forked from fieldtrip/fieldtrip
-
Notifications
You must be signed in to change notification settings - Fork 0
/
ft_artifact_zvalue.m
1134 lines (1046 loc) · 46.5 KB
/
ft_artifact_zvalue.m
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
function [cfg, artifact] = ft_artifact_zvalue(cfg, data)
% FT_ARTIFACT_ZVALUE reads the interesting segments of data from file and identifies
% artifacts by means of thresholding the z-transformed value of the preprocessed raw data.
% Depending on the preprocessing options, this method will be sensitive to EOG, muscle or
% jump artifacts. This procedure only works on continuously recorded data.
%
% Use as
% [cfg, artifact] = ft_artifact_zvalue(cfg)
% with the configuration options
% cfg.dataset = string with the filename
% or
% cfg.headerfile = string with the filename
% cfg.datafile = string with the filename
% and optionally
% cfg.headerformat
% cfg.dataformat
%
% Alternatively you can use it as
% [cfg, artifact] = ft_artifact_zvalue(cfg, data)
% where the input data is a structure as obtained from FT_PREPROCESSING.
%
% The required configuration settings are:
% cfg.trl = structure that defines the data segments of interest. See FT_DEFINETRIAL
% cfg.continuous = 'yes' or 'no' whether the file contains continuous data (default = 'yes')
% and
% cfg.artfctdef.zvalue.channel
% cfg.artfctdef.zvalue.cutoff
% cfg.artfctdef.zvalue.trlpadding
% cfg.artfctdef.zvalue.fltpadding
% cfg.artfctdef.zvalue.artpadding
%
% If you encounter difficulties with memory usage, you can use
% cfg.memory = 'low' or 'high', whether to be memory or computationally efficient, respectively (default = 'high')
%
% The optional configuration settings (see below) are:
% cfg.artfctdef.zvalue.artfctpeak = 'yes' or 'no'
% cfg.artfctdef.zvalue.interactive = 'yes' or 'no'
%
% If you specify artfctpeak='yes', the maximum value of the artifact within its range
% will be found and saved into cfg.artfctdef.zvalue.peaks.
%
% If you specify interactive='yes', a GUI will be started and you can manually
% accept/reject detected artifacts, and/or change the threshold. To control the
% graphical interface via keyboard, use the following keys:
%
% q : Stop
%
% comma : Step to the previous artifact trial
% a : Specify artifact trial to display
% period : Step to the next artifact trial
%
% x : Step 10 trials back
% leftarrow : Step to the previous trial
% t : Specify trial to display
% rightarrow : Step to the next trial
% c : Step 10 trials forward
%
% k : Keep trial
% space : Mark complete trial as artifact
% r : Mark part of trial as artifact
%
% downarrow : Shift the z-threshold down
% z : Specify the z-threshold
% uparrow : Shift the z-threshold down
%
% Use also, e.g. as input to DSS option of ft_componentanalysis
% cfg.artfctdef.zvalue.artfctpeakrange=[-0.25 0.25], for example to indicate range
% around peak to include, saved into cfg.artfctdef.zvalue.dssartifact. The default is
% [0 0]. Range will respect trial boundaries (i.e. be shorter if peak is near
% beginning or end of trial). Samples between trials will be removed; thus this won't
% match .sampleinfo of the data structure.
%
% Configuration settings related to the preprocessing of the data are
% cfg.artfctdef.zvalue.lpfilter = 'no' or 'yes' lowpass filter
% cfg.artfctdef.zvalue.hpfilter = 'no' or 'yes' highpass filter
% cfg.artfctdef.zvalue.bpfilter = 'no' or 'yes' bandpass filter
% cfg.artfctdef.zvalue.bsfilter = 'no' or 'yes' bandstop filter for line noise removal
% cfg.artfctdef.zvalue.dftfilter = 'no' or 'yes' line noise removal using discrete fourier transform
% cfg.artfctdef.zvalue.medianfilter = 'no' or 'yes' jump preserving median filter
% cfg.artfctdef.zvalue.lpfreq = lowpass frequency in Hz
% cfg.artfctdef.zvalue.hpfreq = highpass frequency in Hz
% cfg.artfctdef.zvalue.bpfreq = bandpass frequency range, specified as [low high] in Hz
% cfg.artfctdef.zvalue.bsfreq = bandstop frequency range, specified as [low high] in Hz
% cfg.artfctdef.zvalue.lpfiltord = lowpass filter order
% cfg.artfctdef.zvalue.hpfiltord = highpass filter order
% cfg.artfctdef.zvalue.bpfiltord = bandpass filter order
% cfg.artfctdef.zvalue.bsfiltord = bandstop filter order
% cfg.artfctdef.zvalue.medianfiltord = length of median filter
% cfg.artfctdef.zvalue.lpfilttype = digital filter type, 'but' (default) or 'firws' or 'fir' or 'firls'
% cfg.artfctdef.zvalue.hpfilttype = digital filter type, 'but' (default) or 'firws' or 'fir' or 'firls'
% cfg.artfctdef.zvalue.bpfilttype = digital filter type, 'but' (default) or 'firws' or 'fir' or 'firls'
% cfg.artfctdef.zvalue.bsfilttype = digital filter type, 'but' (default) or 'firws' or 'fir' or 'firls'
% cfg.artfctdef.zvalue.detrend = 'no' or 'yes'
% cfg.artfctdef.zvalue.demean = 'no' or 'yes'
% cfg.artfctdef.zvalue.baselinewindow = [begin end] in seconds, the default is the complete trial
% cfg.artfctdef.zvalue.hilbert = 'no' or 'yes'
% cfg.artfctdef.zvalue.rectify = 'no' or 'yes'
%
% The output argument "artifact" is a Nx2 matrix comparable to the
% "trl" matrix of FT_DEFINETRIAL. The first column of which specifying the
% beginsamples of an artifact period, the second column contains the
% endsamples of the artifactperiods.
