e8eb202f
David Mayerich
added a new ENVI ...
|
1
2
3
4
|
#ifndef STIM_BSQ_H
#define STIM_BSQ_H
#include "../envi/envi_header.h"
|
3fc1d461
heziqi
Ziqi added saveBa...
|
5
|
#include "../envi/binary.h"
|
e8eb202f
David Mayerich
added a new ENVI ...
|
6
|
#include "../envi/bil.h"
|
fc712213
David Mayerich
code simplifications
|
7
8
|
#include <cstring>
#include <utility>
|
e8eb202f
David Mayerich
added a new ENVI ...
|
9
|
#include <vector>
|
3fc1d461
heziqi
Ziqi added saveBa...
|
10
11
12
13
14
15
16
17
18
|
namespace rts{
template <typename T>
class bsq: public binary<T> {
protected:
|
e8eb202f
David Mayerich
added a new ENVI ...
|
19
20
21
|
//envi_header header;
std::vector<double> w; //band wavelengths
|
6708cc25
heziqi
Ziqi added envi c...
|
22
|
unsigned int offset;
|
3fc1d461
heziqi
Ziqi added saveBa...
|
23
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
24
25
|
public:
|
fc712213
David Mayerich
code simplifications
|
26
27
28
|
using binary<T>::open;
using binary<T>::file;
using binary<T>::getSlice;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
29
|
using binary<T>::R;
|
fc712213
David Mayerich
code simplifications
|
30
|
|
e933c14e
David Mayerich
cleaned up the code
|
31
|
//open a file, given the file name and dimensions
|
e8eb202f
David Mayerich
added a new ENVI ...
|
32
|
bool open(std::string filename, unsigned int X, unsigned int Y, unsigned int B, unsigned int header_offset, std::vector<double> wavelengths){
|
3fc1d461
heziqi
Ziqi added saveBa...
|
33
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
34
35
|
//copy the wavelengths to the BSQ file structure
w = wavelengths;
|
6708cc25
heziqi
Ziqi added envi c...
|
36
37
|
//copy the wavelengths to the structure
offset = header_offset;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
38
39
40
41
|
return open(filename, vec<unsigned int>(X, Y, B), header_offset);
return false;
|
3fc1d461
heziqi
Ziqi added saveBa...
|
42
43
44
|
}
|
e933c14e
David Mayerich
cleaned up the code
|
45
|
//retrieve one band (specified by the band index)
|
0e48cc9c
heziqi
Ziqi added getBan...
|
46
|
bool band_index( T * p, unsigned int page){
|
3fc1d461
heziqi
Ziqi added saveBa...
|
47
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
48
|
if (page >= R[2]){ //make sure the bank number is right
|
3fc1d461
heziqi
Ziqi added saveBa...
|
49
50
51
52
|
std::cout<<"ERROR: page out of range"<<std::endl;
return false;
}
|
31394e2a
heziqi
Ziqi added method...
|
53
|
getSlice(p, 2, page);
|
3fc1d461
heziqi
Ziqi added saveBa...
|
54
55
56
|
return true;
}
|
e933c14e
David Mayerich
cleaned up the code
|
57
58
|
//retrieve one band (specified by the wavelength)
bool band( T * p, double wavelength){
|
0e48cc9c
heziqi
Ziqi added getBan...
|
59
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
60
|
unsigned int XY = R[0] * R[1]; //calculate the number of pixels in a band
|
0e48cc9c
heziqi
Ziqi added getBan...
|
61
62
63
64
65
66
67
68
|
unsigned page=0; //bands around the wavelength
T * p1;
T * p2;
//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
|
e8eb202f
David Mayerich
added a new ENVI ...
|
69
|
if ( w[page] > wavelength ){
|
0e48cc9c
heziqi
Ziqi added getBan...
|
70
71
72
73
|
band_index(p, page);
return true;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
74
|
while( w[page] < wavelength )
|
0e48cc9c
heziqi
Ziqi added getBan...
