-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathmain.cpp
2394 lines (1768 loc) · 55.9 KB
/
main.cpp
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
// --------------------------------------------------------------------
//
// This file is part of Luna.
//
// LUNA is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// Luna is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with Luna. If not, see <http://www.gnu.org/licenses/>.
//
// Please see LICENSE.txt for more details.
//
// --------------------------------------------------------------------
#include "luna.h"
#include "main.h"
//
// global resources
//
extern globals global;
extern writer_t writer;
extern logger_t logger;
extern freezer_t freezer;
int main(int argc , char ** argv )
{
//
// initial check for display of all commands
// and save, if writing to log=luna.log
//
std::string cmd_dump = log_commands( argc , argv );
//
// initiate global defintions
//
std::set_new_handler(NoMem);
global.init_defs();
//
// display version info?
//
bool show_version = argc >= 2
&& ( strcmp( argv[1] ,"-v" ) == 0
|| strcmp( argv[1] ,"--version" ) == 0 );
if ( show_version )
{
global.api();
std::cerr << luna_base_version() ;
std::cerr << "Eigen library v"
<< EIGEN_WORLD_VERSION << "."
<< EIGEN_MAJOR_VERSION << "."
<< EIGEN_MINOR_VERSION << "\n";
std::cerr << "sqlite v"
<< sqlite3_libversion() << "\n";
std::exit( globals::retcode );
}
//
// primary usage
//
std::string usage_msg = luna_base_version() +
"url: http://zzz.bwh.harvard.edu/luna/\n"
"primary usage: luna [sample-list|EDF] [n1] [n2] [id=ID] [@param-file] \n"
" [sig=s1,s2] [var1=val1] [-o out.db] [-s COMMANDS] [< command-file]\n";
//
// degenerate command line?
//
if ( argc == 1 && isatty(STDIN_FILENO) )
{
logger << usage_msg << "\n";
logger.off();
std::exit(1);
}
if ( std::cin.eof() || ! std::cin.good() )
Helper::halt( "no input, quitting" );
//
// debug/dummy options (internal testing)
//
if ( argc >= 2 && strcmp( argv[1] ,"-d" ) == 0 )
{
std::string p = argc >= 3 ? argv[2] : "";
std::string p2 = argc >= 4 ? argv[3] : "";
global.api();
proc_dummy( p , p2 );
std::exit( globals::retcode );
}
//
// help mode
//
if ( argc >= 2 && ( strcmp( argv[1] , "-h" ) == 0 || strcmp( argv[1] , "-H" ) == 0 ) )
{
global.api();
const bool primary = strcmp( argv[1] , "-h" ) == 0;
if ( argc == 2 ) // -h
{
std::cerr << "\n" << usage_msg << "\n";
std::cerr << "List of domains\n"
<< "---------------\n";
std::cerr << globals::cmddefs().help_domains()
<< "\n";
std::cerr << "For commands within a domain, add the domain label after -h, e.g.\n"
<< " luna -h annot\n\n";
std::cerr << "For options and output for a given command, add the (upper-case) command after -h, e.g.\n"
<< " luna -h SIGSTATS\n\n";
}
else // --h all
{
std::string p = argv[2] ;
// 'all' list all commands for all domains
if ( p == "all" )
{
std::cerr << globals::cmddefs().help_commands() << "\n";
}
// -h {domain} list all commands (non-verbose)
else if ( globals::cmddefs().is_domain(p) )
{
std::string str = p + " : " + globals::cmddefs().help_domain(p);
std::cerr << "\n"
<< str << "\n"
<< std::string(str.size(),'-')
<< "\n\n"
<< globals::cmddefs().help_commands( p , primary )
<< "\n";
}
// -h {cmd} list all options/tables (verbose)
else if ( globals::cmddefs().is_cmd(p) )
{
std::cerr << globals::cmddefs().help( p , true , true , primary ) << "\n";
}
// otherwise, complain
else
std::cerr << "option [" << p << "] not recognized as a domain or command\n";
}
std::exit(0);
}
//
// Parse the command line
// --> this may execute special commands (e.g. --build)
// and quit, i.e. as we don't want to invoke the
// full output mechansism/banner etc
//
int param_from_command_line;
cmdline_proc_t cmdline = parse_cmdline( argc , argv , ¶m_from_command_line );
//
// mirror log to file?
