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pop_participantinfo.m
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% pop_participantinfo() - GUI for BIDS participant info editing
%
% Usage:
% >> [EEG, pInfoDesc, pInfo] = pop_participantinfo( EEG );
%
% Inputs:
% EEG - EEG dataset structure. May only contain one dataset.
%
% STUDY - (optional) If provided, subject and group information in
% the STUDY will be used to auto-populate participant id and group info.
% Optional input:
% 'default' - generate BIDS participant info using default values without
% popping up the GUI
% Outputs:
% 'EEG' - [struct] Updated EEG structure containing event BIDS information
% in each EEG structure at EEG.BIDS
%
% 'pInfoDesc' - [struct] structure describing BIDS participant fields as you specified.
% See BIDS specification for all suggested fields.
%
% 'pInfo' - [cell] BIDS participant information.
%
% Author: Dung Truong, Arnaud Delorme
%
% This function use sort_nat by Douglas Schwartz with the following
% copyright
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:
%
% 1. Redistributions of source code must retain the above copyright notice,
% this list of conditions and the following disclaimer.
%
% 2. Redistributions in binary form must reproduce the above copyright notice,
% this list of conditions and the following disclaimer in the documentation
% and/or other materials provided with the distribution.
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
% THE POSSIBILITY OF SUCH DAMAGE.
function [EEG, STUDY, command] = pop_participantinfo(EEG,STUDY, varargin)
command = '[EEG, [], command] = pop_participantinfo(EEG);';
%% check if there's already an opened window
if ~isempty(findobj('Tag','pInfoTable'))
errordlg2('A window is already openened for pop_participantinfo');
return
end
%% 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_participantinfo(EEG, STUDY);';
hasSTUDY = true;
end
%% default settings
appWidth = 1300;
appHeight = 600;
bg = [0.65 0.76 1];
fg = [0 0 0.4];
levelThreshold = 20;
fontSize = 12;
[pInfoBIDS, pFields] = newpInfoBIDS();
% pInfo = {};
pInfoDesc = [];
if numel(EEG) == 1
warning('This function can also be applied to multiple dataset (e.g. EEG structures).');
end
% get subjects
% -------------------------
if isfield(EEG(1), 'subject') && ~isempty(EEG(1).subject)
allSubjects = { EEG.subject };
elseif hasSTUDY && isfield(STUDY,'datasetinfo') && isfield(STUDY.datasetinfo(1), 'subject') && ~isempty(STUDY.datasetinfo(1).subject)
allSubjects = { STUDY.datasetinfo.subject };
else
if numel(EEG) == 1
errordlg2('No subject ID found. Please fill in "Subject code" in the next window, then resume.');
EEG = pop_editset(EEG);
elseif hasSTUDY
errordlg2('No subject info found in STUDY. Please add using "Study > Edit study info", then resume.');
end
return
end
emptySubjs = cellfun(@isempty, allSubjects);
if any(emptySubjs)
errordlg2(sprintf('No subject ID found for dataset at index: %s. Please add and resume.', mat2str(find(emptySubjs))));
return
else
uniqueSubjects = sort_nat(unique(allSubjects));
end
%% create UI
f = figure('MenuBar', 'None', 'ToolBar', 'None', 'Name', 'Edit BIDS participant info - pop_participantinfo', 'Color', bg);
f.Position(3) = appWidth;
f.Position(4) = appHeight;
uicontrol(f, 'Style', 'text', 'String', 'Participant information', 'Units', 'normalized','FontWeight','bold','ForegroundColor', fg,'BackgroundColor', bg, 'Position', [0 0.86 0.4 0.1]);
pInfoTbl = uitable(f, 'RowName',[],'ColumnName', [pFields 'HeadCircumference' 'SubjectArtefactDescription'], 'Units', 'normalized', 'FontSize', fontSize, 'Tag', 'pInfoTable', 'ColumnEditable', [false true(1, numel(pFields)) true]);
pInfoTbl.Data = cell(numel(uniqueSubjects), 2+length(pFields));
pInfoTbl.Position = [0.02 0.124 0.38 0.786];
pInfoTbl.CellSelectionCallback = @pInfoCellSelectedCB;
pInfoTbl.CellEditCallback = @pInfoCellEditCB;
% pre-populate pInfo table
for iSubj = 1:length(uniqueSubjects)
indS = strmatch( uniqueSubjects{iSubj}, allSubjects, 'exact' );
curEEG = EEG(indS(1));
% if curEEG has BIDS.pInfo
% pInfo is in format:
% First row participant_id | Gender | ...
