-
Notifications
You must be signed in to change notification settings - Fork 18
/
Copy pathbids_writeeventfile.m
297 lines (279 loc) · 14.4 KB
/
bids_writeeventfile.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
% BIDS_WRITEEVENTFILE - write events.tsv and (if toggled) events.json for individual dataset
% from EEG dataset
%
% Usage:
% bids_writeeventfile(EEG, fileOut, varargin)
%
% Inputs:
% 'EEG' - [struct] the EEG structure
%
% 'fileOut' - [string] filepath of the desired output location with file basename
% e.g. ~/BIDS_EXPORT/sub-01/ses-01/eeg/sub-01_ses-01_task-GoNogo
%
% Optional inputs:
%
% 'stimuli' - [cell] cell array of EEGLAB event type and corresponding file
% names for the stimulus on your computer.
% For example: { 'sound1' '/Users/xxxx/sounds/sound1.mp3';
% 'img1' '/Users/xxxx/sounds/img1.jpg' }
% (the semicolumn above is optional). Alternatively, after
% exporting to BIDS, create a stimuli folder and place your
% stimuli in that folder with a README file describing them.
%
% 'eInfo' - [cell] additional event information columns and their corresponding
% event fields in the EEGLAB event structure in format
% { '<BIDS field1>' '<EEG field1>';
% '<BIDS field2>' '<EEG field2>'}
% Note that EEGLAB event latency, duration, and type are inserted
% automatically as columns "sample" (latency), "onset" (latency in sec), "duration"
% (duration in sec), and "value" (EEGLAB event type). For example
% { 'sample' 'latency';
% 'value' 'type' }
%
% 'eInfoDesc' - [struct] structure describing additional or/and original
% event fields if you wish to redefine these.
% These are EEGLAB event fields listed above.
% See the BIDS format for more information
% eInfo.onset.LongName = 'Event onset'; % change default value
% eInfo.onset.Description = 'Event onset';
% eInfo.onset.Units = 'seconds';
% eInfo.reaction_time.LongName = 'Reaction time';
% eInfo.reaction_time.Units = 'seconds';
%
% 'renametype' - [cell] 2 column cell table for renaming type.
% For example { '2' 'standard';
% '4' 'oddball';
% '128' 'response' }
%
% 'trialtype' - [cell] 2 column cell table indicating the experiment condition of event
% for each event type. Equivalent to BIDS trial_type field. For example { '2' 'go';
% '4' 'nogo' }
%
% 'checkresponse' - [string]
%
% 'individualEventsJson' - [string] specify whether to write events.json
% file specifically for this dataset. Default is 'off' to only have a single
% top-level events.json file for the entire dataset
%
% 'ignoreemptyfields' ['on'|'off'] ignore event field defined in eInfo if
% it not present in the dataset. Setting to 'off' fills a
% column with 'n/a' for that field. Default is 'on'.
