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adding misc function from Cyril
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arno committed Apr 2, 2019
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209 changes: 209 additions & 0 deletions std_tobids.m
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function STUDY = std_tobids(varargin)

% From a STUDY rename files if needed, sort folders, and export metadata
% following the BIDS specification
%
% FORMAT STUDY = std_tobids(STUDY,options)
% options are: 'export_dir' followed by the path
% 'keep_files' being 'yes' (default) or 'no'
% 'update_study' being 'yes' or 'no'
%
% Author: Cyril Pernet - LIMO Team, University of Edinurgh
% Arnaud Delorme, EEGLAB, SCCN, 2018
%

%% options
if nargin == 1
export_dir = STUDY.filepath; % where to make the bids directory
keep_files = 'no'; % copy files to move and rename
update_study = 'yes'; % return study with updated names and paths
else
for in = 2:nargin
if strcmpi(varargin{in},'export_dir') || strcmpi(varargin{in},'exportdir')
export_dir = varargin{in+1};
elseif strcmpi(varargin{in},'keep_files') || strcmpi(varargin{in},'keepfiles')
keep_files = varargin{in+1};
elseif strcmpi(varargin{in},'update_study') || strcmpi(varargin{in},'updatestudy')
update_study = varargin{in+1};
end
end
end

%% get subjects info
N = length(STUDY.subject);
if isempty(STUDY.task)
STUDY.task = inputdlg2('input task name','task info missing'); % @Arno inputdlg2 fails
end
% task name with no space
task = lower(STUDY.task);
task(1) = upper(task(1));
task(find(isspace(STUDY.task))+1) = upper(task(find(isspace(STUDY.task))+1));
task(isspace(task)) = [];


% let's get the index of which files belong to the same subject
datasetindex = cell(N,length(STUDY.session));
if length(STUDY.session) > 1
for subject =1:N
file_index = 1;
for files = 1:length(STUDY.datasetinfo)
if strcmp(STUDY.subject{subject},STUDY.datasetinfo(files).subject)
datasetindex{subject,file_index} = files;
file_index = file_index+1;
end
end
end
else
for subject =1:N
datasetindex{subject} = STUDY.subject{subject};
end
end


% % check if subjects are all together or in different folders
% for files = 1:length(STUDY.datasetinfo)
% paths{files} = STUDY.datasetinfo(files).filepath;
% end

% for each subject, move/rename and export metadata
for subject =1:N
if strncmp(STUDY.subject{subject},'sub-',4)
newname = STUDY.subject{subject};
else
newname = ['sub-' STUDY.subject{subject}];
end

% create sub- folder
if strcmp(export_dir(length(export_dir)),filesep)
export_dir = export_dir(1:end-1);
end
subj_dir = [export_dir filesep newname filesep 'eeg'];
subj_derivatives_dir = [export_dir filesep 'derivatives' filesep newname filesep 'eeg'];
mkdir(subj_dir)

% rename/move files
for run = 1:length(STUDY.session)
if ~isempty(datasetindex{subject,run})
if ischar(datasetindex{subject,run})
tmp = STUDY.datasetinfo(str2num(datasetindex{subject,run}));
else
tmp = STUDY.datasetinfo(datasetindex{subject,run});
end
[~,name,ext]=fileparts(tmp.filename);

if strcmpi(keep_files,'no')
movefile([tmp.filepath filesep tmp.filename],[subj_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_eeg' ext]);
movefile([tmp.filepath filesep name '.fdt'], [subj_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_eeg.fdt']);
elseif strcmpi(keep_files,'yes')
copyfile([tmp.filepath filesep tmp.filename],[subj_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_eeg' ext]);
copyfile([tmp.filepath filesep name '.fdt'], [subj_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_eeg.fdt']);
end
EEG = pop_loadset([subj_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_eeg' ext]);
EEG.setname = [subj_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_eeg'];
EEG.datfile = [newname '_task-' task '_sess-1_run-' num2str(run) '_eeg.fdt'];
% metadata
SF(subject,run) = EEG.srate;
CC(subject,run) = size(EEG.chanlocs,2);
Ref{subject,run} = EEG.ref;