%
% See also FT_REJECTARTIFACT, FT_ARTIFACT_CLIP, FT_ARTIFACT_ECG, FT_ARTIFACT_EOG,
% FT_ARTIFACT_JUMP, FT_ARTIFACT_MUSCLE, FT_ARTIFACT_THRESHOLD, FT_ARTIFACT_ZVALUE
% Copyright (C) 2003-2011, Jan-Mathijs Schoffelen & Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip 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.
%
% FieldTrip 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 FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
% these are used by the ft_preamble/ft_postamble function and scripts
ft_revision = '$Id$';
ft_nargin = nargin;
ft_nargout = nargout;
% do the general setup of the function
ft_defaults
ft_preamble init
ft_preamble provenance
ft_preamble loadvar data
% the ft_abort variable is set to true or false in ft_preamble_init
if ft_abort
return
end
% set default rejection parameters
cfg.headerformat = ft_getopt(cfg, 'headerformat', []);
cfg.dataformat = ft_getopt(cfg, 'dataformat', []);
cfg.memory = ft_getopt(cfg, 'memory', 'high');
cfg.artfctdef = ft_getopt(cfg, 'artfctdef', []);
cfg.artfctdef.zvalue = ft_getopt(cfg.artfctdef, 'zvalue', []);
cfg.artfctdef.zvalue.method = ft_getopt(cfg.artfctdef.zvalue, 'method', 'all');
cfg.artfctdef.zvalue.ntrial = ft_getopt(cfg.artfctdef.zvalue, 'ntrial', 10);
cfg.artfctdef.zvalue.channel = ft_getopt(cfg.artfctdef.zvalue, 'channel', {});
cfg.artfctdef.zvalue.trlpadding = ft_getopt(cfg.artfctdef.zvalue, 'trlpadding', 0);
cfg.artfctdef.zvalue.fltpadding = ft_getopt(cfg.artfctdef.zvalue, 'fltpadding', 0);
cfg.artfctdef.zvalue.artpadding = ft_getopt(cfg.artfctdef.zvalue, 'artpadding', 0);
cfg.artfctdef.zvalue.interactive = ft_getopt(cfg.artfctdef.zvalue, 'interactive', 'no');
cfg.artfctdef.zvalue.cumulative = ft_getopt(cfg.artfctdef.zvalue, 'cumulative', 'yes');
cfg.artfctdef.zvalue.artfctpeak = ft_getopt(cfg.artfctdef.zvalue, 'artfctpeak', 'no');
cfg.artfctdef.zvalue.artfctpeakrange = ft_getopt(cfg.artfctdef.zvalue, 'artfctpeakrange',[0 0]);
% for backward compatibility
cfg.artfctdef = ft_checkconfig(cfg.artfctdef, 'renamed', {'blc', 'demean'});
cfg.artfctdef = ft_checkconfig(cfg.artfctdef, 'renamed', {'blcwindow' 'baselinewindow'});
cfg.artfctdef.zvalue = ft_checkconfig(cfg.artfctdef.zvalue, 'renamed', {'sgn', 'channel'});
cfg.artfctdef.zvalue = ft_checkconfig(cfg.artfctdef.zvalue, 'renamed', {'feedback', 'interactive'});
if isfield(cfg.artfctdef.zvalue, 'artifact')
fprintf('zvalue artifact detection has already been done, retaining artifacts\n');
artifact = cfg.artfctdef.zvalue.artifact;
return
end
% set feedback
cfg.feedback = ft_getopt(cfg, 'feedback', 'text');
% clear old warnings from this stack
ft_warning('-clear')
% flag whether to compute z-value per trial or not, rationale being that if
% there are fluctuations in the variance across trials (e.g. due to
% position differences in MEG measurements) which don't have to do with the artifact per se,
% the detection is compromised (although the data quality is questionable
% when there is a lot of movement to begin with).
