bip.h
68.8 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
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
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
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
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
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
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
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
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
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
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
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
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
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
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
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
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
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
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
1682
1683
1684
1685
1686
1687
1688
1689
#ifndef STIM_BIP_H
#define STIM_BIP_H
#include "../envi/envi_header.h"
#include "../envi/bil.h"
#include "../envi/hsi.h"
#include <cstring>
#include <utility>
//CUDA
#ifdef CUDA_FOUND
#include <cuda_runtime.h>
#include "cublas_v2.h"
#endif
namespace stim{
/**
The BIP class represents a 3-dimensional binary file stored using band interleaved by pixel (BIP) image encoding. The binary file is stored
such that Z-X "frames" are stored sequentially to form an image stack along the y-axis. When accessing the data sequentially on disk,
the dimensions read, from fastest to slowest, are Z, X, Y.
This class is optimized for data streaming, and therefore supports extremely large (terabyte-scale) files. Data is loaded from disk
on request. Functions used to access data are written to support efficient reading.
*/
template <typename T>
class bip: public hsi<T> {
protected:
//std::vector<double> w; //band wavelength
unsigned long long offset; //header offset
using hsi<T>::w; //use the wavelength array in stim::hsi
using hsi<T>::nnz;
using binary<T>::progress;
using hsi<T>::X;
using hsi<T>::Y;
using hsi<T>::Z;
public:
using binary<T>::open;
using binary<T>::file;
using binary<T>::R;
using binary<T>::read_line_0;
bip(){ hsi<T>::init_bip(); }
/// Open a data file for reading using the class interface.
/// @param filename is the name of the binary file on disk
/// @param X is the number of samples along dimension 1
/// @param Y is the number of samples (lines) along dimension 2
/// @param B is the number of samples (bands) along dimension 3
/// @param header_offset is the number of bytes (if any) in the binary header
/// @param wavelengths is an optional STL vector of size B specifying a numerical label for each band
bool open(std::string filename,
unsigned long long X,
unsigned long long Y,
unsigned long long B,
unsigned long long header_offset,
std::vector<double> wavelengths){
//copy the wavelengths to the BSQ file structure
w = wavelengths;
//copy the offset to the structure
offset = header_offset;
return open(filename, vec<unsigned long long>(B, X, Y), header_offset);
}
/// 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.
bool band_index( T * p, unsigned long long page, bool PROGRESS = false){
return binary<T>::read_plane_0(p, page, PROGRESS);
}
/// 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.
bool band( T * p, double wavelength, bool PROGRESS = false){
//if there are no wavelengths in the BSQ file
if(w.size() == 0)
return band_index(p, (unsigned long long)wavelength, PROGRESS);
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned page=0; //bands around the wavelength
//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
if ( w[page] > wavelength ){
band_index(p, page, PROGRESS);
return true;
}
while( w[page] < wavelength )
{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == Z()) {
band_index(p, Z()-1, PROGRESS);
return true;
}
}
if ( wavelength < w[page] )
{
T * p1;
T * p2;
p1=(T*)malloc( XY * sizeof(T)); //memory allocation
p2=(T*)malloc( XY * sizeof(T));
band_index(p1, page - 1);
band_index(p2, page, PROGRESS);
for(unsigned long long i=0; i < XY; i++){
double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
p[i] = (T)(((double)p2[i] - (double)p1[i]) * r + (double)p1[i]);
}
free(p1);
free(p2);
}
else //if the wavelength is equal to a wavelength in header file
{
band_index(p, page, PROGRESS);
}
return true;
}
/// Retrieve a single spectrum (Z-axis line) at a given (x, y) location and stores it in pre-allocated memory.
/// @param p is a pointer to pre-allocated memory at least B * sizeof(T) in size.
/// @param x is the x-coordinate (dimension 1) of the spectrum.
/// @param y is the y-coordinate (dimension 2) of the spectrum.
bool spectrum(T * p, unsigned long long x, unsigned long long y, bool PROGRESS = false){
return read_line_0(p, x, y, PROGRESS); //read a line in the binary YZ plane (dimension order for BIP is ZXY)
}
bool spectrum(T* p, size_t n, bool PROGRESS = false){
size_t y = n / X();
size_t x = n - y * X();
return read_line_0(p, x, y, PROGRESS); //read a line in the binary YZ plane (dimension order for BIP is ZXY)
}
/// Retrieves a band of x values from a given xz plane.
/// @param p is a pointer to pre-allocated memory at least X * sizeof(T) in size
/// @param c is a pointer to an existing XZ plane (size X*Z*sizeof(T))
/// @param wavelength is the wavelength of X values to retrieve
bool read_x_from_xz(T* p, T* c, double wavelength)
{
unsigned long long B = Z();
unsigned long long page=0; //samples around the wavelength
//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
if ( w[page] > wavelength ){
for(unsigned long long j = 0; j < X(); j++)
{
p[j] = c[j * B];
}
return true;
}
while( w[page] < wavelength )
{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == B) {
for(unsigned long long j = 0; j < X(); j++)
{
p[j] = c[(j + 1) * B - 1];
}
return true;
}
}
if ( wavelength < w[page] )
{
T * p1;
T * p2;
p1=(T*)malloc( X() * sizeof(T)); //memory allocation
p2=(T*)malloc( X() * sizeof(T));
//band_index(p1, page - 1);
for(unsigned long long j = 0; j < X(); j++)
{
p1[j] = c[j * B + page - 1];
}
//band_index(p2, page );
for(unsigned long long j = 0; j < X(); j++)
{
p2[j] = c[j * B + page];
}
for(unsigned long long i=0; i < X(); i++){
double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
p[i] = (p2[i] - p1[i]) * r + p1[i];
}
free(p1);
free(p2);
}
else //if the wavelength is equal to a wavelength in header file
{
//band_index(p, page);
for(unsigned long long j = 0; j < X(); j++)
{
p[j] = c[j * B + page];
}
}
return true;
}
/// Retrieve a single pixel and store it in a pre-allocated double array.
bool pixeld(double* p, unsigned long long n){
unsigned long long bandnum = X() * Y(); //calculate numbers in one band
if ( n >= bandnum){ //make sure the pixel number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
unsigned long long B = Z();
T* temp = (T*) malloc(B * sizeof(T)); //allocate space for the raw pixel data
file.seekg(n * B * sizeof(T), std::ios::beg); //point to the certain pixel
file.read((char *)temp, sizeof(T) * B); //read the spectrum from disk to the temp pointer
for(unsigned long long i = 0; i < B; i++) //for each element of the spectrum
p[i] = (double) temp[i]; //cast each element to a double value
free(temp); //free temporary memory
return true;
}
/// 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.
bool pixel(T * p, unsigned long long n){
unsigned long long N = X() * Y(); //calculate numbers in one band
if ( n >= N){ //make sure the pixel number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
file.seekg(n * Z() * sizeof(T), std::ios::beg); //point to the certain pixel
file.read((char *)p, sizeof(T) * Z());
return true;
}
//given a Y ,return a ZX slice
bool read_plane_y(T * p, unsigned long long y){
return binary<T>::read_plane_2(p, y);
}
/// Perform baseline correction given a list of baseline points and stores the result in a new BSQ file.
