Merge pull request #8 from VisLab/main

Corrected syntax error in github actions

.github/workflows/ci.yaml

@@ -20,4 +20,4 @@ jobs:
       - name: Run tests
         uses: matlab-actions/run-command@v1
         with:
-          command: addpath(genpath("hedcode")), addpath(genpath("tests"), runAllTests
+          command: addpath(genpath("hedcode")), addpath(genpath("tests")), runAllTests

hedmat/data_cleaning/eeg_importeventsfilestemp.m

@@ -0,0 +1,211 @@
+% eeg_importeventsfiles - create EEG.event from events.tsv and optionally events.json files
+%
+% Usage:
+%    [EEG, ~, ~, ~] = eeg_importeventsfiles(EEG, eventfile, 'key', value)
+%
+% Inputs:
+%  'EEG'        - [struct] the EEG structure to which event information will be imported
+%  'eventfile'  - [string] path to the events.tsv file. 
+%                 e.g. ~/BIDS_EXPORT/sub-01/ses-01/eeg/sub-01_ses-01_task-GoNogo_events.tsv
+%
+% Optional inputs:
+%  'bids'          - [struct] structure that saves imported BIDS information. Default is []
+%  'eventDescFile' - [string] path to events.json file if applicable. Default is empty
+%  'eventtype'     - [string] BIDS event column to be used as type in EEG.event. Default is 'value'
+%
+%  'usevislab'     - [string] Whether to use VisLab's functions. Default 'off'
+% Outputs:
+%   EEG     - [struct] the EEG structure with event info imported
+%   bids    - [struct] structure that saves BIDS information with event information
+%   eventData - [cell array] imported data from events.tsv
+%   eventDesc - [struct] imported data from events.json
+%
+% Authors: Dung Truong, Arnaud Delorme, 2022
+
+function [EEG, bids, eventData, eventDesc] = eeg_importeventsfiles(EEG, eventfile, varargin)
+g = finputcheck(varargin,  {'eventDescFile'   'string'   [] '';
+                            'bids'            'struct'   [] struct([]);
+                            'eventtype'       'string'   [] 'value' ;
+                            'usevislab'       'string'   { 'on' 'off'} 'off' }, 'eeg_importeventsfiles', 'ignore');
+if isstr(g), error(g); end
+
+if strcmpi(g.usevislab, 'on')
+    [EEG, bids, eventData, eventDesc] = eeg_importeventsfiles(EEG, eventfile, varargin{:}); %change to Kay's function
+    return;
+end
+
+bids = g.bids;
+
+% ---------
+% load files
+eventData = loadfile( eventfile, '');
+eventDesc = loadfile( g.eventDescFile, '');
+
+% ----------
+% event data
+bids(1).eventInfo = {}; % for eInfo. Default is empty. If replacing EEG.event with events.tsv, match field names accordingly
+if isempty(eventData)
+    warning('No data found in events.tsv');
+else
+    events       = struct([]);
+    indSample    = strmatch('sample', lower(eventData(1,:)), 'exact');
+    indType      = strmatch('type', lower(eventData(1,:)), 'exact');
+    indTrialType = strmatch('trial_type', lower(eventData(1,:)), 'exact');
+    if ~isempty(indType) && isempty(indTrialType)
+        eventData(1,indType) = { 'trial_type' }; % renaming type as trial_type because erased below
+    end
+
+    for iField = 1:length(eventData(1,:))
+        eventData{1,iField} = cleanvarname(eventData{1,iField});
+    end
+    indTrial = strmatch( g.eventtype, lower(eventData(1,:)), 'exact');
+    for iEvent = 2:size(eventData,1)
+        events(end+1).latency  = eventData{iEvent,1}*EEG.srate+1; % convert to samples
+        if EEG.trials > 1
+            events(end).epoch = floor(events(end).latency/EEG.pnts)+1;
+        end
+        events(end).duration   = eventData{iEvent,2}*EEG.srate;   % convert to samples
+        bids.eventInfo = {'onset' 'latency'; 'duration' 'duration'}; % order in events.tsv: onset duration
+        if ~isempty(indSample)
+            events(end).sample = eventData{iEvent,indSample} + 1;
+            bids.eventInfo(end+1,:) = {'sample' 'sample'};
+        end
+        for iField = 1:length(eventData(1,:))
+            if ~any(strcmpi(eventData{1,iField}, {'onset', 'duration', 'sample', g.eventtype}))
+                events(end).(eventData{1,iField}) = eventData{iEvent,iField};
+                bids.eventInfo(end+1,:) = { eventData{1,iField} eventData{1,iField} };
+            end
+        end
