add more info and fix typos

Author: marcobarilari

Visual-loc_translational/subfun/doDotMo.m

@@ -5,12 +5,12 @@
 %  0=Right; 90=Up; 180=Left; 270=down
 %
 % Input:
-%   - Cfg: PTB/machine configurations returned by SetParameters and initPTB
-%   - ExpParameters: parameters returned by SetParameters
-%   - logFile: structur that stores the experiment logfile to be saved
+%   - cfg: PTB/machine configurations returned by setParameters and initPTB
+%   - expParameters: parameters returned by setParameters
+%   - logFile: structure that stores the experiment logfile to be saved
 %
 % Output:
-%     - 
+%     -
 %
 % The dots are drawn on a square that contains the round aperture, then any
 % dots outside of the aperture is turned into a NaN so effectively the
@@ -58,7 +58,7 @@
 % [1,1] is the bottom / right of the square that contains the square aperture
 xy = rand(ndots, 2);
 
-% Set a N x 2 matrix that gives jump size in pixels 
+% Set a N x 2 matrix that gives jump size in pixels
 %  pix/sec * sec/frame = pix / frame
 dxdy = repmat(...
     speed * 10/(diamAperture*10) * (3/cfg.monRefresh) ...
@@ -84,69 +84,69 @@
 onset = vbl;
 
 while continueShow
-    
+
     % L are the dots that will be moved
     L = rand(ndots,1) < coh;
-    
+
     % Move the selected dots
     xy(L,:) = xy(L,:) + dxdy(L,:);
-    
+
     % If not 100% coherence, we get new random locations for the other dots
     if sum(~L) > 0
         xy(~L,:) = rand(sum(~L),2);
     end
-    
+
     % Create a logical vector to detect any dot that has:
     % - an xy position inferior to 0
     % - an xy position superior to 1
     % - has exceeded its liftime
     N = any([xy > 1, xy < 0, dotTime > dotLifeTime], 2) ;
-    
+
     % If there is any such dot we relocate it to a new random position
     % and change its lifetime to 1
     if any(N)
         xy(N,:) = rand(sum(N), 2);
         dotTime(N, 1) = 1;
     end
-    
+
     % Convert the dot position to pixels
     xy_pix = floor( xy * diamAperturePix );
-    
+
     % This assumes that zero is at the top left, but we want it to be
     %  in the center, so shift the dots up and left, which just means
     %  adding half of the aperture size to both the x and y direction.
     xy_pix = (xy_pix - diamAperturePix/2)';
-    
+
     % NaN out-of-circle dots
     % We use Pythagore's theorem to figure out which dots are out of the
     % circle
     outCircle = sqrt(xy_pix(1,:).^2 + xy_pix(2,:).^2) + dotSizePix/2 > (diamAperturePix / 2);
     xy_pix(:, outCircle) = NaN;
-    
-    
+
+
     %% PTB draws the dots stimulation
-    
+
     % Draw the fixation cross
     color = expParameters.fixationCrossColor;
     % If this frame shows a target we change the color
     if GetSecs < (onset+targetDuration) && isTarget==1
         color = expParameters.fixationCrossColorTarget;
     end
     drawFixationCross(cfg, expParameters, color)
-    
+
     % Draw the dots
     Screen('DrawDots', cfg.win, xy_pix, dotSizePix, dotColor, cfg.center, 2);
-    
+
     Screen('DrawingFinished', cfg.win, dontClear );
-    
+
     vbl = Screen('Flip', cfg.win, vbl+cfg.ifi, dontClear );
-    
-    
+
+
     %% Update counters
 
     % Check for end of loop
     continueShow = continueShow - 1;
-    
+
     % Add one frame to the dot lifetime to each dot
     dotTime = dotTime + 1;
 