% Second row <value> | <value> |
if isfield(curEEG, 'BIDS') && isfield(curEEG.BIDS,'pInfo')
fnames = curEEG.BIDS.pInfo(1,:); % fields of EEG.BIDS.pInfo
for j=1:numel(pFields)
% if EEG.BIDS.pInfo has pFields{j}
if any(strcmp(pFields{j}, fnames))
pInfoTbl.Data{iSubj,strcmp(pInfoTbl.ColumnName,pFields{j})} = curEEG.BIDS.pInfo{2,strcmp(fnames,pFields{j})};
end
end
else
if isfield(curEEG,'subject')
pInfoTbl.Data{iSubj,strcmp(pInfoTbl.ColumnName, 'participant_id')} = curEEG.subject;
end
if isfield(curEEG,'group') && ~isempty(curEEG.group)
pInfoTbl.Data{iSubj,strcmp(pInfoTbl.ColumnName, 'Group')} = curEEG.group;
end
end
% update HeadCircumference and SubjectArtefactDescription from tInfo
if isfield(curEEG, 'BIDS') && isfield(curEEG.BIDS,'tInfo')
if isfield(curEEG.BIDS.tInfo,'HeadCircumference')
pInfoTbl.Data{iSubj,strcmp(pInfoTbl.ColumnName,'HeadCircumference')} = curEEG.BIDS.tInfo.HeadCircumference;
end
if isfield(curEEG.BIDS.tInfo,'SubjectArtefactDescription')
pInfoTbl.Data{iSubj,strcmp(pInfoTbl.ColumnName,'SubjectArtefactDescription')} = curEEG.BIDS.tInfo.SubjectArtefactDescription;
end
end
end
uicontrol(f, 'Style', 'text', 'String', 'BIDS metadata for participant fields', 'Units', 'normalized','FontWeight','bold','ForegroundColor', fg,'BackgroundColor', bg, 'Position', [0.42 0.86 1-0.42 0.1]);
bidsTbl = uitable(f, 'RowName', pFields, 'ColumnName', {'Description' 'Levels' 'Units' }, 'Units', 'normalized', 'FontSize', fontSize, 'Tag', 'bidsTable');
bidsWidth = (1-0.42-0.02);
bidsTbl.Position = [0.42 0.5 bidsWidth 0.41];
bidsTbl.CellSelectionCallback = @bidsCellSelectedCB;
bidsTbl.CellEditCallback = @bidsCellEditCB;
bidsTbl.ColumnEditable = [true false true];
bidsTbl.ColumnWidth = {appWidth*bidsWidth*2/5,appWidth*bidsWidth/5,appWidth*bidsWidth/5};
units = {' ','ampere','becquerel','candela','coulomb','degree Celsius','farad','gray','henry','hertz','joule','katal','kelvin','kilogram','lumen','lux','metre','mole','newton','ohm','pascal','radian','second','siemens','sievert','steradian','tesla','volt','watt','weber'};
unitPrefixes = {' ','deci','centi','milli','micro','nano','pico','femto','atto','zepto','yocto','deca','hecto','kilo','mega','giga','tera','peta','exa','zetta','yotta'};
bidsTbl.ColumnFormat = {[] [] [] [] units unitPrefixes []};
defaultFields = {'participant_id' 'Gender' 'Age' 'Group' 'HeadCircumference' 'SubjectArtefactDescription'};
uicontrol(f, 'Style', 'pushbutton', 'String', 'Remove column', 'Units', 'normalized', 'Position', [0.4-0.1 0.074 0.1 0.05], 'Callback', {@removeColumnCB, pInfoTbl, defaultFields}, 'Tag', 'removeColumnBtn');
uicontrol(f, 'Style', 'pushbutton', 'String', 'Add/Edit column', 'Units', 'normalized', 'Position', [0.4-0.2 0.074 0.1 0.05], 'Callback', {@editColumnCB, pInfoTbl, defaultFields}, 'Tag', 'addColumnBtn');
uicontrol(f, 'Style', 'pushbutton', 'String', 'Import column(s)', 'Units', 'normalized', 'Position', [0.4-0.3 0.074 0.1 0.05], 'Callback', {@importSpreadsheet}, 'Tag', 'importSpreadsheetBtn');
uicontrol(f, 'Style', 'pushbutton', 'String', 'Ok', 'Units', 'normalized', 'Position', [0.85 0.02 0.1 0.05], 'Callback', @okCB);
uicontrol(f, 'Style', 'pushbutton', 'String', 'Cancel', 'Units', 'normalized', 'Position', [0.7 0.02 0.1 0.05], 'Callback', @cancelCB);
% pre-populate BIDS table
data = cell(length(pFields),length(bidsTbl.ColumnName));
for i=1:length(pFields)
% pre-populate description
field = pFields{i};
if numel(EEG) == 1 || ~isfield(pInfoBIDS.(field),'Levels') % if previous specification of this field didn't include Levels
data{i,strcmp(bidsTbl.ColumnName, 'Levels')} = 'n/a';
elseif isstruct(pInfoBIDS.(field).Levels) && (isempty(pInfoBIDS.(field).Levels) || isempty(fieldnames(pInfoBIDS.(field).Levels)))
data{i,strcmp(bidsTbl.ColumnName, 'Levels')} = 'Click to specify';
else
levelTxt = pInfoBIDS.(field).Levels;
if isstruct(levelTxt)
levelTxt = strjoin(fieldnames(pInfoBIDS.(field).Levels),',');
end
data{i,strcmp(bidsTbl.ColumnName, 'Levels')} = levelTxt;
end
if isfield(pInfoBIDS.(field),'Description')
data{i,strcmp(bidsTbl.ColumnName, 'Description')} = pInfoBIDS.(field).Description;
end
if isfield(pInfoBIDS.(field),'Units')
data{i,strcmp(bidsTbl.ColumnName, 'Units')} = pInfoBIDS.(field).Units;
end
clear('field');
end
bidsTbl.Data = data;
if nargin < 3
%% wait
waitfor(f);
elseif nargin < 4 && ischar(varargin{1}) && strcmp(varargin{1}, 'default')
okCB('','');
end
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
%----- Helper functions ---------------------------------------------------
%% import spreadshet
function importSpreadsheet(~, ~)
% Get spreadsheet
supergui( 'geomhoriz', { 1 1 1 [1 1] }, 'uilist', { ...