|
75
76
77
|
{
page++;
//if wavelength is larger than the last wavelength in header file
|
e8eb202f
David Mayerich
added a new ENVI ...
|
78
79
|
if (page == R[2]) {
getSlice(p, 2, R[2]-1);
|
0e48cc9c
heziqi
Ziqi added getBan...
|
80
81
82
|
return true;
}
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
83
|
if ( wavelength < w[page] )
|
0e48cc9c
heziqi
Ziqi added getBan...
|
84
85
86
87
88
89
|
{
p1=(T*)malloc( XY * sizeof(T)); //memory allocation
p2=(T*)malloc( XY * sizeof(T));
band_index(p1, page - 1);
band_index(p2, page );
for(unsigned i=0; i < XY; i++){
|
e8eb202f
David Mayerich
added a new ENVI ...
|
90
|
double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
|
0e48cc9c
heziqi
Ziqi added getBan...
|
91
92
93
94
95
96
97
98
|
p[i] = (p2[i] - p1[i]) * r + p1[i];
}
}
else //if the wavelength is equal to a wavelength in header file
{
getSlice(p, 2, page);
}
|
0e48cc9c
heziqi
Ziqi added getBan...
|
99
100
101
|
return true;
}
|
3fc1d461
heziqi
Ziqi added saveBa...
|
102
|
//save one pixel of the file into the memory, and return the pointer
|
e933c14e
David Mayerich
cleaned up the code
|
103
|
bool spectrum(T * p, unsigned x, unsigned y){
|
3fc1d461
heziqi
Ziqi added saveBa...
|
104
105
106
|
unsigned int i;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
107
|
if ( x >= R[0] || y >= R[1]){ //make sure the sample and line number is right
|
3fc1d461
heziqi
Ziqi added saveBa...
|
108
109
110
111
|
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
112
113
|
file.seekg((x + y * R[0]) * sizeof(T), std::ios::beg); //point to the certain sample and line
for (i = 0; i < R[3]; i++)
|
3fc1d461
heziqi
Ziqi added saveBa...
|
114
115
|
{
file.read((char *)(p + i), sizeof(T));
|
e8eb202f
David Mayerich
added a new ENVI ...
|
116
|
file.seekg((R[1] * R[0] - 1) * sizeof(T), std::ios::cur); //go to the next band
|
3fc1d461
heziqi
Ziqi added saveBa...
|
117
118
|
}
|
3fc1d461
heziqi
Ziqi added saveBa...
|
119
120
|
return true;
}
|
f0d5a769
heziqi
Ziqi changed the ...
|
121
122
123
124
125
126
|
//baseline correction and save it into file
bool baseline(std::string outname, std::vector<double> wls )
{
unsigned N = wls.size(); //get the number of baseline points
|
31394e2a
heziqi
Ziqi added method...
|
127
|
|
f0d5a769
heziqi
Ziqi changed the ...
|
128
|
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
|
0c748c81
heziqi
Ziqi added save h...
|
129
|
std::string headername = outname + ".hdr"; //the header file name
|
f0d5a769
heziqi
Ziqi changed the ...
|
130
131
|
//simplify image resolution
|
e8eb202f
David Mayerich
added a new ENVI ...
|
132
133
|
unsigned int B = R[2]; //calculate the number of bands
unsigned int XY = R[0] * R[1]; //calculate the number of pixels in a band
|
f0d5a769
heziqi
Ziqi changed the ...
|
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
|
unsigned int S = XY * sizeof(T); //calculate the number of bytes in a band
double ai, bi; //stores the two baseline points wavelength surrounding the current band
double ci; //stores the current band's wavelength
// unsigned aii, bii; //stores the two baseline points number surrounding the current band
unsigned control=0;
T * a; //pointers to the high and low band images
T * b;
T * c; //pointer to the current image
a = (T*)malloc( S ); //memory allocation
b = (T*)malloc( S );
c = (T*)malloc( S );
if (a == NULL || b == NULL || c == NULL){
std::cout<<"ERROR: error allocating memory";
exit(1);
}
//initialize lownum, highnum, low, high
|
e8eb202f
David Mayerich
added a new ENVI ...