/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
/// @param wls is the list of baseline points based on band labels.
bool baseline(std::string outname, std::vector<double> base_pts, unsigned char* mask = NULL, bool PROGRESS = false){
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
unsigned long long N = X() * Y(); //calculate the total number of pixels to be processed
unsigned long long B = Z(); //get the number of bands
T* s = (T*)malloc(sizeof(T) * B); //allocate memory to store a pixel
T* sbc = (T*)malloc(sizeof(T) * B); //allocate memory to store the baseline corrected spectrum
std::vector<T> base_vals; //allocate space for the values at each baseline point
double aw, bw; //surrounding baseline point wavelengths
T av, bv; //surrounding baseline point values
unsigned long long ai, bi; //surrounding baseline point band indices
for(unsigned long long n = 0; n < N; n++){ //for each pixel in the image
if(mask != NULL && !mask[n]){ //if the pixel isn't masked
memset(sbc, 0, sizeof(T) * B); //set the baseline corrected spectrum to zero
}
else{
pixel(s, n); //retrieve the spectrum s
base_vals = hsi<T>::interp_spectrum(s, base_pts); //get the values at each baseline point
ai = bi = 0;
aw = w[0]; //initialize the current baseline points (assume the spectrum starts at 0)
av = s[0];
bw = base_pts[0];
for(unsigned long long b = 0; b < B; b++){ //for each band in the spectrum
while(bi < base_pts.size() && base_pts[bi] < w[b]) //while the current wavelength is higher than the second baseline point
bi++; //move to the next baseline point
if(bi < base_pts.size()){
bw = base_pts[bi]; //set the wavelength for the upper bound baseline point
bv = base_vals[bi]; //set the value for the upper bound baseline point
}
if(bi == base_pts.size()){ //if we have passed the last baseline point
bw = w[B-1]; //set the outer bound to the last spectral band
bv = s[B-1];
}
if(bi != 0){
ai = bi - 1; //set the lower bound baseline point index
aw = base_pts[ai]; //set the wavelength for the lower bound baseline point
av = base_vals[ai]; //set the value for the lower bound baseline point
}
sbc[b] = s[b] - hsi<T>::lerp(w[b], av, aw, bv, bw); //perform the baseline correction and save the new value
}
}
if(PROGRESS) progress = (double)(n+1) / N * 100; //set the current progress
target.write((char*)sbc, sizeof(T) * B); //write the corrected data into destination
} //end for each pixel
free(s);
free(sbc);
target.close();
return true;
}
/// Normalize all spectra based on the value of a single band, storing the result in a new BSQ file.
/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
/// @param w is the label specifying the band that the hyperspectral image will be normalized to.
/// @param t is a threshold specified such that a spectrum with a value at w less than t is set to zero. Setting this threshold allows the user to limit division by extremely small numbers.
bool ratio(std::string outname, double w, unsigned char* mask = NULL, bool PROGRESS = false)
{
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
unsigned long long N = X() * Y(); //calculate the total number of pixels to be processed
unsigned long long B = Z(); //get the number of bands
T* s = (T*)malloc(sizeof(T) * B); //allocate memory to store a pixel
T nv; //stores the value of the normalized band
for(unsigned long long n = 0; n < N; n++){ //for each pixel in the image
if(mask != NULL && !mask[n]) //if the normalization band is below threshold
memset(s, 0, sizeof(T) * B); //set the output to zero
else{
pixel(s, n); //retrieve the spectrum s
nv = hsi<T>::interp_spectrum(s, w); //find the value of the normalization band
for(unsigned long long b = 0; b < B; b++) //for each band in the spectrum
s[b] /= nv; //divide by the normalization value
}
if(PROGRESS) progress = (double)(n+1) / N * 100; //set the current progress
target.write((char*)s, sizeof(T) * B); //write the corrected data into destination
} //end for each pixel
free(s);
target.close();
return true;
}
void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
file.seekg(0, std::ios::beg); //move the pointer to the current file to the beginning
size_t B = Z(); //number of spectral components
size_t XY = X() * Y(); //calculate the number of pixels
size_t Bb = B * sizeof(T); //number of bytes in a spectrum
T* spec = (T*) malloc(Bb); //allocate space for the spectrum
T len;
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
memset(spec, 0, Bb); //set the spectrum to zero
if(mask == NULL || mask[xy]){ //if the pixel is masked
len = 0; //initialize the
file.read((char*)spec, Bb); //read a spectrum
for(size_t b = 0; b < B; b++) //for each band
len += spec[b]*spec[b]; //add the square of the spectral band
len = sqrt(len); //calculate the square of the sum of squared components
for(size_t b = 0; b < B; b++) //for each band
spec[b] /= len; //divide by the length
}
else
file.seekg(Bb, std::ios::cur); //otherwise skip a spectrum
target.write((char*)spec, Bb); //output the normalized spectrum
if(PROGRESS) progress = (double)(xy + 1) / (double)XY * 100; //update the progress
}
}
/// Convert the current BIP file to a BIL file with the specified file name.
