   David Mayerich   fixed metric calc...
1103
1104
  	bool pa_to_pa(void* result, double lb1, double rb1, double lab1, double rab1,
  					double lb2, double rb2, double lab2, double rab2, unsigned char* mask = NULL){
70407ea9   heziqi   Ziqi completed he...
1105
1106
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1107
  				return ((bsq<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1108
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1109
  				return ((bsq<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1110
1111
1112
1113
1114
1115
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1116
  				return ((bil<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1117
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1118
  				return ((bil<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1119
1120
1121
1122
1123
1124
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1125
  				return ((bip<float>*)file)->pa_to_pa((float*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
70407ea9   heziqi   Ziqi completed he...
1126
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1127
  				return ((bip<double>*)file)->pa_to_pa((double*)result, lb1, rb1, lab1, rab1, lb2, rb2, lab2, rab2, mask);
20c212c0   heziqi   Ziqi added functi...
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1139
1140
1141
1142
1143
1144
1145
  	/// Compute the centroid of a baseline corrected peak.
  
  	/// @param lb is the label value for the left baseline point
  	/// @param rb is the label value for the right baseline point
  	/// @param lab is the label for the start of the peak
  	/// @param rab is the label for the end of the peak
  	/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
ba51ae6a   David Mayerich   fixed metric calc...
1146
  	bool centroid(void* result, double lb1, double rb1, double lab1, double rab1, unsigned char* mask = NULL){
517876d6   heziqi   metrics finished ...
1147
1148
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1149
  				return ((bsq<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1150
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1151
  				return ((bsq<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1152
1153
1154
1155
1156
1157
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIL){		//if the infile is bil file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1158
  				return ((bil<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1159
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1160
  				return ((bil<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1161
1162
1163
1164
1165
1166
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else if(header.interleave == envi_header::BIP){		//if the infile is bip file
  			if(header.data_type ==envi_header::float32)
ba51ae6a   David Mayerich   fixed metric calc...
1167
  				return ((bip<float>*)file)->centroid((float*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1168
  			else if(header.data_type == envi_header::float64)
ba51ae6a   David Mayerich   fixed metric calc...
1169
  				return ((bip<double>*)file)->centroid((double*)result, lb1, rb1, lab1, rab1, mask);
517876d6   heziqi   metrics finished ...
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
  			else
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  		}
  
  		else{
  			std::cout<<"ERROR: unidentified file type"<<std::endl;
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1181
  	/// Closes the ENVI file.
edb975b0   David Mayerich   created a stim::e...
1182
1183
  	void close(){
  		if(file == NULL) return;
6708cc25   heziqi   Ziqi added envi c...
1184
1185
  		if(header.interleave == envi_header::BSQ){
  			if(header.data_type ==envi_header::float32)
edb975b0   David Mayerich   created a stim::e...
1186
  				((bsq<float>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1187
  			else if(header.data_type == envi_header::float64)
edb975b0   David Mayerich   created a stim::e...
1188
  				((bsq<double>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1189
1190
1191
1192
1193
1194
1195
1196
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		else if(header.interleave == envi_header::BIL){
  			if(header.data_type ==envi_header::float32)
edb975b0   David Mayerich   created a stim::e...
1197
  				((bil<float>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1198
  			else if(header.data_type == envi_header::float64)
edb975b0   David Mayerich   created a stim::e...
1199
  				((bil<double>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1200
1201
1202
1203
1204
1205
1206
1207
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  
  		else if(header.interleave == envi_header::BIP){
  			if(header.data_type ==envi_header::float32)
edb975b0   David Mayerich   created a stim::e...
1208
  				((bip<float>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1209
  			else if(header.data_type == envi_header::float64)
edb975b0   David Mayerich   created a stim::e...
1210
  				((bip<double>*)file)->close();
6708cc25   heziqi   Ziqi added envi c...
1211
1212
1213
1214
1215
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
e8eb202f   David Mayerich   added a new ENVI ...
1216
  	}
cb455f98   David Mayerich   removed old ENVI ...
1217
1218
1219
1220
1221
  
  	/// Retrieve a single pixel and stores it in pre-allocated memory.
  