+        if ~isempty(indTrial)
+            events(end).type = eventData{iEvent,indTrial};
+            bids.eventInfo(end+1,:) = { g.eventtype 'type' };
+        end                           
+        %                         if size(eventData,2) > 3 && strcmpi(eventData{1,4}, 'response_time') && ~strcmpi(eventData{iEvent,4}, 'n/a')
+        %                             events(end+1).type   = 'response';
+        %                             events(end).latency  = (eventData{iEvent,1}+eventData{iEvent,4})*EEG.srate+1; % convert to samples
+        %                             events(end).duration = 0;
+        %                         end
+    end
+    EEG.event = events; 
+    EEG = eeg_checkset(EEG, 'makeur'); % add urevent
+    EEG = eeg_checkset(EEG, 'eventconsistency');
+end    
+
+% import HED tags if exists
+if ~isempty(g.eventDescFile)
+    if plugin_status('HEDTools')
+        try 
+            fMap = fieldMap.createfMapFromJson(g.eventDescFile);
+            if fMap.hasAnnotation()
+                EEG.etc.tags = fMap.getStruct();
+            end
+        catch ME
+            warning('Unable to import HED tags. Check your _events.json file');
+        end
+    end
+end
+
+% import JSON or TSV file
+% -----------------------
+function data = loadfile(localFile, globalFile)
+[~,~,ext] = fileparts(localFile);
+data = [];
+localFile = dir(localFile);
+if ~isempty(localFile)
+    if strcmpi(ext, '.tsv')
+        data = importtsv( fullfile(localFile(1).folder, localFile(1).name));
+    else
+        if exist('jsondecode.m','file')
+            data = jsondecode( importalltxt( fullfile(localFile(1).folder, localFile(1).name) ));
+        else
+            data = jsonread(fullfile(localFile(1).folder, localFile(1).name));
+        end
+    end        
+elseif ~isempty(globalFile)
+    if strcmpi(ext, '.tsv')
+        data = importtsv( fullfile(globalFile(1).folder, globalFile(1).name));
+    else
+        if exist('jsondecode.m','file')
+            data = jsondecode( importalltxt( fullfile(globalFile(1).folder, globalFile(1).name) ));
+        else
+            data = jsonread(fullfile(globalFile(1).folder, globalFile(1).name));
+        end
+    end
+end
+
+% Import full text file
+% ---------------------
+function str = importalltxt(fileName)
+
+str = [];
+fid =fopen(fileName, 'r');
+while ~feof(fid)
+    str = [str 10 fgetl(fid) ];
+end
+str(1) = [];
+
+% Import tsv file
+% ---------------
+function res = importtsv( fileName)
+
+res = loadtxt( fileName, 'verbose', 'off', 'delim', 9);
+
+for iCol = 1:size(res,2)
+    % search for NaNs in numerical array
+    indNaNs = cellfun(@(x)strcmpi('n/a', x), res(:,iCol));
+    if ~isempty(indNaNs)
+        allNonNaNVals = res(find(~indNaNs),iCol);
+        allNonNaNVals(1) = []; % header
+        testNumeric   = cellfun(@isnumeric, allNonNaNVals);
+        if all(testNumeric)
+            res(find(indNaNs),iCol) = { NaN };
+        elseif ~all(~testNumeric)
+            % Convert numerical value back to string
+            res(:,iCol) = cellfun(@num2str, res(:,iCol), 'uniformoutput', false);
+        end
+    end
+end
+
+function nameout = cleanvarname(namein)
+
+% Routine to remove unallowed characters from strings
+% nameout can be use as a variable or field in a structure
+
+% custom change
+if strcmp(namein,'#')
+    namein = 'nb';
+end
+
+% 1st char must be a letter
+for l=1:length(namein)
+    if isletter(namein(l))
+        nameout = namein(l:end);
+        break % exist for loop
+    end
+end
+
+% remove usual suspects
+stringcheck = [strfind(namein,'('), ...
+    strfind(namein,')') ...
+    strfind(namein,'[') ...
+    strfind(namein,']') ...
+    strfind(namein,'{') ...
+    strfind(namein,'}') ...
+    strfind(namein,'-') ...
+    strfind(namein,'+') ...
+    strfind(namein,'*') ...
+    strfind(namein,'/') ...
+    strfind(namein,'#') ...
+    strfind(namein,'%') ...
+    strfind(namein,'&') ...
+    strfind(namein,'@') ...
+    ];
+
+if ~isempty(stringcheck)
+    nameout(stringcheck) = [];
+end
+
+% last check
+if ~isvarname(nameout)
+    error('the variable name to use is still invalid, check chars to remove')
+end