pertrial = strcmp(cfg.artfctdef.zvalue.method, 'trial');
demeantrial = strcmp(cfg.artfctdef.zvalue.method, 'trialdemean');
if pertrial
if isfield(cfg.artfctdef.zvalue, 'ntrial') && cfg.artfctdef.zvalue.ntrial>0
pertrial = cfg.artfctdef.zvalue.ntrial;
else
ft_error('you should specify cfg.artfctdef.zvalue.ntrial, and it should be > 0');
end
end
% the data can be passed as input arguments or can be read from disk
hasdata = exist('data', 'var');
if ~hasdata
% only cfg given, read data from disk
cfg = ft_checkconfig(cfg, 'dataset2files', 'yes');
hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat);
trl = cfg.trl;
else
% check whether the value for trlpadding makes sense
if cfg.artfctdef.zvalue.trlpadding > 0
% negative trlpadding is allowed with in-memory data
ft_error('you cannot use positive trlpadding with in-memory data');
end
% check if the input data is valid for this function
data = ft_checkdata(data, 'datatype', 'raw', 'hassampleinfo', 'yes');
cfg = ft_checkconfig(cfg, 'forbidden', {'dataset', 'headerfile', 'datafile'});
hdr = ft_fetch_header(data);
trl = data.sampleinfo;
end
% set default cfg.continuous
if ~isfield(cfg, 'continuous')
if hdr.nTrials==1
cfg.continuous = 'yes';
else
cfg.continuous = 'no';
end
end
trlpadding = round(cfg.artfctdef.zvalue.trlpadding*hdr.Fs);
fltpadding = round(cfg.artfctdef.zvalue.fltpadding*hdr.Fs);
artpadding = round(cfg.artfctdef.zvalue.artpadding*hdr.Fs);
trl(:,1) = trl(:,1) - trlpadding; % pad the trial with some samples, in order to detect
trl(:,2) = trl(:,2) + trlpadding; % artifacts at the edges of the relevant trials.
if size(trl, 2) >= 3
trl(:,3) = trl(:,3) - trlpadding; % the offset can ofcourse be adjusted as well
elseif hasdata
% reconstruct offset
for tr=1:size(trl, 1)
% account for 0 might not be in data.time
t0 = interp1(data.time{tr}, 1:numel(data.time{tr}), 0, 'linear', 'extrap');
trl(tr, 3) = -t0+1 - trlpadding;
end
else
% assuming that the trial starts at t=0s
trl(:, 3) = trl(:, 1);
end
trllength = trl(:,2) - trl(:,1) + 1; % length of each trial
numtrl = size(trl,1);
cfg.artfctdef.zvalue.trl = trl; % remember where we are going to look for artifacts
cfg.artfctdef.zvalue.channel = ft_channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
numsgn = length(sgnind);
thresholdsum = strcmp(cfg.artfctdef.zvalue.cumulative, 'yes');
if numsgn<1
ft_error('no channels selected');
end
% read the data and apply preprocessing options
sumval = zeros(numsgn, 1);
sumsqr = zeros(numsgn, 1);
numsmp = zeros(numsgn, 1);
ft_progress('init', cfg.feedback, ['searching for artifacts in ' num2str(numsgn) ' channels']);
for trlop = 1:numtrl
ft_progress(trlop/numtrl, 'searching in trial %d from %d\n', trlop, numtrl);
if strcmp(cfg.memory, 'low') % store nothing in memory
if hasdata
dat = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous, 'no'), 'skipcheckdata', 1);
else
dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
end
dat = preproc(dat, cfg.artfctdef.zvalue.channel, offset2time(0, hdr.Fs, size(dat,2)), cfg.artfctdef.zvalue, fltpadding, fltpadding);
if trlop==1 && ~pertrial
sumval = zeros(size(dat,1), 1);
sumsqr = zeros(size(dat,1), 1);
numsmp = zeros(size(dat,1), 1);
numsgn = size(dat,1);
elseif trlop==1 && pertrial
sumval = zeros(size(dat,1), numtrl);
sumsqr = zeros(size(dat,1), numtrl);
numsmp = zeros(size(dat,1), numtrl);
numsgn = size(dat,1);
end
if ~pertrial
% accumulate the sum and the sum-of-squares
sumval = sumval + nansum(dat,2);
sumsqr = sumsqr + nansum(dat.^2,2);
numsmp = numsmp + size(dat,2);
else
% store per trial the sum and the sum-of-squares
sumval(:,trlop) = sum(dat,2);
sumsqr(:,trlop) = sum(dat.^2,2);
numsmp(:,trlop) = size(dat,2);
end
else % store all data in memory, saves computation time
if hasdata
dat{trlop} = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous, 'no'), 'skipcheckdata', 1);
else
dat{trlop} = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
end
dat{trlop} = preproc(dat{trlop}, cfg.artfctdef.zvalue.channel, offset2time(0, hdr.Fs, size(dat{trlop},2)), cfg.artfctdef.zvalue, fltpadding, fltpadding);
if trlop==1 && ~pertrial
sumval = zeros(size(dat{1},1), 1);
sumsqr = zeros(size(dat{1},1), 1);
numsmp = zeros(size(dat{1},1), 1);
numsgn = size(dat{1},1);
elseif trlop==1 && pertrial
sumval = zeros(size(dat{1},1), numtrl);
sumsqr = zeros(size(dat{1},1), numtrl);
numsmp = zeros(size(dat{1},1), numtrl);
