Prevent unwanted timer callback calls in the execution queue

Hi, I made a GUI in guide with the following purpose: A random number appears in one of two boxes on the screen and the user is supposed to press either left or right on the keyboard depending on whether the number is even or odd. This is done through a windowkeypressfcn that only reacts to these two button presses apart from 'return' to start and 'escape' to end the session. After a key has been pressed the boxes are cleared and another number appears after 0.5-2s - chosen randomly using the pause() function. If the user fails to respond within 2.5 s the timer callback gets called, the boxes cleared and another number appears after 0.5-2s again. I am basically tracking their response times (using tic and toc) and in case the timer callback gets called I know they are being too slow. The important thing is that the user sees the number in one of the boxes changing every time one of the 2 functions is called! Ok, I create a timer object the following way

handles.timer = timer('ExecutionMode','fixedSpacing','BusyMode','drop','StartDelay',2.5,'Period',2.5,'TimerFcn', {@update_boxes,hObject});

The timer gets stopped every time the gui enters the button press callback function and started again when it exits the function. Same goes for the timer callback. The GUI works fine apart from one (very unlikely but still) scenario: If the user completely goofs off and doesn't press anything for a while, the timer function at some point (usually after it has been called twice or three times consecutively - so in the twice case the user hasn't reacted for 5s+ x1+x2, where x1 and x2 are random numbers from the interval 0.5-2s )gets executed twice in such a way that the user only sees one number change even though 2 occurred. I save all the numbers that were presented and in this case there are more numbers in the output vector than I have actually seen. I would assume that it has something to do with the examples presented here: http://www.mathworks.nl/help/matlab/matlab_prog/handling-timer-queuing-conflicts.html.

I assume that the timer callback execution gets queued up (whatever I set for the 'BusyMode' parameter, at least one instance will be in the queue..) and called at some point when the random 0.5-2s pauses add up. How can I fix this? Is there a way not to put the timer callback execution in the queue but delete it? I thought about creating and deleting a new timer object each time but I can't do that since I'm in the timer callback function and it also doesn't seem like an elegant solution...

Sorry for the long post... Here's the code in case it helps:

%%%% Key press fcn

function figure1_WindowKeyPressFcn(hObject, eventdata, handles)

if handles.firstiteration==0 %if it's not the first iteration save the responses
    % check whether keystorke occured while boxes were blank, if so
    % disregard it
    if ~(strcmp(get(handles.eo_numberl,'String'),'')&& strcmp(get(handles.eo_numberr,'String'),''))
        switch eventdata.Key
            case 'leftarrow'
                % get the reaction time and save it
                timing_var=toc;
                handles.responsetimes = [handles.responsetimes,timing_var];
                % stop timer and evaluate
                if strcmp(get(handles.timer, 'Running'), 'on')
                    stop(handles.timer);
                end

                  set(handles.eo_numberl, 'string', '');
                  set(handles.eo_numberr, 'string', '');
                  pause_dur = 0.5 + (2-0.5).*rand(1);% pause between 0.5 and 2s
                  pause(pause_dur);
                  % compare number and response and save both
                  handles.responses = [handles.responses,1];
                  handles.rand_numbers = [handles.rand_numbers,handles.number];
                  handles.number = randi(8,1,1);% generate random number
                  % choose window to show number in
                  choose_window = round(rand(1));
                  if choose_window == 0
                      set(handles.eo_numberl, 'string', num2str(handles.number));
                      set(handles.eo_numberr, 'string', '');
                  elseif choose_window == 1;
                      set(handles.eo_numberr, 'string', num2str(handles.number));
                      set(handles.eo_numberl, 'string', '');
                  end
                  tic
              case 'rightarrow'
                  % get the reaction time and save it
                  timing_var=toc;
                  handles.responsetimes = [handles.responsetimes,timing_var];
                  % stop timer and evaluate
                  if strcmp(get(handles.timer, 'Running'), 'on')
                      stop(handles.timer);
                  end
                  % get the reaction time and save it
                  set(handles.eo_numberl, 'string', '');
                  set(handles.eo_numberr, 'string', '');
                  pause_dur = 0.5 + (2-0.5).*rand(1);% pause between 0.5 and 2s
                  pause(pause_dur);
                  % compare number and response and save both
                  handles.responses = [handles.responses,0];
                  handles.rand_numbers = [handles.rand_numbers,handles.number];
                  handles.number = randi(8,1,1);% generate random number
                  % choose window to show number in
                  choose_window = round(rand(1));
                  if choose_window == 0
                      set(handles.eo_numberl, 'string', num2str(handles.number));
                      set(handles.eo_numberr, 'string', '');
                  elseif choose_window == 1;
                      set(handles.eo_numberr, 'string', num2str(handles.number));
                      set(handles.eo_numberl, 'string', '');
                  end
                  tic;
              case('escape')
                  figure1_CloseRequestFcn(hObject, eventdata, handles);
                  return;
              otherwise
                  return;
          end
          % start timer again
          % Only start timer if it is not running
          if strcmp(get(handles.timer, 'Running'), 'off')
              start(handles.timer);
          end
          % if it takes more than 2.5s to press a button move on to the
          % next number
      end
  else
      % start with enter
      if strcmp(eventdata.Key,'return')
          set(handles.startexp, 'visible','off');
          set(handles.text2, 'visible', 'on');
          set(handles.eo_numberr, 'visible','on');
          set(handles.eo_numberl, 'visible','on');
          % if it's the first keystroke, don't take reaction time into account
          disp('************************************************************************************');
          %         pause_dur = 0.5 + (2-0.5).*rand(1);% pause between 0.5 and 2s
          pause_dur = 2.5;
          pause(pause_dur);
          % start the playback
          play(handles.player);
          handles.firstiteration =0;
          handles.number = randi(8,1,1);% generate random number
          % choose window to show number in
          choose_window = round(rand(1));
          if choose_window == 0
              set(handles.eo_numberl, 'string', num2str(handles.number));
              set(handles.eo_numberr, 'string', '');
          elseif choose_window == 1;
              set(handles.eo_numberr, 'string', num2str(handles.number));
              set(handles.eo_numberl, 'string', '');
          end
          % start timer again
          start(handles.timer);
          tic;
          % if it takes more than 2.5s to press a button move on to the
          % next number
      elseif strcmp(eventdata.Key,'escape')
          figure1_CloseRequestFcn(hObject, eventdata, handles);
          return;
      end
  end
  guidata(hObject, handles);

