Transparency in PlotPosteriorComparison

MemExperiments/ColorWorkingMemoryExperiment.asv

@@ -0,0 +1,235 @@
+% COLORWORKINGMEMORYEXPERIMENT Runs a color working memory task
+% a la Zhang & Luck (2008). The task requires memory for the color of
+% briefly presented squares. Participants then report the color of a single
+% probed square using a continuous report task.
+%
+%   ColorWorkingMemoryExperiment();
+%
+%	Preferences can be found down at the bottom, beginning on line 197.
+%
+
+function ColorWorkingMemoryExperiment()
+
+  try
+    prepareEnvironment;
+    window = openWindow();
+    prefs = getPreferences()
+
+    % Put up instructions and wait for keypress.
+    instruct(window);
+    returnToFixation(window, window.centerX, window.centerY, prefs.fixationSize)
+
+    WaitSecs(1);
+
+    % Get rects for each item.
+    rects = cell(1, max(prefs.setSizes));
+    for i = 1:max(prefs.setSizes)
+      rects{i} = circularArrayRects([0, 0, prefs.squareSize, prefs.squareSize], ...
+        i, prefs.radius, window.centerX, window.centerY)';
+    end
+
+    colorWheelLocations = colorwheelLocations(window,prefs);
+
+    for trialIndex = 1:length(prefs.fullFactorialDesign)
+
+      % Determine how many items there are on this trial and the duration.
+      nItems = prefs.setSizes(prefs.fullFactorialDesign(prefs.order(trialIndex), 1));
+      retentionInterval = prefs.retentionIntervals(prefs.fullFactorialDesign(prefs.order(trialIndex), 2));
+
+      % Pick an item to test.
+      itemToTest(trialIndex) = PsychRandSample(1:nItems);
+
+      % Pick the colors for this trial.
+      colorsInDegrees{trialIndex} = ceil(rand(1, nItems)*360);
+
+      % Draw fixation.
+      drawFixation(window, window.centerX, window.centerY, prefs.fixationSize);
+
+      % Draw the stimulus.
+      colorsToDisplay = prefs.colorwheel(colorsInDegrees{trialIndex}, :)';
+      Screen('FillRect', window.onScreen, colorsToDisplay, rects{nItems});
+
+      % Post the stimulus and wait.
+      Screen('Flip', window.onScreen);
+      WaitSecs(prefs.stimulusDuration);
+
+      % Remove stimulus, return to blank, wait for retention interval to pass.
+      returnToFixation(window, window.centerX, window.centerY, prefs.fixationSize);
+      WaitSecs(retentionInterval);
+
+      % Choose a circle to test, then display the response screen.
+      data.presentedColor(trialIndex) = deg2rad(colorsInDegrees{trialIndex}(itemToTest(trialIndex)));
+      colorsOfTest = repmat([120 120 120], nItems, 1);
+      colorsOfTest(itemToTest(trialIndex), :) = [145 145 145];
+      drawFixation(window, window.centerX, window.centerY, prefs.fixationSize);
+      Screen('FillRect', window.onScreen, colorsOfTest', rects{nItems});
+
+      drawColorWheel(window, prefs);
+
+      % Wait for click.
+      SetMouse(window.centerX, window.centerY);
+      ShowCursor('Arrow');
+
+      % If mouse button is already down, wait for release.
+      [x, y, buttons]GetMouse(window.onScreen);
+      while any(buttons)
+        [x, y, buttons] = GetMouse(window.onScreen);
+      end
+
+      everMovedFromCenter = false;
+      while ~any(buttons)
+
+        drawColorWheel(window, prefs);
+
+        [x,y,buttons] = GetMouse(window.onScreen);
+        [minDistance, minDistanceIndex] = min(sqrt((colorWheelLocations(1, :) - x).^2 + (colorWheelLocations(2, :) - y).^2));
+
+        if(minDistance < 250)
+          everMovedFromCenter = true;
+        end
+
+        if(everMovedFromCenter)
+          colorsOfTest(itemToTest(trialIndex), :) = prefs.colorwheel(minDistanceIndex,:);
+        else
+          colorsOfTest(itemToTest(trialIndex), :) = [145 145 145];
+        end
+
+        drawFixation(window, window.centerX, window.centerY, prefs.fixationSize);
+        Screen('FillRect', window.onScreen, colorsOfTest', rects{nItems});
+        drawColorWheel(window, prefs);
+        Screen('Flip', window.onScreen);
+      end
+      data.reportedColor(trialIndex) = deg2rad(minDistanceIndex);
+      while any(buttons) % wait for release
+        [x,y,buttons] = GetMouse(window.onScreen);
+      end
+
+      HideCursor
+
+      % Return to fixation.
+      returnToFixation(window, window.centerX, window.centerY, prefs.fixationSize);
+      WaitSecs(0.5);
+    end
+
+    % Preliminary analysis of results.
+    data.error = (180/pi) .* (angle(exp(1i*data.reportedColor)./exp(1i*data.presentedColor)));
+    data.setSize = prefs.setSizes(prefs.fullFactorialDesign(prefs.order, 1));