|
156
|
ai=w[0];
|
f0d5a769
heziqi
Ziqi changed the ...
|
157
158
159
|
//if no baseline point is specified at band 0,
//set the baseline point at band 0 to 0
|
e8eb202f
David Mayerich
added a new ENVI ...
|
160
|
if(wls[0] != w[0]){
|
f0d5a769
heziqi
Ziqi changed the ...
|
161
162
163
164
165
166
|
bi = wls[control];
memset(a, (char)0, S);
}
//else get the low band
else{
control += 1;
|
e933c14e
David Mayerich
cleaned up the code
|
167
|
band(a, ai);
|
f0d5a769
heziqi
Ziqi changed the ...
|
168
169
170
|
bi = wls[control];
}
//get the high band
|
e933c14e
David Mayerich
cleaned up the code
|
171
|
band(b, bi);
|
f0d5a769
heziqi
Ziqi changed the ...
|
172
173
174
175
176
|
//correct every band
for(unsigned cii = 0; cii < B; cii++){
//update baseline points, if necessary
|
e8eb202f
David Mayerich
added a new ENVI ...
|
177
|
if( w[cii] >= bi && cii != B - 1) {
|
f0d5a769
heziqi
Ziqi changed the ...
|
178
179
180
181
182
183
184
185
186
|
//if the high band is now on the last BL point?
if (control != N-1) {
control++; //increment the index
std::swap(a, b); //swap the baseline band pointers
ai = bi;
bi = wls[control];
|
e933c14e
David Mayerich
cleaned up the code
|
187
|
band(b, bi);
|
f0d5a769
heziqi
Ziqi changed the ...
|
188
189
190
|
}
//if the last BL point on the last band of the file?
|
e8eb202f
David Mayerich
added a new ENVI ...
|
191
|
else if ( wls[control] < w[B - 1]) {
|
f0d5a769
heziqi
Ziqi changed the ...
|
192
193
194
195
196
197
|
std::swap(a, b); //swap the baseline band pointers
memset(b, (char)0, S); //clear the high band
ai = bi;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
198
|
bi = w[B - 1];
|
f0d5a769
heziqi
Ziqi changed the ...
|
199
200
201
202
203
|
}
}
//get the current band
band_index(c, cii);
|
e8eb202f
David Mayerich
added a new ENVI ...
|
204
|
ci = w[cii];
|
f0d5a769
heziqi
Ziqi changed the ...
|
205
206
207
208
|
//perform the baseline correction
for(unsigned i=0; i < XY; i++){
double r = (double) (ci - ai) / (double) (bi - ai);
|
92e4cf05
heziqi
include file fixed
|
209
|
c[i] =(T) ( c[i] - (b[i] - a[i]) * r - a[i] );
|
f0d5a769
heziqi
Ziqi changed the ...
|
210
211
212
213
214
|
}
target.write(reinterpret_cast<const char*>(c), S); //write the corrected data into destination
}
|
0c748c81
heziqi
Ziqi added save h...
|
215
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
216
|
//header.save(headername); //save the new header file
|
f0d5a769
heziqi
Ziqi changed the ...
|
217
218
219
220
221
222
223
|
free(a);
free(b);
free(c);
target.close();
return true;
}
|
089d9c81
heziqi
Ziqi added normal...
|
224
225
|
// normalize the BSQ file
|
e933c14e
David Mayerich
cleaned up the code
|
226
|
bool normalize(std::string outname, double w)
|
089d9c81
heziqi
Ziqi added normal...
|
227
|
{
|
e8eb202f
David Mayerich
added a new ENVI ...
|
228
229
|
unsigned int B = R[2]; //calculate the number of bands
unsigned int XY = R[0] * R[1]; //calculate the number of pixels in a band
|
089d9c81
heziqi
Ziqi added normal...