%%% Timer callback

function update_boxes(hObject,eventdata,hfigure)

handles = guidata(hfigure);

   if strcmp(get(handles.timer, 'Running'), 'on')
      %%%%%%this part is wrong
      stop(handles.timer);
  end
  if ~(strcmp(get(handles.eo_numberl, 'String'),'') && strcmp(get(handles.eo_numberr, 'String'),''))&& (handles.timerfcnflag == 0)
      handles.timerfcnflag = 1;
      handles.timerfcnflag
      disp('timerfcn');

      % timing_var=toc;
      % save invalid reaction time

      handles.responsetimes = [handles.responsetimes,-1];

      set(handles.eo_numberl, 'string', '');
      set(handles.eo_numberr, 'string', '');
      pause_dur = 0.5 + (2-0.5).*rand(1);% pause between 0.5 and 2s
      pause(pause_dur);
      handles.responses = [handles.responses,2];
      handles.rand_numbers = [handles.rand_numbers,handles.number];
      choose_window = round(rand(1));
      handles.number = randi(8,1,1);% generate random number
      if choose_window == 0
          set(handles.eo_numberl, 'string', num2str(handles.number));
          set(handles.eo_numberr, 'string', '');
          % start measuring responsetime again
          tic;
      elseif choose_window == 1;
          set(handles.eo_numberr, 'string', num2str(handles.number));
          set(handles.eo_numberl, 'string', '');
          % start measuring responsetime again
          tic;
      end

      % start timer again
      % Only start timer if it is not running
      if strcmp(get(handles.timer, 'Running'), 'off')
          %%%%%%this part is wrong
          start(handles.timer);
      end
      handles.timerfcnflag = 0;
      handles.timerfcnflag
  end
  % if it takes more than 2.5s to press a button move on to the
  % next number etc
  guidata(hfigure, handles);

[Jan]

I do not understand the question. Could you narrow it down to 3 or 4 sentences?

[Nemanja]

Hi Jan, sorry I'm not sure how to describe it... Ok, so what I want is for the timer to start running when the gui starts, stop if a button is pressed within 2.5 s and start again at the end of the buttonpress callback and wait for input again and repeat until the gui is closed. If the button is not pressed in 2.5s, I want to call the timer callback, and start the timer again at the end of it, wait for input and repeat until the gui is closed. So the timer callback should only be called if in an iteration the input takes more than 2.5s. However, if I just open the gui and wait, so press nothing, the timer callback gets called more often than it should - so not every 2.5s (+ whatever delay is caused by the callback execution) but 2 consecutive calls occur every now and then. I don't know why this is and how to fix it. Hope this clears it up a bit...

[Nemanja]

I figured it out... I was stopping the timer whenever the timer callback is entered and starting it again before it is left. Since I set the period to 2.5s and busymode to 'fixedSpacing' this was unnecessary and messed things up. It's working now and that's good but I'd still like to understand what actually goes wrong when you call the stop and start within the timer callback.