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Merge branch 'master' of github.com:sccn/bids-matlab-tools
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@arnodelorme
arnodelorme committed Oct 12, 2021
2 parents 19b67fc + c35fb60 commit dabf9e9
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Showing 5 changed files with 103 additions and 75 deletions.
71 changes: 49 additions & 22 deletions bids_export.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -265,6 +265,7 @@ function bids_export(files, varargin)
'chanlookup' 'string' {} '';
'defaced' 'string' {'on' 'off'} 'on';
'createids' 'string' {'on' 'off'} 'on';
'singleEventsJson' 'string' {'on' 'off'} 'on';
'exportext' 'string' { 'edf' 'eeglab' } 'eeglab';
'README' 'string' {} '';
'CHANGES' 'string' {} '' ;
Expand All @@ -277,8 +278,20 @@ function bids_export(files, varargin)
% deleting folder
fprintf('Exporting data to %s...\n', opt.targetdir);
if exist(opt.targetdir,'dir')
disp('Deleting folder...')
rmdir(opt.targetdir, 's');
uilist = { ...
{ 'Style', 'text', 'string', 'Output directory exists and all current files will be deleted if continue', 'fontweight', 'bold' }, ...
{ 'Style', 'text', 'string', 'Would you want to proceed?'}, ...
};
geometry = { [1] [1]};
geomvert = [1 1 ];
[results,userdata,isOk,restag] = inputgui( 'geometry', geometry, 'geomvert', geomvert, 'uilist', uilist, 'title', 'Warning');
if isempty(isOk)
disp('BIDS export cancelled...')
return
else
disp('Deleting folder...')
rmdir(opt.targetdir, 's');
end
end

disp('Creating sub-directories...')
Expand Down Expand Up @@ -445,11 +458,20 @@ function bids_export(files, varargin)

% prepare event file information (_events.json)
% ----------------------------
eInfoDescFields = { 'LongName' 'optional' 'char' '';
'Levels' 'optional' 'struct' struct([]);
'Description' 'optional' 'char' '';
'Units' 'optional' 'char' '';
'TermURL' 'optional' 'char' '';
'HED' 'optional' 'struct' struct([])};
fields = fieldnames(opt.eInfoDesc);
for iField = 1:length(fields)
descFields{1,4} = fields{iField};
if ~isfield(opt.eInfoDesc, fields{iField}), opt.eInfoDesc(1).(fields{iField}) = struct([]); end
opt.eInfoDesc.(fields{iField}) = checkfields(opt.eInfoDesc.(fields{iField}), descFields, 'eInfoDesc');
opt.eInfoDesc.(fields{iField}) = checkfields(opt.eInfoDesc.(fields{iField}), eInfoDescFields, 'eInfoDesc');
end
if strcmpi(opt.singleEventsJson, 'on')
jsonwrite(fullfile(opt.targetdir, ['task-' opt.taskName '_events.json' ]), opt.eInfoDesc,struct('indent',' '));
end

% Write README files (README)
Expand Down Expand Up @@ -739,8 +761,9 @@ function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata, exportE
[folderOut,fileOut,~] = fileparts(fileOut);
fileOut = fullfile(folderOut,fileOut);
if ~isempty(EEG.event)
jsonwrite([ fileOut(1:end-3) 'events.json' ], opt.eInfoDesc,struct('indent',' '));

if strcmpi(opt.singleEventsJson,'off')
jsonwrite([ fileOut(1:end-3) 'events.json' ], opt.eInfoDesc,struct('indent',' '));
end
% --- _events.tsv

fid = fopen( [ fileOut(1:end-3) 'events.tsv' ], 'w');
Expand All @@ -757,7 +780,7 @@ function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata, exportE
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, 'usertags'), opt.eInfo(end+1,:) = { 'HED' 'usertags' }; 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'))
Expand All @@ -783,7 +806,7 @@ function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata, exportE
end

% reorder fields so it matches BIDS
fieldOrder = { 'onset' 'duration' 'sample' 'trial_type' 'response_time' 'stim_file' 'value' 'HED' };
fieldOrder = { 'onset' 'duration' 'sample' 'trial_type' 'response_time' 'stim_file' 'value'}; % 'HED' }; % remove HED from default column in events.tsv as HED tags should be put in events.json instead
newOrder = [];
for iField = 1:length(fieldOrder)
ind = strmatch(fieldOrder{iField}, opt.eInfo(:,1)', 'exact');
Expand Down Expand Up @@ -926,21 +949,21 @@ function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata, exportE
end
str{end+1} = eventValue;

