create valid suffix for MRI filenames

Author: Remi-Gau

src/createFilename.m

@@ -99,21 +99,39 @@
 
     cfg.fileName.suffix.run = ['_run-' sprintf(cfg.fileName.pattern, cfg.subject.runNb)];
 
+    %% MRI
     % set values for the suffixes for the different fields in the BIDS name
     fields2Check = { ...
+        'acquisition', ...
         'contrastEnhancement', ...
+        'echo', ...
         'phaseEncodingDirection', ...
         'reconstruction', ...
+        };
+    
+    targetFields = { ...
+        'acq', ...
+        'ce', ...
         'echo', ...
-        'acquisition'
+        'dir', ...
+        'rec', ...
         };
 
     for iField = 1:numel(fields2Check)
+        
         if isempty (cfg.mri.(fields2Check{iField})) %#ok<*GFLD>
+            
             cfg.fileName.suffix.mri.(fields2Check{iField}) = ''; %#ok<*SFLD>
+            
         else
+            
+            % upper camelCase and remove invalid characters
+            thisField = getfield(cfg.mri, fields2Check{iField});
+            [~, validFieldName] = createValidName(thisField);
+            
             cfg.fileName.suffix.mri.(fields2Check{iField}) = ...
-                ['_' fields2Check{iField} '-' getfield(cfg.mri, fields2Check{iField})];
+                ['_' targetFields{iField} '-' validFieldName];
+            
         end
     end
 

src/subfun/createTaskName.m renamed to src/subfun/createValidName.m

@@ -1,17 +1,17 @@
-function [taskName, taskNameValid] = createTaskName(taskName)
+function [name, nameValid] = createValidName(name)
     % [taskName, taskNameValid] = createTaskName(taskName)
     %
     % 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)));
+    spaceIdx = regexp(name, '[a-zA-Z0-9]*', 'start');
+    name(spaceIdx(2:end)) = upper(name(spaceIdx(2:end)));
 
     % remove invalid characters
-    [unvalidCharacters] = regexp(taskName, '[^a-zA-Z0-9]');
-    taskNameValid = taskName;
-    taskNameValid(unvalidCharacters) = [];
+    [unvalidCharacters] = regexp(name, '[^a-zA-Z0-9]');
+    nameValid = name;
+    nameValid(unvalidCharacters) = [];
 
 end

src/subfun/transferInfoToBids.m

@@ -5,7 +5,7 @@
     % 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);
+        [taskName, taskNameValid] = createValidName(cfg.task.name);
         fieldsToSet.fileName.task = taskNameValid;
         fieldsToSet.bids.meg.TaskName = taskName;
         fieldsToSet.bids.mri.TaskName = taskName;

tests/test_checkCFG.m

@@ -124,4 +124,4 @@ function test_checkCfgBasic()
 
     expectedCfgStructure = orderfields(expectedCfgStructure);
 
-end
+end

tests/test_createFilename.m

@@ -94,6 +94,53 @@ function test_createFilenameMriEyetracker()
 
 end
 
+
+function test_createFilenameMriSuffix()
+
+    outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
+
+    %% set up
+
+    cfg.verbose = false;
+    cfg.subject.subjectGrp = 'ssri';
+    cfg.subject.subjectNb = 3;
+    cfg.subject.sessionNb = 4;
+    cfg.subject.runNb = 5;
+    cfg.task.name = 'rest';
+    cfg.dir.output = outputDir;
+
+    cfg.eyeTracker.do = false;
+    cfg.testingDevice = 'mri';
+    
+    cfg.mri.reconstruction = 'fast recon';
+    cfg.mri.contrastEnhancement = 'test';
+    cfg.mri.phaseEncodingDirection = 'y pos';
+    cfg.mri.echo = '1';
+    cfg.mri.acquisition = ' new tYpe';
+
+    cfg = createFilename(cfg);
+
+    %% data to test against
+
+    funcDir = fullfile(outputDir, 'source', 'sub-ssri003', 'ses-004', 'func');
+
+    baseFilename = 'sub-ssri003_ses-004_task-rest';
+
+    eventFilename = ['sub-ssri003_ses-004_task-rest',  ...
+        '_acq-newTYpe_ce-test_dir-yPos_rec-fastRecon', ...
+        '_run-005_echo-1_events_date-' ...
+        cfg.fileName.date '.tsv'];
+
+    %% tests
+    % make sure the func dir is created
+    assertTrue(exist(funcDir, 'dir') == 7);
+
+    % make sure the right filenames are created
+    assertEqual(cfg.fileName.base, baseFilename)
+    assertEqual(cfg.fileName.events, eventFilename);
+
+end
+
 function test_createFilenameEeg()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');

tests/test_createTaskName.m renamed to tests/test_createValidName.m

@@ -1,4 +1,4 @@
-function test_suite = test_createTaskName %#ok<*STOUT>
+function test_suite = test_createValidName %#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
@@ -12,7 +12,7 @@ function test_createTaskNameRemoveInvalidCharacters()
 
     taskName = '&|@#-_(§!{})[]ù%£+/=:;.?,\<> visual task';
 
-    [taskName, taskNameValid] = createTaskName(taskName);
+    [~, taskNameValid] = createValidName(taskName);
 
     [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
 
@@ -22,15 +22,15 @@ function test_createTaskNameRemoveInvalidCharacters()
     %% set up
     taskName = ' 09 visual task';
 
-    [taskName, taskNameValid] = createTaskName(taskName);
+    [~, taskNameValid] = createValidName(taskName);
 
     [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
 
     %% test
     assertTrue(isempty(unvalidCharacters));
 
     taskName = 'foo bar';
-    [taskName, taskNameValid] = createTaskName(taskName);
+    [taskName, taskNameValid] = createValidName(taskName);
     assert(isequal(taskName, 'foo Bar'));
     assert(isequal(taskNameValid, 'fooBar'));
 
@@ -40,7 +40,7 @@ function test_createTaskNameCamelCase()
 
     %% set up
     taskName = 'foo bar';
-    [taskName, taskNameValid] = createTaskName(taskName);
+    [taskName, taskNameValid] = createValidName(taskName);
 
     %% test
     assertEqual(taskName, 'foo Bar');