Merge remote-tracking branch 'cpp-lln-lab/master'

Author: CerenB

README.md

@@ -41,26 +41,18 @@ expParameters.subjectNb = 1;
 expParameters.sessionNb = 1;
 expParameters.runNb = 1;
 
-% Use the verbose switch to know where your data is being saved
-expParameters.verbose = true;
-
-% In case you are using en eyetracker
+% by default we assume you are running things on a behavioral PC with no eyetracker
 cfg.eyeTracker = false;
+cfg.testingDevice = 'PC';
 
-% if the device is set to 'PC' then the data will be saved
-% in the `beh` folder
-cfg.device = 'PC';
-
-% if the device is set to 'scanner' then the data will be saved
-% in the `func` folder
-% cfg.device = 'scanner';
-
-% check that cfg and exparameters have all the necessary information
-% and fill in any missing field
-expParameters = checkCFG(cfg, expParameters);
+% if the testing device is set to 'PC' then the data will be saved in the `beh` folder
+% if set to 'mri' then the data will be saved in the `func` folder
+% cfg.testingDevice = 'mri';
+% if set to 'eeg' then the data will be saved in the `eeg` folder
+% cfg.testingDevice = 'eeg';
 
-% create the filenames
-expParameters = createFilename(cfg, expParameters);
+% create the filenames: this include a step to check that all the information is there (checkCFG)
+[cfg, expParameters] = createFilename(cfg, expParameters);
 
 % initialize the events files with the typical BIDS
 % columns (onsets, duration, trial_type)
@@ -96,6 +88,9 @@ saveEventsFile('close', expParameters, logFile);
 
 Get subject, run and session number and make sure they are positive integer values.
 
+By default this will return `expParameters.session = 1` even if you asked it to omit enquiring about sessions. This means
+that the folder tree will always include a session folder.
+
 ```matlab
 [expParameters] = userInputs(cfg, expParameters)
 ```
@@ -111,19 +106,21 @@ it will only ask you about session
 
 if you use it with `expParameters.askGrpSess = [1 1]`
 it will ask you about both
-this is the defaut
+this is the default
 
 
 ### createFilename
 
 Create the BIDS compliant directories  and filenames (but not the files) for the behavioral
 output for this subject / session / run.
 
+The folder tree will always include a session folder.
+
 Will also create the right filename for the eye-tracking data file.
 
 For the moment the date of acquisition is appended 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 behavioral experiment if cfg.testingDevice is set to 'PC'
+-   can work for fMRI experiment if cfg.testingDevice is set to 'mri'
 -   can work for simple eyetracking data if cfg.eyeTracker is set to 1
 
 ### saveEventsFile

checkCFG.m

@@ -1,56 +1,74 @@
-function [expParameters, cfg] = checkCFG(cfg, expParameters)
-    % check that we have all the fields that we need in the experiment
-    % parameters
+function [cfg, expParameters] = checkCFG(cfg, expParameters)
+    % 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( ...
+    %% set the expParameters defaults
+    
+    fieldsToSet.verbose = 0;
+    fieldsToSet.outputDir = fullfile( ...
             fileparts(mfilename('fullpath')), ...
             '..', ...
             'output');
-    end
-
-    % set empty values for a series of field if they have not been specified
-    % '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
-    % 'subjectGrp' in case no group was provided
-    % 'sessionNb'  in case no session was provided
-
-    fields2Check = { ...
-        'ce', ...
-        'dir', ...
-        'rec', ...
-        'echo', ...
-        'acq', ...
-        'subjectGrp', ...
-        'sessionNb'};
 
-    for iField = 1:numel(fields2Check)
-        if ~isfield(expParameters, fields2Check{iField})
-            expParameters = setfield(expParameters, fields2Check{iField}, []); %#ok<SFLD>
-        end
+    fieldsToSet.subjectGrp = []; % in case no group was provided
+    fieldsToSet.sessionNb = []; % in case no session was provided
+    fieldsToSet.askGrpSess = [true true];
+    
+    % BIDS
+    
+    % dataset description json
+    % required
+    fieldsToSet.bids.datasetDescription.json.Name = '';
+    fieldsToSet.bids.datasetDescription.json.BIDSVersion = '';
+    % recommended
+    fieldsToSet.bids.datasetDescription.json.License = '';
+    fieldsToSet.bids.datasetDescription.json.Authors = {''};
+    fieldsToSet.bids.datasetDescription.json.Acknowledgements = '';
+    fieldsToSet.bids.datasetDescription.json.HowToAcknowledge = '';
+    fieldsToSet.bids.datasetDescription.json.Funding = {''};
+    fieldsToSet.bids.datasetDescription.json.ReferencesAndLinks = {''};
+    fieldsToSet.bids.datasetDescription.json.DatasetDOI = '';
+    
+    % mri
+    % for json
+    fieldsToSet.MRI.repetitionTime = [];
+    % for file naming
+    fieldsToSet.MRI.ce = [];
+    fieldsToSet.MRI.dir = []; % phase encoding direction of acquisition for fMRI
+    fieldsToSet.MRI.rec = []; % reconstruction of fMRI images
+    fieldsToSet.MRI.echo = []; % echo fMRI images
+    fieldsToSet.MRI.acq = []; % acquisition of fMRI images
+    
+    %% loop through the defaults and set them in expParameters if they don't exist
+    names = fieldnames(fieldsToSet);
+    
+    for i = 1:numel(names)
+        expParameters = setFieldToIfNotPresent(...
+            expParameters, ...
+            names{i}, ...
+            getfield(fieldsToSet, names{i})); %#ok<GFLD>
+    end
+    
+    %% set the cfg defaults
+    
+    clear fieldsToSet
+    fieldsToSet.testingDevice = 'pc';
+    fieldsToSet.eyeTracker = false;
+    
+    % loop through the defaults and set them in cfg if they don't exist
+    names = fieldnames(fieldsToSet);
+    
+    for i = 1:numel(names)
+        cfg = setFieldToIfNotPresent(...
+            cfg, ...
+            names{i}, ...
+            getfield(fieldsToSet, names{i})); %#ok<GFLD>
     end
 
-    % set false value for a series of field if they have not been specified
-    fields2CheckFalse = { ...
-        'eyeTracker'
-        };
+end
 
-    for iField = 1:numel(fields2CheckFalse)
-        if ~isfield(cfg, fields2CheckFalse{iField})
-            cfg = setfield(cfg, fields2CheckFalse{iField}, false); %#ok<SFLD>
-        end
-    end
 
-    % other defaults
-    if ~isfield(expParameters, 'askGrpSess')
-        expParameters.askGrpSess = [true true];
+function struct = setFieldToIfNotPresent(struct, fieldName, value)
+    if ~isfield(struct, fieldName)
+        struct = setfield(struct, fieldName, value); %#ok<SFLD>
     end
-
-end
+end