  	/// @param p is a pointer to pre-allocated memory at least sizeof(T) in size.
  	/// @param n is an integer index to the pixel using linear array indexing.
bfe9c6db   heziqi   added feature_mat...
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
  	bool pixel(void * p, unsigned n){
  		if(header.interleave == envi_header::BSQ){
  			if(header.data_type ==envi_header::float32)
  				return ((bsq<float>*)file)->pixel((float*)p, n);
  			else if(header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->pixel((double*)p, n);
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  		else if(header.interleave == envi_header::BIL){
  			if(header.data_type ==envi_header::float32)
  				return ((bil<float>*)file)->pixel((float*)p, n);
  			else if(header.data_type == envi_header::float64)
  				return ((bil<double>*)file)->pixel((double*)p, n);
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  		else if(header.interleave == envi_header::BIP){
  			if(header.data_type ==envi_header::float32)
  				return ((bip<float>*)file)->pixel((float*)p, n);
  			else if(header.data_type == envi_header::float64)
  				return ((bip<double>*)file)->pixel((double*)p, n);
  			else{
  				std::cout<<"ERROR: unidentified data type"<<std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
e8eb202f   David Mayerich   added a new ENVI ...
1255
  
cb455f98   David Mayerich   removed old ENVI ...
1256
  	/// Saves a header file describing the current ENVI file parameters.
e8eb202f   David Mayerich   added a new ENVI ...
1257
1258
1259
1260
1261
1262
1263
1264
  	bool save_header(std::string filename){
  
  		//save the header file here
  		header.save(filename);
  
  		return true;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1265
1266
1267
1268
  	/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
  
  	/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
  	/// @param wavelength is a floating point value (usually a wavelength in spectral data) used as a label for the band to be copied.
63fc1df8   David Mayerich   added an inverse ...
1269
  	bool band(void* ptr, double wavelength, bool PROGRESS = false){
d1d8ef91   David Mayerich   added band readin...
1270
1271
1272
  
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1273
  				return ((bsq<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1274
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1275
  				return ((bsq<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1276
1277
1278
1279
1280
1281
1282
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1283
  				return ((bil<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1284
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1285
  				return ((bil<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1286
1287
1288
1289
1290
1291
1292
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1293
  				return ((bip<float>*)file)->band((float*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1294
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1295
  				return ((bip<double>*)file)->band((double*)ptr, wavelength, PROGRESS);
081f2c9f   heziqi   made bip bil file...
1296
1297
1298
1299
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
d1d8ef91   David Mayerich   added band readin...
1300
  		}
ee4dea28   David Mayerich   fixed errors in c...
1301
  		return false;
1582ce07   David Mayerich   added band_index(...
1302
1303
  	}
  
735a2a24   David Mayerich   started testing o...
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
  	// Retrieve a spectrum at the specified 1D location
  
  	/// @param ptr is a pointer to pre-allocated memory of size B*sizeof(T)
  	/// @param x is the 1D coordinate of the spectrum
  	template<typename T>
  	void spectrum(T* ptr, size_t n, bool PROGRESS = false){
  