case 'HED'
hed = 'n/a';
if isfield(EEG.event, tmpField) && ~isempty(EEG.event(iEvent).(tmpField))
hed = EEG.event(iEvent).(tmpField);
else
if isfield(EEG.event, 'usertags') && ~isempty(EEG.event(iEvent).usertags)
hed = EEG.event(iEvent).usertags;
if isfield(EEG.event, 'hedtags') && ~isempty(EEG.event(iEvent).hedtags)
hed = [hed ',' EEG.event(iEvent).hedtags];
end
elseif isfield(EEG.event, 'hedtags') && ~isempty(EEG.event(iEvent).hedtags)
hed = EEG.event(iEvent).hedtags;
end
end
str{end+1} = hed;
% case 'HED'
% hed = 'n/a';
% if isfield(EEG.event, tmpField) && ~isempty(EEG.event(iEvent).(tmpField))
% hed = EEG.event(iEvent).(tmpField);
% else
% if isfield(EEG.event, 'HED') && ~isempty(EEG.event(iEvent).usertags)
% hed = EEG.event(iEvent).usertags;
% if isfield(EEG.event, 'hedtags') && ~isempty(EEG.event(iEvent).hedtags)
% hed = [hed ',' EEG.event(iEvent).hedtags];
% end
% elseif isfield(EEG.event, 'hedtags') && ~isempty(EEG.event(iEvent).hedtags)
% hed = EEG.event(iEvent).hedtags;
% end
% end
% str{end+1} = hed;

otherwise
if isfield(EEG.event, opt.eInfo{iField,2})
Expand Down Expand Up @@ -1161,6 +1184,10 @@ function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata, exportE
s = setfield(s, {1}, f{iRow,1}, f{iRow,4});
end
elseif ~isempty(f{iRow,3}) && ~isa(s.(f{iRow,1}), f{iRow,3}) && ~strcmpi(s.(f{iRow,1}), 'n/a')
% if it's HED in eInfoDesc, allow string also
if strcmp(structName,'eInfoDesc') && strcmp(f{iRow,1}, 'HED') && isa(s.(f{iRow,1}), 'char')
return
end
error(sprintf('Parameter %s.%s must be a %s', structName, f{iRow,1}, f{iRow,3}));
end
end
Expand Down
4 changes: 2 additions & 2 deletions eegplugin_bids.m
View file
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)
Expand Down
80 changes: 39 additions & 41 deletions pop_eventinfo.m
View file
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
9 changes: 5 additions & 4 deletions pop_exportbids.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -59,10 +59,11 @@
{ 'Style', 'pushbutton', 'string', 'Edit participants' 'tag' 'participants' 'callback' cb_participants }, ...
{ 'Style', 'pushbutton', 'string', 'Edit event info' 'tag' 'events' 'callback' cb_events }, ...
{ 'Style', 'checkbox', 'string', 'Do not use participants ID and create anonymized participant ID instead' 'tag' 'newids' }, ...
{ 'Style', 'checkbox', 'string', 'Use single top-level events.json' 'tag' 'eventsJson' }, ...
};
relSize = 0.7;
geometry = { [1] [1] [1-relSize relSize*0.8 relSize*0.2] [1-relSize relSize] [1] [1] [1 1 1] [1] };
geomvert = [1 0.2 1 1 1 3 1 1 ];
geometry = { [1] [1] [1-relSize relSize*0.8 relSize*0.2] [1-relSize relSize] [1] [1] [1 1 1] [1] [1]};
geomvert = [1 0.2 1 1 1 3 1 1 1];
userdata.EEG = EEG;
userdata.STUDY = STUDY;
[results,userdata,~,restag] = inputgui( 'geometry', geometry, 'geomvert', geomvert, 'uilist', uilist, 'helpcom', 'pophelp(''pop_exportbids'');', 'title', 'Export EEGLAB STUDY to BIDS -- pop_exportbids()', 'userdata', userdata );
Expand All @@ -80,10 +81,10 @@
% end

% options
options = { 'targetdir' restag.outputfolder 'License' restag.license 'CHANGES' restag.changes 'createids' fastif(restag.newids, 'on', 'off') };
options = { 'targetdir' restag.outputfolder 'License' restag.license 'CHANGES' restag.changes 'createids' fastif(restag.newids, 'on', 'off') 'singleEventsJson' fastif(restag.eventsJson, 'on', 'off')};

if ~isfield(EEG(1), 'BIDS') % none of the edit button was clicked
EEG = pop_eventinfo(EEG, 'default');
EEG = pop_eventinfo(EEG, STUDY, 'default');
EEG = pop_participantinfo(EEG, STUDY, 'default');
EEG = pop_taskinfo(EEG, 'default');
end
Expand Down
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