|
230
231
232
233
234
235
236
237
238
239
240
|
unsigned int S = XY * sizeof(T); //calculate the number of bytes in a band
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
T * b; //pointers to the certain wavelength band
T * c; //pointer to the current image
b = (T*)malloc( S ); //memory allocation
c = (T*)malloc( S );
|
e933c14e
David Mayerich
cleaned up the code
|
241
|
band(b, w); //get the certain band into memory
|
089d9c81
heziqi
Ziqi added normal...
|
242
243
244
245
246
247
248
249
250
251
252
|
for(unsigned j = 0; j < B; j++)
{
band_index(c, j); //get the current band into memory
for(unsigned i = 0; i < XY; i++)
{
c[i] = c[i] / b[i];
}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
253
|
//header.save(headername); //save the new header file
|
089d9c81
heziqi
Ziqi added normal...
|
254
255
256
257
258
259
|
free(b);
free(c);
target.close();
return true;
}
|
f0d5a769
heziqi
Ziqi changed the ...
|
260
|
|
421219ba
heziqi
Ziqi added bip.h ...
|
261
262
263
|
//convert BSQ file to BIP file and save it
bool bip(std::string outname)
{
|
f6169dea
heziqi
Ziqi completed bi...
|
264
265
266
267
268
269
|
std::string temp = outname + "_temp";
std::string headtemp = temp + ".hdr";
//first creat a temporary bil file and convert bsq file to bil file
bil(temp);
rts::bil<T> n;
|
e933c14e
David Mayerich
cleaned up the code
|
270
|
if(n.open(temp, R[0], R[1], R[2], offset, w)==false){ //open infile
|
f6169dea
heziqi
Ziqi completed bi...
|
271
272
|
std::cout<<"ERROR: unable to open input file"<<std::endl;
exit(1);
|
421219ba
heziqi
Ziqi added bip.h ...
|
273
|
}
|
f6169dea
heziqi
Ziqi completed bi...
|
274
275
276
277
278
|
//then convert bil file to bip file
n.bip(outname);
n.close();
remove(temp.c_str());
remove(headtemp.c_str());
|
421219ba
heziqi
Ziqi added bip.h ...
|
279
280
|
return true;
}
|
c25e7d0d
heziqi
speed of bip.base...
|
281
282
283
284
285
|
//convert BSQ file to BIL file and save it
bool bil(std::string outname)
{
//simplify image resolution
|
6708cc25
heziqi
Ziqi added envi c...
|
286
|
unsigned int L = R[0] * R[2] * sizeof(T); //calculate the number of bytes of a ZX slice
|
e8eb202f
David Mayerich
added a new ENVI ...
|
287
|
unsigned int jump = (R[1] - 1) * R[0] * sizeof(T);
|
c25e7d0d
heziqi
speed of bip.base...
|
288
289
290
291
292
293
294
|
std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
T * p; //pointer to the current spectrum
p = (T*)malloc(L);
|
e8eb202f
David Mayerich
added a new ENVI ...
|
295
|
for ( unsigned i = 0; i < R[1]; i++)
|
c25e7d0d
heziqi
speed of bip.base...
|
296
|
{
|
e8eb202f
David Mayerich
added a new ENVI ...
|
297
298
|
file.seekg(R[0] * i * sizeof(T), std::ios::beg);
for ( unsigned j = 0; j < R[2]; j++ )
|
c25e7d0d
heziqi
speed of bip.base...
|
299
|
{
|
e8eb202f
David Mayerich
added a new ENVI ...
|
300
|
file.read((char *)(p + j * R[0]), sizeof(T) * R[0]);
|
c25e7d0d
heziqi
speed of bip.base...