  		void* temp = alloc_array(header.bands);		//allocate space for the output array
  
  		if(header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if(header.data_type ==envi_header::float32){
  				((bsq<float>*)file)->spectrum((float*)temp, n, PROGRESS);
  				cast<T, float>(ptr, (float*)temp, header.bands);
  			}
  			else if (header.data_type == envi_header::float64){
  				((bsq<double>*)file)->spectrum((double*)temp, n, PROGRESS);
  				cast<T, double>(ptr, (double*)temp, header.bands);
  			}
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32){
  				((bil<float>*)file)->spectrum((float*)temp, n, PROGRESS);
  				cast<T, float>(ptr, (float*)temp, header.bands);
  			}
  			else if (header.data_type == envi_header::float64){
  				((bil<double>*)file)->spectrum((double*)temp, n, PROGRESS);
  				cast<T, double>(ptr, (double*)temp, header.bands);
  			}
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32){
  				((bip<float>*)file)->spectrum((float*)temp, n, PROGRESS);
d4aa4cf7   David Mayerich   fixed the in-memo...
1344
  				float test = ((float*)temp)[0];
735a2a24   David Mayerich   started testing o...
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
  				cast<T, float>(ptr, (float*)temp, header.bands);
  			}
  			else if (header.data_type == envi_header::float64){
  				((bip<double>*)file)->spectrum((double*)temp, n, PROGRESS);
  				cast<T, double>(ptr, (double*)temp, header.bands);
  			}
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  	}
  
  	/// Retrieve a spectrum from the specified (x, y) location
  
  	/// @param ptr is a pointer to pre-allocated memory of size B*sizeof(T)
  	/// @param x is the x-coordinate of the spectrum
  	/// @param y is the y-coordinate of the spectrum
  	template<typename T>
d0ef98e3   David Mayerich   fixed a Linux com...
1364
  	void spectrum(T* ptr, size_t x, size_t y, bool PROGRESS = false){
735a2a24   David Mayerich   started testing o...
1365
  
c4dd399a   David Mayerich   fixed a Linux com...
1366
  		spectrum<T>(ptr, y * header.samples + x, PROGRESS);
724ec347   David Mayerich   simplified the EN...
1367
1368
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1369
1370
1371
1372
  	/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
  
  	/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
  	/// @param page <= B is the integer number of the band to be copied.
9d3ba0b1   David Mayerich   added stim::hsi a...
1373
  	bool band_index(void* ptr, unsigned long long b){
081f2c9f   heziqi   made bip bil file...
1374
1375
  		if (header.interleave == envi_header::BSQ){		//if the infile is bsq file
  			if (header.data_type == envi_header::float32)
1582ce07   David Mayerich   added band_index(...
1376
  				return ((bsq<float>*)file)->band_index((float*)ptr, b);
081f2c9f   heziqi   made bip bil file...
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
  			else if (header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->band_index((double*)ptr, b);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
  				return ((bil<float>*)file)->band_index((float*)ptr, b);
  			else if (header.data_type == envi_header::float64)
  				return ((bil<double>*)file)->band_index((double*)ptr, b);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				return ((bip<float>*)file)->band_index((float*)ptr, b);
  			else if (header.data_type == envi_header::float64)
  				return ((bip<double>*)file)->band_index((double*)ptr, b);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
1582ce07   David Mayerich   added band_index(...
1403
1404
  		}
  		return false;
d1d8ef91   David Mayerich   added band readin...
1405
  	}
f92397d2   David Mayerich   fixed a Win32 bug...
1406
  
cb455f98   David Mayerich   removed old ENVI ...
1407
1408
1409
1410
  	/// Calculate the mean value for all masked (or valid) pixels in a band and returns the average spectrum
  
  	/// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
  	/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
35a7195f   David Mayerich   added median spec...
1411
  	bool mean_spectrum(double * p, double* std, unsigned char* mask, bool PROGRESS = false){
a43c4fe1   heziqi   Added crop in env...
1412
1413
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
35a7195f   David Mayerich   added median spec...
1414
  				return ((bsq<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1415
  			else if (header.data_type == envi_header::float64)
35a7195f   David Mayerich   added median spec...
1416
  				return ((bsq<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1417
1418
1419
1420
1421
1422
1423
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
35a7195f   David Mayerich   added median spec...
1424
  				return ((bil<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1425
  			else if (header.data_type == envi_header::float64)
35a7195f   David Mayerich   added median spec...
1426
  				return ((bil<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1427
1428
1429
1430
1431
1432
1433
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
35a7195f   David Mayerich   added median spec...
1434
  				return ((bip<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1435
  			else if (header.data_type == envi_header::float64)
35a7195f   David Mayerich   added median spec...
1436
  				return ((bip<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1437
1438
1439
1440
1441
1442
1443
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
e8eb202f   David Mayerich   added a new ENVI ...
1444
  