//
if ( globals::write_log )
{
logger.write_log( Helper::expand( globals::log_file ) );
// if we previously did a command-line dump (w/ --log) then
// write that out now - it will already have been sent to std::cerr
// before the logger was started properly
if ( cmd_dump != "" ) logger.print_to_file( cmd_dump );
}
//
// banner
//
logger.banner( globals::version , globals::date );
//
// initialize output to a STOUT db or not?
//
if ( cmd_t::stout_file.find( globals::indiv_wildcard ) != std::string::npos )
{
cmd_t::has_indiv_wildcard = true;
cmd_t::stout_template = cmd_t::stout_file;
}
//
// text-table mode?
//
if ( cmd_t::plaintext_mode )
{
writer.use_plaintext( cmd_t::plaintext_root );
}
// else was an output db specified?
else if ( cmd_t::stout_file != "" )
{
// if using indiv-specific output databases, postpone this...
if ( ! cmd_t::has_indiv_wildcard )
{
// if not append-mode, first wipe it
if ( ! cmd_t::append_stout_file )
Helper::deleteFile( cmd_t::stout_file );
writer.attach( cmd_t::stout_file );
}
}
// otherwise, just send to std out
else
writer.nodb();
//
// branch off to run any cmdline driven special functions not already done
// then quit
//
if ( cmdline != NOPROC )
{
exec_cmdline_procs( cmdline , argc, argv, param_from_command_line ) ;
std::exit(0);
}
//
// if here, we're expecting to apply luna commands to one or more data inputs
// --> iterate through the primary sample-list
//
int processed = 0, failed = 0;
int actually_processed = 0;
while ( ! std::cin.eof() )
{
cmd_t cmd ; // scans STDIN for next command
if ( cmd.empty() ) break;
++processed;
if ( ! cmd.valid() )
++failed;
else
{
// process command ( most will iterate over 1 or more EDFs)
if ( cmd.process_edfs() )
process_edfs(cmd);
else // handle any exceptions
{
// [ currently, this single exception not used ...
// --> if needed, better to hook in as a command-line
// function
// i.e. commands where we do not simply iterate over the
// EDF filelist; note, these currently are only
// applicable in the single command mode;
if ( cmd.is( 0 , "INTERVALS" ) )
proc_intervals( cmd.param(0) , cmd.data() );
}
}
// if received command from the -s option, we are all done
if ( cmd_t::cmdline_cmds != "" ) break;
}
//
// wrap up
//
logger << "...processed " << processed << " command set(s), ";
if ( failed == 0 ) logger << " all of which passed" << "\n";
else logger << failed << " of which failed\n";
std::exit( globals::retcode );
}
void process_edfs( cmd_t & cmd )
{
//
// Iterate over some or all of a list of EDFs and annotations,
// performing one or more commands
//
if ( cmd.num_cmds() == 0 ) return; // nothing to do
if ( ! Helper::fileExists( cmd.data() ) )
Helper::halt( "could not find file list, " + cmd.data() );
//
// Open sample-list, or working with single EDF (or ASCII file)?
