mh autofix

Author: Remi-Gau

manualTests/test_makeRawDataset.m

@@ -1,75 +1,75 @@
 function test_makeRawDataset()
-    
+
     outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
-    
+
     if isdir(outputDir)
         rmdir(outputDir, 's');
     end
-    
+
     %% set up
     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.testingDevice = 'mri';
-    
+
     %% MRI task data
     cfg.mri.repetitionTime = 1.56;
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'testtask';
     cfg.task.instructions = 'do this';
-    
+
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
     logFile.extraColumns.is_Fixation.length = 1;
-    
+
     cfg = createFilename(cfg);
-    
+
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
     createJson(cfg, extraInfo);
-    
+
     createDatasetDescription(cfg);
-    
+
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
-    
+
     % ROW 2: normal events : all info is there
     logFile(1, 1).onset = 2;
     logFile(end, 1).trial_type = 'MotionUp';
     logFile(end, 1).duration = 3;
     logFile(end, 1).Speed = 2;
     logFile(end, 1).is_Fixation = true;
     logFile(end, 1).LHL24 = 1:3;
-    
+
     % ROW 3: missing info (speed, LHL24)
     logFile(1, 1).onset = 3;
     logFile(end, 1).trial_type = 'static';
     logFile(end, 1).duration = 4;
     logFile(end, 1).is_Fixation = false;
-    
+
     % ROW 4: missing info (duration is missing and speed is empty)
     logFile(2, 1).onset = 4;
     logFile(end, 1).trial_type = 'BLUES';
     logFile(end, 1).Speed = [];
     logFile(end, 1).is_Fixation = true;
     logFile(end, 1).LHL24 = rand(1, 3);
-    
+
     % ROW 5: missing info (array is not the right size)
     logFile(5, 1).onset = 5;
     logFile(end, 1).trial_type = 'jazz';
     logFile(end, 1).duration = 3;
     logFile(end, 1).LHL24 = rand(1, 2);
-    
+
     saveEventsFile('save', cfg, logFile);
-    
+
     % close the file
     saveEventsFile('close', cfg, logFile);
-    
+
     % add dummy stim data
     stimLogFile = saveEventsFile('open_stim', cfg, logFile);
     for i = 1:100
@@ -85,169 +85,168 @@ function test_makeRawDataset()
 
     %% MRI bold rest data and fancy suffixes
     clear cfg;
-    
+
     cfg.dir.output = outputDir;
-    
+
     cfg.testingDevice = 'mri';
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     % deal with MRI suffixes
     cfg.suffix.reconstruction = 'fast recon';
     cfg.suffix.contrastEnhancement = 'test';
     cfg.suffix.phaseEncodingDirection = 'y pos';
     cfg.suffix.echo = '1';
     cfg.suffix.acquisition = ' new tYpe';
-    
+
     cfg.mri.repetitionTime = 1.56;
-    
+
     cfg.task.name = 'rest';
-    
+
     cfg = createFilename(cfg);
-    
+
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
     createJson(cfg, extraInfo);
-    
-    
+
     %% EEG data and fancy suffixes
     clear cfg;
-    
+
     cfg.dir.output = outputDir;
-    
+
     cfg.testingDevice = 'eeg';
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'target practice';
     cfg.task.instructions = 'do this';
-    
+
     cfg.bids.eeg.EEGReference = 'Cz';
     cfg.bids.eeg.SamplingFrequency = 2400;
     cfg.bids.eeg.PowerLineFrequency = 50;
     cfg.bids.eeg.SoftwareFilters = 'n/a';
 