{ 'style', 'text', 'string', 'Warning: First row must contains column headers!', 'fontweight', 'bold' },...
{ 'style', 'text', 'string', 'Supported file formats: .txt, .csv, .tsv, .xlsx, .xls' }, { }, ...
{ 'style', 'pushbutton' , 'string', 'Cancel', 'callback', 'close(gcbf)' } ...
{ 'style', 'pushbutton' , 'string', 'OK', 'callback', @proceed } } );
function proceed(~,~)
close(gcbf); % close column header warning dialog
[name, path] = uigetfile2({'*'}, 'Choose spreadsheet file');
filepath = '';
allowedFormats = {'.txt', '.csv', '.tsv', '.xlsx', '.xls'};
if ~isequal(name, 0)
filepath = fullfile(path, name);
if ~any(endsWith(filepath, allowedFormats))
supergui( 'geomhoriz', { 1 1 1 1 }, 'uilist', { ...
{ 'style', 'text', 'string', 'Selected file format is NOT among those supported'},...
{ 'style', 'text', 'string', '(.txt, .csv, .tsv, .xlsx, .xls)' }, { }, ...
{ 'style', 'pushbutton' , 'string', 'Ok', 'callback', 'close(gcbf)' } ...
} );
filepath = '';
end
else
close(gcbf);
end
clear tmpfolder;
% Load spreadsheet
if ~isempty(filepath)
try
warning('OFF', 'MATLAB:table:ModifiedAndSavedVarnames')
if endsWith(filepath,'.tsv')
T = readtable(filepath, 'filetype', 'text');
else
T = readtable(filepath);
end
catch
errordlg2('Error importing data.');
return
end
columns = T.Properties.VariableNames;
columns = ["(none)" columns];
pTable = findobj('Tag', 'pInfoTable');
columnMap = containers.Map('KeyType','char','ValueType','char');
idColumn = '';
% Match spreadsheet columns with GUI columns
[~, ~, ~, structout] = inputgui('geometry', {[1 1] [1 1] [1 1] [1 1] [1 1] [1 1] 1 1 1 1}, 'geomvert', [1 1 1 1 1 1 1 1 1 5], 'uilist', {...
{'Style', 'text', 'string', 'Participant ID column* (required)', 'fontweight', 'bold', 'fontsize', 14} ...
{'Style', 'popupmenu', 'string', columns, 'Tag', 'ID_Column', 'Callback', @idSelected} ...
{'Style', 'text', 'string', 'Age column'} ...
{'Style', 'popupmenu', 'string', columns, 'Tag', 'Age_Column', 'Callback', @fieldSelected} ...
{'Style', 'text', 'string', 'Gender column'} ...
{'Style', 'popupmenu', 'string', columns, 'Tag', 'Gender_Column', 'Callback', @fieldSelected} ...
{'Style', 'text', 'string', 'Group column'} ...
{'Style', 'popupmenu', 'string', columns, 'Tag', 'Group_Column', 'Callback', @fieldSelected} ...
{'Style', 'text', 'string', 'Head circumference column'} ...
{'Style', 'popupmenu', 'string', columns, 'Tag', 'HeadCircumference_Column', 'Callback', @fieldSelected} ...
{'Style', 'text', 'string', 'Subject artefact column'} ...
{'Style', 'popupmenu', 'string', columns, 'Tag', 'SubjectArtefactDescription_Column', 'Callback', @fieldSelected} ...
{} ...
{'Style', 'checkbox', 'string', 'Choose additional spreadsheet columns to import', 'Tag', 'HasAdditionalCols', 'fontweight', 'bold', 'callback', @chooseColumnSelected} ...
{'Style', 'text', 'string', '(Hold Ctrl or Shift for multi-select)'} ...
{'Style', 'listbox', 'string', columns(2:end), 'Tag', 'SpreadsheetColumns', 'max', 2, 'Enable', 'off'} ...
});
if ~isempty(structout)
if isempty(idColumn) || strcmp(idColumn, '(none)')
supergui( 'geomhoriz', { 1 1 1 }, 'uilist', { ...