//
std::string f = cmd.data();
// use .edf (or .EDF extension, or .rec or .edfz or .edf.gz ) to
// indicate 'single EDF' mode, '.rec'
f = f.substr( (int)f.size() - 4 >= 0 ? (int)f.size() - 4 : 0 );
bool single_edf = Helper::iequals( f , ".edf" ) || Helper::iequals( f , ".rec" ) ;
if ( ! single_edf )
{
// also test .edfz or .edf.gz
f = cmd.data();
f = f.substr( (int)f.size() - 5 >= 0 ? (int)f.size() - 5 : 0 );
if ( Helper::iequals( f , ".edfz" ) )
single_edf = true;
else
{
f = cmd.data();
f = f.substr( (int)f.size() - 7 >= 0 ? (int)f.size() - 7 : 0 );
if ( Helper::iequals( f , ".edf.gz" ) )
single_edf = true;
}
}
// also allow .sedf for Luna summary EDF
if ( ! single_edf )
{
std::string f2 = cmd.data();
f2 = f2.substr( (int)f2.size() - 5 >= 0 ? (int)f2.size() - 5 : 0 );
if ( Helper::iequals( f2 , ".sedf" ) ) single_edf = true;
}
// use presence of --fs command-line option to indicate 'single ASCII file' mode
bool single_txt = globals::param.has( "-fs" );
if ( single_txt ) single_edf = true;
// use presence of '.' name to indicate an empty EDF
// also (below) allow '.' from SLIST, i.e. incase we have annot-only datasets
bool empty_edf = f == "." ;
if ( empty_edf ) single_edf = true;
std::ifstream EDFLIST;
if ( ! single_edf )
EDFLIST.open( cmd.data().c_str() , std::ios::in );
//
// Do we have a search path for EDFs and ANNOTs?
//
bool has_project_path = globals::param.has( "path" );
if ( has_project_path )
{
if ( single_edf ) Helper::halt( "cannot specify project path in single EDF mode" );
globals::project_path = globals::param.value( "path" );
// does this folder exist?
if ( ! Helper::fileExists( globals::project_path ) )
Helper::halt( "could not find project path , " + globals::project_path );
if ( globals::project_path[ globals::project_path.size() - 1 ] != globals::folder_delimiter )
globals::project_path = globals::project_path + globals::folder_delimiter ;
logger << "path : " << globals::project_path << "\n";
}
//
// Report on any slices
//
if ( ! single_edf )
{
if ( globals::sample_list_min != -1 || globals::sample_list_max != -1 )
{
if ( globals::sample_list_min == globals::sample_list_max )
logger << "row(s) : #" << globals::sample_list_min << " ( n = 1 )\n";
else
logger << "row(s) : #" << globals::sample_list_min << " -> #"
<< globals::sample_list_max
<< " ( n = " << globals::sample_list_max - globals::sample_list_min + 1 << " )\n";
}
else if ( globals::sample_list_ids.size() )
logger << "rows(s) : #'s from id arg ( n = "
<< globals::sample_list_ids.size() << " )\n";
else
logger << "row(s) : all\n";
}
//
// Start iterating through it
//
int processed = 0;
int actual = 0;
while ( single_edf || ! EDFLIST.eof() )
{
// each line should contain (tab-delimited)
// 1 ID
// 2 EDF file
// 3+ other optional ANNOT files for that EDF
std::string rootname;
std::string edffile;
std::vector<std::string> tok;
if ( ! single_edf )
{
std::string line;
Helper::safe_getline( EDFLIST , line);
if ( line == "" ) continue;
//
// If we are only looking at a subset of the sample list,
// might skip here
//
if ( globals::sample_list_min != -1 || globals::sample_list_max != -1 )
{
int line_n = processed + 1;
if ( line_n < globals::sample_list_min ||
line_n > globals::sample_list_max )
{
++processed;
continue;
}
}
// parse by tabs
tok = Helper::parse( line , "\t" );
if ( tok.size() < 2 )
Helper::halt( "requires (ID) | EDF file | (optional ANNOT files)" );
// allow '.' missing value for annots?
if ( tok.size() == 3 && tok[2] == "." ) tok.resize(2);
// ignore SL annots?
if ( globals::skip_sl_annots ) tok.resize(2);
// allow annot field to be comma delimited? expand out here
if ( tok.size() == 3 )
{
std::vector<std::string> annot_fields = Helper::parse( tok[2] , globals::file_list_delimiter );
if ( annot_fields.size() > 1 )
{
tok.resize( 2 + annot_fields.size() );
for (int a=0; a<annot_fields.size();a++)
tok[a+2] = annot_fields[a];
}
}
// remove any quotes (e.g. we're okay to have spaces in names now, as tab delim
for (int t=1;t<tok.size();t++)
tok[t] = Helper::unquote( tok[t] );
// add in project path to relative paths?