     cfg = createFilename(cfg);
-    
+
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
     createJson(cfg, extraInfo);
-    
+
     %% iEEG data and fancy suffixes
     clear cfg;
-    
+
     cfg.dir.output = outputDir;
-    
+
     cfg.testingDevice = 'ieeg';
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'implanted target practice';
     cfg.task.instructions = 'do this';
-    
+
     cfg.bids.ieeg.iEEGReference = 'Cz';
     cfg.bids.ieeg.SamplingFrequency = 2400;
     cfg.bids.ieeg.PowerLineFrequency = 50;
     cfg.bids.ieeg.SoftwareFilters = 'n/a';
-    
+
     cfg = createFilename(cfg);
-    
+
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
     createJson(cfg, extraInfo);
-    
+
     %% MEG data and fancy suffixes
     clear cfg;
-    
+
     cfg.dir.output = outputDir;
-    
+
     cfg.testingDevice = 'meg';
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'magnetic target practice';
     cfg.task.instructions = 'do this';
-    
+
     cfg.bids.meg.SamplingFrequency = 2400;
     cfg.bids.meg.PowerLineFrequency = 60;
     cfg.bids.meg.DewarPosition = 'upright';
     cfg.bids.meg.SoftwareFilters = 'n/a';
     cfg.bids.meg.DigitizedLandmarks = false;
     cfg.bids.meg.DigitizedHeadPoints = false;
-    
+
     cfg = createFilename(cfg);
-    
+
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
     createJson(cfg, extraInfo);
-    
+
     %% beh data and fancy suffixes
     clear cfg;
-    
+
     cfg.dir.output = outputDir;
-    
+
     cfg.testingDevice = 'pc';
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'easy target practice';
     cfg.task.instructions = 'do this';
-    
+
     cfg = createFilename(cfg);
-    
+
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
     createJson(cfg, extraInfo);
-    
+
     %% add dummy data
     subjectDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001');
     funcDir = fullfile(subjectDir, 'func');
-    
+
     boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';
-    
+
     copyfile( ...
         fullfile('dummyData', 'dummyData.nii.gz'), ...
         fullfile(funcDir, boldFilename));
-    
+
     boldFilename = ['sub-001_ses-001_task-rest',  ...
         '_acq-newTYpe_ce-test_dir-yPos_rec-fastRecon', ...
         '_run-001_echo-1_bold.nii.gz'];
-    
+
     copyfile( ...
         fullfile('dummyData', 'dummyData.nii.gz'), ...
         fullfile(funcDir, boldFilename));
-    
+
     eegDir = fullfile(subjectDir, 'eeg');
     megDir = fullfile(subjectDir, 'meg');
     ieegDir = fullfile(subjectDir, 'ieeg');
     behDir = fullfile(subjectDir, 'beh');
-    
+
     eegFilename = 'sub-001_ses-001_task-targetPractice_run-001_eeg.edf';
     megFilename = 'sub-001_ses-001_task-magneticTargetPractice_run-001_meg.fif';
     ieegFilename = 'sub-001_ses-001_task-implantedTargetPractice_run-001_ieeg.edf';
     behFilename = 'sub-001_ses-001_task-easyTargetPractice_run-001_beh.tsv';
-    
+
     copyfile( ...
         fullfile('dummyData', 'dummyData.nii.gz'), ...
         fullfile(eegDir, eegFilename));
-    
+
     copyfile( ...
         fullfile('dummyData', 'dummyData.nii.gz'), ...
         fullfile(megDir, megFilename));
-    
+
     copyfile( ...
         fullfile('dummyData', 'dummyData.nii.gz'), ...
         fullfile(ieegDir, ieegFilename));
-    
+
     copyfile( ...
         fullfile('dummyData', 'dummyData.nii.gz'), ...
         fullfile(behDir, behFilename));
-    
+
     %% actually do the conversion of the source data thus created
     clear;
-    
+
     outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
     cfg.dir.output = outputDir;
     convertSourceToRaw(cfg);
-    
+
 end

src/checkCFG.m

@@ -221,7 +221,7 @@
     fieldsToSet.bids.ieeg.TaskName = '';
 
     fieldsToSet.bids.ieeg.Instructions = '';
-    
+
     fieldsToSet.bids.ieeg.iEEGReference = '';
 
     fieldsToSet.bids.ieeg.SamplingFrequency = [];

src/subfun/removeAllDateSuffix.m

@@ -1,39 +1,38 @@
 function removeAllDateSuffix(rawDir, subjName, sesName)
     % removeAllDateSuffix(rawDir, subjName, sesName)
     %
-    
+
     labels = {'func', 'bold', 'eeg', 'ieeg', 'meg', 'beh'};
-    
+
     for iModality = 1:numel(labels)
-        
+
         subjectPath = fullfile(rawDir, subjName, sesName, labels{iModality});
-        
+
         if exist(subjectPath, 'dir')
-            
+
             % do events
             filenames = file_utils('List', subjectPath, ...
                 sprintf('^%s.*_task-.*_events_date-.*$', subjName));
-            
+
             removeDateSuffix(filenames, subjectPath);
-            
-            
+
             for iLabel = 1:numel(labels)
                 filenames = file_utils('List', subjectPath, ...
                     sprintf('^%s.*_task-.*_%s_date-.*$', subjName, labels{iLabel}));
-                
+
                 removeDateSuffix(filenames, subjectPath);
             end
-            
+
             % do stim
             filenames = file_utils('List', subjectPath, ...
                 sprintf('^%s.*_task-.*_stim_date-.*tsv$', subjName));
             compressFiles(filenames, subjectPath);
             filenames = file_utils('List', subjectPath, ...
                 sprintf('^%s.*_task-.*_stim_date-.*tsv.gz$', subjName));
             removeDateSuffix(filenames, subjectPath);
-            
+
         end
-        
+
     end
 end
 
@@ -43,11 +42,11 @@ function compressFiles(filenames, subjectPath)
     else
         filenames = cellstr(filenames);
     end
-    
+
     for i = 1:numel(filenames)
-        
+
         gzip(fullfile(subjectPath, filenames{i}));
         delete(fullfile(subjectPath, filenames{i}));
-        
+
     end
 end