/// @param outname is the name of the output BIL file to be saved to disk.
bool bil(std::string outname, bool PROGRESS = false)
{
unsigned long long S = X() * Z() * sizeof(T); //calculate the number of bytes in a ZX slice
std::ofstream target(outname.c_str(), std::ios::binary);
//std::string headername = outname + ".hdr";
T * p; //pointer to the current ZX slice for bip file
p = (T*)malloc(S);
T * q; //pointer to the current XZ slice for bil file
q = (T*)malloc(S);
for ( unsigned long long i = 0; i < Y(); i++)
{
read_plane_y(p, i);
for ( unsigned long long k = 0; k < Z(); k++)
{
unsigned long long ks = k * X();
for ( unsigned long long j = 0; j < X(); j++)
q[ks + j] = p[k + j * Z()];
if(PROGRESS) progress = (double)(i * Z() + k+1) / (Y() * Z()) * 100;
}
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
}
free(p);
free(q);
target.close();
return true;
}
/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lp is a pointer to an array holding the band image for the left baseline point
/// @param rp is a pointer to an array holding the band image for the right baseline point
/// @param wavelength is the label value for the requested baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
unsigned long long XY = X() * Y();
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
for(unsigned long long i=0; i < XY; i++){
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param bandwavelength is the label value for the desired baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
bool height(double lb, double rb, double bandwavelength, T* result){
T* lp;
T* rp;
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
band(lp, lb);
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
free(lp);
free(rp);
return true;
}
/// Calculate the area under the spectrum between two specified points and stores the result in a pre-allocated array.
/// @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 value for the left bound (start of the integration)
/// @param rab is the label value for the right bound (end of the integration)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
bool area(double lb, double rb, double lab, double rab, T* result){
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
memset(result, (char)0, S);
//find the wavelenght position in the whole band
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long 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 (lab >= w[ai]){
ai++;
}
while (rab <= w[bi]){
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((rab - w[bi]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
}
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
}
//calculate the area
ai++;
for(unsigned long long i = ai; i <= bi ;i++)
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
for(unsigned long long j = 0; j < XY; j++)
{
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
/// 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
bool ph_to_ph(T* result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask = NULL){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
//get the two peak band
height(lb1, rb1, pos1, p1);
height(lb2, rb2, pos2, p2);
//calculate the ratio in result
for(unsigned long long i = 0; i < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// 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
bool pa_to_ph(T* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, unsigned char* mask = NULL){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
height(lb2, rb2, pos, p2);
//calculate the ratio in result
for(unsigned long long i = 0; i < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// Compute the ratio between two peak areas.
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param lab1 is the label value for the left bound (start of the integration) of the first peak (numerator)
/// @param rab1 is the label value for the right bound (end of the integration) of the first peak (numerator)
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param lab2 is the label value for the left bound (start of the integration) of the second peak (denominator)
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
bool pa_to_pa(T* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, unsigned char* mask = NULL){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
area(lb2, rb2, lab2, rab2, p2);
//calculate the ratio in result
for(unsigned long long i = 0; i < X() * Y(); i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// Compute the definite integral 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 definite integral
/// @param rab is the label for the end of the definite integral
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
bool x_area(double lb, double rb, double lab, double rab, T* result){
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
memset(result, (char)0, S);
//find the wavelenght position in the whole band
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long 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 (lab >= w[ai]){
ai++;
}
while (rab <= w[bi]){
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((rab - w[bi]) * (rab + w[bi]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
}
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
}
//calculate f(x) times x
ai++;
for(unsigned long long i = ai; i <= bi ;i++)
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
for(unsigned long long j = 0; j < XY; j++)
{
result[j] += (T)((w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
/// 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
bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
//get the area and the peak band
x_area(lb, rb, lab, rab, p1);
area(lb, rb, lab, rab, p2);
//calculate the ratio in result
for(unsigned long long i = 0; i < X() * Y(); i++){
if(mask == NULL || mask[i])
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
/// Create a mask based on a given band and threshold value.
/// All pixels in the
/// specified band greater than the threshold are true and all pixels less than the threshold are false.
/// @param mask_band is the band used to specify the mask
/// @param threshold is the threshold used to determine if the mask value is true or false
/// @param p is a pointer to a pre-allocated array at least X * Y in size
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
band(temp, mask_band, PROGRESS);
for (unsigned long long i = 0; i < X() * Y();i++) {
if (temp[i] < threshold)
mask[i] = 0;
else
mask[i] = 255;
}
free(temp);
return true;
}
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
/// @param outfile is the name of the masked output file
/// @param p is a pointer to memory of size X * Y, where p(i) = 0 for pixels that will be set to zero.
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
std::ofstream target(outfile.c_str(), std::ios::binary);
unsigned long long ZX = Z() * X(); //calculate the number of values in a page (XZ in BIP)
unsigned long long L = ZX * sizeof(T); //calculate the number of bytes in a page
T * temp = (T*)malloc(L); //allocate space for that page
for (unsigned long long i = 0; i < Y(); i++) //for each page (Y in BIP)
{
read_plane_y(temp, i); //load that page (it's pointed to by temp)
for ( unsigned long long j = 0; j < X(); j++) //for each X value
{
for (unsigned long long k = 0; k < Z(); k++) //for each B value (band)
{
if (p[i * X() + j] == 0) //if the mask value is zero
temp[j * Z() + k] = 0; //set the pixel value to zero
else //otherwise just continue
continue;
}
}
target.write(reinterpret_cast<const char*>(temp), L); //write the edited band data into target file