%
% Authors: Dung Truong, Arnaud Delorme, 2022
function bids_writeeventfile(EEG, fileOut, varargin)
opt = finputcheck(varargin, {
'stimuli' 'cell' {} {};
'eInfo' 'cell' {} {};
'omitsample' 'string' {'on' 'off'} {'off'};
'eInfoDesc' 'struct' {} struct([]);
'renametype' 'cell' {} {};
'trialtype' 'cell' {} {};
'checkresponse' 'string' {} '';
'ignoreemptyfields' 'string' {'on' 'off'} 'on';
'individualEventsJson' 'string' {'on' 'off'} 'off';
}, 'write_events_files');
if isstr(opt), error(opt); end
% write event file information
% --- _events.json
[folderOut,fileOut,~] = fileparts(fileOut);
fileOut = fullfile(folderOut,fileOut);
if ~isempty(EEG.event)
if strcmpi(opt.individualEventsJson,'on')
jsonwrite([ fileOut '_events.json' ], opt.eInfoDesc,struct('indent',' '));
end
% --- _events.tsv
fid = fopen( [ fileOut '_events.tsv' ], 'w');
% -- parse eInfo
if isempty(opt.eInfo)
if isfield(EEG.event, 'onset') opt.eInfo(end+1,:) = { 'onset' 'onset' };
else opt.eInfo(end+1,:) = { 'onset' 'latency' }; end
opt.eInfo(end+1,:) = { 'duration' 'duration' };
opt.eInfo(end+1,:) = { 'sample' 'latency' };
if isfield(EEG.event, 'trial_type') opt.eInfo(end+1,:) = { 'trial_type' 'trial_type' };
elseif ~isempty(opt.trialtype) opt.eInfo(end+1,:) = { 'trial_type' 'xxxx' }; end % to be filled with event type based on opt.trialtype mapping
if isfield(EEG.event, 'value') opt.eInfo(end+1,:) = { 'value' 'value' };
else opt.eInfo(end+1,:) = { 'value' 'type' }; end
if isfield(EEG.event, 'response_time'), opt.eInfo(end+1,:) = { 'response_time' 'response_time' }; end
if isfield(EEG.event, 'stim_file'), opt.eInfo(end+1,:) = { 'stim_file' 'stim_file' }; end
if isfield(EEG.event, 'HED'), opt.eInfo(end+1,:) = { 'HED' 'HED' }; end
else
bids_fields = opt.eInfo(:,1);
if ~any(strcmp(bids_fields,'onset'))
if isfield(EEG.event, 'onset')
opt.eInfo(end+1,:) = { 'onset' 'onset' };
else
opt.eInfo(end+1,:) = { 'onset' 'latency' };
end
end
if ~any(strcmp(bids_fields,'duration')), opt.eInfo(end+1,:) = { 'duration' 'duration' }; end
if ~any(strcmp(bids_fields,'sample')) && isfield(EEG.event, 'latency'), opt.eInfo(end+1,:) = { 'sample' 'latency' }; end
if ~any(strcmp(bids_fields,'value'))
if isfield(EEG.event, 'value')
opt.eInfo(end+1,:) = { 'value' 'value' };
else
opt.eInfo(end+1,:) = { 'value' 'type' };
end
end
if ~isempty(opt.trialtype), opt.eInfo(end+1,:) = { 'trial_type' 'xxxx' }; end
end
if ~isempty(opt.stimuli)
opt.eInfo(end+1,:) = { 'stim_file' '' };
end
% reorder fields to put required and default fields first
fieldOrder = { 'onset' 'duration' 'sample' 'value'}; % 'HED' }; % remove HED from default column in events.tsv as HED tags should be put in events.json instead
% 'trial_type' 'response_time' 'stim_file' }; % no longer required by BIDS by default
newOrder = [];
for iField = 1:length(fieldOrder)
ind = strmatch(fieldOrder{iField}, opt.eInfo(:,1)', 'exact');
newOrder = [ newOrder ind ];
end
remainingInd = setdiff([1:size(opt.eInfo,1)], newOrder);
newOrder = [ newOrder remainingInd];
opt.eInfo = opt.eInfo(newOrder,:);
% scan events
eventFields = fieldnames(EEG.event);
for iEvent = 1:length(EEG.event)
str = {};
for iField = 1:size(opt.eInfo,1)
if iField > 2 && isempty(strmatch(opt.eInfo{iField,2}, eventFields, 'exact')) && strcmpi(opt.ignoreemptyfields, 'on')
if iEvent == 1
fprintf('Field %s not found in the dataset events and ignored\n', opt.eInfo{iField,2} )
if iField == size(opt.eInfo,1)
fprintf(fid, '\n');
end
end
