make functions more verbose

checkCFG.m

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

createFilename.m

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

createFilename.m~

@@ -0,0 +1,132 @@
+function expParameters = createFilename(expParameters, cfg)
+% create the BIDS compliant directories and filenames for the behavioral output for this subject /
+% session / run.
+% Will also create the right filename for the eyetracking data file.
+%
+% For the moment the date of acquisition is appreneded to the filename
+%
+% can work for behavioral experiment if cfg.device is set to 'PC'
+% can work for fMRI experiment if cfg.device is set to 'scanner'
+% can work for simple eyetracking data if cfg.eyeTracker is set to 1
+%
+% BOLD
+% sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
+%
+% iEEG
+% sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json
+%
+% EEG
+% sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>
+%
+% EYETRACKER
+% sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>
+
+zeroPadding = 3;
+pattern = ['%0' num2str(zeroPadding) '.0f'];
+
+dateFormat = 'yyyymmdd_HHMM';
+
+% Setting some defaults: no need to change things here
+expParameters = checkCFG(expParameters);
+
+% extract input
+subjectGrp = expParameters.subjectGrp;
+subjectNb = expParameters.subjectNb;
+sessionNb = expParameters.sessionNb;
+runNb = expParameters.runNb;
+
+expParameters.date = datestr(now, dateFormat);
+
+% output dir
+expParameters.outputDir = fullfile (...
+    expParameters.outputDir, ...
+    'source', ...
+    ['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
+    ['ses-', sprintf(pattern, sessionNb)]);
+
+% create base filename
+expParameters.fileName.base = ...
+    ['sub-', subjectGrp, sprintf(pattern, subjectNb), ...
+    '_ses-', sprintf(pattern, sessionNb) , ...
+    '_task-', expParameters.task];
+
+runSuffix = ['_run-' sprintf(pattern, runNb)];
+
+
+switch lower(cfg.device)
+    case 'pc'
+        modality = 'beh';
+    case 'scanner'
+        modality = 'func';
+    otherwise
+        modality = 'beh';
+end
+
+expParameters.modality = modality;
+
+
+% set values for the suffixes for the different fields in the BIDS name
+fields2Check = { ...
+    'ce', ...
+    'dir', ...  % For BIDS file naming: phase encoding direction of acquisition for fMRI
+    'rec', ...  % For BIDS file naming: reconstruction of fMRI images
+    'echo', ... % For BIDS file naming: echo fMRI images
+    'acq'       % For BIDS file naming: acquisition of fMRI images
+    };
+
+for iField = 1:numel(fields2Check)
+    if isempty (getfield(expParameters, fields2Check{iField}) ) %#ok<*GFLD>
+        expParameters = setfield(expParameters, [fields2Check{iField} 'Suffix'], ...
+            ''); %#ok<*SFLD>
+    else
+        expParameters = setfield(expParameters, [fields2Check{iField} 'Suffix'], ...
+            ['_' fields2Check{iField} '-' getfield(expParameters, fields2Check{iField})]);
+    end
+end
+
+
+%% create directories
+[~, ~, ~] = mkdir(expParameters.outputDir);
+[~, ~, ~] = mkdir(fullfile(expParameters.outputDir, modality));
+
+if cfg.eyeTracker
+    [~, ~, ~] = mkdir(fullfile(expParameters.outputDir, 'eyetracker'));
+end
+
+
+%% create filenames
+
+switch modality
+
+    case 'beh'
+
+        expParameters.fileName.events = ...
+            [expParameters.fileName.base, runSuffix, '_events_date-' expParameters.date '.tsv'];
+
+    case 'func'
+
+        expParameters.fileName.events = ...
+            [expParameters.fileName.base, ...
+            expParameters.acqSuffix, expParameters.ceSuffix, ...
+            expParameters.dirSuffix, expParameters.recSuffix, ...
+            runSuffix, expParameters.echoSuffix, ...
+            '_events_date-' expParameters.date '.tsv'];
+
+end
+
+if cfg.eyeTracker
+
+    expParameters.fileName.eyetracker = ...
+        [expParameters.fileName.base, expParameters.acqSuffix, ...
+        runSuffix, '_eyetrack_date-' expParameters.date '.edf'];
+
+end
+
+if expParameters.verbose
+    fprintf(1,'\nData will be saved in this directory:\n\n%s\')
+    expParameters.outputDir
+    expParameters.fileName
+end
+
+
+end

saveEventsFile.m

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

saveEventsFile.m~

@@ -0,0 +1,79 @@
+function [ logFile ] = saveEventsFile(input, expParameters, logFile, varargin)
+
+if nargin<3 || isempty(logFile)
+    logFile = struct();
+end
+
+switch input
+
+    case 'open'
+
+        logFile = struct();
+
+        % Initialize txt logfiles and empty fields for the standard BIDS
+        %  event file
+        logFile.eventLogFile = fopen(...
+            fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.events), ...
+            'w');
+
+        % print the basic BIDS columns
+        fprintf(logFile.eventLogFile, '%s\t%s\t%s\t', 'onset', 'trial_type', 'duration');
+
+        % print any extra column specified by the user
+        %  also prepare an empty field in the structure to collect data
+        %  for those
+        for iExtraColumn = 1:numel(varargin)
+            fprintf(logFile.eventLogFile,'%s\t', lower(varargin{iExtraColumn}));
+        end
+
+        % next line so we start printing at the right place
+        fprintf(logFile.eventLogFile, '\n');
+
+
+    case 'save'
+
+        % appends to the logfile all the data stored in the structure
+        % first with the standard BIDS data and then any extra things
+        for iEvent = 1:size(logFile,1)
+
+            fprintf(logFile(1).eventLogFile,'%f\t%s\t%f\t',...
+                logFile(iEvent).onset, ...
+                logFile(iEvent).trial_type, ...
+                logFile(iEvent).duration);
+
+            for iExtraColumn = 1:numel(varargin)
+
+                % if the field we are looking for does not exist or is empty in the
+                % input logFile structure we will write a NaN otherwise we
+                % write its content
+
+                if ~isfield(logFile, varargin{iExtraColumn})
+                    data = [];
+                else
+                    data = getfield(logFile(iEvent), varargin{iExtraColumn});
+                end
+
+                if isempty(data)
+                    data = NaN;
+                end
+
+                if ischar(data)
+                    fprintf(logFile(1).eventLogFile, '%s\t', data);
+                else
+                    fprintf(logFile(1).eventLogFile, '%f\t', data);
+                end
+
+            end
+
+            fprintf(logFile(1).eventLogFile, '\n');
+        end
+
+    case 'close'
+
+        % close txt log file
+        fclose(logFile(1).eventLogFile);
+
+        if expParameters.verbose
+        fullfile(expParameters.outputDir, expParameters.modality, expParameters.fileName.events)
+
+end

tests/test_createFilename.m

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

tests/test_saveEventsFile.m

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