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Remi-GauRemi-Gau
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Merge pull request #11 from Remi-Gau/remi-talk_to_me
make functions more verbose
2 parents accb67c + e05df07 commit 3ccbe22

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7 files changed

+247
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‎checkCFG.m‎

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@@ -2,6 +2,10 @@
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% check that we have all the fields that we need in the experiment
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% parameters
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if ~isfield(expParameters, 'verbose') || isempty(expParameters.verbose)
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expParameters.verbose = 0;
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end
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if ~isfield(expParameters, 'outputDir')
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expParameters.outputDir = fullfile(...
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fileparts(mfilename('fullpath')), ...

‎createFilename.m‎

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@@ -122,5 +122,25 @@
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end
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if expParameters.verbose
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fprintf(1,'\nData will be saved in this directory:\n\t%s\n', ...
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fullfile(expParameters.outputDir, modality));
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fprintf(1,'\nData will be saved in this file:\n\t%s\n', ...
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expParameters.fileName.events);
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if cfg.eyeTracker
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fprintf(1,'\nEyetracking data will be saved in this directory:\n\t%s\n', ...
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fullfile(expParameters.outputDir, 'eyetracker'));
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fprintf(1,'\nEyetracking data will be saved in this file:\n\t%s\n', ...
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expParameters.fileName.eyetracker);
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end
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end
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end

‎createFilename.m~‎

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function expParameters = createFilename(expParameters, cfg)
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% create the BIDS compliant directories and filenames for the behavioral output for this subject /
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% session / run.
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% Will also create the right filename for the eyetracking data file.
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%
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% For the moment the date of acquisition is appreneded to the filename
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%
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% can work for behavioral experiment if cfg.device is set to 'PC'
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% can work for fMRI experiment if cfg.device is set to 'scanner'
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% can work for simple eyetracking data if cfg.eyeTracker is set to 1
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%
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% BOLD
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% sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
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%
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% iEEG
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% sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json
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%
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% EEG
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% sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>
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%
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% EYETRACKER
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% sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>
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zeroPadding = 3;
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pattern = ['%0' num2str(zeroPadding) '.0f'];
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dateFormat = 'yyyymmdd_HHMM';
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% Setting some defaults: no need to change things here
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expParameters = checkCFG(expParameters);
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% extract input
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subjectGrp = expParameters.subjectGrp;
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subjectNb = expParameters.subjectNb;
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sessionNb = expParameters.sessionNb;
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runNb = expParameters.runNb;
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expParameters.date = datestr(now, dateFormat);
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% output dir
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expParameters.outputDir = fullfile (...
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expParameters.outputDir, ...
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'source', ...
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['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
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['ses-', sprintf(pattern, sessionNb)]);
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% create base filename
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expParameters.fileName.base = ...
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['sub-', subjectGrp, sprintf(pattern, subjectNb), ...
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'_ses-', sprintf(pattern, sessionNb) , ...
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'_task-', expParameters.task];
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runSuffix = ['_run-' sprintf(pattern, runNb)];
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switch lower(cfg.device)
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case 'pc'
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modality = 'beh';
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case 'scanner'
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modality = 'func';
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otherwise
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modality = 'beh';
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end
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expParameters.modality = modality;
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% set values for the suffixes for the different fields in the BIDS name
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fields2Check = { ...
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'ce', ...
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'dir', ... % For BIDS file naming: phase encoding direction of acquisition for fMRI
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'rec', ... % For BIDS file naming: reconstruction of fMRI images
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'echo', ... % For BIDS file naming: echo fMRI images
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'acq' % For BIDS file naming: acquisition of fMRI images
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};
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for iField = 1:numel(fields2Check)
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if isempty (getfield(expParameters, fields2Check{iField}) ) %#ok<*GFLD>
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expParameters = setfield(expParameters, [fields2Check{iField} 'Suffix'], ...
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''); %#ok<*SFLD>
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else
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expParameters = setfield(expParameters, [fields2Check{iField} 'Suffix'], ...
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['_' fields2Check{iField} '-' getfield(expParameters, fields2Check{iField})]);
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end
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end
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%% create directories
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[~, ~, ~] = mkdir(expParameters.outputDir);
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[~, ~, ~] = mkdir(fullfile(expParameters.outputDir, modality));
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if cfg.eyeTracker
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[~, ~, ~] = mkdir(fullfile(expParameters.outputDir, 'eyetracker'));
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end
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%% create filenames
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switch modality
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case 'beh'
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expParameters.fileName.events = ...
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[expParameters.fileName.base, runSuffix, '_events_date-' expParameters.date '.tsv'];
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case 'func'
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expParameters.fileName.events = ...
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[expParameters.fileName.base, ...
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expParameters.acqSuffix, expParameters.ceSuffix, ...
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expParameters.dirSuffix, expParameters.recSuffix, ...
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runSuffix, expParameters.echoSuffix, ...
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'_events_date-' expParameters.date '.tsv'];
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end
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if cfg.eyeTracker
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expParameters.fileName.eyetracker = ...
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[expParameters.fileName.base, expParameters.acqSuffix, ...
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runSuffix, '_eyetrack_date-' expParameters.date '.edf'];
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end
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if expParameters.verbose
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fprintf(1,'\nData will be saved in this directory:\n\n%s\')
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expParameters.outputDir
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expParameters.fileName
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end
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end

