Exp server test (#203)

* Started expServer tests

* Added more tests; bug fix for older versions

* Removed validation functions for old MATLAB versions; added documentation

* More coverage, documentation

* Draws text to screen during calibration #128

* Fix for #4

* Added structAssign test; rewardId tests

* Typo fix in structAssign_test

* Finished tests for expServer

* #156

* Returned listener delete to cleanup

* Stricter tolerance in AlyxPanel_test; bug fix for rounding negative numbers

* Update alyx-matlab submodule

* Minor changes to documentation

* Update CHANGELOG.md

* Typo fix; 'off' -> false for safety

Author: k1o0

+eui/AlyxPanel.m

@@ -679,7 +679,7 @@ function dispWaterReq(obj, src, ~)
                     obj.WaterRemaining = remainder;
                 end
             catch me
-                d = me.message; %FIXME: JSON no longer returned
+                d = me.message;
                 if isfield(d, 'detail') && strcmp(d.detail, 'Not found.')
                     set(obj.WaterRequiredText, 'ForegroundColor', 'black',...
                         'String', sprintf('Subject %s not found in alyx', obj.Subject));
@@ -761,12 +761,12 @@ function log(obj, varargin)
           %   Examples:
           %     eui.AlyxPanel.round(0.8437, 'up') % 0.85
           %     eui.AlyxPanel.round(12.65, 'up', 3) % 12.6
-          %     eui.AlyxPanel.round(12.6, 'down'), 12);
+          %     eui.AlyxPanel.round(12.6, 'down') % 12
           %
           % See also ROUND
             if nargin < 2; direction = 'nearest'; end
             if nargin < 3; N = 2; end
-            c = 10.^(N-ceil(log10(a)));
+            c = 10.^(N-ceil(log10(abs(a))));
             c(c==Inf) = 0;
             switch direction
                 case 'up'

+hw/+ptb/Window.m

@@ -612,14 +612,35 @@ function applyCalibration(obj, cal)
       Screen('LoadNormalizedGammaTable', obj.PtbHandle, gammaTable);
     end
 
-    function c = calibration(obj, dev, lightIn, clockIn, clockOut)
-      % Creates a calibration file automatically using the light meter
+    function c = calibration(obj, dev, lightIn, clockIn, clockOut, makePlot)
+      % CALIBRATION Performs a gamma calibration for the screen
+      %  Requires the user to hold a photodiode, connected to a NI-DAQ,
+      %  against the screen in order to perform gamma calibration, and
+      %  returns the results as a struct.
+      %  
+      %  Inputs:
+      %    dev (int) : NI DAQ device ID to which the photodiode is
+      %      connected
+      %    lightIn (char) : analogue input channel name to which the
+      %      photodiode is connected
+      %    clockIn (char) : analogue input channel name for clocking pulse
+      %    clockOut (char) : digital output channel name for clocking pulse
+      %    makePlot (bool) : flag for making photodiode signal plot
+      % 
+      %  Output:
+      %    c (struct) : calibration struct containing refresh rate and
+      %      gamma tables
+      %
+      % See also calibrationStruct, applyCalibration
 
       %first load a default gamma table
       stdGammaTable = repmat(linspace(0, 1 - 1/256, 256)',[1 3]);
       disp('Loading standard gamma table');
       Screen('LoadNormalizedGammaTable', obj.PtbHandle, stdGammaTable);
 
+      if nargin < 6
+        makePlot = true;
+      end
       if nargin < 5
         clockOut = 'port1/line0';
       end
@@ -647,37 +668,37 @@ function applyCalibration(obj, cal)
       %% assess the delay between digital and analog
 
       [xc, lags ] = xcorr(light, clock, 1000, 'coeff');
-%       figure; plot(lags,xc)
       [~,imax] = max(xc);
       ishift = lags(imax);
       delay = 1000*ishift/acqRate; % in ms
-      fprintf('Digital is ahead of screen by %2.2f ms\n',delay);
-      
+      delayMsg = sprintf('Digital is ahead of screen by %2.2f ms\n', delay);
+      fprintf(delayMsg);
+
       % correct the data
       clock = circshift(clock,[ishift,0]);
 
       %% plot the data
-      
-      ns = length(light);
-      tt = (1:ns)/acqRate;
-      
-      figure; plot(tt,clock);
-      ylabel('clock signal'); title('Clock'); 
-      
-      upCrossings = find(diff( clock > 1 ) ==  1);
-      dnCrossings = find(diff( clock > 1 ) == -1);
-      
-      figure; clf
-      for iC = 1:length(upCrossings)
-        plot(tt(upCrossings(iC))*[1 1],[0 5],'-', ...
-          'color', 0.8*[1 1 1] ); hold on
+      if makePlot
+        ns = length(light);
+        tt = (1:ns)/acqRate;
+        
+        figure; plot(tt,clock);
+        ylabel('clock signal'); title('Clock');
+        
+        upCrossings = find(diff( clock > 1 ) ==  1);
+        dnCrossings = find(diff( clock > 1 ) == -1);
+        
+        figure; clf
+        for iC = 1:length(upCrossings)
+          plot(tt(upCrossings(iC))*[1 1],[0 5],'-', ...
+            'color', 0.8*[1 1 1] ); hold on
+        end
+        plot( tt, light ); hold on
+        xlabel('Time (s)');
+        ylabel('Photodiode Signal (Volts)');
+        set(gca,'ylim',[0 1.1*max(light)]);
+        title(delayMsg);
       end
-      plot( tt, light ); hold on
-      xlabel('Time (s)');
-      ylabel('Photodiode Signal (Volts)');
-      set(gca,'ylim',[0 1.1*max(light)]);
-      title(sprintf('In this plot. digital has been delayed by %2.2f ms', delay));
-      
       %% interpret the results
 
       nsteps = length(steps); % length(UpCrossings)/3;

+hw/Window.m

@@ -37,6 +37,12 @@
   end
 
   methods (Abstract)
+    % Opens a window into which stimuli can be drawn
+     open(obj)
+     
+     % Closes the window if currently open
+     close(obj)
+    
      % Flips offscreen buffer to window, "validating" it
      % 
      % [TIME, INVALIDFRAMES, VALIDATIONLAG] = flip(WHEN) performs flip as
@@ -63,14 +69,16 @@
     % fillRect(COLOUR, RECT)
     fillRect(obj, colour, rect)
 
-    %Creates the texture on this device from an image matrix
+    % Creates the texture on this device from an image matrix
     tex = makeTexture(obj, image)
 
-    deleteTextures(obj) %Deletes any textures created on this device
+    % Deletes any textures created on this device
+    deleteTextures(obj)
 
-    %Change alpha blending factors
+    % Changes alpha blending factors
     [oldSrcFactor, oldDestFactor] = setAlphaBlending(obj, srcFactor, destFactor)
 
+    % Draws text to the screen
     [nx, ny] = drawText(obj, text, x, y, colour, vSpacing, wrapAt)
   end