allow createBoldJson to add extra content to a json file

Author: Remi-Gau

manualTests/testData/extra_bold.json

@@ -0,0 +1,10 @@
+{
+    "Instructions": "",
+    "RepetitionTime": [],
+    "SliceTiming": [],
+    "TaskDescription": "",
+    "TaskName": "testtask",
+    "extraInfo": {
+        "nestedExtraInfo": "something extra"
+    }
+}

manualTests/test_createBoldJson.m

@@ -0,0 +1,50 @@
+function test_suite = test_createBoldJson %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_createBoldJsonExtra()
+
+    outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
+
+    %% set up
+
+    cfg.verbose = false;
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'testtask';
+
+    cfg.dir.output = outputDir;
+
+    cfg.testingDevice = 'mri';
+
+    cfg = createFilename(cfg);
+
+    logFile = saveEventsFile('init', cfg); %#ok<*NASGU>
+    
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+
+    createBoldJson(cfg, extraInfo);
+
+    %% check content
+    fileName = strrep(cfg.fileName.events, '_events', '_bold');
+    fileName = strrep(fileName, '.tsv', '.json');
+    
+    actualStruct = bids.util.jsondecode(fullfile( ...
+        cfg.dir.outputSubject, ...
+        cfg.fileName.modality, ...
+        fileName));
+
+    % data to test against
+    expectedStruct = bids.util.jsondecode( ...
+        fullfile(pwd, 'testData', 'extra_bold.json'));
+
+    % test
+    assertEqual(expectedStruct, actualStruct);
+
+end

manualTests/test_makeRawDataset.m

@@ -29,7 +29,8 @@ function test_makeRawDataset()
 
     cfg = createFilename(cfg);
 
-    createBoldJson(cfg);
+    extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
+    createBoldJson(cfg, extraInfo);
 
     createDatasetDescription(cfg);
 

src/createBoldJson.m

@@ -1,11 +1,17 @@
-function createBoldJson(cfg)
-    % createBoldJson(cfg)
+function createBoldJson(cfg, extraInfo)
+    % createBoldJson(cfg, extraInfo)
     %
     % Creates the side car JSON file for a BOLD functional run.
     % This will only contain the minimum BIDS requirement and will likey be less
     % complete than the info you could from DICOM conversion.
+    %
+    % Extra content can be added to the JSON file
 
     opts.Indent = '    ';
+    
+    if nargin<2
+        extraInfo = struct();
+    end
 
     fileName = strrep(cfg.fileName.events, '_events', '_bold');
     fileName = strrep(fileName, '.tsv', '.json');
@@ -16,6 +22,15 @@ function createBoldJson(cfg)
         fileName);
 
     jsonContent = cfg.bids.mri;
+    
+    % add content of extraInfo to the JSON content
+    if ~isstruct(extraInfo)
+        warning('additional info added to a json file must be a structure')
+    end   
+    fieldList = fieldnames(extraInfo);
+    for iField = 1:numel(fieldList)
+        jsonContent.(fieldList{iField}) =  extraInfo.(fieldList{iField});
+    end
 
     bids.util.jsonencode(fileName, jsonContent, opts);