{ 'style', 'text', 'string', 'Participant ID column was not set. Abort.' }, { }, ...
{ 'style', 'pushbutton' , 'string', 'Ok', 'callback', 'close(gcbf)' } ...
} );
else
listboxCols = columns(2:end);
if structout.HasAdditionalCols == 1
importData(listboxCols(structout.SpreadsheetColumns));
else
importData([]);
end
end
end
end
function idSelected(src,~)
val = src.Value;
str = src.String;
column = str{val};
if ~strcmp(column, "(none)")
idColumn = column;
end
end
function fieldSelected(src,~)
fieldName = split(src.Tag, '_');
fieldName = fieldName{1};
val = src.Value;
str = src.String;
column = str{val};
if ~strcmp(column, "(none)")
columnMap(fieldName) = column;
end
end
function chooseColumnSelected(src,~)
if src.Value == 1
set(findobj('Tag', 'SpreadsheetColumns'), 'Enable', 'on');
else
set(findobj('Tag', 'SpreadsheetColumns'), 'Enable', 'off');
end
end
% import subject data from spreadsheet to GUI
function importData(additionalCols)
pIDColIndex = strcmp(pTable.ColumnName, "participant_id");
% participant ids
allGUIRows = pTable.Data(:, pIDColIndex); % all participants in GUI
matchedGUIRows = []; %
matchedSpreadsheetRows = zeros(numel(allGUIRows),1); % index of row in spreadsheet that matches GUI row
for r=1:numel(allGUIRows)
matchedIdx = find(strcmp(allGUIRows{r}, T.(idColumn)));
if ~isempty(matchedIdx)
matchedGUIRows = [matchedGUIRows r];
matchedSpreadsheetRows(r) = matchedIdx;
end
end
if numel(matchedGUIRows) < numel(allGUIRows)
unmatchedSubjs = setdiff(1:numel(allGUIRows),matchedGUIRows);
if numel(unmatchedSubjs) == numel(allGUIRows)
errordlg2('No matched subject between dataset and spreadsheet found.');
return
else
errordlg2(sprintf('%d subjects (%s) not found in spreadsheet.', numel(unmatchedSubjs), strjoin(allGUIRows(unmatchedSubjs), ',')));
return
end
end
matchedSpreadsheetRows = matchedSpreadsheetRows(matchedSpreadsheetRows > 0); % only keep those that match
if numel(matchedSpreadsheetRows) < numel(T.(idColumn))
warndlg2('There are more subjects in spreadsheet than in the dataset. Importing data only for those in dataset...');
end
% process additional columns
for c=1:numel(additionalCols)
col = additionalCols{c};
if ~strcmp(pTable.ColumnName, col), addNewColumn(col); end
columnMap(col) = col; % same name
end
% copy data
keySet = keys(columnMap);
for k=1:columnMap.Count
spreadsheetCol = columnMap(keySet{k});
spreadsheetColData = T.(spreadsheetCol);
for r=1:numel(matchedGUIRows)
if isnumeric(spreadsheetColData(1))
pTable.Data{matchedGUIRows(r), strcmp(pTable.ColumnName, keySet{k})} = spreadsheetColData(matchedSpreadsheetRows(r));
elseif iscell(spreadsheetColData(1))
pTable.Data{matchedGUIRows(r), strcmp(pTable.ColumnName, keySet{k})} = spreadsheetColData{matchedSpreadsheetRows(r)};
end
end
end
end
end
end
%% callback handle for cancel button
function cancelCB(~, ~)
clear('eventBIDS');
close(f);
end
%% callback handle for ok button
function okCB(~, ~)
% prepare return struct
pTable = findobj('Tag', 'pInfoTable');
fields = fieldnames(pInfoBIDS);
for idx=1:length(fields)
field = fields{idx};
pInfoDesc.(field).Description = pInfoBIDS.(field).Description;
% Only add Units and Levels to pInfoDesc if they have values
if ~isempty(pInfoBIDS.(field).Units)
pInfoDesc.(field).Units = pInfoBIDS.(field).Units;
end
if (isstruct(pInfoBIDS.(field).Levels) && ~isempty(pInfoBIDS.(field).Levels) && ~isempty(fieldnames(pInfoBIDS.(field).Levels))) || (ischar(pInfoBIDS.(field).Levels) && ~strcmp(pInfoBIDS.(field).Levels, 'n/a'))
pInfoDesc.(field).Levels = pInfoBIDS.(field).Levels;
end
end
for e=1:numel(EEG)
if ~isfield(EEG(e),'BIDS')
EEG(e).BIDS = [];
end
tInfo = struct('HeadCircumference', [], 'SubjectArtefactDescription', "");
if isfield(EEG(e).BIDS,'tInfo')
tInfo = EEG(e).BIDS.tInfo;
end
if ~isempty(EEG(e).subject)
rowIdx = strcmp(EEG(e).subject, pTable.Data(:, strcmp('participant_id', pTable.ColumnName)));
elseif hasSTUDY && ~isempty(STUDY.datasetinfo(1).subject) % assuming order of STUDY.datasetinfo matches with order of EEG in the EEG array