+    data.retentionInterval = prefs.retentionIntervals(prefs.fullFactorialDesign(prefs.order,2));
+
+    save data.mat data prefs
+    postpareEnvironment;
+
+  catch ME
+      rethrow(ME)
+    postpareEnvironment;
+    psychrethrow(psychlasterror);
+
+  end % end try/catch
+end % end whole colorworkingmemoryscript
+
+function prepareEnvironment
+
+  clear all;
+  HideCursor;
+
+  commandwindow; % Select the command window to avoid typing in open scripts
+
+  % Seed the random number generator.
+  % RandStream.setDefaultStream was renamed to RandStream.setGlobalStream in
+  % R2011a
+  if verLessThan('matlab','7.12')
+    RandStream.setDefaultStream(RandStream('mt19937ar', 'seed', sum(100*clock)));
+  else
+    RandStream.setGlobalStream(RandStream('mt19937ar', 'seed', sum(100*clock)));
+  end
+
+  ListenChar(2); % Don't print to MATLAB command window
+end
+
+function postpareEnvironment
+  ShowCursor;
+  ListenChar(0);
+  Screen('CloseAll');
+end
+
+function instruct(window)
+  Screen('TextSize', window.onScreen, window.fontsize);
+  Screen('DrawText', window.onScreen, 'Remember the colors. Click to begin.', 100, 100, 255);
+  Screen('Flip', window.onScreen);
+  GetClicks(window.onScreen);
+end
+
+function drawFixation(window, fixationX, fixationY, fixationSize)
+  Screen('DrawDots', window.onScreen, [fixationX, fixationY], fixationSize, 255);
+end
+
+function offsets = circularArrayOffsets(n, centerX, centerY, radius, rotation)
+  degreeStep = 360/n;
+  offsets = [sind(0:degreeStep:(360-degreeStep) + rotation)'.* radius, ...
+             cosd(0:degreeStep:(360-degreeStep) + rotation)'.* radius];
+end
+
+function rects = circularArrayRects(rect, nItems, radius, centerX, centerY)
+  coor = circularArrayOffsets(nItems, centerX, centerY, radius, 0) + repmat([centerX centerY], nItems, 1);
+  rects = [coor(:, 1)-rect(3)/2 , coor(:, 2)-rect(3)/2, coor(:, 1)+rect(3)/2, coor(:, 2)+rect(3)/2];
+end
+
+function returnToFixation(window, fixationX, fixationY, fixationSize)
+  Screen('FillRect', window.onScreen, window.bcolor);
+  Screen('DrawDots', window.onScreen, [fixationX, fixationY], fixationSize, 255);
+  Screen('Flip', window.onScreen);
+end
+
+function window = openWindow()
+  window.screenNumber = max(Screen('Screens'));
+  window.onScreen = Screen('OpenWindow', window.screenNumber, [128 128 128]);
+  Screen('BlendFunction', window.onScreen, 'GL_SRC_ALPHA', 'GL_ONE_MINUS_SRC_ALPHA');
+  [window.screenX, window.screenY] = Screen('WindowSize', window.onScreen); % check resolution
+  window.screenRect  = [0, 0, window.screenX, window.screenY]; % screen rect
+  window.centerX = window.screenX * 0.5; % center of screen in X direction
+  window.centerY = window.screenY * 0.5; % center of screen in Y direction
+  window.centerXL = floor(mean([0, window.centerX])); % center of left half of screen in X direction
+  window.centerXR = floor(mean([window.centerX, window.screenX])); % center of right half of screen in X direction
+
+  % Basic drawing and screen variables.
+  window.black    = BlackIndex(window.onScreen);
+  window.white    = WhiteIndex(window.onScreen);
+  window.gray     = mean([window.black window.white]);
+  window.fontsize = 24;
+  window.bcolor   = window.gray;
+end
+
+function drawColorWheel(window, prefs)
+  colorWheelLocations = [cosd(1:360).*prefs.colorWheelRadius + window.centerX; ...
+    sind(1:360).*prefs.colorWheelRadius + window.centerY];
+  colorWheelSizes = 20;
+  Screen('DrawDots', window.onScreen, colorWheelLocations, colorWheelSizes, prefs.colorwheel', [], 1);
+end
+
+function L = colorwheelLocations(window,prefs)
+  L = [cosd(1:360).*prefs.colorWheelRadius + window.centerX; ...
+       sind(1:360).*prefs.colorWheelRadius + window.centerY];
+end
+
+function prefs = getPreferences
+  prefs.nTrialsPerCondition = 2;
+  prefs.setSizes = [2,4];
+  prefs.retentionIntervals = [0.250, 0.5, 1];
+  prefs.stimulusDuration = 0.250;
+  prefs.squareSize = 75; % size of each stimulus object, in pixels
+  prefs.radius = 180;
+  prefs.fixationSize = 3;
+
+  % Colorwheel details.
+  prefs.colorWheelRadius = 350;
+  prefs.colorwheel = load('colorwheel360.mat', 'fullcolormatrix');
+  prefs.colorwheel = prefs.colorwheel.fullcolormatrix;
+
+  % Randomize trial order of full factorial design order.
+  prefs.fullFactorialDesign = fullfact([length(prefs.setSizes), ...
+    length(prefs.retentionIntervals), ...
+    prefs.nTrialsPerCondition]);
+
+  prefs.order = Shuffle(1:length(prefs.fullFactorialDesign));
+  prefs.nTrials = length(prefs.fullFactorialDesign);
+end