% check derivatives and update .set
if exist([tmp.filepath filesep STUDY.subject{subject} '.daterp'],'file') || ...
exist([tmp.filepath filesep STUDY.subject{subject} '.daterpim'],'file') || ...
exist([tmp.filepath filesep STUDY.subject{subject} '.datspec'],'file') || ...
exist([tmp.filepath filesep STUDY.subject{subject} '.dattimef'],'file')
name = STUDY.subject{subject}; % otherwise comes from STUDY.datasetinfo, depends if computed from study or not
end

if exist([tmp.filepath filesep name '.daterp'],'file')
if ~exist(subj_derivatives_dir,'dir'); mkdir(subj_derivatives_dir); end
if strcmpi(keep_files,'no')
movefile([tmp.filepath filesep name '.daterp'], [subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-erp_eeg.daterp']);
elseif strcmpi(keep_files,'yes')
copyfile([tmp.filepath filesep name '.daterp'], [subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-erp_eeg.daterp']);
end
EEG.etc.datafiles.daterp = [subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-erp_eeg.daterp'];
end

if exist([tmp.filepath filesep name '.daterpim'],'file')
if ~exist(subj_derivatives_dir,'dir'); mkdir(subj_derivatives_dir); end
if strcmpi(keep_files,'no')
movefile([tmp.filepath filesep name '.daterpim'],[subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-erpimg_eeg.daterpim']);
elseif strcmpi(keep_files,'yes')
copyfile([tmp.filepath filesep name '.daterpim'],[subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-erpimg_eeg.daterpim']);
end
EEG.etc.datafiles.daterpim = [subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-erpimg_eeg.daterpim'];
end

if exist([tmp.filepath filesep name '.datspec'],'file')
if ~exist(subj_derivatives_dir,'dir'); mkdir(subj_derivatives_dir); end
if strcmpi(keep_files,'no')
movefile([tmp.filepath filesep name '.datspec'],[subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-spectrum_eeg.datspec']);
elseif strcmpi(keep_files,'yes')
copyfile([tmp.filepath filesep name '.datspec'],[subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-spectrum_eeg.datspec']);
EEG.etc.datafiles.datspec = [subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-spectrum_eeg.datspec'];
end
end

if exist([tmp.filepath filesep name '.dattimef'],'file')
if ~exist(subj_derivatives_dir,'dir'); mkdir(subj_derivatives_dir); end
if strcmpi(keep_files,'no')
movefile([tmp.filepath filesep name '.dattimef'],[subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-timefrequency_eeg.dattimef']);
elseif strcmpi(keep_files,'yes')
copyfile([tmp.filepath filesep name '.dattimef'],[subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-timefrequency_eeg.dattimef']);
EEG.etc.datafiles.dattimef = [subj_derivatives_dir filesep newname '_task-' task '_sess-1_run-' num2str(run) '_desc-timefrequency_eeg.dattimef'];
end
end

% resave the .set with updated info
pop_saveset(EEG,'savemode','resave');

% export metadata
if run == 1
electrodes_to_tsv(EEG);
end
channelloc_to_tsv(EEG);
events_to_tsv(EEG);
end

if strcmpi(update_study,'yes')
STUDY.datasetinfo(subject).filepath = subj_dir;
STUDY.datasetinfo(subject).filename = [newname '_task-' task '_sess-1_run-' num2str(run) '_eeg' ext];
STUDY.datasetinfo(subject).subject = newname;
STUDY.subject{subject} = newname;
end
end
end

% update task name
if strcmpi(update_study,'yes')
STUDY.task = task;
STUDY = pop_savestudy(STUDY,'savemode','resave');
end

% finish of with root metadata
% ----------------------------
% make *_eeg.json
PLF = str2num(cell2mat(inputdlg('What was the Power Line Frequency?','BIDS spec requirement')));
if size(unique(Ref),1) > 1
warning('difference referencing scheme found of this dataset')
Ref = cell2mat(inputdlg('What was the reference?','BIDS spec requirement'));
end

json = struct('TaskName',task, ...
'SamplingFrequency', mean(SF(:)), ...
'EEGChannelCount', max(CC(:)), ...
'EEGReference', unique(Ref), ...
'PowerLineFrequency', PLF, ...
'SoftwareFilters', ' ');
jsonwrite([export_dir filesep task '_eeg.json'],json,struct('indent',' '))

% make a participants table and save
age = zeros(N,1);
sex = repmat(' ',[N 1]);
t = table(STUDY.subject',age,sex,'VariableNames',{'participant_id','age','sex'});
writetable(t,[export_dir filesep 'Participants.tsv'],'FileType','text','Delimiter','\t');
warndlg('Job done, but metadata created need editing','BIDS spec','modal')




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