// (but keep absolute paths as they are)
if ( has_project_path )
{
for (int t=1;t<tok.size();t++)
{
if ( tok[t][0] != globals::folder_delimiter )
tok[t] = globals::project_path + tok[t];
}
}
// extract main items (ID, signal EDF)
rootname = tok[0];
edffile = tok[1];
// swap in new ID?
rootname = cmd_t::remap_id( rootname );
// else, do we have an 'ID' check? (id=ID does not match so skip)
if ( globals::sample_list_ids.size() )
{
if ( globals::sample_list_ids.find( rootname )
== globals::sample_list_ids.end() )
{
++processed;
continue;
}
}
// skip=ID matches
if ( globals::sample_list_ids_skips.size() )
{
if ( globals::sample_list_ids_skips.find( rootname )
!= globals::sample_list_ids_skips.end() )
{
++processed;
continue;
}
}
}
else
{
edffile = cmd.data();
rootname = edffile;
// remove .edf from ID, making file name ==> ID
if ( Helper::file_extension( rootname , "edf" ) )
rootname = rootname.substr( 0 , rootname.size() - 4 );
else if ( Helper::file_extension( rootname , "edfz" ) )
rootname = rootname.substr( 0 , rootname.size() - 5 );
else if ( Helper::file_extension( rootname , "edf.gz" ) )
rootname = rootname.substr( 0 , rootname.size() - 7 );
tok.resize(2);
tok[0] = rootname;
tok[1] = edffile;
}
//
// File in exclude list? (or not in an include list?)
//
bool include = true;
if ( globals::id_excludes.find( rootname ) != globals::id_excludes.end() )
include = false;
if ( globals::id_includes.size() != 0
&& globals::id_includes.find( rootname ) == globals::id_includes.end() )
include = false;
if ( ! include )
{
logger << "\n"
<< "___________________________________________________________________\n"
<< " **********************************\n"
<< " * Skipping EDF " << rootname << "\n"
<< " **********************************\n"
<< "\n";
++processed;
continue; // to the next EDF in the list
}
//
// Begin running through the series of commands
//
logger << "\n___________________________________________________________________\n"
<< "Processing: " << rootname
<< " [ #" << processed+1 << " ]" << "\n";
//
// Do we need to open an individual-specific out-db?
//
if ( cmd_t::has_indiv_wildcard )
{
if ( cmd_t::plaintext_mode )
Helper::halt( "cannot specify -t and have ^ wild card" );
cmd_t::stout_file = cmd_t::resolved_outdb( rootname , cmd_t::stout_template );
// if not append-mode, first wipe it
if ( ! cmd_t::append_stout_file )
Helper::deleteFile( cmd_t::stout_file );
writer.attach( cmd_t::stout_file );
logger << " writing to " << writer.name() << "\n";
}
//
// Begin transaction
//
writer.begin();
writer.clear_tags();
writer.id( rootname , edffile );
//
// Unset 'problem' and 'empty' flags (i.e. for bailing for this individual)
//
globals::problem = false;
globals::empty = false;
//
// Limited to specific signals to load in?