rowIdx = strcmp(STUDY.datasetinfo(e).subject, pTable.Data(:, strcmp('participant_id', pTable.ColumnName)));
end
if isempty(pTable.Data{rowIdx,strcmp('HeadCircumference',pTable.ColumnName)})
if isfield(tInfo, 'HeadCircumference')
tInfo = rmfield(tInfo, 'HeadCircumference');
end
else
if ~isnumeric(pTable.Data{rowIdx,strcmp('HeadCircumference',pTable.ColumnName)})
tInfo.HeadCircumference = str2double(pTable.Data{rowIdx,strcmp('HeadCircumference',pTable.ColumnName)});
else
tInfo.HeadCircumference = pTable.Data{rowIdx,strcmp('HeadCircumference',pTable.ColumnName)};
end
end
if isempty(pTable.Data{rowIdx,strcmp('SubjectArtefactDescription',pTable.ColumnName)})
if isfield(tInfo, 'SubjectArtefactDescription')
tInfo = rmfield(tInfo,'SubjectArtefactDescription');
end
else
if ~ischar(pTable.Data{rowIdx, strcmp('SubjectArtefactDescription',pTable.ColumnName)})
tInfo.SubjectArtefactDescription = char(pTable.Data{rowIdx,strcmp('SubjectArtefactDescription',pTable.ColumnName)});
else
tInfo.SubjectArtefactDescription = pTable.Data{rowIdx,strcmp('SubjectArtefactDescription',pTable.ColumnName)};
end
end
EEG(e).BIDS.tInfo = tInfo;
EEG(e).BIDS.pInfoDesc = pInfoDesc;
colIdx = 1:numel(pTable.ColumnName);
colIdx = colIdx(~strcmp('HeadCircumference',pTable.ColumnName) & ~strcmp('SubjectArtefactDescription',pTable.ColumnName)); % these are not pInfo fields
EEG(e).BIDS.pInfo = [pFields; pTable.Data(rowIdx,colIdx)];
EEG(e).saved = 'no';
EEG(e).history = [EEG(e).history command];
end
clear('pInfoBIDS');
close(f);
end
%% add new column to pInfo GUI table
% used by both import and editColumn button
function addNewColumn(newColName)
% input validation
newField = checkFormat(newColName);
pFields = [pFields newField];
% add to pInfoBIDS structure
pInfoBIDS.(newField).Description = '';
pInfoBIDS.(newField).Levels = struct([]);
pInfoBIDS.(newField).Units = '';
% update Tables
pInfoTbl.ColumnName = [pInfoTbl.ColumnName;newField];
temp = pInfoTbl.Data;
pInfoTbl.Data = cell(size(pInfoTbl.Data,1), size(pInfoTbl.Data,2)+1);
pInfoTbl.Data(:,1:size(temp,2)) = temp;
pInfoTbl.ColumnEditable = [pInfoTbl.ColumnEditable true];
bidsTbl.RowName = [bidsTbl.RowName;newField];
temp = bidsTbl.Data;
bidsTbl.Data = cell(size(bidsTbl.Data,1)+1, size(bidsTbl.Data,2));
bidsTbl.Data(1:size(temp,1),:) = temp;
bidsTbl.Data{end,strcmp(bidsTbl.ColumnName, 'Levels')} = 'Click to specify';
end
%% callback handle for Add/Edit Column button
function editColumnCB(~, ~, table, defaultBIDSFields)
allowedFields = ['(none)' setdiff(table.ColumnName', defaultBIDSFields)];
[~, ~, ~, structout] = inputgui('geometry', {[1 1] 1 [1 1 1 1]}, 'geomvert', [1 1 1], 'uilist', {...
{'Style', 'text', 'string', 'New column name (no space):'} ...
{'Style', 'edit', 'Tag', 'new_name'} ...
{} ...
{'Style', 'text', 'string', 'Rename column'} ...
{'Style', 'popupmenu', 'string', allowedFields, 'Tag', 'renamed_column_target'} ...
{'Style', 'text', 'string', 'to:'} ...
{'Style', 'edit', 'Tag', 'renamed_column_dest'} ...
});
if ~isempty(structout)
if ~isempty(structout.new_name)
addNewColumn(structout.new_name);
end
if ~isempty(structout.renamed_column_target) && structout.renamed_column_target > 1
targetColumn = allowedFields{structout.renamed_column_target};
if ~isempty(structout.renamed_column_dest)
renameColumn(targetColumn, structout.renamed_column_dest);
end
end
end
function renameColumn(target, destination)
% input validation
colName = checkFormat(destination);
pFields = strrep(pFields, target, colName);
% update pInfoBIDS structure
if isfield(pInfoBIDS, target)
pInfoBIDS.(colName) = pInfoBIDS.(target);
pInfoBIDS = rmfield(pInfoBIDS, target);
end
% update Tables
colIdx = strcmp(pInfoTbl.ColumnName,target);
if any(colIdx)
pInfoTbl.ColumnName{colIdx} = colName;
end
rowIdx = strcmp(bidsTbl.RowName, target);
if any(rowIdx)
bidsTbl.RowName{rowIdx} = colName;
end
end
end
%% callback handle for Add/Edit Column button
function removeColumnCB(~, ~, table, defaultBIDSFields)
allowedFields = ['(none)' setdiff(table.ColumnName', defaultBIDSFields)];
[~, ~, ~, structout] = inputgui('geometry', {[1 1]}, 'geomvert', 1, 'uilist', {...