numsgn = size(dat{1},1);
end
if ~pertrial
% accumulate the sum and the sum-of-squares
sumval = sumval + nansum(dat{trlop},2);
sumsqr = sumsqr + nansum(dat{trlop}.^2,2);
numsmp = numsmp + size(dat{trlop},2);
else
% store per trial the sum and the sum-of-squares
sumval(:,trlop) = sum(dat{trlop},2);
sumsqr(:,trlop) = sum(dat{trlop}.^2,2);
numsmp(:,trlop) = size(dat{trlop},2);
end
end
end % for trlop
ft_progress('close');
if pertrial>1
sumval = ft_preproc_smooth(sumval, pertrial)*pertrial;
sumsqr = ft_preproc_smooth(sumsqr, pertrial)*pertrial;
numsmp = ft_preproc_smooth(numsmp, pertrial)*pertrial;
end
% compute the average and the standard deviation
datavg = sumval./numsmp;
datstd = sqrt(sumsqr./numsmp - (sumval./numsmp).^2);
if strcmp(cfg.memory, 'low')
fprintf('\n');
end
zmax = cell(1, numtrl);
zsum = cell(1, numtrl);
zindx = cell(1, numtrl);
% create a vector that indexes the trials, or is all 1, in order
% to a per trial z-scoring, or use a static std and mean (used in lines 317
% and 328)
if pertrial
indvec = 1:numtrl;
else
indvec = ones(1,numtrl);
end
for trlop = 1:numtrl
if strcmp(cfg.memory, 'low') % store nothing in memory (note that we need to preproc AGAIN... *yawn*
fprintf('.');
if hasdata
dat = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous, 'no'));
else
dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
end
dat = preproc(dat, cfg.artfctdef.zvalue.channel, offset2time(0, hdr.Fs, size(dat,2)), cfg.artfctdef.zvalue, fltpadding, fltpadding);
zmax{trlop} = -inf + zeros(1,size(dat,2));
zsum{trlop} = zeros(1,size(dat,2));
zindx{trlop} = zeros(1,size(dat,2));
nsmp = size(dat,2);
zdata = (dat - datavg(:,indvec(trlop)*ones(1,nsmp)))./datstd(:,indvec(trlop)*ones(1,nsmp)); % convert the filtered data to z-values
zsum{trlop} = nansum(zdata,1); % accumulate the z-values over channels
[zmax{trlop},ind] = max(zdata,[],1); % find the maximum z-value and remember it
zindx{trlop} = sgnind(ind); % also remember the channel number that has the largest z-value
else
% initialize some matrices
zmax{trlop} = -inf + zeros(1,size(dat{trlop},2));
zsum{trlop} = zeros(1,size(dat{trlop},2));
zindx{trlop} = zeros(1,size(dat{trlop},2));
nsmp = size(dat{trlop},2);
zdata = (dat{trlop} - datavg(:,indvec(trlop)*ones(1,nsmp)))./datstd(:,indvec(trlop)*ones(1,nsmp)); % convert the filtered data to z-values
zsum{trlop} = nansum(zdata,1); % accumulate the z-values over channels
[zmax{trlop},ind] = max(zdata,[],1); % find the maximum z-value and remember it
zindx{trlop} = sgnind(ind); % also remember the channel number that has the largest z-value
end
% This alternative code does the same, but it is much slower
% for i=1:size(zmax{trlop},2)
% if zdata{trlop}(i)>zmax{trlop}(i)
% % update the maximum value and channel index
% zmax{trlop}(i) = zdata{trlop}(i);
% zindx{trlop}(i) = sgnind(sgnlop);
% end
% end
end % for trlop
if demeantrial
for trlop = 1:numtrl
zmax{trlop} = zmax{trlop}-mean(zmax{trlop},2);
zsum{trlop} = zsum{trlop}-mean(zsum{trlop},2);
end
end
%for sgnlop=1:numsgn
% % read the data and apply preprocessing options
% sumval = 0;
% sumsqr = 0;
% numsmp = 0;
% fprintf('searching channel %s ', cfg.artfctdef.zvalue.channel{sgnlop});
% for trlop = 1:numtrl
% fprintf('.');
% if hasdata
% dat{trlop} = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', sgnind(sgnlop), 'checkboundary', strcmp(cfg.continuous, 'no'));
% else
% dat{trlop} = read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', sgnind(sgnlop), 'checkboundary', strcmp(cfg.continuous, 'no'));
% end
% dat{trlop} = preproc(dat{trlop}, cfg.artfctdef.zvalue.channel(sgnlop), hdr.Fs, cfg.artfctdef.zvalue, [], fltpadding, fltpadding);
% % accumulate the sum and the sum-of-squares
% sumval = sumval + sum(dat{trlop},2);
% sumsqr = sumsqr + sum(dat{trlop}.^2,2);
% numsmp = numsmp + size(dat{trlop},2);
% end % for trlop
%
% % compute the average and the standard deviation
% datavg = sumval./numsmp;
% datstd = sqrt(sumsqr./numsmp - (sumval./numsmp).^2);
%
% for trlop = 1:numtrl
% if sgnlop==1
% % initialize some matrices
% zdata{trlop} = zeros(size(dat{trlop}));
% zmax{trlop} = -inf + zeros(size(dat{trlop}));
% zsum{trlop} = zeros(size(dat{trlop}));
% zindx{trlop} = zeros(size(dat{trlop}));
% end
% zdata{trlop} = (dat{trlop} - datavg)./datstd; % convert the filtered data to z-values