if(PROGRESS) progress = (double)(i+1) / (double)Y() * 100;
}
target.close(); //close the target file
free(temp); //free allocated memory
return true; //return true
}
/// Copies all spectra corresponding to nonzero values of a mask into a pre-allocated matrix of size (B x P)
/// 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 = p*B + b
/// @param matrix is the destination for the pixel data
/// @param mask is the mask
bool sift(T* matrix, unsigned char* mask = NULL, bool PROGRESS = false){
size_t Bbytes = sizeof(T) * Z();
size_t XY = X() * Y();
T* band = (T*) malloc( Bbytes ); //allocate space for a line
file.seekg(0, std::ios::beg); //seek to the beginning of the file
size_t p = 0; //create counter variables
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
if(mask == NULL || mask[xy]){ //if the current pixel is masked
file.read( (char*)band, Bbytes ); //read the current line
for(size_t b = 0; b < Z(); b++){ //copy each band value to the sifted matrix
size_t i = p * Z() + b; //calculate the index in the sifted matrix
matrix[i] = band[b]; //store the current value in the line at the correct matrix location
}
p++; //increment the pixel pointer
}
else
file.seekg(Bbytes, std::ios::cur); //otherwise skip this band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
return true;
}
/// Saves to disk only those spectra corresponding to mask values != 0
bool sift(std::string outfile, unsigned char* mask, bool PROGRESS = false){
//reset the file pointer to the beginning of the file
file.seekg(0, std::ios::beg);
// open an output stream
std::ofstream target(outfile.c_str(), std::ios::binary);
//allocate space for a single spectrum
unsigned long long B = Z();
T* spectrum = (T*) malloc(B * sizeof(T));
//calculate the number of pixels in a band
unsigned long long XY = X() * Y();
//for each pixel
unsigned long long skip = 0; //number of spectra to skip
for(unsigned long long x = 0; x < XY; x++){
//if the current pixel isn't masked
if( mask[x] == 0){
//increment the number of skipped pixels
skip++;
}
//if the current pixel is masked
else{
//skip the intermediate pixels
file.seekg(skip * B * sizeof(T), std::ios::cur);
//set the skip value to zero
skip = 0;
//read this pixel into memory
file.read((char *)spectrum, B * sizeof(T));
//write this pixel out
target.write((char *)spectrum, B * sizeof(T));
}
if(PROGRESS) progress = (double) (x+1) / XY * 100;
}
//close the output file
target.close();
free(spectrum);
return true;
}
bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
// open an output stream
std::ofstream target(outfile.c_str(), std::ios::binary);
//reset the file pointer to the beginning of the file
file.seekg(0, std::ios::beg);
//allocate space for a single spectrum
unsigned long long B = Z();
T* spectrum = (T*) malloc(B * sizeof(T));
//allocate space for a spectrum of zeros
T* zeros = (T*) malloc(B * sizeof(T));
memset(zeros, 0, B * sizeof(T));
//calculate the number of pixels in a band
unsigned long long XY = samples * lines;
//for each pixel
unsigned long long skip = 0; //number of spectra to skip
for(unsigned long long x = 0; x < XY; x++){
//if the current pixel isn't masked
if( mask[x] == 0){
//write a bunch of zeros
target.write((char *)zeros, B * sizeof(T));
}
//if the current pixel is masked
else{
//read a pixel into memory
file.read((char *)spectrum, B * sizeof(T));
//write this pixel out
target.write((char *)spectrum, B * sizeof(T));
}
if(PROGRESS) progress = (double)(x + 1) / XY * 100;
}
//close the output file
target.close();
free(spectrum);
//progress = 100;
return true;
}
/// 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 avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
unsigned long long XY = X() * Y(); //calculate the total number of pixels in the HSI
T* temp = (T*)malloc(sizeof(T) * Z()); //allocate space for the current spectrum to be read
memset(p, 0, sizeof(double) * Z()); //initialize the average spectrum to zero (0)
//for (unsigned j = 0; j < Z(); j++){
// p[j] = 0;
//}
unsigned long long count = nnz(mask); //calculate the number of masked pixels
for (unsigned long long i = 0; i < XY; i++){ //for each pixel in the HSI
if (mask == NULL || mask[i] != 0){ //if the pixel is masked
pixel(temp, i); //get the spectrum
for (unsigned long long j = 0; j < Z(); j++){ //for each spectral component
p[j] += (double)temp[j] / (double)count; //add the weighted value to the average
}
}
if(PROGRESS) progress = (double)(i+1) / XY * 100; //increment the progress
}
free(temp);
return true;
}
#ifdef CUDA_FOUND
/// Calculate the covariance matrix for masked pixels using cuBLAS
/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
bool co_matrix_cublas(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
cudaError_t cudaStat;
cublasStatus_t stat;
cublasHandle_t handle;
progress = 0; //initialize the progress to zero (0)
unsigned long long XY = X() * Y(); //calculate the number of elements in a band image
unsigned long long B = Z(); //calculate the number of spectral elements
double* s = (double*)malloc(sizeof(double) * B); //allocate space for the spectrum that will be pulled from the file
double* s_dev; //declare a device pointer that will store the spectrum on the GPU
double* A_dev; //declare a device pointer that will store the covariance matrix on the GPU
double* avg_dev; //declare a device pointer that will store the average spectrum
cudaStat = cudaMalloc(&s_dev, B * sizeof(double)); //allocate space on the CUDA device for the spectrum
cudaStat = cudaMalloc(&A_dev, B * B * sizeof(double)); //allocate space on the CUDA device for the covariance matrix
cudaStat = cudaMemset(A_dev, 0, B * B * sizeof(double)); //initialize the covariance matrix to zero (0)
cudaStat = cudaMalloc(&avg_dev, B * sizeof(double)); //allocate space on the CUDA device for the average spectrum
stat = cublasSetVector((int)B, sizeof(double), avg, 1, avg_dev, 1); //copy the average spectrum to the CUDA device
double ger_alpha = 1.0/(double)XY; //scale the outer product by the inverse of the number of samples (mean outer product)
double axpy_alpha = -1; //multiplication factor for the average spectrum (in order to perform a subtraction)
stat = cublasCreate(&handle); //create a cuBLAS instance
if (stat != CUBLAS_STATUS_SUCCESS) { //test the cuBLAS instance to make sure it is valid
printf ("CUBLAS initialization failed\n");
return EXIT_FAILURE;
}
for (unsigned long long xy = 0; xy < XY; xy++){ //for each pixel
if (mask == NULL || mask[xy] != 0){
pixeld(s, xy); //retreive the spectrum at the current xy pixel location
stat = cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1); //copy the spectrum from the host to the device
stat = cublasDaxpy(handle, (int)B, &axpy_alpha, avg_dev, 1, s_dev, 1); //subtract the average spectrum
stat = cublasDsyr(handle, CUBLAS_FILL_MODE_UPPER, (int)B, &ger_alpha, s_dev, 1, A_dev, (int)B); //calculate the covariance matrix (symmetric outer product)
}
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
}
cublasGetMatrix((int)B, (int)B, sizeof(double), A_dev, (int)B, co, (int)B); //copy the result from the GPU to the CPU
cudaFree(A_dev); //clean up allocated device memory
cudaFree(s_dev);
cudaFree(avg_dev);
for(unsigned long long i = 0; i < B; i++){ //copy the upper triangular portion to the lower triangular portion
for(unsigned long long j = i+1; j < B; j++){
co[B * i + j] = co[B * j + i];
}
}
return true;
}
#endif
/// Calculate the covariance matrix for all masked pixels in the image with 64-bit floating point precision.