35a7195f   David Mayerich   added median spec...
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
  	/// Calculate the mean value for all masked (or valid) pixels in a band and returns the average spectrum
  
  	/// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
  	/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
  	bool median_spectrum(double* m, unsigned char* mask, bool PROGRESS = false){
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				return ((bsq<float>*)file)->median_spectrum(m, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->median_spectrum(m, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else{
  			std::cout<<"ERROR: median calculation is only supported for BSQ interleave types. Convert to process."<<std::endl;
  			exit(1);
  		}
  		return false;
  	}
  
cb455f98   David Mayerich   removed old ENVI ...
1467
1468
1469
1470
1471
  	/// Calculate the covariance matrix for all masked pixels in the image.
  
  	/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
  	/// @param avg is a pointer to memory of size B that stores the average spectrum
  	/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
dd5aab2f   David Mayerich   fixed errors in s...
1472
  	bool co_matrix(double* co, double* avg, unsigned char* mask, int cuda_device, bool PROGRESS = false){
a43c4fe1   heziqi   Added crop in env...
1473
  		if (header.interleave == envi_header::BSQ){
63fc1df8   David Mayerich   added an inverse ...
1474
1475
  			std::cout<<"ERROR: calculating the covariance matrix for a BSQ file is impractical; convert to BIL or BIP first"<<std::endl;
  			exit(1);
a43c4fe1   heziqi   Added crop in env...
1476
1477
1478
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
dd5aab2f   David Mayerich   fixed errors in s...
1479
  				return ((bil<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1480
  			else if (header.data_type == envi_header::float64)
dd5aab2f   David Mayerich   fixed errors in s...
1481
  				return ((bil<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1482
1483
1484
1485
1486
1487
1488
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
dd5aab2f   David Mayerich   fixed errors in s...
1489
  				return ((bip<float>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1490
  			else if (header.data_type == envi_header::float64)
dd5aab2f   David Mayerich   fixed errors in s...
1491
  				return ((bip<double>*)file)->co_matrix(co, avg, mask, cuda_device, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1492
1493
1494
1495
1496
1497
1498
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
0df38ff3   heziqi   fixed head detached
1499
  
334547d8   sam   changes for mnf: ...
1500
1501
1502
1503
1504
  	/// Calculate the covariance of noise matrix for all masked pixels in the image.
  
  	/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
  	/// @param avg is a pointer to memory of size B that stores the average spectrum
  	/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
dd5aab2f   David Mayerich   fixed errors in s...
1505
  	bool coNoise_matrix(double* coN, double* avg, unsigned char* mask, int cuda_device = 0, bool PROGRESS = false){
334547d8   sam   changes for mnf: ...
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
  		if (header.interleave == envi_header::BSQ){
  			std::cout<<"ERROR: calculating the covariance matrix of noise for a BSQ file is impractical; convert to BIP first"<<std::endl;
  			exit(1);
  		}
  
  
  		else if (header.interleave == envi_header::BIL){
  		        std::cout<<"ERROR: calculating the covariance matrix of noise for a BIL file is impractical; convert to BIP first"<<std::endl;
                  exit(1);
  			 }
  
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
dd5aab2f   David Mayerich   fixed errors in s...
1519
  				return ((bip<float>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
334547d8   sam   changes for mnf: ...
1520
  			else if (header.data_type == envi_header::float64)
dd5aab2f   David Mayerich   fixed errors in s...
1521
  				return ((bip<double>*)file)->coNoise_matrix(coN, avg, mask, cuda_device, PROGRESS);
334547d8   sam   changes for mnf: ...
1522
1523
1524
1525
1526
1527
1528
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
e8eb202f   David Mayerich   added a new ENVI ...
1529
  
cb455f98   David Mayerich   removed old ENVI ...
1530
1531
1532
1533
1534
1535
1536
  	/// Crop a region of the image and save it to a new file.
  