//
const std::set<std::string> * inp_signals = NULL;
if ( cmd.signals().size() > 0 ) inp_signals = &cmd.signals();
//
// load EDF
//
annotation_set_t annotations;
edf_t edf( &annotations );
bool okay = true;
//
// Read a single input from ASCII
//
if ( single_txt )
{
int fs = globals::param.requires_int( "-fs" );
std::string startdate = globals::param.has("-date") ? globals::param.value( "-date" ) : "01.01.00" ;
std::string starttime = globals::param.has("-time") ? globals::param.value( "-time" ) : "00.00.00" ;
std::string id = globals::param.has("-id") ? globals::param.value( "-id" ) : rootname ;
std::vector<std::string> labels;
if ( globals::param.has("-chs" ) ) labels = globals::param.strvector( "-chs" );
okay = edf.read_from_ascii( edffile ,
id ,
fs ,
labels ,
startdate , starttime );
}
else if ( empty_edf || edffile == "." ) // i.e. sample-list empty EDF called for
{
//
// Generate an empty EDF
//
const int nr = globals::param.has( "-nr" )
? globals::param.requires_int( "-nr" )
: 60 * 60 * 6 ; // 6 hr default
const int rs = globals::param.has( "-rs" )
? globals::param.requires_int( "-rs" )
: 1 ; // in full seconds (integer)
const std::string startdate = globals::param.has("-date")
? globals::param.value( "-date" )
: "01.01.00" ;
const std::string starttime = globals::param.has("-time")
? globals::param.value( "-time" )
: "00.00.00" ;
const std::string id = globals::param.has("-id")
? globals::param.value( "-id" )
: rootname ;
okay = edf.init_empty( id , nr , rs , startdate , starttime );
}
else // attach an EDF from disk
okay = edf.attach( edffile , rootname , inp_signals );
//
// Check status of attached data, whatever the source
//
if ( ! okay )
{
globals::problem = true;
logger << "**warning: problem loading "
<< edffile << ", skipping..." << "\n";
if ( globals::write_naughty_list )
{
logger << "**writing ID " << edf.id << " to " << globals::naughty_list << "\n";
std::ofstream PROBLEMS( globals::naughty_list.c_str() , std::ios_base::app );
PROBLEMS << edf.id << "\n";
PROBLEMS.close();
}
writer.commit();
continue;
}
//
// ensure we've cleaned the freezer (except this new self)
//
freezer.clean( &edf );
//
// Check labels are still unique given aliases
//
edf.header.check_channels();
//
// Give annotations some basic details about the EDF
//
edf.annotations->set( &edf );
//
// Add additional annotations?
//
for (int i=0;i<globals::annot_files.size();i++)
{
// if absolute path given, add in as in /home/joe/etc
if ( globals::annot_files[i][0] == globals::folder_delimiter )
tok.push_back( globals::annot_files[i] );
else // project path may be "" if not set; but if set, will end in /
tok.push_back( globals::project_path + globals::annot_files[i] );
}
//
// Attach annotations
//
if ( ! globals::skip_nonedf_annots )
{
for (int i=2;i<tok.size();i++)
{
std::string fname = Helper::expand( tok[i] );
if ( fname[ fname.size() - 1 ] == globals::folder_delimiter )
{
// this means we are specifying a folder, in which case search for all files that
// start id_<ID>_* and attach thoses
DIR * dir;
struct dirent *ent;
if ( (dir = opendir ( fname.c_str() ) ) != NULL )
{
/* print all the files and directories within directory */
while ((ent = readdir (dir)) != NULL)
{
std::string fname2 = ent->d_name;
// only annot files (.xml, .ftr, .annot, .eannot)
if ( Helper::file_extension( fname2 , "annot" ) ||
Helper::file_extension( fname2 , "txt" ) ||
Helper::file_extension( fname2 , "tsv" ) ||
Helper::file_extension( fname2 , "xml" ) ||
Helper::file_extension( fname2 , "ameta" ) ||
Helper::file_extension( fname2 , "stages" ) ||
Helper::file_extension( fname2 , "eannot" ) )
{
edf.load_annotations( fname + fname2 );
}
}
closedir (dir);