% zsum{trlop} = zsum{trlop} + zdata{trlop}; % accumulate the z-values over channels
% zmax{trlop} = max(zmax{trlop}, zdata{trlop}); % find the maximum z-value and remember it
% zindx{trlop}(zmax{trlop}==zdata{trlop}) = sgnind(sgnlop); % also remember the channel number that has the largest z-value
%
% % This alternative code does the same, but it is much slower
% % for i=1:size(zmax{trlop},2)
% % if zdata{trlop}(i)>zmax{trlop}(i)
% % % update the maximum value and channel index
% % zmax{trlop}(i) = zdata{trlop}(i);
% % zindx{trlop}(i) = sgnind(sgnlop);
% % end
% % end
% end
% fprintf('\n');
%end % for sgnlop
for trlop = 1:numtrl
zsum{trlop} = zsum{trlop} ./ sqrt(numsgn);
end
% always create figure
% keypress to enable keyboard uicontrol
h = figure('KeyPressFcn', @keyboard_cb);
set(h, 'visible', 'off');
opt.artcfg = cfg.artfctdef.zvalue;
opt.artval = {};
opt.artpadding = artpadding;
opt.cfg = cfg;
opt.channel = 'artifact';
opt.hdr = hdr;
opt.numtrl = size(trl,1);
opt.quit = 0;
opt.threshold = cfg.artfctdef.zvalue.cutoff;
opt.thresholdsum = thresholdsum;
opt.trialok = true(1,opt.numtrl); % OK by means of objective criterion
opt.keep = zeros(1,opt.numtrl); % OK overruled by user +1 to keep, -1 to reject, start all zeros for callback to work
opt.trl = trl;
opt.trlop = 1;
opt.updatethreshold = true;
opt.zmax = zmax;
opt.zsum = zsum;
if ~thresholdsum
opt.zval = zmax;
else
opt.zval = zsum;
end
opt.zindx = zindx;
if ~hasdata
opt.data = {};
else
opt.data = data;
end
if strcmp(cfg.artfctdef.zvalue.interactive, 'yes')
set(h, 'visible', 'on');
set(h, 'CloseRequestFcn', @cleanup_cb);
% give graphical feedback and allow the user to modify the threshold
set(h, 'position', [100 200 900 400]);
h1 = axes('position', [0.05 0.15 0.4 0.8]);
h2 = axes('position', [0.5 0.57 0.45 0.38]);
h3 = axes('position', [0.5 0.15 0.45 0.32]);
opt.h1 = h1;
opt.h2 = h2;
opt.h3 = h3;
setappdata(h, 'opt', opt);
artval_cb(h);
redraw_cb(h);
% make the user interface elements for the data view, the order of the elements
% here is from left to right and should match the order in the documentation
uicontrol('tag', 'width1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'stop', 'userdata', 'q');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'comma');
uicontrol('tag', 'width1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'artifact', 'userdata', 'a');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'period');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<<', 'userdata', 'x');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'leftarrow');
uicontrol('tag', 'width1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'trial', 'userdata', 't');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'rightarrow');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>>', 'userdata', 'c');
uicontrol('tag', 'width3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'keep trial', 'userdata', 'k');
uicontrol('tag', 'width3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'reject full', 'userdata', 'space');
uicontrol('tag', 'width3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'reject part', 'userdata', 'r');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'downarrow');
uicontrol('tag', 'width3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'threshold', 'userdata', 'z');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'uparrow');
%uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'control+uparrow')
%uicontrol('tag', 'width1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'channel', 'userdata', 'c')
%uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'control+downarrow')
ft_uilayout(h, 'tag', 'width1', 'width', 0.10, 'height', 0.05);
ft_uilayout(h, 'tag', 'width2', 'width', 0.05, 'height', 0.05);
ft_uilayout(h, 'tag', 'width3', 'width', 0.12, 'height', 0.05);
ft_uilayout(h, 'tag', 'width1', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'width2', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'width3', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'width1', 'retag', 'viewui');
ft_uilayout(h, 'tag', 'width2', 'retag', 'viewui');
ft_uilayout(h, 'tag', 'width3', 'retag', 'viewui');
ft_uilayout(h, 'tag', 'viewui', 'BackgroundColor', [0.8 0.8 0.8], 'hpos', 'auto', 'vpos', 0.005);
while opt.quit==0
uiwait(h);
opt = getappdata(h, 'opt');
end
else
% compute the artifacts given the settings in the cfg