Visual-loc_translational/subfun/expDesign.m

@@ -3,6 +3,8 @@
 %
 % The conditions are consecutive static and motion blocks (Gives better results than randomised).
 %
+% It can be run as a stand alone without inputs to display a visual example of possible design.
+%
 % EVENTS
 %  The numEventsPerBlock should be a multiple of the number of "base"
 %  listed in the motionDirections and staticDirections (4 at the moment).
@@ -22,12 +24,12 @@
 %   - ExpParameters.designBlockNames      = cell array (nr_blocks, 1) with the
 %    name for each block
 %
-%   - ExpParameters.designDirections      = array (nr_blocks, numEventsPerBlock) 
+%   - ExpParameters.designDirections      = array (nr_blocks, numEventsPerBlock)
 %    with the direction to present in a given block
 %       - 0 90 180 270 indicate the angle
 %       - -1 indicates static
 %
-%   - ExpParameters.designSpeeds          = array (nr_blocks, numEventsPerBlock) * speedEvent;
+%   - ExpParameters.designSpeeds          = array (nr_blocks, numEventsPerBlock) * speedEvent
 %
 %   - ExpParameters.designFixationTargets = array (nr_blocks, numEventsPerBlock)
 %   showing for each event if it should be accompanied by a target
@@ -103,14 +105,14 @@
 expParameters.designFixationTargets = zeros(nrBlocks, numEventsPerBlock);
 
 for iMotionBlock = 1:numRepetitions
-    
+
     expParameters.designDirections( motionIndex(iMotionBlock), :) = Shuffle(motionDirections);
     expParameters.designDirections( staticIndex(iMotionBlock), :) = Shuffle(staticDirections);
-    
+
 end
 
 for iBlock = 1:nrBlocks
-    
+
     % Set block name
     switch condition{iBlock}
         case 'static'
@@ -119,55 +121,55 @@
             thisBlockName = {'motion'};
     end
     expParameters.designBlockNames(iBlock) = thisBlockName;
-    
-    
+
+
     % set target
     % if there are 2 targets per block we make sure that they are at least
     % 2 events apart
     % targets cannot be on the first or last event of a block
-    
+
     chosenTarget = [];
-    
+
     tmpTarget = numTargets(iBlock);
-    
+
     switch tmpTarget
-        
+
         case 1
-            
+
             chosenTarget = randsample(2:numEventsPerBlock-1, tmpTarget, false);
-            
+
         case 2
-            
+
             targetDifference = 0;
-            
+
             while targetDifference <= 2
                 chosenTarget = randsample(2:numEventsPerBlock-1, tmpTarget, false);
                 targetDifference = (max(chosenTarget) - min(chosenTarget));
-            end  
-            
+            end
+
     end
-    
+
     expParameters.designFixationTargets(iBlock, chosenTarget) = 1;
-    
+
 end
 
 
 %% Visualize the design matrix
 if displayFigs
-    
+
     uniqueNames = unique(expParameters.designBlockNames) ;
-    
+
     Ind = zeros(length(expParameters.designBlockNames), length(uniqueNames)) ;
-    
+
     for i = 1:length(uniqueNames)
         CondInd(:,i) = find(strcmp(expParameters.designBlockNames, uniqueNames{i})) ; %#ok<*AGROW>
         Ind(CondInd(:,i), i) = 1 ;
     end
-    
+
     imagesc(Ind)
-    
+
     set(gca, ...
         'XTick',1:length(uniqueNames),...
         'XTickLabel', uniqueNames)
-    
+
 end

Visual-loc_translational/subfun/wait4Trigger.m

@@ -1,33 +1,33 @@
 function wait4Trigger(Cfg)
 
 if strcmp(Cfg.device,'Scanner')
-    
+
     fprintf('Waiting for trigger \n');
-    
+
     DrawFormattedText(Cfg.win,'Waiting For Trigger',...
         'center', 'center', Cfg.textColor);
     Screen('Flip', Cfg.win);
-    
+
     triggerCounter=0;
-    
+
     while triggerCounter < Cfg.numTriggers
 
         [keyIsDown, ~, keyCode, ~] = KbCheck(-1);
-        
+
         if strcmp(KbName(keyCode),Cfg.triggerKey)
-            
+
             triggerCounter = triggerCounter+1 ;
-            
+
             fprintf('Trigger %s \n', num2str(triggerCounter));
-            
+
             DrawFormattedText(Cfg.win,['Trigger ',num2str(triggerCounter)],'center', 'center', Cfg.textColor);
             Screen('Flip', Cfg.win);
-            
+
             while keyIsDown
                 [keyIsDown, ~, ~, ~] = KbCheck(-1);
             end
-            
+
         end
     end
 end
-end
+end