Merge pull request #53 from cpp-lln-lab/remi-retinotopy_update

update from retinotopy

Author: Remi-Gau

checkCFG.m

@@ -12,7 +12,7 @@
 
     %% set the expParameters defaults
 
-    fieldsToSet.verbose = 0;
+    fieldsToSet.verbose = false;
     fieldsToSet.outputDir = fullfile( ...
         fileparts(mfilename('fullpath')), ...
         '..', ...
@@ -57,6 +57,7 @@
     %% set the cfg defaults
 
     clear fieldsToSet;
+    fieldsToSet.verbose = false;
     fieldsToSet.testingDevice = 'pc';
     fieldsToSet.eyeTracker = false;
 

checkCppBidsDependencies.m

@@ -1,11 +1,25 @@
 function checkCppBidsDependencies
 
     pth = fileparts(mfilename('fullpath'));
-    addpath(fullfile(pth, 'lib', 'JSONio'));
-    addpath(fullfile(pth, 'lib', 'bids-matlab'));
+    
+    checkSubmodule(fullfile(pth, 'lib', 'JSONio'))
+    checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'))
+    
     addpath(fullfile(pth, 'lib', 'utils'));
     addpath(fullfile(pth, 'subfun'));
 
-    printCredits()
+    printCreditsCppBids();
+
+end
 
+function checkSubmodule(pth)
+    % If external dir is empty throw an exception
+    % and ask user to update submodules.
+    if numel(dir(pth)) <= 2 % Means that the external is empty
+        error(['Git submodules are not cloned!', ...
+              'Try this in your terminal:', ...
+              ' git submodule update --recursive ']);
+    else
+        addpath(pth);
+    end
 end

createFilename.m

@@ -34,6 +34,9 @@
     expParameters = setFilenames(cfg, expParameters);
 
     talkToMe(cfg, expParameters);
+    
+    cfg = orderfields(cfg);
+    expParameters = orderfields(expParameters);
 
 end
 

printCredits.m renamed to printCreditsCppBids.m

@@ -1,4 +1,4 @@
-function printCredits()
+function printCreditsCppBids()
 
     version = '0.0.1';
 

saveEventsFile.m

@@ -185,7 +185,7 @@
         'w');
 
     % print the basic BIDS columns
-    fprintf(logFile.fileID, '%s\t%s\t%s\t', 'onset', 'duration', 'trial_type');
+    fprintf(logFile.fileID, '%s\t%s\t%s', 'onset', 'duration', 'trial_type');
 
     printHeaderExtraColumns(logFile);
 
@@ -207,7 +207,7 @@ function printHeaderExtraColumns(logFile)
 
             headerName = returnHeaderName(namesExtraColumns{iExtraColumn}, nbCol, iCol);
 
-            fprintf(logFile.fileID, '%s\t', headerName);
+            fprintf(logFile.fileID, '\t%s', headerName);
 
         end
 
@@ -239,7 +239,7 @@ function printHeaderExtraColumns(logFile)
         if any(isnan(data))
             warning('Missing some %s data for this event.', namesExtraColumns{iExtraColumn});
             disp(logFile(iEvent));
-        elseif  all(isnan(data)) || strcmp(data, 'n/a')
+        elseif  all(isnan(data))
             warning('Missing %s data for this event.', namesExtraColumns{iExtraColumn});
             disp(logFile(iEvent));
         end