/// @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
bool co_matrix(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
#ifdef CUDA_FOUND
int dev_count;
cudaGetDeviceCount(&dev_count); //get the number of CUDA devices
cudaDeviceProp prop;
cudaGetDeviceProperties(&prop, 0); //get the property of the first device
if(dev_count > 0 && prop.major != 9999) //if the first device is not an emulator
return co_matrix_cublas(co, avg, mask, PROGRESS); //use cuBLAS to calculate the covariance matrix
#endif
progress = 0;
//memory allocation
unsigned long long XY = X() * Y();
unsigned long long B = Z();
T* temp = (T*)malloc(sizeof(T) * B);
unsigned long long count = nnz(mask); //count the number of masked pixels
//initialize covariance matrix
memset(co, 0, B * B * sizeof(double));
//calculate covariance matrix
double* co_half = (double*) malloc(B * B * sizeof(double)); //allocate space for a higher-precision intermediate matrix
double* temp_precise = (double*) malloc(B * sizeof(double));
memset(co_half, 0, B * B * sizeof(double)); //initialize the high-precision matrix with zeros
unsigned long long idx; //stores i*B to speed indexing
for (unsigned long long xy = 0; xy < XY; xy++){
if (mask == NULL || mask[xy] != 0){
pixel(temp, xy); //retreive the spectrum at the current xy pixel location
for(unsigned long long b = 0; b < B; b++) //subtract the mean from this spectrum and increase the precision
temp_precise[b] = (double)temp[b] - (double)avg[b];
idx = 0;
for (unsigned long long b0 = 0; b0 < B; b0++){ //for each band
for (unsigned long long b1 = b0; b1 < B; b1++)
co_half[idx++] += temp_precise[b0] * temp_precise[b1];
}
}
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
idx = 0;
for (unsigned long long i = 0; i < B; i++){ //copy the precision matrix to both halves of the output matrix
for (unsigned long long j = i; j < B; j++){
co[j * B + i] = co[i * B + j] = co_half[idx++] / (double) count;
}
}
free(temp);
free(temp_precise);
return true;
}
#ifdef CUDA_FOUND
/// Calculate the covariance matrix of Noise for masked pixels using cuBLAS
/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
bool coNoise_matrix_cublas(double* coN, double* avg, unsigned char *mask, bool PROGRESS = false){
cudaError_t cudaStat;
cublasStatus_t stat;
cublasHandle_t handle;
progress = 0; //initialize the progress to zero (0)
unsigned long long XY = X() * Y(); //calculate the number of elements in a band image
unsigned long long B = Z(); //calculate the number of spectral elements
double* s = (double*)malloc(sizeof(double) * B); //allocate space for the spectrum that will be pulled from the file
double* s_dev; //declare a device pointer that will store the spectrum on the GPU
double* s2_dev; // device pointer on the GPU
cudaStat = cudaMalloc(&s2_dev, B * sizeof(double)); // allocate space on the CUDA device
cudaStat = cudaMemset(s2_dev, 0, B * sizeof(double)); // initialize s2_dev to zero (0)
double* A_dev; //declare a device pointer that will store the covariance matrix on the GPU
double* avg_dev; //declare a device pointer that will store the average spectrum
cudaStat = cudaMalloc(&s_dev, B * sizeof(double)); //allocate space on the CUDA device for the spectrum
cudaStat = cudaMalloc(&A_dev, B * B * sizeof(double)); //allocate space on the CUDA device for the covariance matrix
cudaStat = cudaMemset(A_dev, 0, B * B * sizeof(double)); //initialize the covariance matrix to zero (0)
cudaStat = cudaMalloc(&avg_dev, B * sizeof(double)); //allocate space on the CUDA device for the average spectrum
stat = cublasSetVector((int)B, sizeof(double), avg, 1, avg_dev, 1); //copy the average spectrum to the CUDA device
double ger_alpha = 1.0/(double)XY; //scale the outer product by the inverse of the number of samples (mean outer product)
double axpy_alpha = -1; //multiplication factor for the average spectrum (in order to perform a subtraction)
stat = cublasCreate(&handle); //create a cuBLAS instance
if (stat != CUBLAS_STATUS_SUCCESS) { //test the cuBLAS instance to make sure it is valid
printf ("CUBLAS initialization failed\n");
return EXIT_FAILURE;
}
for (unsigned long long xy = 0; xy < XY; xy++){ //for each pixel
if (mask == NULL || mask[xy] != 0){
pixeld(s, xy); //retreive the spectrum at the current xy pixel location
stat = cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1); //copy the spectrum from the host to the device
stat = cublasDaxpy(handle, (int)B, &axpy_alpha, avg_dev, 1, s_dev, 1); //subtract the average spectrum
cudaMemcpy(s2_dev, s_dev + 1 , (B-1) * sizeof(double), cudaMemcpyDeviceToDevice); //copy B-1 elements from shifted source data (s_dev) to device pointer (s2_dev )
stat = cublasDaxpy(handle, (int)B, &axpy_alpha, s2_dev, 1, s_dev, 1); //Minimum/Maximum Autocorrelation Factors (MAF) method : subtranct each pixel from adjacent pixel (z direction is choosed to do so , which is almost the same as x or y direction or even average of them )
stat = cublasDsyr(handle, CUBLAS_FILL_MODE_UPPER, (int)B, &ger_alpha, s_dev, 1, A_dev, (int)B); //calculate the covariance matrix (symmetric outer product)
}
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
}
cublasGetMatrix((int)B, (int)B, sizeof(double), A_dev, (int)B, coN, (int)B); //copy the result from the GPU to the CPU
cudaFree(A_dev); //clean up allocated device memory
cudaFree(s_dev);
cudaFree(s2_dev);
cudaFree(avg_dev);
for(unsigned long long i = 0; i < B; i++){ //copy the upper triangular portion to the lower triangular portion
for(unsigned long long j = i+1; j < B; j++){
coN[B * i + j] = coN[B * j + i];
}
}
return true;
}
#endif
/// Calculate the covariance of noise matrix for all masked pixels in the image with 64-bit floating point precision.
