update checkCFG

Author: Remi-Gau

checkCFG.m

@@ -12,8 +12,9 @@
 
     fieldsToSet.verbose = false;
 
-    cfg.fileName.zeroPadding = 3;
-    cfg.fileName.dateFormat = 'yyyymmddHHMM';
+    fieldsToSet.fileName.task = '';
+    fieldsToSet.fileName.zeroPadding = 3;
+    fieldsToSet.fileName.dateFormat = 'yyyymmddHHMM';
 
     fieldsToSet.dir.output = fullfile( ...
         fileparts(mfilename('fullpath')), ...
@@ -35,31 +36,26 @@
     %% BIDS
 
     fieldsToSet = datasetDescriptionDefaults(fieldsToSet);
-
     fieldsToSet = mriJsonDefaults(fieldsToSet);
-    if isfield(cfg, 'task') && isfield(cfg.task, 'name')
-        fieldsToSet.bids.mri.TaskName = cfg.task.name;
-    end
-
     fieldsToSet = megJsonDefaults(fieldsToSet);
-    if isfield(cfg, 'task') && isfield(cfg.task, 'name')
-        fieldsToSet.bids.meg.TaskName = cfg.task.name;
-    end
-
+    
+    fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
+    
     cfg = setDefaultFields(cfg, fieldsToSet);
 
 end
 
 function fieldsToSet = mriDefaults(fieldsToSet)
 
-    % for file naming
-    fieldsToSet.fileName.mri.ce = [];
-    fieldsToSet.fileName.mri.dir = []; % phase encoding direction of acquisition for fMRI
-    fieldsToSet.fileName.mri.rec = []; % reconstruction of fMRI images
-    fieldsToSet.fileName.mri.echo = []; % echo fMRI images
-    fieldsToSet.fileName.mri.acq = []; % acquisition of fMRI images
+    % for file naming and JSON    
+    fieldsToSet.mri.contrastEnhancement = [];
+    fieldsToSet.mri.phaseEncodingDirection = [];
+    fieldsToSet.mri.reconstruction = [];
+    fieldsToSet.mri.echo = [];
+    fieldsToSet.mri.acquisition = [];
+    fieldsToSet.mri.repetitionTime = [];
 
-    fieldsToSet.fileName.mri = orderfields(fieldsToSet.fileName.mri);
+    fieldsToSet.mri = orderfields(fieldsToSet.mri);
 
 end
 
@@ -189,4 +185,4 @@
 
     fieldsToSet.bids.meg = orderfields(fieldsToSet.bids.meg);
 
-end
+end

tests/test_checkCFG.m

@@ -19,15 +19,15 @@ function test_checkCFG()
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
 
-    cfg.task.name = 'testtask';
+    cfg.task.name = 'test task';
 
     cfg.dir.output = outputDir;
 
     cfg.bids.datasetDescription.Name = 'dummy';
     cfg.bids.datasetDescription.BIDSVersion = '1.0.0';
     cfg.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
 
-    cfg.bids.mri.RepetitionTime = 1.56;
+    cfg.mri.repetitionTime = 1.56;
 
     cfg.testingDevice = 'mri';
 
@@ -42,13 +42,18 @@ function test_checkCFG()
 
     expectedStructure.dir.output = outputDir;
 
-    expectedStructure.task.name = 'testtask';
+    expectedStructure.task.name = 'test task';
+    
     expectedStructure.testingDevice = 'mri';
 
+    expectedStructure.mri.repetitionTime = 1.56;
+    
+    expectedStructure.fileName.task = 'testTask';
+    
     expectedStructure.bids.mri.RepetitionTime = 1.56;
-    expectedStructure.bids.mri.TaskName = 'testtask';
+    expectedStructure.bids.mri.TaskName = 'test Task';
 
-    expectedStructure.bids.meg.TaskName = 'testtask';
+    expectedStructure.bids.meg.TaskName = 'test Task';
 
     expectedStructure.bids.datasetDescription.Name = 'dummy';
     expectedStructure.bids.datasetDescription.BIDSVersion =  '1.0.0';
@@ -70,16 +75,18 @@ function test_checkCFG()
 
     expectedStructure.verbose = 0;
 
+    expectedStructure.fileName.task = '';
     expectedStructure.fileName.zeroPadding = 3;
     expectedStructure.fileName.dateFormat = 'yyyymmddHHMM';
 
     expectedStructure.eyeTracker.do = false;
 
-    expectedStructure.fileName.mri.ce = [];
-    expectedStructure.fileName.mri.dir = [];
-    expectedStructure.fileName.mri.rec = [];
-    expectedStructure.fileName.mri.echo = [];
-    expectedStructure.fileName.mri.acq = [];
+    expectedStructure.mri.contrastEnhancement = [];
+    expectedStructure.mri.phaseEncodingDirection = [];
+    expectedStructure.mri.reconstruction = [];
+    expectedStructure.mri.echo = [];
+    expectedStructure.mri.acquisition = [];
+    expectedStructure.mri.repetitionTime = [];
 
     expectedStructure.bids.mri.RepetitionTime = [];
     expectedStructure.bids.mri.SliceTiming = '';