Merge pull request #115 from TomasLenc/tomas-dev

enable setting column Levels properties

Author: Remi-Gau

lib/bids-matlab

@@ -25,14 +25,15 @@ function test_createDataDictionaryBasic()
 
     cfg = createFilename(cfg);
 
+    logFile.extraColumns = {'Speed', 'LHL24'};
+
+    logFile = saveEventsFile('init', cfg, logFile);
+
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
-    logFile = saveEventsFile('init', cfg, logFile);
 
     logFile = saveEventsFile('open', cfg, logFile);
 
-    createDataDictionary(cfg, logFile);
-
     %% check that the file has the right path and name
 
     % data to test against
@@ -53,16 +54,17 @@ function test_createDataDictionaryBasic()
     % test_createDataDictionary>test_createDataDictionaryBasic:48
     %   (/github/workspace/tests/test_createDataDictionary.m)
 
-    %     actualStruct = bids.util.jsondecode(fullfile(funcDir, jsonFilename));
-    %
-    %     % data to test against
-    %     expectedStruct = bids.util.jsondecode( ...
-    %                                           fullfile(pwd, ...
-    %     'testData', ...
-    %         'eventsDataDictionary.json'));
-    %
-    %     % test
-    %     assertTrue(isequal(expectedStruct, actualStruct));
+    actualStruct = bids.util.jsondecode(fullfile(funcDir, jsonFilename));
+
+    % data to test against
+    expectedStruct = bids.util.jsondecode( ...
+                                          fullfile( ...
+                                                   pwd, ...
+                                                   'testData', ...
+                                                   'eventsDataDictionary.json'));
+
+    % test
+    assertTrue(isequal(expectedStruct, actualStruct));
 
 end
 
@@ -85,18 +87,18 @@ function test_createDataDictionaryStim()
 
     cfg = createFilename(cfg);
 
+    stimLogFile.extraColumns = {'Speed', 'LHL24', 'is_Fixation'};
+
+    stimLogFile = saveEventsFile('init_stim', cfg, stimLogFile);
+
     stimLogFile.extraColumns.Speed.length = 1;
     stimLogFile.extraColumns.LHL24.length = 3;
     stimLogFile.extraColumns.is_Fixation.length = 1;
 
     stimLogFile.SamplingFrequency = 100;
     stimLogFile.StartTime = 0;
 
-    stimLogFile = saveEventsFile('init', cfg, stimLogFile);
-
-    stimLogFile = saveEventsFile('open_stim', cfg, stimLogFile);
-
-    createDataDictionary(cfg, stimLogFile);
+    stimLogFile = saveEventsFile('open', cfg, stimLogFile);
 
     %% check that the file has the right path and name
 
@@ -118,4 +120,16 @@ function test_createDataDictionaryStim()
     % test_createDataDictionary>test_createDataDictionaryBasic:48
     %   (/github/workspace/tests/test_createDataDictionary.m)
 
+    actualStruct = bids.util.jsondecode(fullfile(funcDir, jsonFilename));
+
+    % data to test against
+    expectedStruct = bids.util.jsondecode( ...
+                                          fullfile( ...
+                                                   pwd, ...
+                                                   'testData', ...
+                                                   'stimDataDictionary.json'));
+
+    % test
+    assertTrue(isequal(expectedStruct, actualStruct));
+
 end

tests/test_createDataDictionary.m renamed to manualTests/test_createDataDictionary.m

@@ -23,13 +23,17 @@ function test_makeRawDataset()
 
     cfg.task.name = 'testtask';
     cfg.task.instructions = 'do this';
+    
+    cfg.verbosity = 0;
+    
+    cfg = createFilename(cfg);
 
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
     logFile.extraColumns.is_Fixation.length = 1;
 
-    cfg = createFilename(cfg);
-
+    logFile = saveEventsFile('init', cfg, logFile);
+    
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
     createJson(cfg, extraInfo);
 
@@ -72,20 +76,21 @@ function test_makeRawDataset()
 