/// @param coN 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
bool coNoise_matrix(double* coN, double* avg, unsigned char *mask, bool PROGRESS = false){
#ifdef CUDA_FOUND
int dev_count;
cudaGetDeviceCount(&dev_count); //get the number of CUDA devices
cudaDeviceProp prop;
cudaGetDeviceProperties(&prop, 0); //get the property of the first device
if(dev_count > 0 && prop.major != 9999) //if the first device is not an emulator
return coNoise_matrix_cublas(coN, avg, mask, PROGRESS); //use cuBLAS to calculate the covariance matrix
#endif
progress = 0;
//memory allocation
unsigned long long XY = X() * Y();
unsigned long long B = Z();
T* temp = (T*)malloc(sizeof(T) * B);
unsigned long long count = nnz(mask); //count the number of masked pixels
//initialize covariance matrix of noise
memset(coN, 0, B * B * sizeof(double));
//calculate covariance matrix
double* coN_half = (double*) malloc(B * B * sizeof(double)); //allocate space for a higher-precision intermediate matrix
double* temp_precise = (double*) malloc(B * sizeof(double));
memset(coN_half, 0, B * B * sizeof(double)); //initialize the high-precision matrix with zeros
unsigned long long idx; //stores i*B to speed indexing
for (unsigned long long xy = 0; xy < XY; xy++){
if (mask == NULL || mask[xy] != 0){
pixel(temp, xy); //retreive the spectrum at the current xy pixel location
for(unsigned long long b = 0; b < B; b++) //subtract the mean from this spectrum and increase the precision
temp_precise[b] = (double)temp[b] - (double)avg[b];
for(unsigned long long b2 = 0; b2 < B-1; b2++) //Minimum/Maximum Autocorrelation Factors (MAF) method : subtranct each pixel from adjacent pixel (z direction is choosed to do so , which is almost the same as x or y direction or even average of them )
temp_precise[b2] -= temp_precise[b2+1];
idx = 0;
for (unsigned long long b0 = 0; b0 < B; b0++){ //for each band
for (unsigned long long b1 = b0; b1 < B; b1++)
coN_half[idx++] += temp_precise[b0] * temp_precise[b1];
}
}
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
idx = 0;
for (unsigned long long i = 0; i < B; i++){ //copy the precision matrix to both halves of the output matrix
for (unsigned long long j = i; j < B; j++){
coN[j * B + i] = coN[i * B + j] = coN_half[idx++] / (double) count;
}
}
free(temp);
free(temp_precise);
return true;
}
#ifdef CUDA_FOUND
/// Project the spectra onto a set of basis functions
/// @param outfile is the name of the new binary output file that will be created
/// @param center is a spectrum about which the data set will be rotated (ex. when performing mean centering)
/// @param basis a set of basis vectors that the data set will be projected onto (after centering)
/// @param M is the number of basis vectors
/// @param mask is a character mask used to limit processing to valid pixels
bool project_cublas(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask = NULL, bool PROGRESS = false){
cudaError_t cudaStat;
cublasStatus_t stat;
cublasHandle_t handle;
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
progress = 0; //initialize the progress to zero (0)
unsigned long long XY = X() * Y(); //calculate the number of elements in a band image
unsigned long long B = Z(); //calculate the number of spectral elements
double* s = (double*)malloc(sizeof(double) * B); //allocate space for the spectrum that will be pulled from the file
double* s_dev; //declare a device pointer that will store the spectrum on the GPU
cudaStat = cudaMalloc(&s_dev, B * sizeof(double)); //allocate space on the CUDA device for the spectrum
double* basis_dev; // device pointer on the GPU
cudaStat = cudaMalloc(&basis_dev, M * B * sizeof(double)); // allocate space on the CUDA device
cudaStat = cudaMemset(basis_dev, 0, M * B * sizeof(double)); // initialize basis_dev to zero (0)
/// transposing basis matrix (because cuBLAS is column-major)
double *basis_Transposed = (double*)malloc(M * B * sizeof(double));
memset(basis_Transposed, 0, M * B * sizeof(double));
for (int i = 0; i<M; i++)
for (int j = 0; j<B; j++)
basis_Transposed[i+j*M] = basis[i*B+j];
stat = cublasSetMatrix((int)M, (int)B, sizeof(double),basis_Transposed, (int)M, basis_dev, (int)M); //copy the basis_Transposed matrix to the CUDA device (both matrices are stored in column-major format)
double* center_dev; //declare a device pointer that will store the center (average)
cudaStat = cudaMalloc(¢er_dev, B * sizeof(double)); //allocate space on the CUDA device for the center (average)
stat = cublasSetVector((int)B, sizeof(double), center, 1, center_dev, 1); //copy the center vector (average) to the CUDA device (from host to device)
double* A = (double*)malloc(sizeof(double) * M); //allocate space for the projected pixel on the host
double* A_dev; //declare a device pointer that will store the projected pixel on the GPU
cudaStat = cudaMalloc(&A_dev,M * sizeof(double)); //allocate space on the CUDA device for the projected pixel
cudaStat = cudaMemset(A_dev, 0,M * sizeof(double)); //initialize the projected pixel to zero (0)
double axpy_alpha = -1; //multiplication factor for the center (in order to perform a subtraction)
double axpy_alpha2 = 1; //multiplication factor for the matrix-vector multiplication
double axpy_beta = 0; //multiplication factor for the matrix-vector multiplication (there is no second scalor)
stat = cublasCreate(&handle); //create a cuBLAS instance
if (stat != CUBLAS_STATUS_SUCCESS) { //test the cuBLAS instance to make sure it is valid
printf ("CUBLAS initialization failed\n");
return EXIT_FAILURE;
}
T* temp = (T*)malloc(sizeof(T) * M); //allocate space for the projected pixel to be written on the disc
size_t i;
for (unsigned long long xy = 0; xy < XY; xy++){ //for each pixel
if (mask == NULL || mask[xy] != 0){
pixeld(s, xy); //retreive the spectrum at the current xy pixel location
stat = cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1); //copy the spectrum from the host to the device
stat = cublasDaxpy(handle, (int)B, &axpy_alpha, center_dev, 1, s_dev, 1); //subtract the center (average)
stat = cublasDgemv(handle,CUBLAS_OP_N,(int)M,(int)B,&axpy_alpha2,basis_dev,(int)M,s_dev,1,&axpy_beta,A_dev,1); //performs the matrix-vector multiplication
stat = cublasGetVector((int)B, sizeof(double), A_dev, 1, A, 1); //copy the projected pixel to the host (from GPU to CPU)
//std::copy<double*, T*>(A, A + M, temp);
for(i = 0; i < M; i++) temp[i] = (T)A[i]; //casting projected pixel from double to whatever T is
}
target.write(reinterpret_cast<const char*>(temp), sizeof(T) * M); //write the projected vector
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
}
//clean up allocated device memory
cudaFree(A_dev);
cudaFree(s_dev);
cudaFree(basis_dev);
cudaFree(center_dev);
free(A);
free(s);
free(temp);
target.close(); //close the output file
return true;
}
#endif
/// Project the spectra onto a set of basis functions
/// @param outfile is the name of the new binary output file that will be created
/// @param center is a spectrum about which the data set will be rotated (ex. when performing mean centering)
/// @param basis a set of basis vectors that the data set will be projected onto (after centering)
/// @param M is the number of basis vectors
/// @param mask is a character mask used to limit processing to valid pixels
bool project(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask = NULL, bool PROGRESS = false){
#ifdef CUDA_FOUND
int dev_count;