{'Style', 'text', 'string', 'Column to remove (*cannot be undone):'} ...
{'Style', 'popupmenu', 'string', allowedFields, 'Tag', 'removed_column'} ...
});
if ~isempty(structout)
if ~isempty(structout.removed_column) && structout.removed_column > 1
removedColumn = allowedFields{structout.removed_column};
removeColumn(removedColumn);
end
end
function removeColumn(colName)
pFields(strcmp(pFields, colName)) = [];
% remove from pInfoBIDS structure
if isfield(pInfoBIDS, colName)
pInfoBIDS = rmfield(pInfoBIDS, colName);
end
% update Tables
colIdx = strcmp(pInfoTbl.ColumnName,colName);
if any(colIdx)
pInfoTbl.Data(:, colIdx) = [];
pInfoTbl.ColumnName(colIdx) = [];
end
rowIdx = strcmp(bidsTbl.RowName, colName);
if any(rowIdx)
bidsTbl.Data(rowIdx,:) = [];
bidsTbl.RowName(rowIdx) = [];
end
end
end
%% callback handle for cell selection in the participant info table
function pInfoCellSelectedCB(~, obj)
removeLevelUI();
tbl = obj.Source;
if ~isempty(obj.Indices)
uicontrol(f, 'Style', 'text', 'String', tbl.Data{obj.Indices(1), 1}, 'Units', 'normalized', 'Position',[0.02 0 0.38 0.08], 'HorizontalAlignment', 'left', 'FontSize',11,'FontAngle','italic','ForegroundColor', fg,'BackgroundColor', bg);
if strcmp(obj.Source.ColumnName{obj.Indices(2)}, 'SubjectArtefactDescription')
uicontrol(f, 'Style', 'text', 'String', 'Input for Subject Artefact Description', 'Units', 'normalized', 'Position',[0.42 0.43 0.68 0.05], 'HorizontalAlignment', 'left','FontAngle','italic','ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'cellContentHeader');
uicontrol(f, 'Style', 'edit', 'String', obj.Source.Data{obj.Indices(1),obj.Indices(2)}, 'Units', 'normalized', 'Max',2,'Min',0,'Position',[0.42 0.23 0.5 0.2], 'HorizontalAlignment', 'left', 'Callback', {@artefactCB, obj}, 'Tag', 'cellContentMsg');
end
end
end
%% callback handle for cell edit in pInfo table
function pInfoCellEditCB(~, obj, input)
row = obj.Indices(1);
col = obj.Indices(2);
pTbl = obj.Source;
if ~isempty(pTbl.Data{row, strcmp('participant_id', pTbl.ColumnName)})
if exist('input','var') % called from edit box for artefact description
entered = input;
else
entered = obj.EditData;
end
% for each row of the pInfo table
for r=1:size(pTbl.Data,1)
% if same subject with celected cell then copy value to that row as well
participantColIdx = find(strcmp(pTbl.ColumnName,'participant_id'));
if strcmp(pTbl.Data{r,participantColIdx}, pTbl.Data{row,participantColIdx})
pTbl.Data{r,col} = entered;
end
end
end
end
%% callback handle for cell selection in the BIDS table
function bidsCellSelectedCB(~, obj)
if size(obj.Indices,1) == 1
removeLevelUI();
row = obj.Indices(1);
col = obj.Indices(2);
field = obj.Source.RowName{row};
columnName = obj.Source.ColumnName{col};
if strcmp(columnName, 'Levels')
createLevelUI('','',obj,field);
elseif strcmp(columnName, 'Description')
uicontrol(f, 'Style', 'text', 'String', sprintf('%s (%s):',columnName, 'full description of the field'), 'Units', 'normalized', 'Position',[0.42 0.43 0.68 0.05], 'HorizontalAlignment', 'left','FontAngle','italic','ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'cellContentHeader');
uicontrol(f, 'Style', 'edit', 'String', obj.Source.Data{row,col}, 'Units', 'normalized', 'Max',2,'Min',0,'Position',[0.42 0.23 0.5 0.2], 'HorizontalAlignment', 'left', 'Callback', {@descriptionCB, obj,field}, 'Tag', 'cellContentMsg');
end
end
end
%% callback handle for cell edit in BIDS table
function bidsCellEditCB(~, obj)
field = obj.Source.RowName{obj.Indices(1)};
column = obj.Source.ColumnName{obj.Indices(2)};
if ~strcmp(column, 'Levels')
pInfoBIDS.(field).(column) = obj.EditData;
end
end
function descriptionCB(src,~,obj,field)
obj.Source.Data{obj.Indices(1),obj.Indices(2)} = src.String;
pInfoBIDS.(field).Description = src.String;
end
function artefactCB(src,~,obj)
obj.Source.Data{obj.Indices(1),obj.Indices(2)} = src.String;
pInfoCellEditCB(src, obj, src.String);
end