  	/// @param outfile is the file name for the new cropped image
  	/// @param x0 is the lower-left x pixel coordinate to be included in the cropped image
  	/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
  	/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
  	/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
c8c976a9   David Mayerich   replaced CImg wit...
1537
1538
1539
1540
1541
1542
1543
1544
  	bool crop(std::string outfile,
  			  unsigned long long x0, 
  			  unsigned long long y0, 
  			  unsigned long long x1, 
  			  unsigned long long y1, 
  			  unsigned long long b0, 
  			  unsigned long long b1, 
  			  bool PROGRESS = false){
a43c4fe1   heziqi   Added crop in env...
1545
  
177c7863   David Mayerich   updated the ENVI ...
1546
1547
  		//save the header for the cropped file
  		stim::envi_header new_header = header;
f78ceb64   David Mayerich   fixed BIP croppin...
1548
1549
1550
  		new_header.samples = x1 - x0 + 1;
  		new_header.lines = y1 - y0 + 1;
  		new_header.bands = b1 - b0 + 1;
177c7863   David Mayerich   updated the ENVI ...
1551
  		std::vector<double>::const_iterator first = new_header.wavelength.begin() + b0;
f78ceb64   David Mayerich   fixed BIP croppin...
1552
  		std::vector<double>::const_iterator last = new_header.wavelength.begin() + b1 + 1;
177c7863   David Mayerich   updated the ENVI ...
1553
1554
1555
  		new_header.wavelength = std::vector<double>(first, last);
  		new_header.save(outfile + ".hdr");
  
a43c4fe1   heziqi   Added crop in env...
1556
1557
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1558
  				return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1559
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1560
  				return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1561
1562
1563
1564
1565
1566
1567
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1568
  				return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1569
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1570
  				return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1571
1572
1573
1574
1575
1576
1577
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
63fc1df8   David Mayerich   added an inverse ...
1578
  				return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1579
  			else if (header.data_type == envi_header::float64)
63fc1df8   David Mayerich   added an inverse ...
1580
  				return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1, PROGRESS);
a43c4fe1   heziqi   Added crop in env...
1581
1582
1583
1584
1585
1586
1587
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		return false;
  	}
0df38ff3   heziqi   fixed head detached
1588
  
bb61cb18   David Mayerich   added subimage fu...
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
  	void subimages(std::string outfile, size_t nx, size_t ny, unsigned char* mask, bool PROGRESS = false){
  		
  		size_t nnz = 0;													//initialize the number of subimages to zero
  		for(size_t i = 0; i < header.lines * header.samples; i++)		//for each pixel in the mask
  			if(mask[i]) nnz++;											//if the pixel is valid, add a subimage
  
  
  		//save the header for the cropped file
  		stim::envi_header new_header = header;
  		new_header.samples = nx;									//calculate the width of the output image (concatenated subimages)
  		new_header.lines = nnz * ny;											//calculate the height of the output image (height of subimages)
  		
  
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->subimages(outfile, nx, ny, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->subimages(outfile, nx, ny, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			std::cout << "ERROR: unidentified data type" << std::endl;
  			exit(1);
  		}
  		else if (header.interleave == envi_header::BIP){
  			std::cout << "ERROR: unidentified data type" << std::endl;
  			exit(1);
  		}
  
  		new_header.save(outfile + ".hdr");									//save the header for the output file
  	}
  
dc8eb8aa   David Mayerich   added band trimmi...
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
1650
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
  	/// Remove a list of bands from the ENVI file
  