MemExperiments/ColorWorkingMemoryExperiment.m

@@ -37,7 +37,7 @@ function ColorWorkingMemoryExperiment()
       retentionInterval = prefs.retentionIntervals(prefs.fullFactorialDesign(prefs.order(trialIndex), 2));
 
       % Pick an item to test.
-      itemToTest(trialIndex) = RandSample(1:nItems);
+      itemToTest(trialIndex) = PsychRandSample(1:nItems);
 
       % Pick the colors for this trial.
       colorsInDegrees{trialIndex} = ceil(rand(1, nItems)*360);
@@ -71,7 +71,7 @@ function ColorWorkingMemoryExperiment()
       ShowCursor('Arrow');
 
       % If mouse button is already down, wait for release.
-      GetMouse(window.onScreen);
+      [x, y, buttons] = GetMouse(window.onScreen);
       while any(buttons)
         [x, y, buttons] = GetMouse(window.onScreen);
       end
@@ -134,7 +134,13 @@ function ColorWorkingMemoryExperiment()
   commandwindow; % Select the command window to avoid typing in open scripts
 
   % Seed the random number generator.
-  RandStream.setDefaultStream(RandStream('mt19937ar', 'seed', sum(100*clock)));
+  % RandStream.setDefaultStream was renamed to RandStream.setGlobalStream in
+  % R2011a
+  if verLessThan('matlab','7.12')
+    RandStream.setDefaultStream(RandStream('mt19937ar', 'seed', sum(100*clock)));
+  else
+    RandStream.setGlobalStream(RandStream('mt19937ar', 'seed', sum(100*clock)));
+  end
 
   ListenChar(2); % Don't print to MATLAB command window
 end

MemPlots/PlotPosteriorComparison.m

@@ -1,6 +1,6 @@
 %PLOTPOSTERIORCOMPARISON Show multiple posteriors at once (e.g., for two conditions)
 %
-%    figHand = PlotPosteriorComparison(posteriors, paramNames)
+%    figHand = PlotPosteriorComparison(posteriors, paramNames, conditionOrder)
 %
 %  Example usage:
 %   posteriorSamples1 = MCMC(MemDataset(1), model);
@@ -12,7 +12,12 @@
 % Posteriors can be either fullPosteriors or posteriorSamples or a mixture
 % of the two.
 %
-function figHand = PlotPosteriorComparison(posteriors, paramNames)
+% The optional third argument "conditionOrder" can be used to plot 
+% condition names instead of numbers. The output from 
+% [datasets, conditionOrder] = SplitDataByCondition(data)
+% can be recycled.
+%
+function figHand = PlotPosteriorComparison(posteriors, paramNames, conditionOrder)
   % Show 2x2 correlation for each variable with each other to look for
   % structure; Visualize both as a scatter and as a 2D histogram
   figHand = figure;
@@ -28,7 +33,11 @@
   end
   N = length(paramNames);
   subplot(N,N,sub2ind([N N],N,1));
-  l = legend(cl, num2str((1:length(posteriors))'), 'Location', 'NorthEast');
+  if exist('conditionOrder','var')
+      l = legend(cl, conditionOrder, 'Location', 'NorthEast');
+  else
+      l = legend(cl, num2str((1:length(posteriors))'), 'Location', 'NorthEast');
+  end
   pos = get(l, 'Position');
   set(l, 'Position', [pos(1)+0.05, pos(2)+0.04, pos(3), pos(4)]);
 end
@@ -67,8 +76,13 @@
     [n,x] = hist(posteriorSamples.vals(:,p));
     n = n./max(n(:));
     h1=bar(x,n, 'FaceColor',cols(w,:),'EdgeColor',cols(w,:));
-    hPatch = findobj(h1,'Type','patch');
-    set(hPatch,'FaceAlpha',0.4);
+    %different transparency handles starting R2014b
+    if verLessThan('matlab','8.5')
+        hPatch = findobj(h1,'Type','patch');
+        set(hPatch,'FaceAlpha',0.4);
+    else
+        h1.FaceAlpha = 0.4;
+    end
     axis tight;
     xlim([min(xlim)-(max(xlim)-min(xlim))/3 max(xlim)+(max(xlim)-min(xlim))/3]);
     set(gca, 'YTick', []);