     % add dummy stim data
     stimLogFile.extraColumns.Speed.length = 1;
-    stimLogFile.extraColumns.LHL24.length = 3;
+    stimLogFile.extraColumns.LHL24.length = 1;
     stimLogFile.extraColumns.is_Fixation.length = 1;
 
     stimLogFile.SamplingFrequency = cfg.mri.repetitionTime;
     stimLogFile.StartTime = 0;
 
-    stimLogFile = saveEventsFile('open_stim', cfg, stimLogFile);
+    stimLogFile = saveEventsFile('init_stim', cfg, stimLogFile);
+    stimLogFile = saveEventsFile('open', cfg, stimLogFile);
     for i = 1:100
         stimLogFile(i, 1).onset = cfg.mri.repetitionTime * i;
         stimLogFile(i, 1).trial_type = 'test';
         stimLogFile(i, 1).duration = 1;
         stimLogFile(i, 1).Speed = rand(1);
         stimLogFile(i, 1).is_Fixation = rand > 0.5;
-        stimLogFile(i, 1).LHL24 = randn(1, 3);
+        stimLogFile(i, 1).LHL24 = randn();
     end
     saveEventsFile('save', cfg, stimLogFile);
     saveEventsFile('close', cfg, stimLogFile);

tests/test_createDatasetDescription.m renamed to manualTests/test_createDatasetDescription.m

@@ -17,33 +17,23 @@ function createDataDictionary(cfg, logFile)
     fileName = strrep(logFile(1).filename, '.tsv', '.json');
     fullFilename = getFullFilename(fileName, cfg);
 
-    jsonContent = setJsonContent(fullFilename, logFile);
+    jsonContent = setJsonContent(logFile);
 
     opts.Indent = '    ';
+
     bids.util.jsonencode(fullFilename, jsonContent, opts);
 
 end
 
-function jsonContent = setJsonContent(fullFilename, logFile)
+function jsonContent = setJsonContent(logFile)
 
-    % transfer content of extra fields to json content
-    namesExtraColumns = returnNamesExtraColumns(logFile);
+    % regular _events file: add default _event file fields to the json content
+    if ~isfield(logFile, 'isStim') || isempty(logFile.isStim) || ~logFile.isStim
 
-    % default content for events file that will be overriddent if we are dealing
-    % with a stim file
-    jsonContent = struct( ...
-                         'onset', struct( ...
-                                         'Description', 'time elapsed since experiment start', ...
-                                         'Units', 's'), ...
-                         'trial_type', struct( ...
-                                              'Description', 'types of trial', ...
-                                              'Levels', ''), ...
-                         'duration', struct( ...
-                                            'Description', 'duration of the event', ...
-                                            'Units', 's') ...
-                        );
-
-    if ismember('_stim', fullFilename)
+        jsonContent = logFile.columns;
+
+        % _stim file: write stim-specific fields to the json content
+    elseif logFile.isStim
 
         samplingFrequency = nan;
         startTime = nan;
@@ -59,9 +49,11 @@ function createDataDictionary(cfg, logFile)
                              'SamplingFrequency', samplingFrequency, ...
                              'StartTime',  startTime, ...
                              'Columns', []);
-
     end
 
+    % transfer content of extra fields to json content
+    namesExtraColumns = returnNamesExtraColumns(logFile);
+
     for iExtraColumn = 1:numel(namesExtraColumns)
 
         nbCol = returnNbColumns(logFile, namesExtraColumns{iExtraColumn});
@@ -70,10 +62,8 @@ function createDataDictionary(cfg, logFile)
 
             headerName = returnHeaderName(namesExtraColumns{iExtraColumn}, nbCol, iCol);
 
-            if ismember('_stim', fullFilename)
-
+            if isfield(logFile, 'isStim') && ~isempty(logFile.isStim) && logFile.isStim
                 jsonContent.Columns{end + 1} = headerName;
-
             end
 
             jsonContent.(headerName) = ...