setappdata(h, 'opt', opt);
artval_cb(h);
end
h = getparent(h);
opt = getappdata(h, 'opt');
% convert to one long vector
dum = zeros(1,max(opt.trl(:,2)));
for trlop=1:opt.numtrl
dum(opt.trl(trlop,1):opt.trl(trlop,2)) = opt.artval{trlop};
end
artval = dum;
% find the padded artifacts and put them in a Nx2 trl-like matrix
artbeg = find(diff([0 artval])== 1);
artend = find(diff([artval 0])==-1);
artifact = [artbeg(:) artend(:)];
if strcmp(cfg.artfctdef.zvalue.artfctpeak, 'yes')
cnt=1;
shift=opt.trl(1,1)-1;
for tt=1:opt.numtrl
if tt==1
tind{tt}=find(artifact(:,2)<opt.trl(tt,2));
else
tind{tt}=intersect(find(artifact(:,2)<opt.trl(tt,2)),find(artifact(:,2)>opt.trl(tt-1,2)));
end
artbegend=[(artifact(tind{tt},1)-opt.trl(tt,1)+1) (artifact(tind{tt},2)-opt.trl(tt,1)+1)];
for rr=1:size(artbegend,1)
[mx,mxnd]=max(opt.zval{tt}(artbegend(rr,1):artbegend(rr,2)));
peaks(cnt)=artifact(tind{tt}(rr),1)+mxnd-1;
dssartifact(cnt,1)=max(peaks(cnt)+cfg.artfctdef.zvalue.artfctpeakrange(1)*hdr.Fs,opt.trl(tt,1));
dssartifact(cnt,2)=min(peaks(cnt)+cfg.artfctdef.zvalue.artfctpeakrange(2)*hdr.Fs,opt.trl(tt,2));
peaks(cnt)=peaks(cnt)-shift;
dssartifact(cnt,:)=dssartifact(cnt,:)-shift;
cnt=cnt+1;
end
if tt<opt.numtrl
shift=shift+opt.trl(tt+1,1)-opt.trl(tt,2)-1;
end
clear artbegend
end
cfg.artfctdef.zvalue.peaks=peaks';
cfg.artfctdef.zvalue.dssartifact=dssartifact;
end
% remember the artifacts that were found
cfg.artfctdef.zvalue.artifact = artifact;
% also update the threshold
cfg.artfctdef.zvalue.cutoff = opt.threshold;
fprintf('detected %d artifacts\n', size(artifact,1));
delete(h);
% do the general cleanup and bookkeeping at the end of the function
ft_postamble provenance
ft_postamble previous data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function artval_cb(h, eventdata)
opt = getappdata(h, 'opt');
artval = cell(1,opt.numtrl);
for trlop=1:opt.numtrl
if opt.thresholdsum
% threshold the accumulated z-values
artval{trlop} = opt.zsum{trlop}>opt.threshold;
else
% threshold the max z-values
artval{trlop} = opt.zmax{trlop}>opt.threshold;
end
% pad the artifacts
artbeg = find(diff([0 artval{trlop}])== 1);
artend = find(diff([artval{trlop} 0])==-1);
artbeg = artbeg - opt.artpadding;
artend = artend + opt.artpadding;
artbeg(artbeg<1) = 1;
artend(artend>length(artval{trlop})) = length(artval{trlop});
for artlop=1:length(artbeg)
artval{trlop}(artbeg(artlop):artend(artlop)) = 1;
end
opt.trialok(trlop) = isempty(artbeg);
end
for trlop = find(opt.keep==1 & opt.trialok==0)
% overrule the objective criterion, i.e. keep the trial when the user
% wants to keep it
artval{trlop}(:) = 0;
end
for trlop = find(opt.keep<0 & opt.trialok==1)
% if the user specifies that the trial is not OK
% reject the whole trial if there is no extra-threshold data,
% otherwise use the artifact as found by the thresholding
if opt.thresholdsum && opt.keep(trlop)==-1
% threshold the accumulated z-values
artval{trlop} = opt.zsum{trlop}>opt.threshold;
elseif opt.keep(trlop)==-1
% threshold the max z-values
artval{trlop} = opt.zmax{trlop}>opt.threshold;
elseif opt.keep(trlop)==-2
artval{trlop}(:) = 1;
end
% pad the artifacts
artbeg = find(diff([0 artval{trlop}])== 1);
artend = find(diff([artval{trlop} 0])==-1);
artbeg = artbeg - opt.artpadding;
artend = artend + opt.artpadding;
artbeg(artbeg<1) = 1;
artend(artend>length(artval{trlop})) = length(artval{trlop});
if ~isempty(artbeg)
for artlop=1:length(artbeg)
artval{trlop}(artbeg(artlop):artend(artlop)) = 1;
end
else
artval{trlop}(:) = 1;
end
end
for trlop = find(opt.keep==-2 & opt.trialok==0)
% if the user specifies the whole trial to be rejected define the whole
% segment to be bad
artval{trlop}(:) = 1;
% pad the artifacts
artbeg = find(diff([0 artval{trlop}])== 1);
artend = find(diff([artval{trlop} 0])==-1);
artbeg = artbeg - opt.artpadding;
artend = artend + opt.artpadding;
artbeg(artbeg<1) = 1;
artend(artend>length(artval{trlop})) = length(artval{trlop});
if ~isempty(artbeg)
for artlop=1:length(artbeg)
artval{trlop}(artbeg(artlop):artend(artlop)) = 1;
end
else
artval{trlop}(:) = 1;
end
end
opt.artval = artval;
setappdata(h, 'opt', opt);
uiresume;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function keyboard_cb(h, eventdata)
% If a mouseclick was made, use that value. If not, determine the key that
% corresponds to the uicontrol element that was activated.
