mh autofix

Author: Remi-Gau

checkCFG.m

@@ -38,16 +38,16 @@
     fieldsToSet = datasetDescriptionDefaults(fieldsToSet);
     fieldsToSet = mriJsonDefaults(fieldsToSet);
     fieldsToSet = megJsonDefaults(fieldsToSet);
-    
+
     fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
-    
+
     cfg = setDefaultFields(cfg, fieldsToSet);
 
 end
 
 function fieldsToSet = mriDefaults(fieldsToSet)
 
-    % for file naming and JSON    
+    % for file naming and JSON
     fieldsToSet.mri.contrastEnhancement = [];
     fieldsToSet.mri.phaseEncodingDirection = [];
     fieldsToSet.mri.reconstruction = [];
@@ -185,4 +185,4 @@
 
     fieldsToSet.bids.meg = orderfields(fieldsToSet.bids.meg);
 
-end
+end

createFilename.m

@@ -102,10 +102,10 @@
     % set values for the suffixes for the different fields in the BIDS name
     fields2Check = { ...
         'contrastEnhancement', ...
-        'phaseEncodingDirection', ...  % For BIDS file naming: phase encoding direction of acquisition for fMRI
-        'reconstruction', ...  % For BIDS file naming: reconstruction of fMRI images
-        'echo', ... % For BIDS file naming: echo fMRI images
-        'acquisition'       % For BIDS file naming: acquisition of fMRI images
+        'phaseEncodingDirection', ...
+        'reconstruction', ...
+        'echo', ...
+        'acquisition'
         };
 
     for iField = 1:numel(fields2Check)

subfun/createTaskName.m

@@ -4,15 +4,14 @@
     % Name of the task (for resting state use the "rest" prefix). No two tasks
     % should have the same name. Task label is derived from this field by
     % removing all non alphanumeric ([a-zA-Z0-9]) characters.
-       
+
     % camel case: upper case for first letter for all words but the first one
     spaceIdx = regexp(taskName, '[a-zA-Z0-9]*', 'start');
     taskName(spaceIdx(2:end)) = upper(taskName(spaceIdx(2:end)));
-    
+
     % remove invalid characters
     [unvalidCharacters] = regexp(taskName, '[^a-zA-Z0-9]');
     taskNameValid = taskName;
     taskNameValid(unvalidCharacters) = [];
-    
-end
 
+end

subfun/transferInfoToBids.m

@@ -1,16 +1,16 @@
 function fieldsToSet = transferInfoToBids(fieldsToSet, cfg)
     % transfer any info that might have been provided by the user to the
     % relevant field for its reuse for BIDS filenames or JSON later
-    
+
     if isfield(cfg, 'task') && isfield(cfg.task, 'name')
         [taskName, taskNameValid] = createTaskName(cfg.task.name);
         fieldsToSet.fileName.task = taskNameValid;
         fieldsToSet.bids.meg.TaskName = taskName;
         fieldsToSet.bids.mri.TaskName = taskName;
     end
-        
+
     if isfield(cfg, 'mri') && isfield(cfg.mri, 'repetitionTime')
         fieldsToSet.bids.mri.RepetitionTime = cfg.mri.repetitionTime;
     end
-    
-end
+
+end

tests/test_checkCFG.m

@@ -43,13 +43,13 @@ function test_checkCFG()
     expectedStructure.dir.output = outputDir;
 
     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 = 'test Task';
 

tests/test_createFilename.m

@@ -50,7 +50,7 @@ function test_createFilename()
     cfg.subject.subjectNb = 2;
     cfg.subject.sessionNb = 2;
     cfg.subject.runNb = 2;
-    cfg.task.name = 'testTask';
+    cfg.task.name = 'test task';
     cfg.dir.output = outputDir;
 
     cfg.eyeTracker.do = true;
@@ -93,7 +93,7 @@ function test_createFilename()
     cfg.subject.subjectNb = 3;
     cfg.subject.sessionNb = 1;
     cfg.subject.runNb = 1;
-    cfg.task.name = 'testTask';
+    cfg.task.name = 'test task';
     cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'eeg';

tests/test_createTaskName.m

@@ -1,28 +1,25 @@
 function test_createTaskName()
     %
-    
+
     taskName = '&|@#-_(§!{})[]ù%£+/=:;.?,\<> visual task';
-    
-    [taskName, taskNameValid] = createTaskName(taskName)
-    
+
+    [taskName, taskNameValid] = createTaskName(taskName);
+
     [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
-    
+
     assert(isempty(unvalidCharacters));
-    
-    
+
     taskName = ' 09 visual task';
-    
-    [taskName, taskNameValid] = createTaskName(taskName)
-    
+
+    [taskName, taskNameValid] = createTaskName(taskName);
+
     [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
-    
+
     assert(isempty(unvalidCharacters));
-    
-    
+
     taskName = 'foo bar';
-    [taskName, taskNameValid] = createTaskName(taskName)
-    assert(isequal(taskName, 'foo Bar'))
-    assert(isequal(taskNameValid, 'fooBar'))
-    
-end
+    [taskName, taskNameValid] = createTaskName(taskName);
+    assert(isequal(taskName, 'foo Bar'));
+    assert(isequal(taskNameValid, 'fooBar'));
 
+end

tests/test_transferInfoToBids.m

@@ -1,35 +1,35 @@
 function test_transferInfoToBids()
-    
+
     %%
     cfg = struct();
     fieldsToSet = struct();
     cfg = transferInfoToBids(fieldsToSet, cfg);
-    
+
     expectedStruct = struct();
-    
-    assert(isequal(expectedStruct, fieldsToSet))
-    
+
+    assert(isequal(expectedStruct, fieldsToSet));
+
     %%
     cfg.task.name = 'foo bar';
-    
+
     fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
-    
+
     expectedStruct.fileName.task = 'fooBar';
     expectedStruct.bids.meg.TaskName = 'foo Bar';
     expectedStruct.bids.mri.TaskName = 'foo Bar';
-    
-    assert(isequal(expectedStruct, fieldsToSet))
-    
+
+    assert(isequal(expectedStruct, fieldsToSet));
+
     %%
-    clear cfg fieldsToSet expectedStruct
-    
+    clear cfg fieldsToSet expectedStruct;
+
     cfg.mri.repetitionTime = 1.56;
-    
+
     fieldsToSet = struct();
     fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
 
     expectedStruct.bids.mri.RepetitionTime = 1.56;
-    
-    assert(isequal(expectedStruct, fieldsToSet))
-    
-end
+
+    assert(isequal(expectedStruct, fieldsToSet));
+
+end