function createLevelUI(~,~,table,field)
removeLevelUI();
lvlHeight = 0.43;
if numel(EEG) == 1
uicontrol(f, 'Style', 'text', 'String', 'Documentation of levels does not apply to single dataset - edit at the study level.', 'Units', 'normalized', 'Position', [0.42 lvlHeight bidsWidth 0.05],'ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'levelEditMsg');
elseif strcmp(field, 'Participant_ID') || strcmp(field, 'Age')
uicontrol(f, 'Style', 'text', 'String', 'Levels editing does not apply to this field.', 'Units', 'normalized', 'Position', [0.42 lvlHeight bidsWidth 0.05],'ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'levelEditMsg');
else
pTable = findobj('Tag', 'pInfoTable');
if numel(pTable) > 1
pTable = pTable(1);
end
colIdx = strcmp(pTable.ColumnName, field);
levelCellText = table.Source.Data{strcmp(table.Source.RowName, field), strcmp(table.Source.ColumnName, 'Levels')}; % text (fieldName-Levels) cell. if 'n/a' then no action, 'Click to..' then conditional action, '<value>,...' then get levels
% retrieve all unique values
values = pTable.Data(:,colIdx);
idx = cellfun(@isempty, values);
levels = unique(values(~idx))';
if strcmp(levelCellText,'n/a')
uicontrol(f, 'Style', 'text', 'String', 'Levels editing does not apply to this field.', 'Units', 'normalized', 'Position', [0.42 lvlHeight bidsWidth 0.05],'ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'levelEditMsg');
elseif isempty(levels)
uicontrol(f, 'Style', 'text', 'String', 'No value found. Please specify values in Participant information table.', 'Units', 'normalized', 'Position', [0.42 lvlHeight 0.58 0.05],'ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'levelEditMsg');
elseif strcmp('Click to specify', levelCellText) && length(levels) > levelThreshold
msg = sprintf('\tThere are more than %d unique levels for field %s.\nAre you sure you want to specify levels for it?', levelThreshold, field);
c4 = uicontrol(f, 'Style', 'text', 'String', msg, 'Units', 'normalized', 'FontWeight', 'bold', 'ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'confirmMsg');
c4.Position = [0.42 lvlHeight-0.05 0.58 0.1];
c5 = uicontrol(f, 'Style', 'pushbutton', 'String', 'Yes', 'Units', 'normalized','Tag', 'confirmBtn', 'Callback', {@ignoreThresholdCB,table,field});
c5.Position = [0.42+0.58/2-0.1/2 lvlHeight-0.1 0.1 0.05];
else
% build table data
t = cell(length(levels),2);
for lvl=1:length(levels)
formattedLevel = checkFormat(levels{lvl}); % put level in the right format for indexing. Number is prepended by 'x'
t{lvl,1} = formattedLevel;
if ~isempty(pInfoBIDS.(field).Levels) && isfield(pInfoBIDS.(field).Levels, formattedLevel)
t{lvl,2} = pInfoBIDS.(field).Levels.(formattedLevel);
end
end
% create UI
uicontrol(f, 'Style', 'text', 'String', ['Describe the categorical values of participant field ' field], 'Units', 'normalized', 'HorizontalAlignment', 'left', 'Position', [0.52 0.45 0.53 0.05],'FontWeight', 'bold','ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'levelEditMsg');
msg = 'BIDS allows you to describe the level for each of your categorical field. Describing levels helps other researchers to understand your experiment better';
uicontrol(f, 'Style', 'text', 'String', msg, 'Units', 'normalized', 'HorizontalAlignment', 'Left','Position', [0.42 0.02 0.15 0.36],'ForegroundColor', fg,'BackgroundColor', bg, 'Tag', 'levelMsg');
h = uitable(f, 'Data', t(:,2), 'ColumnName', {'Description'}, 'RowName', t(:,1), 'Units', 'normalized', 'Position', [0.58 0.08 0.4 0.36], 'FontSize', fontSize, 'Tag', 'levelEditTbl', 'CellEditCallback',{@levelEditCB,field},'ColumnEditable',true);
h.ColumnWidth = {appWidth*0.4*0.9};
end
end
end
function ignoreThresholdCB(~,~,table, field)
table.Source.Data{strcmp(table.Source.RowName, field), strcmp(table.Source.ColumnName, 'Levels')} = 'Click to specify below (ignore max number of levels threshold)';
createLevelUI('','',table,field);
end
function levelEditCB(~, obj, field)