  	/// @param outfile is the file name for the output hyperspectral image (with trimmed bands)
  	/// @param b is an array of bands to be eliminated
  	void trim(std::string outfile, std::vector<size_t> trimmed, bool PROGRESS = false){
  		
  		envi_header h = header;
  		h.bands = header.bands - trimmed.size();			//calculate the new number of bands
  		if(header.wavelength.size() != 0)
  			h.wavelength.resize(h.bands);
  		if(header.band_names.size() != 0)
  			h.band_names.resize(h.bands);
  		size_t it = 0;									//allocate an index into the trimmed bands array
  		size_t i = 0;
  		for(size_t b = 0; b < header.bands; b++){		//for each band
  			if(b != trimmed[it]){
  				if(h.wavelength.size()) h.wavelength[i] = header.wavelength[b];
  				if(h.band_names.size()) h.band_names[i] = header.band_names[i];
  				i++;
  			}
  			else it++;
  		}
  		h.save(outfile + ".hdr");
  
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				return ((bsq<float>*)file)->trim(outfile, trimmed, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bsq<double>*)file)->trim(outfile, trimmed, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
  				return ((bil<float>*)file)->trim(outfile, trimmed, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bil<double>*)file)->trim(outfile, trimmed, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				return ((bip<float>*)file)->trim(outfile, trimmed, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				return ((bip<double>*)file)->trim(outfile, trimmed, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		
  
  	}
  
2ce6954b   David Mayerich   added the ability...
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
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
  	/// Combine two ENVI images along the Y axis
  
  	/// @param outfile is the combined file to be output
  	/// @param C is the ENVI object for the image to be combined
  	void combine(std::string outfile, envi C, long long x, long long y, bool PROGRESS = false){
  		envi_header h = header;
  		
  		long long left = std::min<long long>(0, x);													//calculate the left edge of the final image
  		long long right = std::max<long long>((long long)header.samples, C.header.samples + x);		//calculate the right edge of the final image
  		long long top = std::min<long long>(0, y);													//calculate the top edge of the final image
  		long long bottom = std::max<long long>((long long)header.lines, C.header.lines + y);		//calculate the bottom edge of the final image
  
  		h.samples = right - left;
  		h.lines = bottom - top;
  	
  		h.save(outfile + ".hdr");
  
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->combine(outfile, (bsq<float>*)C.file, x, y, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->combine(outfile, (bsq<double>*)C.file, x, y, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
  				((bil<float>*)file)->combine(outfile, (bil<float>*)C.file, x, y, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bil<double>*)file)->combine(outfile, (bil<double>*)C.file, x, y, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				((bip<float>*)file)->combine(outfile, (bip<float>*)C.file, x, y, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bip<double>*)file)->combine(outfile, (bip<double>*)C.file, x, y, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  	}
9b2a5d71   David Mayerich   implemented finit...
1730
  
82a7c08c   David Mayerich   added an append c...
1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
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
1790
1791
  	void append(std::string outfile, envi C, bool PROGRESS = false) {
  		if (C.header.samples != header.samples ||									//verify that the images are the same size
  			C.header.lines != header.lines) {
  			std::cout << "ERROR - appended images must be the same size: input = [" << header.samples << " x " << header.lines << "], output = [" << C.header.samples << " x " << C.header.lines << "]" << std::endl;
  			exit(1);
  		}
  		if (C.header.interleave != header.interleave) {
  			std::cout << "ERROR - appended images must have the same interleave format" << std::endl;
  			exit(1);
  		}
  
  		stim::envi_header new_header = header;												//create a header for the output image
  		new_header.bands = header.bands + C.header.bands;									//calculate the number of bands in the new image
  
  		if (header.wavelength.size() != 0 && C.header.wavelength.size() != 0) {				//if both files contain wavelength information
  			for (size_t b = 0; b < C.header.wavelength.size(); b++)
  				new_header.wavelength.push_back(C.header.wavelength[b]);					//append the wavelength labels to the new header array
  		}
  		else new_header.wavelength.clear();
  