|
301
302
303
304
|
file.seekg(jump, std::ios::cur); //go to the next band
}
target.write(reinterpret_cast<const char*>(p), L); //write XZ slice data into target file
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
305
306
|
//header.interleave = rts::envi_header::BIL; //change the type of file in header file
//header.save(headername);
|
c25e7d0d
heziqi
speed of bip.base...
|
307
308
309
310
311
|
free(p);
target.close();
return true;
}
|
20c212c0
heziqi
Ziqi added functi...
|
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
|
//providing the left and the right bound data, return baseline-corrected band height
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
unsigned XY = R[0] * R[1];
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
for(unsigned i=0; i < XY; i++){
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
//untested
//providing the left and the right bound wavelength, return baseline-corrected band height
bool height(double lb, double rb, double bandwavelength){
T* lp;
T* rp;
T* result;
lp = (T*) malloc(sizeof(R[0] * R[1] * sizeof(T))); //memory allocation
rp = (T*) malloc(sizeof(R[0] * R[1] * sizeof(T)));
|
2b10d15c
David Mayerich
updated framework...
|
336
|
result = (T*) malloc(sizeof(R[0] * R[1] * sizeof(T)));
|
20c212c0
heziqi
Ziqi added functi...
|
337
338
339
340
341
342
343
344
345
|
band(lp, lb); //get the data of the left bounbd and the right bound
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
346
|
|
20c212c0
heziqi
Ziqi added functi...
|
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
|
//calculate the area between two bound point(including baseline correction)
bool area(double lb, double rb){
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
T* result; //area result
unsigned XY = R[0] * R[1];
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
result = (T*) malloc(S);
memset(result, (char)0, S);
//find the wavelenght position in the whole band
unsigned int n = w.size();
unsigned int ai = 0; //left bound position
unsigned int bi = n - 1; //right bound position
//to make sure the left and the right bound are in the bandwidth
if (lb < w[0] || rb < w[0] || lb > w[n-1] || rb >w[n-1]){
std::cout<<"ERROR: left bound or right bound out of bandwidth"<<std::endl;
exit(1);
}
//to make sure rigth bound is bigger than left bound
else if(lb > rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
exit(1);
}
//get the position of lb and rb
while (lb >= w[ai]){
ai++;
}
while (rb <= w[bi]){
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
baseline_band(lb, rb, lp, rp, w[bi], cur); //ending part
for(unsigned j = 0; j < XY; j++){
result[j] += (rb - w[bi]) * cur[j] / 2.0;
}
baseline_band(lb, rb, lp, rp, w[ai], cur); //beginnning part
for(unsigned j = 0; j < XY; j++){
result[j] += (w[ai] - lb) * cur[j] / 2.0;
}
//calculate the area
ai++;
for(unsigned i = ai; i <= bi ;i++)
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
for(unsigned j = 0; j < XY; j++)
{
result[j] += (w[ai] - w[ai-1]) * (cur[j] + cur2[j]) / 2.0;
}
std::swap(cur,cur2); //swap the band pointers
}
///////////////for testing use
std::ofstream text("area_result.txt",std::ios::out);
for (unsigned i = 0; i < 640; i++)
{
for (unsigned j = 0; j < 384; j++)
{
text<<result[i*384+j]<<", ";
}
text<<std::endl;
}
///////////////
return true;
}
|
4a6f666c
heziqi
Added mask method
|
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
|
//create mask file
bool mask(unsigned char* p, double mask_band, double threshold){
T* temp = (T*)malloc(R[0] * R[1] * sizeof(T)); //allocate memory for the certain band
band(temp, mask_band);
for (unsigned int i = 0; i < R[0] * R[1]; i++) {
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
}
return true;
}
|
f6169dea
heziqi
Ziqi completed bi...
|
447
448
449
450
451
|
//close the file
bool close(){
file.close();
return true;
}
|
31394e2a
heziqi
Ziqi added method...
|
452
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
453
454
|
};
}
|
31394e2a
heziqi
Ziqi added method...
|
455
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
456
457
|
#endif
|
fc712213
David Mayerich
code simplifications
|
458
|
|