level = checkFormat(obj.Source.RowName{obj.Indices(1)});
description = obj.EditData;
if isempty(pInfoBIDS.(field).Levels)
temp = [];
temp.(level) = description;
pInfoBIDS.(field).Levels = temp;
else
pInfoBIDS.(field).Levels.(level) = description;
end
specified_levels = fieldnames(pInfoBIDS.(field).Levels);
% Update main table
mainTable = findobj('Tag','bidsTable');
mainTable.Data{strcmp(field,mainTable.RowName),strcmp('Levels',mainTable.ColumnName)} = strjoin(specified_levels, ',');
end
function bidsFieldSelected(src, ~, table, row, col)
val = src.Value;
str = src.String;
selected = str{val};
table.Data{row,col} = selected;
field = table.RowName{row};
eventBIDS.(field).BIDSField = selected;
end
function formatted = checkFormat(str)
if ~isempty(str2num(str))
formatted = ['x' str];
else
formatted = strrep(str,' ','_'); %replace space with _
end
end
function removeLevelUI()
% remove old ui items of level section if exist
h = findobj('Tag', 'levelEditMsg');
if ~isempty(h)
delete(h);
end
h = findobj('Tag', 'levelEditTbl');
if ~isempty(h)
delete(h);
end
h = findobj('Tag', 'confirmMsg');
if ~isempty(h)
delete(h);
end
h = findobj('Tag', 'confirmBtn');
if ~isempty(h)
delete(h);
end
h = findobj('Tag', 'noBidsMsg');
if ~isempty(h)
delete(h);
end
h = findobj('Tag', 'cellContentMsg');
if ~isempty(h)
delete(h);
end
h = findobj('Tag', 'cellContentHeader');
if ~isempty(h)
delete(h);
end
h = findobj('Tag', 'selectBIDSMsg');
if ~isempty(h)
delete(h);
end
h = findobj('Tag', 'selectBIDSDD');
if ~isempty(h)
delete(h);
end
h = findobj('Tag', 'levelMsg');
if ~isempty(h)
delete(h);
end
end
function [pBIDS, pFields] = newpInfoBIDS()
pBIDS = getpInfoDesc();
if isempty(pBIDS)
pFields = { 'participant_id' 'Gender' 'Age' 'Group'};
for idx=1:length(pFields)
if strcmp(pFields{idx}, 'participant_id')
pBIDS.participant_id.Description = 'Unique participant label';
pBIDS.participant_id.Units = '';
pBIDS.participant_id.Levels = 'n/a';
elseif strcmp(pFields{idx}, 'Gender')
pBIDS.Gender.Description = 'Participant gender';
pBIDS.Gender.Levels = struct;
pBIDS.Gender.Units = '';
elseif strcmp(pFields{idx}, 'Age')
pBIDS.Age.Description = 'Participant age (years)';
pBIDS.Age.Units = 'years';
pBIDS.Age.Levels = 'n/a';
elseif strcmp(pFields{idx}, 'Group')
pBIDS.Group.Description = 'Participant group label';
pBIDS.Group.Units = '';
pBIDS.Group.Levels = struct;
end
end
else
pFields = fieldnames(pBIDS)';
for p=1:numel(pFields)
if ~isfield(pBIDS.(pFields{p}), 'Units')
if strcmp(pFields{p}, 'Age')
pBIDS.(pFields{p}).Units = 'years';
else
pBIDS.(pFields{p}).Units = '';
end
end
if ~isfield(pBIDS.(pFields{p}), 'Levels')
if strcmp(pFields{p}, 'Age') || strcmp(pFields{p}, 'participant_id')
pBIDS.(pFields{p}).Levels = 'n/a';
else
pBIDS.(pFields{p}).Levels = struct;
end
end
end
end
% Get BIDS information
function info = getpInfoDesc()
hasBIDS = arrayfun(@(x) isfield(x,'BIDS') && ~isempty(x.BIDS),EEG);
if sum(hasBIDS) == 0 %if no BIDS found for any EEG
info = [];
else % at least one EEG has BIDS
if sum(hasBIDS) < numel(EEG) % not all have BIDS
warning('Not all EEG contains BIDS information.');
end
haspInfoDesc = arrayfun(@(x) isfield(x,'BIDS') && isfield(x.BIDS,'pInfoDesc') && ~isempty(x.BIDS.pInfoDesc),EEG);
if sum(haspInfoDesc) == 0
info = [];
else % at least one EEG has BIDS.pInfoDesc
try
bids = [EEG(haspInfoDesc).BIDS];
allpInfoDesc = [bids.pInfoDesc];
if numel(allpInfoDesc) < numel(EEG)
info = EEG(find(haspInfoDesc,1)).BIDS.pInfoDesc;
warning('Not all EEG contains BIDS information. Using BIDS information of EEG(%d)...',find(haspInfoDesc,1));
else
info = allpInfoDesc(1);
fprintf('Using BIDS information of the first dataset for all datasets...\n');
end
catch % field inconsistent
info = EEG(find(haspInfoDesc,1)).BIDS.pInfoDesc;
warning('Inconsistence found in BIDS information across STUDY datasets. Using BIDS information of EEG(%d)...',find(haspInfoDesc,1));
end
end
end
end
end
end