mh autofix

Author: Remi-Gau

checkCFG.m

@@ -7,7 +7,7 @@
     if nargin < 1 || isempty(cfg)
         cfg = struct();
     end
-    
+
     checkCppBidsDependencies(cfg);
 
     %% list the defaults to set

checkCppBidsDependencies.m

@@ -1,7 +1,7 @@
 function checkCppBidsDependencies(cfg)
     % checkCppBidsDependencies()
     %
-    
+
     pth = fileparts(mfilename('fullpath'));
 
     checkSubmodule(fullfile(pth, 'lib', 'JSONio'));

convertSourceToRaw.m

@@ -6,7 +6,7 @@ function convertSourceToRaw(cfg)
     % - creates dummy README and CHANGE file
     % - copy source dir to raw dir
     % - remove the date suffix (_date-YYYYMMDDHHMM) from the files where it is present
-    % 
+    %
 
     sourceDir = fullfile(cfg.dir.output, 'source');
     rawDir = fullfile(cfg.dir.output, 'rawdata');

createFilename.m

@@ -11,34 +11,34 @@
     %
     %
     % See test_createFilename in the test folder for more details on how to use it.
-    
+
     cfg = checkCFG(cfg);
-    
+
     cfg.fileName.pattern = ['%0' num2str(cfg.fileName.zeroPadding) '.0f'];
     cfg.fileName.date = datestr(now, cfg.fileName.dateFormat);
-    
+
     if ~isfield(cfg, 'task')
         error('createFilename: missing a task name. i.e cfg.task.name');
     end
-    
+
     cfg = getModality(cfg);
-    
+
     cfg = createDirectories(cfg);
-    
+
     cfg = setSuffixes(cfg);
-    
+
     cfg = setFilenames(cfg);
-    
+
     talkToMe(cfg);
-    
+
     cfg = orderfields(cfg);
     cfg.fileName = orderfields(cfg.fileName);
     cfg.dir = orderfields(cfg.dir);
-    
+
 end
 
 function cfg = getModality(cfg)
-    
+
     switch lower(cfg.testingDevice)
         case 'pc'
             modality = 'beh';
@@ -53,52 +53,52 @@
         otherwise
             modality = 'beh';
     end
-    
+
     cfg.fileName.modality = modality;
-    
+
 end
 
 function [subjectGrp, subjectNb, sessionNb, modality, taskName] = extractInput(cfg)
-    
+
     subjectGrp = cfg.subject.subjectGrp;
     subjectNb = cfg.subject.subjectNb;
     sessionNb = cfg.subject.sessionNb;
     modality = cfg.fileName.modality;
     taskName = cfg.fileName.task;
-    
+
     if isempty(sessionNb)
         sessionNb = 1;
     end
-    
+
 end
 
 function cfg = createDirectories(cfg)
-    
+
     [subjectGrp, subjectNb, sessionNb, modality] = extractInput(cfg);
-    
+
     pattern = cfg.fileName.pattern;
-    
+
     % output dir
     cfg.dir.outputSubject = fullfile ( ...
         cfg.dir.output, ...
         'source', ...
         ['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
         ['ses-', sprintf(pattern, sessionNb)]);
-    
+
     [~, ~, ~] = mkdir(cfg.dir.output);
     [~, ~, ~] = mkdir(cfg.dir.outputSubject);
     [~, ~, ~] = mkdir(fullfile(cfg.dir.outputSubject, modality));
-    
+
     if cfg.eyeTracker.do
         [~, ~, ~] = mkdir(fullfile(cfg.dir.outputSubject, 'eyetracker'));
     end
-    
+
 end
 
 function cfg = setSuffixes(cfg)
-    
+
     cfg.fileName.suffix.run = ['_run-' sprintf(cfg.fileName.pattern, cfg.subject.runNb)];
-    
+
     % set values for the suffixes for the different fields in the BIDS name
     fields2Check = { ...
         'contrastEnhancement', ...
@@ -107,7 +107,7 @@
         'echo', ...
         'acquisition'
         };
-    
+
     for iField = 1:numel(fields2Check)
         if isempty (cfg.mri.(fields2Check{iField})) %#ok<*GFLD>
             cfg.fileName.suffix.mri.(fields2Check{iField}) = ''; %#ok<*SFLD>
@@ -116,85 +116,85 @@
                 ['_' fields2Check{iField} '-' getfield(cfg.mri, fields2Check{iField})];
         end
     end
-    
+
     cfg.fileName.suffix = orderfields(cfg.fileName.suffix);
-    
+
 end
 