if isa(eventdata, 'matlab.ui.eventdata.ActionData') % only the case when clicked with mouse
curKey = get(h, 'userdata');
elseif isa(eventdata, 'matlab.ui.eventdata.KeyData') % only when key was pressed
if isempty(eventdata.Character) && any(strcmp(eventdata.Key, {'control', 'shift', 'alt', '0'}))
% only a modifier key was pressed
return
end
if isempty(eventdata.Modifier)
curKey = eventdata.Key;
else
curKey = [sprintf('%s+', eventdata.Modifier{:}) eventdata.Key];
end
elseif isfield(eventdata, 'Key') % only when key was pressed
curKey = eventdata.Key;
elseif isempty(eventdata) % matlab2012b returns an empty double upon a mouse click
curKey = get(h, 'userdata');
else
ft_error('cannot process user input, please report this on http://bugzilla.fieldtriptoolbox.org including your MATLAB version');
end
h = getparent(h); % otherwise h is empty if isa [...].ActionData
opt = getappdata(h, 'opt');
switch strtrim(curKey)
case 'leftarrow' % change trials
opt.trlop = max(opt.trlop - 1, 1); % should not be smaller than 1
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
case 'x'
opt.trlop = max(opt.trlop - 10, 1); % should not be smaller than 1
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
case 'rightarrow'
opt.trlop = min(opt.trlop + 1, opt.numtrl); % should not be larger than the number of trials
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
case 'c'
opt.trlop = min(opt.trlop + 10, opt.numtrl); % should not be larger than the number of trials
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
case 'uparrow' % change threshold
opt.threshold = opt.threshold+0.5;
opt.updatethreshold = true;
setappdata(h, 'opt', opt);
artval_cb(h, eventdata);
redraw_cb(h, eventdata);
opt = getappdata(h, 'opt'); % grab the opt-structure from the handle because it has been adjusted in the callbacks
opt.updatethreshold = false;
setappdata(h, 'opt', opt);
case 'downarrow'
opt.threshold = opt.threshold-0.5;
opt.updatethreshold = true;
setappdata(h, 'opt', opt);
artval_cb(h, eventdata);
redraw_cb(h, eventdata);
opt = getappdata(h, 'opt'); % grab the opt-structure from the handle because it has been adjusted in the callbacks
opt.updatethreshold = false;
setappdata(h, 'opt', opt);
case 'period' % change artifact
artfctindx = find(opt.trialok == 0);
sel = find(artfctindx>opt.trlop);
if ~isempty(sel)
opt.trlop = artfctindx(sel(1));
end
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
case 'comma'
artfctindx = find(opt.trialok == 0);
sel = find(artfctindx<opt.trlop);
if ~isempty(sel)
opt.trlop = artfctindx(sel(end));
end
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
% case 'control+uparrow' % change channel
% if strcmp(opt.channel, 'artifact')
% [dum, indx] = max(opt.zval);
% sgnind = opt.zindx(indx);
% else
% if ~isempty(opt.data)
% sgnind = match_str(opt.channel, opt.data.label);
% selchan = match_str(opt.artcfg.channel, opt.channel);
% else
% sgnind = match_str(opt.channel, opt.hdr.label);
% selchan = match_str(opt.artcfg.channel, opt.channel);
% end
% end
% numchan = numel(opt.artcfg.channel);
% chansel = min(selchan+1, numchan);
% % convert numeric array into cell-array with channel labels
% opt.channel = tmpchan(chansel);
% setappdata(h, 'opt', opt);
% redraw_cb(h, eventdata);
% case 'c' % select channel
% select = match_str([opt.artcfg.channel;{'artifact'}], opt.channel);
% opt.channel = select_channel_list([opt.artcfg.channel;{'artifact'}], select);
% setappdata(h, 'opt', opt);
% redraw_cb(h, eventdata);
% case 'control+downarrow'
% tmpchan = [opt.artcfg.channel;{'artifact'}]; % append the 'artifact' channel
% chansel = match_str(tmpchan, opt.channel);
% chansel = max(chansel-1, 1);
% % convert numeric array into cell-array with channel labels
% opt.channel = tmpchan(chansel);
% setappdata(h, 'opt', opt);
% redraw_cb(h, eventdata);
case 'a'
% select the artifact to display
response = inputdlg(sprintf('artifact trial to display'), 'specify', 1, {num2str(opt.trlop)});
if ~isempty(response)
artfctindx = find(opt.trialok == 0);
sel = str2double(response);
sel = min(numel(artfctindx), sel);
sel = max(1, sel);
opt.trlop = artfctindx(sel);
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
end
case 'q'
setappdata(h, 'opt', opt);
cleanup_cb(h);
case 't'
% select the trial to display
response = inputdlg(sprintf('trial to display'), 'specify', 1, {num2str(opt.trlop)});
if ~isempty(response)
opt.trlop = str2double(response);
opt.trlop = min(opt.trlop, opt.numtrl); % should not be larger than the number of trials