  		if (header.band_names.size() != 0 && C.header.band_names.size() != 0) {				//if both files contain band name information
  			for (size_t b = 0; b < C.header.band_names.size(); b++)
  				new_header.band_names.push_back(C.header.band_names[b]);					//append the wavelength labels to the new header array
  		}
  		else new_header.wavelength.clear();
  
  		new_header.save(outfile + ".hdr");													//save the output
  
  		if (header.interleave == envi_header::BSQ) {
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->append(outfile, (bsq<float>*)C.file, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->append(outfile, (bsq<double>*)C.file, PROGRESS);
  			else {
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL) {
  			if (header.data_type == envi_header::float32)
  				((bil<float>*)file)->append(outfile, (bil<float>*)C.file, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bil<double>*)file)->append(outfile, (bil<double>*)C.file, PROGRESS);
  			else {
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP) {
  			if (header.data_type == envi_header::float32)
  				((bip<float>*)file)->append(outfile, (bip<float>*)C.file, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bip<double>*)file)->append(outfile, (bip<double>*)C.file, PROGRESS);
  			else {
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  	}
  
9b2a5d71   David Mayerich   implemented finit...
1792
1793
1794
1795
1796
1797
1798
  	/// Convolve the given band range with a kernel specified by a vector of coefficients.
  
  	/// @param outfile is the combined file to be output
  	/// @param c is an array of coefficients
  	/// @param start is the band to start processing (the first coefficient starts here)
  	/// @param nbands is the number of bands to process
  	/// @param center is the index for the center coefficient for the kernel (used to set the wavelengths in the output file)
9d77bbd9   David Mayerich   updates for HSIvi...
1799
  	void convolve(std::string outfile, std::vector<double> C, size_t start, size_t end, size_t center = 0, unsigned char* mask = NULL, bool PROGRESS = false){
9b2a5d71   David Mayerich   implemented finit...
1800
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
  		size_t nbands = end - start + 1;
  		envi_header h = header;												//copy the current header
  		h.bands = nbands;													//set the number of new bands
  		if(header.wavelength.size() != 0){
  			h.wavelength.resize(nbands);									//set the number of wavelengths to the number of bands
  			for(size_t b = 0; b < nbands; b++)
  				h.wavelength[b] = header.wavelength[b+center];
  		}
  		if(header.band_names.size() != 0){
  			h.band_names.resize(nbands);
  			for(size_t b = 0; b < nbands; b++)
  				h.band_names[b] = header.band_names[b+center];
  		}
  		h.save(outfile + ".hdr");											//save the new header
  
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1817
  				((bsq<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1818
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1819
  				((bsq<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1820
1821
1822
1823
1824
1825
1826
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1827
  				((bil<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1828
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1829
  				((bil<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1830
1831
1832
1833
1834
1835
1836
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1837
  				((bip<float>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1838
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1839
  				((bip<double>*)file)->convolve(outfile, C, start, end, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1840
1841
1842
1843
1844
1845
1846
1847
1848
1849
1850
1851
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  	}
  
