gtSequenceMedianRefs: now accepts empty workingdirectory input

Signed-off-by: preischig <preischig@gmail.com>

1_preprocessing/gtSequenceMedianRefs.m

@@ -36,7 +36,7 @@ disp('gtSequenceMedianRefs.m  -  graintracking specific version')
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % load('parameters.mat');
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-if ~exist('workingdirectory', 'var')
+if ~exist('workingdirectory', 'var') || isempty(workingdirectory)
     workingdirectory=pwd;
 end
 cd(workingdirectory)
@@ -122,11 +122,12 @@ for n=0:acq.refon:nimages
             i=i+1;
           pause(2)
           if i>2000 % timeout
-              cd(parameters.acq.dir);
+              fprintf('\nTimeout. Exiting...\n')
+			  cd(parameters.acq.dir);
               return
           end
         end
-        fprintf('Found something!\n')
+        fprintf('Found file.\n')
       end
 
       if exist(fname_ref,'file')
@@ -144,6 +145,7 @@ for n=0:acq.refon:nimages
       fprintf('Now performing median...\n')
       refC=squeeze(median(ref));
       info.datatype='uint16';
+	  fprintf('Saving file: %s\n', fname_refC)
       edf_write(refC,fname_refC, info);
     end