}
else
Helper::halt( "could not open folder " + fname );
}
else
{
// only annot files (.xml, .ftr, .annot, .eannot)
// i.e. skip .sedf files that might also be specified as
// attached to this EDF
if ( Helper::file_extension( fname , "annot" ) ||
Helper::file_extension( fname , "txt" ) ||
Helper::file_extension( fname , "tsv" ) ||
Helper::file_extension( fname , "xml" ) ||
Helper::file_extension( fname , "ameta" ) ||
Helper::file_extension( fname , "stages" ) ||
Helper::file_extension( fname , "eannot" ) )
{
edf.load_annotations( fname );
}
else
Helper::halt( "did not recognize annotation file extension: " + fname );
}
}
}
//
// Attach EDF Annotations, potentially
//
if ( edf.header.edfplus )
{
// must read if EDF+D (but only the time-track will be taken in)
// if EDF+C, then look at 'skip-edf-annots' flag
if ( edf.header.continuous && ! globals::skip_edf_annots )
edf.annotations->from_EDF( edf , edf.edfz_ptr() );
else if ( ! edf.header.continuous )
edf.annotations->from_EDF( edf , edf.edfz_ptr() );
}
//
// Now, all annotations (except EPOCH-ANNOT) are attached and can be reported on
//
std::vector<std::string> names = edf.annotations->names();
if ( names.size() > 0 ) logger << "\n annotations:\n";
for (int a = 0 ; a < names.size() ; a++ )
{
annot_t * annot = edf.annotations->find( names[a] );
if ( annot == NULL ) Helper::halt( "internal problem in list_all_annotations()" );
// do not show special annots [ duration_hms, duration_sec, epoch_sec, start_hms ]
if ( annot->special() ) continue;
const int num_events = annot->num_interval_events();
const int nf = annot->types.size();
// verbose mode
if ( globals::verbose )
{
logger << " [" << names[a] << "] "
<< num_events << " instance(s)"
<< " (from " << annot->file << ")\n";
// list instance IDs (up to 4) if multiple or differnt from annot name
// but only if there are >1 unique value, *and* the number of unique values
// does not equal the total instance count (i.e. do not print if just time-stamp
// or count for each ID, only if some coding
std::set<std::string> instance_ids = annot->instance_ids();
if ( instance_ids.size() > 0 && instance_ids.size() != num_events )
{
if ( ! ( instance_ids.size() == 1
&& ( *instance_ids.begin() == names[a] || *instance_ids.begin() == "." ) ) )
{
logger << " " << instance_ids.size() << " instance IDs: ";
std::set<std::string>::const_iterator ii = instance_ids.begin();
int icnt = 0 ;
while ( ii != instance_ids.end() )
{
logger << " " << *ii ;
++icnt;
if ( icnt > 4 ) { logger << " ..." ; break; }
++ii;
}
logger << "\n";
}
}
// lists meta-data
if ( nf > 1 )
{
logger << " w/ " << nf << " field(s):";
std::map<std::string,globals::atype_t>::const_iterator aa = annot->types.begin();
while ( aa != annot->types.end() )
{
logger << " " << aa->first << "[" << globals::type_name[ aa->second ] << "]";
++aa;
}
logger << "\n";
}
}
//
// else non-verbose annotaiton listing
//
else
{
if ( a != 0 && a % 4 == 0 ) logger << "\n ";
else if ( a != 0 ) logger << " |";
else logger << " ";
logger << " " << names[a] << " (x" << num_events << ")";
}
}
logger << "\n";
//
// Automatically generate channel type variables based on attached EDF
//
cmd.define_channel_type_variables( edf );
//
// Set special 'id' variable to EDF ID
//
cmd_t::ivars[ edf.id ][ "id" ] = edf.id;
//
// List any individual level variables (including new channel type variables, and ${id})
//
if ( cmd_t::ivars.find( edf.id ) != cmd_t::ivars.end() )
{
logger << "\n variables:\n";
const std::map<std::string,std::string> & newvars = cmd_t::ivars.find( edf.id )->second;
std::map<std::string,std::string>::const_iterator vv = newvars.begin();
int icnt = 0 ;
while ( vv != newvars.end() )