cudaGetDeviceCount(&dev_count); //get the number of CUDA devices
cudaDeviceProp prop;
cudaGetDeviceProperties(&prop, 0); //get the property of the first device
if(dev_count > 0 && prop.major != 9999) //if the first device is not an emulator
return project_cublas(outfile,center,basis,M,mask,PROGRESS); //use cuBLAS to calculate the covariance matrix
#endif
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
//std::string headername = outfile + ".hdr"; //the header file name
//memory allocation
unsigned long long XY = X() * Y();
unsigned long long B = Z();
T* s = (T*)malloc(sizeof(T) * B); //allocate space for the spectrum
T* rs = (T*)malloc(sizeof(T) * M); //allocate space for the projected spectrum
double* bv; //pointer to the current projection vector
for(unsigned long long xy = 0; xy < XY; xy++){ //for each spectrum in the image
memset(rs, 0, sizeof(T) * M);
if(mask == NULL || mask[xy]){
pixel(s, xy); //load the spectrum
for(unsigned long long m = 0; m < M; m++){ //for each basis vector
bv = &basis[m * B]; //assign 'bv' to the beginning of the basis vector
for(unsigned long long b = 0; b < B; b++){ //for each band
rs[m] += (T)(((double)s[b] - center[b]) * bv[b]); //center the spectrum and perform the projection
}
}
}
target.write(reinterpret_cast<const char*>(rs), sizeof(T) * M); //write the projected vector
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
free(s); //free temporary storage arrays
free(rs);
target.close(); //close the output file
return true;
}
bool inverse(std::string outfile, double* center, double* basis, unsigned long long B, unsigned long long C = 0, bool PROGRESS = false){
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
std::string headername = outfile + ".hdr"; //the header file name
//memory allocation
unsigned long long XY = X() * Y();
if(C == 0) C = Z(); //if no coefficient number is given, assume all are used
C = std::min<unsigned long long>(C, Z()); //set the number of coefficients (the user can specify fewer)
T* coeff = (T*)malloc(sizeof(T) * Z()); //allocate space for the coefficients
T* s = (T*)malloc(sizeof(T) * B); //allocate space for the spectrum
double* bv; //pointer to the current projection vector
for(unsigned long long xy = 0; xy < XY; xy++){ //for each pixel in the image (expressed as a set of coefficients)
pixel(coeff, xy); //load the coefficients
memset(s, 0, sizeof(T) * B); //initialize the spectrum to zero (0)
for(unsigned long long c = 0; c < C; c++){ //for each basis vector coefficient
bv = &basis[c * B]; //assign 'bv' to the beginning of the basis vector
for(unsigned long long b = 0; b < B; b++){ //for each component of the basis vector
s[b] += (T)((double)coeff[c] * bv[b] + center[b]); //calculate the contribution of each element of the basis vector in the final spectrum
}
}
target.write(reinterpret_cast<const char*>(s), sizeof(T) * B); //write the projected vector
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
free(coeff); //free temporary storage arrays
free(s);
target.close(); //close the output file
return true;
}
/// 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
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){
//calculate the new number of samples, lines, and bands
unsigned long long samples = x1 - x0;
unsigned long long lines = y1 - y0;
unsigned long long bands = b1 - b0;
//calculate the length of one cropped spectrum
unsigned long long L = bands * sizeof(T);
//unsigned long long L = Z() * sizeof(T);
//allocate space for the spectrum
T* temp = (T*)malloc(L);
//open an output file for binary writing
std::ofstream out(outfile.c_str(), std::ios::binary);
//seek to the first pixel in the cropped image
file.seekg( (y0 * X() * Z() + x0 * Z() + b0) * sizeof(T), std::ios::beg);
//distance between sample spectra in the same line
unsigned long long jump_sample = ( (Z() - b1) + b0 ) * sizeof(T);
//distance between sample spectra in adjacent lines
unsigned long long jump_line = (X() - x1) * Z() * sizeof(T);
//unsigned long long sp = y0 * X() + x0; //start pixel
//for each pixel in the image
for (unsigned y = 0; y < lines; y++)
{
for (unsigned x = 0; x < samples; x++)
{
//read the cropped spectral region
file.read( (char*) temp, L );
//pixel(temp, sp + x + y * X());
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
file.seekg(jump_sample, std::ios::cur);
if(PROGRESS) progress = (double)((y+1) * samples + x + 1) / (lines * samples) * 100;
}
file.seekg(jump_line, std::ios::cur);
}
free(temp);
return true;
}
/// 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> band_array, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
file.seekg(0, std::ios::beg); //move to the beginning of the input file
size_t B = Z(); //calculate the number of elements in a spectrum
size_t Bdst = Z() - band_array.size(); //calculate the number of elements in an output spectrum
size_t Bb = B * sizeof(T); //calculate the number of bytes in a spectrum
size_t XY = X() * Y(); //calculate the number of pixels in the image
T* src = (T*)malloc(Bb); //allocate space to store an input spectrum
T* dst = (T*)malloc(Bdst * sizeof(T)); //allocate space to store an output spectrum
size_t i; //index into the band array
size_t bdst; //index into the output array
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
i = 0;
bdst = 0;
file.read((char*)src, Bb); //read a spectrum
for(size_t b = 0; b < B; b++){ //for each band
if(b != band_array[i]){ //if the band isn't trimmed
dst[bdst] = src[b]; //copy the band value to the output spectrum
bdst++;
}
else i++; //otherwise increment i
}
out.write((char*)dst, Bdst * sizeof(T)); //write the output spectrum
if(PROGRESS) progress = (double)(xy + 1) / (double) XY * 100;
}
free(src);
free(dst);
}
/// Combine two BIP images along the Y axis
/// @param outfile is the combined file to be output
/// @param infile is the input file stream for the image to combine with this one
/// @param Sx is the size of the second image along X
/// @param Sy is the size of the second image along Y
/// @param offset is a shift (negative or positive) in the combined image to the left or right
void combine(std::string outfile, bip<T>* C, long long xp, long long yp, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
file.seekg(0, std::ios::beg); //move to the beginning of both files
C->file.seekg(0, std::ios::beg);
size_t S[2]; //size of the output band image
size_t p0[2]; //position of the current image in the output
size_t p1[2]; //position of the source image in the output
hsi<T>::calc_combined_size(xp, yp, C->X(), C->Y(), S[0], S[1], p0[0], p0[1], p1[0], p1[1]); //calculate the image placement parameters
size_t spec_bytes = Z() * sizeof(T); //calculate the number of bytes in a spectrum
T* spec = (T*)malloc(spec_bytes); //allocate space for a spectrum
for(size_t y = 0; y < S[1]; y++){ //for each pixel in the destination image
for(size_t x = 0; x < S[0]; x++){
if(x >= p0[0] && x < p0[0] + X() && y >= p0[1] && y < p0[1] + Y()) //if this pixel is in the current image
file.read((char*)spec, spec_bytes);
else if(x >= p1[0] && x < p1[0] + C->X() && y >= p1[1] && y < p1[1] + C->Y()) //if this pixel is in the source image
C->file.read((char*)spec, spec_bytes);
else
memset(spec, 0, spec_bytes);
out.write((char*)spec, spec_bytes); //write to the output file
}
if(PROGRESS) progress = (double)( (y+1) * S[0] + 1) / (double) (S[0] * S[1]) * 100;
}
}
/// Convolve the given band range with a kernel specified by a vector of coefficients.
