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make it work with STUDY
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@dungscout96
dungscout96 committed Oct 8, 2021
1 parent cac70fb commit f9c7c70
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Showing 2 changed files with 41 additions and 43 deletions.
4 changes: 2 additions & 2 deletions eegplugin_bids.m
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Original file line number Diff line number Diff line change
Expand Up @@ -44,8 +44,8 @@
% create BIDS menus
% -----------------
comtaskinfo = [trystrs.no_check '[EEG,LASTCOM] = pop_taskinfo(EEG);' catchstrs.store_and_hist ];
comsubjinfo = [trystrs.no_check '[EEG,LASTCOM] = pop_participantinfo(EEG,STUDY);' catchstrs.store_and_hist ];
comeventinfo = [trystrs.no_check '[EEG,LASTCOM] = pop_eventinfo(EEG);' catchstrs.store_and_hist ];
comsubjinfo = [trystrs.no_check '[EEG,STUDY,LASTCOM] = pop_participantinfo(EEG,STUDY);' catchstrs.store_and_hist ];
comeventinfo = [trystrs.no_check '[EEG,STUDY,LASTCOM] = pop_eventinfo(EEG,STUDY);' catchstrs.store_and_hist ];
% comvalidatebids = [ trystrs.no_check 'if plugin_askinstall(''bids-validator'',''pop_validatebids'') == 1 pop_validatebids() end' catchstrs.add_to_hist ];
bids = findobj(fig, 'label', 'BIDS tools');
if isempty(bids)
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80 changes: 39 additions & 41 deletions pop_eventinfo.m
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Original file line number Diff line number Diff line change
Expand Up @@ -14,29 +14,36 @@
% 'EEG' - [struct] Updated EEG structure containing event BIDS information
% in each EEG structure at EEG.BIDS.eInfoDesc and EEG.BIDS.eInfo
%
% 'eInfoDesc' - [struct] structure describing BIDS event fields as you specified.
% 'eInfoDesc' - [struct] structure describing BIDS event fields as you specified.
% See BIDS specification for all suggested fields.
%
% 'eInfo' - [cell] BIDS event fields and their corresponding
% 'eInfo' - [cell] BIDS event fields and their corresponding
% event fields in the EEGLAB event structure. Note that
% EEGLAB event latency, duration, and type are inserted
% automatically as columns "onset" (latency in sec), "duration"
% (duration in sec), "value" (EEGLAB event type)
%
% Author: Dung Truong, Arnaud Delorme
function [EEG, command] = pop_eventinfo(EEG, varargin)
function [EEG, STUDY, command] = pop_eventinfo(EEG, STUDY, varargin)
%% check if there's already an opened window
if ~isempty(findobj('Tag','eventBidsTable'))
errordlg2('A window is already openened for pop_eventinfo');
return
end

command = '[EEG, command] = pop_eventinfo(EEG)';
command = '[EEG, [], command] = pop_eventinfo(EEG)';
%% if STUDY is provided, check for consistency
hasSTUDY = false;
if exist('STUDY','var') && ~isempty(STUDY)
[STUDY, EEG] = pop_checkdatasetinfo(STUDY, EEG);
command = '[EEG, STUDY, command] = pop_eventinfo(EEG, STUDY);';
hasSTUDY = true;
end

% perform check to make sure EEG.event is consistent across EEG
if isempty(EEG(1).event)
errordlg2('EEG.event is empty for first dataset');
return

return
end
try
eventFields = fieldnames([EEG.event]);
Expand All @@ -48,7 +55,7 @@
warning('There is mismatch in number of fields in EEG.event structures. Using fields of EEG(%d) which has the highest number of fields (%d).', index, num);
end
end
bidsFields = {'onset', 'duration', 'trial_type','value','stim_file','sample','response_time'};%,'HED'};
bidsFields = {'onset', 'duration', 'trial_type','value','stim_file','sample','response_time'};
eventFields = setdiff(eventFields, 'latency');
% define global variables
% -----------------------
Expand All @@ -63,7 +70,7 @@
fontSize = 12;

% Use GUI
if nargin < 2
if nargin < 3
% create UI
f = figure('MenuBar', 'None', 'ToolBar', 'None', 'Name', 'Edit BIDS event info - pop_eventinfo', 'Color', bg);
f.Position(3) = appWidth;
Expand Down Expand Up @@ -110,7 +117,7 @@
if isfield(eventBIDS.(field), 'Levels') && ~isempty(eventBIDS.(field).Levels)
data{i,strcmp(tbl.ColumnName, 'Levels')} = strjoin(fieldnames(eventBIDS.(field).Levels),',');
else
if strcmp(field, 'onset') || strcmp(field, "sample") || strcmp(field, "duration") || strcmp(field, "HED")
if strcmp(field, 'onset') || strcmp(field, "sample") || strcmp(field, "duration")
data{i,strcmp(tbl.ColumnName, 'Levels')} = 'n/a';
else
data{i,strcmp(tbl.ColumnName, 'Levels')} = 'Click to specify below';
Expand All @@ -122,7 +129,7 @@
tbl.Data = data;
waitfor(f);
% Use default value - pop_eventinfo(EEG,'default') called
elseif nargin < 3 && ischar(varargin{1}) && strcmp(varargin{1}, 'default')
elseif nargin < 4 && ischar(varargin{1}) && strcmp(varargin{1}, 'default')
done();
end