else
if iEvent == 1
if strcmpi(opt.omitsample, 'off') || ~isequal(opt.eInfo{iField,1}, 'sample')
if iField == 1
fprintf(fid, '%s', opt.eInfo{iField,1});
else
fprintf(fid, '\t%s', opt.eInfo{iField,1});
end
if iField == size(opt.eInfo,1)
fprintf(fid, '\n');
end
end
end
tmpField = opt.eInfo{iField,2};
if strcmpi(tmpField, 'n/a')
str{end+1} = tmpField;
else
switch opt.eInfo{iField,1}
case 'onset'
onset = (EEG.event(iEvent).(tmpField)-1)/EEG.srate;
str{end+1} = num2str(onset, 10);
case 'duration'
if isfield(EEG.event, tmpField) && ~isempty(EEG.event(iEvent).(tmpField))
duration = num2str(EEG.event(iEvent).(tmpField)/EEG.srate, 10);
else
duration = 'n/a';
end
if isempty(duration) || strcmpi(duration, 'NaN')
duration = 'n/a';
end
str{end+1} = duration;
case 'sample'
if ~strcmpi(opt.omitsample, 'on')
if isfield(EEG.event, tmpField)
sample = num2str(EEG.event(iEvent).(tmpField)-1);
else
sample = 'n/a';
end
if isempty(sample) || strcmpi(sample, 'NaN')
sample = 'n/a';
end
str{end+1} = sample;
end
case 'trial_type'
% trial type (which is the experimental condition - not the same as EEGLAB)
if isfield(EEG.event(iEvent), tmpField) && ~isempty(EEG.event(iEvent).(tmpField))
trialType = EEG.event(iEvent).(tmpField);
if isnumeric(trialType)
trialType = num2str(trialType);
end
str{end+1} = trialType;
else
str{end+1} = 'n/a';
end
case 'response_time'
if isfield(EEG.event, tmpField)
response_time = num2str(EEG.event(iEvent).(tmpField));
else
response_time = 'n/a';
end
if isempty(response_time) || strcmpi(response_time, 'NaN')
response_time = 'n/a';
end
str{end+1} = response_time;
case 'stim_file'
if isempty(tmpField)
indStim = strmatch(EEG.event(iEvent).type, opt.stimuli(:,1));
if ~isempty(indStim)
stim_file = opt.stimuli{indStim, 2};
else
stim_file = 'n/a';
end
elseif isfield(EEG.event, tmpField)
if ~isempty(opt.stimuli)
error('Cannot use "stim_file" as a BIDS event field and use the "stimuli" option')
end
stim_file = num2str(EEG.event(iEvent).(tmpField));
else
stim_file = 'n/a';
end
if isempty(stim_file) || strcmpi(stim_file, 'NaN')
stim_file = 'n/a';
end
str{end+1} = stim_file;
case 'value'
if isfield(EEG.event, tmpField) && ~isempty(EEG.event(iEvent).(tmpField))
if isempty(opt.renametype)
eventValue = num2str(EEG.event(iEvent).(tmpField));
else
posType = strmatch(num2str(EEG.event(iEvent).(tmpField)), opt.renametype(:,1), 'exact');
if ~isempty(posType)
eventValue = opt.renametype{posType,2};
else
eventValue = num2str(EEG.event(iEvent).(tmpField));
end
end
if ~isempty(opt.checkresponse)
if iEvent+1 <= length(EEG.event) && strcmpi(EEG.event(iEvent+1).type, opt.checkresponse) && ~strcmpi(EEG.event(iEvent).type, opt.checkresponse)
eventValue = [ eventValue '_with_reponse' ];
response_time = (EEG.event(iEvent+1).latency - EEG.event(iEvent).latency)/EEG.srate;
str{end-1} = num2str(response_time*1000,'%1.0f');
end
end
else
eventValue = 'n/a';
end
if isequal(eventValue, 'NaN') || isempty(eventValue)
eventValue = 'n/a';
end
str{end+1} = eventValue;
otherwise
if isfield(EEG.event, opt.eInfo{iField,2})
tmpVal = EEG.event(iEvent).(opt.eInfo{iField,2});
if isnumeric(tmpVal)
tmpVal = num2str(tmpVal);
elseif iscell(tmpVal)
tmpVal = tmpVal{1};
end
if isequal(tmpVal, 'NaN') || isempty(tmpVal)
tmpVal = 'n/a';
end
else
tmpVal = 'n/a';
end
assert(ischar(tmpVal));
str{end+1} = tmpVal;
end % switch
end
end
end
strConcat = sprintf('%s\t', str{:});
fprintf(fid, '%s\n', strConcat(1:end-1));
end
fclose(fid);
end