/// @param outfile is an already open stream to the output file
/// @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)
void convolve(std::string outfile, std::vector<double> C, size_t start, size_t end, unsigned char* mask = NULL, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
size_t N = end - start + 1; //number of bands in the output spectrum
size_t Nb = N * sizeof(T); //size of the output spectrum in bytes
size_t B = Z(); //calculate the number of values in a spectrum
size_t Bb = B * sizeof(T); //calculate the size of a spectrum in bytes
file.seekg(0, std::ios::beg); //move to the beginning of the input file
size_t nC = C.size(); //get the number of bands that the kernel spans
T* inspec = (T*)malloc(Bb); //allocate space for the input spectrum
T* outspec = (T*)malloc(Nb); //allocate space for the output spectrum
size_t XY = X() * Y(); //number of pixels in the image
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
file.read((char*)inspec, Bb); //read an input spectrum
memset(outspec, 0, Nb); //set the output spectrum to zero (0)
if(mask == NULL || mask[xy]){
for(size_t b = 0; b < N; b++){ //for each component of the spectrum
for(size_t c = 0; c < nC; c++){ //for each coefficient in the kernel
outspec[b] += (T)(inspec[b + start + c] * C[c]); //perform the sum/multiply part of the convolution
}
}
}
out.write((char*)outspec, Nb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
void deriv(std::string outfile, size_t d, size_t order, const std::vector<double> w, unsigned char* mask = NULL, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
size_t B = Z(); //calculate the number of values in a spectrum
size_t Bb = B * sizeof(T); //calculate the size of a spectrum in bytes
bool UNIFORM = true;
double ds = w[1] - w[0]; //initialize ds
for(size_t b = 1; b < B; b++) //test to see if the spectral spacing is uniform (if it is, convolution is much faster)
if(w[b] - w[b-1] != ds) UNIFORM = false;
size_t nC = order + d; //approximating a derivative requires order + d samples
file.seekg(0, std::ios::beg); //move to the beginning of the input file
T* inspec = (T*)malloc(Bb); //allocate space for the input spectrum
T* outspec = (T*)malloc(Bb); //allocate space for the output spectrum
size_t XY = X() * Y(); //number of pixels in the image
size_t mid = (size_t)(nC / 2); //calculate the mid point of the kernel
size_t iw; //index to the first wavelength used to evaluate the derivative at this band
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
file.read((char*)inspec, Bb); //read an input spectrum
memset(outspec, 0, Bb); //set the output spectrum to zero (0)
if(mask == NULL || mask[xy]){
iw = 0;
for(size_t b = 0; b < mid; b++){ //for each component of the spectrum
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
}
std::vector<double> w_pts(w.begin(), w.begin() + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[0], w_pts, d); //get the optimal sample weights
for(size_t b = mid; b <= B - (nC - mid); b++){
iw = b - mid;
if(!UNIFORM){ //if the spacing is non-uniform, we have to re-calculate these points every iteration
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
}
for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
}
iw = B - nC;
for(size_t b = B - (nC - mid) + 1; b < B; b++){
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
}
}
out.write((char*)outspec, Bb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
bool multiply(std::string outname, double v, unsigned char* mask = NULL, bool PROGRESS = false){
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
unsigned long long N = X() * Y(); //calculate the total number of pixels to be processed
unsigned long long B = Z(); //get the number of bands
T* s = (T*)malloc(sizeof(T) * B); //allocate memory to store a pixel
for(unsigned long long n = 0; n < N; n++){ //for each pixel in the image
if(mask == NULL || mask[n]){ //if the pixel is masked
for(size_t b = 0; b < B; b++) //for each band in the spectrum
s[b] *= (T)v; //multiply
}
if(PROGRESS) progress = (double)(n+1) / N * 100; //set the current progress
target.write((char*)s, sizeof(T) * B); //write the corrected data into destination
} //end for each pixel
free(s); //free the spectrum
target.close(); //close the output file
return true;
}
bool add(std::string outname, double v, unsigned char* mask = NULL, bool PROGRESS = false){
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
unsigned long long N = X() * Y(); //calculate the total number of pixels to be processed
unsigned long long B = Z(); //get the number of bands
T* s = (T*)malloc(sizeof(T) * B); //allocate memory to store a pixel
for(unsigned long long n = 0; n < N; n++){ //for each pixel in the image
if(mask == NULL || mask[n]){ //if the pixel is masked
for(size_t b = 0; b < B; b++) //for each band in the spectrum
s[b] += (T)v; //multiply
}
if(PROGRESS) progress = (double)(n+1) / N * 100; //set the current progress
target.write((char*)s, sizeof(T) * B); //write the corrected data into destination
} //end for each pixel
free(s); //free the spectrum
target.close(); //close the output file
return true;
}
/// Close the file.
bool close(){
file.close();
return true;
}
};
}
#endif