opt.trlop = max(opt.trlop, 1); % should not be smaller than 1
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
end
case 'z'
% select the threshold
response = inputdlg('z-threshold', 'specify', 1, {num2str(opt.threshold)});
if ~isempty(response)
opt.threshold = str2double(response);
opt.updatethreshold = true;
setappdata(h, 'opt', opt);
artval_cb(h, eventdata);
redraw_cb(h, eventdata);
opt = getappdata(h, 'opt'); % grab the opt-structure from the handle because it has been adjusted in the callbacks
opt.updatethreshold = false;
setappdata(h, 'opt', opt);
end
case 'k'
opt.keep(opt.trlop) = 1;
setappdata(h, 'opt', opt);
artval_cb(h);
redraw_cb(h);
case 'r'
% only of the trial contains a partial artifact
if opt.trialok(opt.trlop) == 0
opt.keep(opt.trlop) = -1;
end
setappdata(h, 'opt', opt);
artval_cb(h);
redraw_cb(h);
case 'space'
opt.keep(opt.trlop) = -2;
setappdata(h, 'opt', opt);
artval_cb(h);
redraw_cb(h);
case 'control+control'
% do nothing
case 'shift+shift'
% do nothing
case 'alt+alt'
% do nothing
otherwise
setappdata(h, 'opt', opt);
% this should be consistent with the help of the function
fprintf('----------------------------------------------------------------------\n');
fprintf(' q : Stop\n');
fprintf('\n');
fprintf(' comma : Step to the previous artifact trial\n');
fprintf(' a : Specify artifact trial to display\n');
fprintf(' period : Step to the next artifact trial\n');
fprintf('\n');
fprintf(' x : Step 10 trials back\n');
fprintf(' leftarrow : Step to the previous trial\n');
fprintf(' t : Specify trial to display\n');
fprintf(' rightarrow : Step to the next trial\n');
fprintf(' c : Step 10 trials forward\n');
fprintf('\n');
fprintf(' k : Keep trial\n');
fprintf(' space : Mark complete trial as artifact\n');
fprintf(' r : Mark part of trial as artifact\n');
fprintf('\n');
fprintf(' downarrow : Shift the z-threshold down\n');
fprintf(' z : Specify the z-threshold\n');
fprintf(' uparrow : Shift the z-threshold down\n');
fprintf('----------------------------------------------------------------------\n');
end
clear curKey;
uiresume(h);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function redraw_cb(h, eventdata)
h = getparent(h);
opt = getappdata(h, 'opt');
% make a local copy of the relevant variables
trlop = opt.trlop;
artval = opt.artval{trlop};
zindx = opt.zindx{trlop};
zval = opt.zval{trlop};
cfg = opt.cfg;
artcfg = opt.artcfg;
hdr = opt.hdr;
trl = opt.trl;
trlpadsmp = round(artcfg.trlpadding*hdr.Fs);
channel = opt.channel;
% determine the channel with the highest z-value to be displayed
% this is default behaviour but can be overruled in the gui
if strcmp(channel, 'artifact')
[dum, indx] = max(zval);
sgnind = zindx(indx);
else
if ~isempty(opt.data)
sgnind = match_str(channel, opt.data.label);
else
sgnind = match_str(channel, hdr.label);
end
end
if ~isempty(opt.data)
data = ft_fetch_data(opt.data, 'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous, 'no'));
else
data = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous, 'no'));
end
% data = preproc(data, '', hdr.Fs, artcfg, [], artcfg.fltpadding, artcfg.fltpadding);
% the string us used as title and printed in the command window
str = sprintf('trial %3d of %d, channel %s', trlop, size(trl,1), hdr.label{sgnind});
fprintf('showing %s\n', str);
%-----------------------------
% plot summary in left subplot
subplot(opt.h1); hold on;
% plot as a blue line only once
if isempty(get(opt.h1, 'children'))
for k = 1:opt.numtrl
xval = opt.trl(k,1):opt.trl(k,2);
if opt.thresholdsum
yval = opt.zsum{k};
else
yval = opt.zmax{k};
end
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'b', 'displayname', 'data');
xlabel('samples');
ylabel('z-value');
end
end
h1children = get(opt.h1, 'children');
% plot trial box
boxhandle = findall(h1children, 'displayname', 'highlight');
if isempty(boxhandle)
% draw it
xval = trl(opt.trlop,1):trl(opt.trlop,2);
if opt.thresholdsum
yval = opt.zsum{opt.trlop};
else
yval = opt.zmax{opt.trlop};
end
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'm', 'linewidth', 2, 'displayname', 'highlight');
else
% update it
xval = trl(opt.trlop,1):trl(opt.trlop,2);
if opt.thresholdsum
yval = opt.zsum{opt.trlop};
else
yval = opt.zmax{opt.trlop};
end
set(boxhandle, 'XData', xval);
set(boxhandle, 'YData', yval);
end
% plot as red lines the suprathreshold data points
thrhandle = findall(h1children, 'displayname', 'reddata');
if isempty(thrhandle)
% they have to be drawn
for k = 1:opt.numtrl
xval = trl(k,1):trl(k,2);
if opt.thresholdsum
yval = opt.zsum{k};