 function cfg = setFilenames(cfg)
-    
+
     [subjectGrp, subjectNb, sessionNb, modality, taskName] = extractInput(cfg);
-    
+
     pattern = cfg.fileName.pattern;
-    
+
     runSuffix = cfg.fileName.suffix.run;
     acqSuffix = cfg.fileName.suffix.mri.acquisition ;
     ceSuffix = cfg.fileName.suffix.mri.contrastEnhancement ;
     dirSuffix = cfg.fileName.suffix.mri.phaseEncodingDirection ;
     recSuffix = cfg.fileName.suffix.mri.reconstruction ;
     echoSuffix = cfg.fileName.suffix.mri.echo;
-    
+
     thisDate = cfg.fileName.date;
-    
+
     cfg.fileName.datasetDescription = fullfile ( ...
         cfg.dir.output, ...
         'dataset_description.json');
-    
+
     % create base fileName
     fileNameBase = ...
         ['sub-', subjectGrp, sprintf(pattern, subjectNb), ...
         '_ses-', sprintf(pattern, sessionNb), ...
         '_task-', taskName];
     cfg.fileName.base = fileNameBase;
-    
+
     switch modality
-        
+
         case 'func'
-            
+
             cfg.fileName.events = ...
                 [fileNameBase, ...
                 acqSuffix, ceSuffix, ...
                 dirSuffix, recSuffix, ...
                 runSuffix, echoSuffix, ...
                 '_events_date-' thisDate '.tsv'];
-            
+
         otherwise
-            
+
             cfg.fileName.events = ...
                 [fileNameBase, runSuffix, '_events_date-' thisDate '.tsv'];
-            
+
     end
-    
+
     cfg.fileName.stim = strrep(cfg.fileName.events, 'events', 'stim');
-    
+
     if cfg.eyeTracker.do
         cfg.fileName.eyetracker = ...
             [fileNameBase, acqSuffix, ...
             runSuffix, '_eyetrack_date-' thisDate '.edf'];
     end
-    
+
 end
 
 function talkToMe(cfg)
-    
+
     if cfg.verbose
-        
+
         fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
             fullfile(cfg.dir.outputSubject, cfg.fileName.modality));
-        
+
         fprintf(1, '\nData will be saved in this file:\n\t%s\n', ...
             cfg.fileName.events);
-        
+
         if cfg.eyeTracker.do
-            
+
             fprintf(1, '\nEyetracking data will be saved in this directory:\n\t%s\n', ...
                 fullfile(cfg.dir.outputSubject, 'eyetracker'));
-            
+
             fprintf(1, '\nEyetracking data will be saved in this file:\n\t%s\n', ...
                 cfg.fileName.eyetracker);
-            
+
         end
-        
+
     end
-    
+
 end

printCreditsCppBids.m

@@ -1,25 +1,25 @@
 function printCreditsCppBids(cfg)
-    
+
     verbose = true;
     if ~isempty(cfg) && isfield(cfg, 'verbose') && ~isempty(cfg.verbose)
         verbose = cfg.verbose;
     end
-    
+
     if verbose
-        
+
         version = '0.0.1';
-        
+
         contributors = { ...
             'Rémi Gau', ...
             'Marco Barilari', ...
             'Ceren Battal'};
-        
+
         % DOI_URL = 'https://doi.org/10.5281/zenodo.3554331.';
-        
+
         repoURL = 'https://github.com/cpp-lln-lab/CPP_BIDS';
-        
+
         fprintf('\n\n');
-        
+
         disp('___________________________________________________');
         disp('___________________________________________________');
         disp('                                                   ');
@@ -28,26 +28,26 @@ function printCreditsCppBids(cfg)
         disp('       | (__|  _/  _/ | _ \| || |) \__ \');
         disp('        \___|_| |_|   |___/___|___/|___/');
         disp('                                                   ');
-        
+
         splash = 'Thank you for using the CPP BIDS - version %s. ';
         fprintf(splash, version);
         fprintf('\n\n');
-        
+
         fprintf('Current list of contributors includes:\n');
         for iCont = 1:numel(contributors)
             fprintf(' %s\n', contributors{iCont});
         end
         fprintf('\b\n\n');
-        
+
         % fprintf('Please cite using the following DOI: \n %s\n\n', DOI_URL)
-        
+
         fprintf('For bug report, suggestions or contributions see: \n %s\n\n', repoURL);
-        
+
         disp('___________________________________________________');
         disp('___________________________________________________');
-        
+
         fprintf('\n\n');
-        
+
     end
-    
+
 end