Expand Down Expand Up @@ -201,8 +208,12 @@ function done()

% prepare return struct
fields = fieldnames(eventBIDS);
if isfield(EEG.etc,'tags')
hedTags = EEG.etc.tags;
fMap = [];
if hasSTUDY && isfield(STUDY.etc, 'tags')
hedTags = STUDY.etc.tags;
fMap = fieldMap.createfMapFromStruct(hedTags);
elseif isfield(EEG(1).etc,'tags')
hedTags = EEG(1).etc.tags;
fMap = fieldMap.createfMapFromStruct(hedTags);
end
for k=1:length(fields)
Expand All @@ -229,18 +240,23 @@ function done()
if isfield(eventBIDS.(bidsField),'Levels') && ~isempty(eventBIDS.(bidsField).Levels) && ~strcmp(eventBIDS.(bidsField).Levels,'n/a')
eInfoDesc.(bidsField).Levels = eventBIDS.(bidsField).Levels;
end
% parse HED
if isfield(EEG.etc,'tags')
% parse HED if exists
if ~isempty(fMap)
tMap = fMap.getMap(eegField);
if ~isempty(tMap)
if ~isempty(tMap) && tMap.hasAnnotation()
codes = tMap.getCodes();
if numel(codes) == 1 && strcmp(codes{1},'HED')
tList = tMap.getValue('HED');
eInfoDesc.(bidsField).HED = tagList.stringify(tList.getTags());
if tList.hasAnnotation()
eInfoDesc.(bidsField).HED = tagList.stringify(tList.getTags());
end
else
for c=1:numel(codes)
tList = tMap.getValue(codes{c});
eInfoDesc.(bidsField).HED.(codes{c}) = tagList.stringify(tList.getTags());
% only add HED tags for the ones that
if tList.hasAnnotation()
eInfoDesc.(bidsField).HED.(codes{c}) = tagList.stringify(tList.getTags());
end
end
end
end
Expand All @@ -250,12 +266,12 @@ function done()
end
end
end
if numel(EEG) == 1
command = '[EEG, eInfoDesc, eInfo] = pop_eventinfo(EEG);';
else
command = '[EEG, eInfoDesc, eInfo] = pop_eventinfo(EEG);';
end

% add info to STUDY if exists
if hasSTUDY
STUDY.BIDS.eInfoDesc = eInfoDesc;
STUDY.BIDS.eInfo = eInfo;
end
% add info to EEG structs
for e=1:numel(EEG)
EEG(e).BIDS.eInfoDesc = eInfoDesc;
Expand Down Expand Up @@ -380,9 +396,7 @@ function createLevelUI(~,~,table,field)
removeLevelUI();
matchedRow = strcmp(table.Source.Data(:, strcmp(table.Source.ColumnName, 'BIDS Field')), field);
levelCellText = table.Source.Data{matchedRow, strcmp(table.Source.ColumnName, 'Levels')}; % text @ (field, Levels) cell. if 'n/a' then no action, 'Click to..' then conditional action, '<value>,...' then get levels
if strcmp(field, 'HED')
uicontrol(f, 'Style', 'text', 'String', 'Levels editing not applied for HED. Use ''pop_tageeg(EEG)'' of HEDTools plug-in to edit event HED tags', 'Units', 'normalized', 'Position', [0.01 0.45 1 0.05],'ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'levelEditMsg');
elseif strcmp(field, 'onset') || strcmp(field, 'sample') || strcmp(field, 'duration')
if strcmp(field, 'onset') || strcmp(field, 'sample') || strcmp(field, 'duration')
uicontrol(f, 'Style', 'text', 'String', 'Levels editing not applied for field with continuous values.', 'Units', 'normalized', 'Position', [0.01 0.45 1 0.05],'ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'levelEditMsg');
else
% retrieve all unique values from EEG.event.(field).
Expand Down Expand Up @@ -619,23 +633,7 @@ function removeLevelUI()
event.value.Units = '';
event.value.Levels = [];
event.value.TermURL = '';
% elseif strcmp(fields{idx}, 'HED') && any(strcmp(eventFields, 'usertags'))
% if isfield(EEG(1).event, 'usertags')
% event.HED.EEGField = 'usertags';
% else
% event.HED.EEGField = '';
% end
% event.HED.LongName = 'Hierarchical Event Descriptor';
% event.HED.Description = 'Tags describing the nature of the event';
% event.HED.Levels = [];
% event.HED.Units = '';
% event.HED.TermURL = '';
elseif strcmp(fields{idx}, 'duration')
% if isfield(EEG(1).event, 'duration')
% event.HED.EEGField = 'duration';
% else
% event.HED.EEGField = '';
% end
event.duration.LongName = 'Event duration';
event.duration.Description = 'Duration of the event (measured from onset) in seconds. Must always be either zero or positive. A "duration" value of zero implies that the delta function or event is so short as to be effectively modeled as an impulse.';
event.duration.Units = 'second';
Expand Down

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