  	/// Approximates the nth derivative of the spectra to the specified order
  
  	/// @param outfile is the file where the derivative approximation will be saved
  	/// @n is the derivative to be calculated
  	/// @order is the order of the error (must be even)
9d77bbd9   David Mayerich   updates for HSIvi...
1852
  	void deriv(std::string outfile, size_t d, size_t order, unsigned char* mask = NULL, bool PROGRESS = false){
9b2a5d71   David Mayerich   implemented finit...
1853
1854
1855
  		header.save(outfile + ".hdr");
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1856
  				((bsq<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1857
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1858
  				((bsq<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1859
1860
1861
1862
1863
1864
1865
1866
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1867
  				((bil<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1868
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1869
  				((bil<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1870
1871
1872
1873
1874
1875
1876
1877
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
9d77bbd9   David Mayerich   updates for HSIvi...
1878
  				((bip<float>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1879
  			else if (header.data_type == envi_header::float64)
9d77bbd9   David Mayerich   updates for HSIvi...
1880
  				((bip<double>*)file)->deriv(outfile, d, order, header.wavelength, mask, PROGRESS);
9b2a5d71   David Mayerich   implemented finit...
1881
1882
1883
1884
1885
1886
1887
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		exit(1);
  	}
278c622b   David Mayerich   finished Windows ...
1888
1889
1890
1891
1892
1893
1894
1895
1896
1897
1898
1899
1900
1901
1902
1903
1904
1905
1906
1907
1908
1909
1910
1911
1912
1913
1914
1915
1916
1917
1918
1919
1920
1921
1922
1923
1924
1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
1936
1937
1938
1939
1940
1941
1942
1943
1944
1945
1946
1947
1948
1949
1950
1951
1952
1953
1954
1955
1956
1957
1958
1959
1960
1961
  
  	void multiply(std::string outfile, double v, unsigned char* mask = NULL, bool PROGRESS = false){
  		header.save(outfile + ".hdr");
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
  				((bil<float>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bil<double>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				((bip<float>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bip<double>*)file)->multiply(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		exit(1);
  	}
  
  	void add(std::string outfile, double v, unsigned char* mask = NULL, bool PROGRESS = false){
  		header.save(outfile + ".hdr");
  		if (header.interleave == envi_header::BSQ){
  			if (header.data_type == envi_header::float32)
  				((bsq<float>*)file)->add(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bsq<double>*)file)->add(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIL){
  			if (header.data_type == envi_header::float32)
  				((bil<float>*)file)->add(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bil<double>*)file)->add(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  
  		else if (header.interleave == envi_header::BIP){
  			if (header.data_type == envi_header::float32)
  				((bip<float>*)file)->add(outfile, v, mask, PROGRESS);
  			else if (header.data_type == envi_header::float64)
  				((bip<double>*)file)->add(outfile, v, mask, PROGRESS);
  			else{
  				std::cout << "ERROR: unidentified data type" << std::endl;
  				exit(1);
  			}
  		}
  		exit(1);
  	}
9d34229e   David Mayerich   restructured the ...
1962
1963
1964
1965
1966
  
  	
  
  
  	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...
1967
  		if(samples == 0) samples = header.bands;
9d34229e   David Mayerich   restructured the ...
1968
1969
1970
1971
1972
1973
1974
1975
1976
1977
1978
1979
1980
1981
  		double B = (double)header.bands;
  		double delta = header.wavelength[1] - header.wavelength[0];					//calculate spacing in the current domain
  		double span = samples * delta;											//calculate the span in the current domain
  		double fft_delta = 1.0 / span;												//calculate the span in the FFT domain
  		double fft_max = fft_delta * samples/2;										//calculate the maximum range of the FFT
  
  		if(band_max > fft_max) band_max = fft_max;									//the user gave a band outside of the FFT range, reset the band to the maximum available
  		size_t start_i = (size_t)std::ceil(band_min / fft_delta);					//calculate the first band to store
  		size_t size_i = (size_t)std::floor(band_max / fft_delta) - start_i + 1;		//calculate the number of bands to store
  		size_t end_i = start_i + size_i - 1;										//last band number
  
  		envi_header new_header = header;
  		new_header.bands = size_i;
  		new_header.set_wavelengths(start_i * fft_delta, fft_delta);
6e9cf1ac   David Mayerich   fixed image bug i...
1982
  		new_header.wavelength_units = "inv_" + header.wavelength_units;
9d34229e   David Mayerich   restructured the ...
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
  		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 ...
2000
  };	//end ENVI
e8eb202f   David Mayerich   added a new ENVI ...
2001
2002
2003
2004
  
  }	//end namespace rts
  
  #endif