‎saveEventsFile.m‎

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@@ -73,4 +73,13 @@
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% close txt log file
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fclose(logFile(1).eventLogFile);
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if expParameters.verbose
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fprintf(1,'\nData were saved in this file:\n\n%s\n\n', ...
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fullfile(...
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expParameters.outputDir, ...
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expParameters.modality, ...
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expParameters.fileName.events));
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end
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end

‎saveEventsFile.m~‎

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function [ logFile ] = saveEventsFile(input, expParameters, logFile, varargin)
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if nargin<3 || isempty(logFile)
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logFile = struct();
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end
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switch input
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case 'open'
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logFile = struct();
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% Initialize txt logfiles and empty fields for the standard BIDS
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% event file
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logFile.eventLogFile = fopen(...
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fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.events), ...
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'w');
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% print the basic BIDS columns
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fprintf(logFile.eventLogFile, '%s\t%s\t%s\t', 'onset', 'trial_type', 'duration');
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% print any extra column specified by the user
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% also prepare an empty field in the structure to collect data
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% for those
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for iExtraColumn = 1:numel(varargin)
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fprintf(logFile.eventLogFile,'%s\t', lower(varargin{iExtraColumn}));
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end
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% next line so we start printing at the right place
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fprintf(logFile.eventLogFile, '\n');
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case 'save'
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% appends to the logfile all the data stored in the structure
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% first with the standard BIDS data and then any extra things
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for iEvent = 1:size(logFile,1)
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fprintf(logFile(1).eventLogFile,'%f\t%s\t%f\t',...
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logFile(iEvent).onset, ...
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logFile(iEvent).trial_type, ...
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logFile(iEvent).duration);
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for iExtraColumn = 1:numel(varargin)
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% if the field we are looking for does not exist or is empty in the
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% input logFile structure we will write a NaN otherwise we
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% write its content
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if ~isfield(logFile, varargin{iExtraColumn})
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data = [];
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else
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data = getfield(logFile(iEvent), varargin{iExtraColumn});
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end
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if isempty(data)
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data = NaN;
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end
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if ischar(data)
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fprintf(logFile(1).eventLogFile, '%s\t', data);
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else
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fprintf(logFile(1).eventLogFile, '%f\t', data);
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end
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end
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fprintf(logFile(1).eventLogFile, '\n');
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end
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case 'close'
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% close txt log file
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fclose(logFile(1).eventLogFile);
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if expParameters.verbose
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fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.events)
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end

‎tests/test_createFilename.m‎

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@@ -9,6 +9,7 @@ function test_createFilename()
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expParameters.sessionNb = 1;
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expParameters.runNb = 1;
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expParameters.task = 'testtask';
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expParameters.verbose = 1;
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cfg.eyeTracker = true;
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cfg.device = 'PC';

‎tests/test_saveEventsFile.m‎

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Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@ function test_saveEventsFile()
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expParameters.sessionNb = 1;
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expParameters.runNb = 1;
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expParameters.task = 'testtask';
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expParameters.verbose = 1;
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cfg.eyeTracker = false;
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cfg.device = 'scanner';
@@ -72,4 +73,4 @@ function test_saveEventsFile()
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assert(isequal(C{4}{2}, 'NaN')); % check that empty values are entered as NaN
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assert(isequal(C{4}{4}, 'NaN')); % check that missing fields are entered as NaN
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assert(isequal(str2num(C{5}{4}), 3)); % check values entered properly
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assert(isequal(str2double(C{5}{4}), 3)); % check values entered properly

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