refactor first part of the exp

marcobarilari · marcobarilari · commit 52576dd2229a · 2020-06-22T23:23:16.000+02:00
diff --git a/ALocalizer.m b/ALocalizer.m
@@ -1,121 +1,26 @@
-%function mirror_runMTLocalizer
-clear all;
-clc
-
-%8 trials =  370 sec (without trigger) =6.17 minutes
-% if TR =2 Sec.    370 sec / 2 (TR) = 185 TRs (without trigger) + 4 = 189 TRs  
-% if TR =2.5 Sec.  370 sec / 2 (TR) = 148 TRs (without trigger) + 4 = 152 TRs 
-
-%% To correct for the y-axis problem inside the scanner
-%  where the lower 1/3 of the screen is not appearing because of coil indicate which device the script is running on, on PC, the middle of the
-%  y axis will be the middle of the screen, on the Scanner, the middle of y-axis will be the middle of the upper 2/3 of the screen, because the
-%  lower 1/3 is not visible due to the coil in the scanner.
-device = 'Scanner';
-%device = 'PC';
-
-fprintf('Connected Device is %s \n\n',device);
-
-% Original Script Written by Sam Weiller to localize MT+/V5
-% Adapted by M.Rezk to localize MT/MST (Huk,2002)
-%% Start me up
-% Get the subject Name
-SubjName = input('Subject Name: ','s');
-       if isempty(SubjName)
-          SubjName = 'trial';
-       end
-
-fprintf('Auditory MT Localizer \n\n')
-
 %% Experiment Parametes
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-initial_wait = 5;                                                              % seconds to have a blank screen at the beginning, the scans will be discarded until                                                                              % the magnetic field is homogenous                                                                         
-finalWait = 5;
-%blockDur = 16;                                                                 % Block duration [should be a multiple of osc (below)]                                                                               
-ISI = 0.1;             % Interstimulus Interval between events in the block.
-ibi = 6;                                                                       % Inter-block duration in seconds (time between blocks)
-nrBlocks = 14;                                                                 % Number of trials , where 1 block = 1 block of all conditions (static and motion)
-numEventsPerBlock = 12;
-range_targets = [0 2];                                                         % range of number of targets in each block (from 2 to 5 targets in each block)
-
-mirror_width= 11.5;                                                            % Width (x-axis) of the mirror (in cm)
-v_dist      = 14;                                                              % viewing distance from the mirror (cm) "in this script we use mirror"
-fix_r       = 0.15;                                                            % radius of fixation point (deg)
-
-%Audiofile_duration = 16 ;                                                      % Length of the Audio file (in seconds)
-%Stop_audiofile = blockDur ;                                                    % Let the audio file play for x Seconds
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%                                               % 1 Cycle = one inward and outward motion together
 %% Experimental Design
-% function "experimental_design" while assign the blocks, conditions, and 
+% function "experimental_design" while assign the blocks, conditions, and
 % the number of targets that will be used in the motion localizer
-%[names,targets,condition] = experimental_design(nrBlocks,range_targets);  
+%[names,targets,condition] = experimental_design(nrBlocks,range_targets);
 [names,targets,condition,directions,isTarget] = experimental_design(nrBlocks,numEventsPerBlock,range_targets) ;
 
 numBlocks = length(names);                                                     % Create a variable with the number of blocks in the whole experiment
 
 
-%% InitializePsychAudio;
-InitializePsychSound(1);
-
-[soundData, freq] = loadAudioFiles(SubjName);
-phandle = PsychPortAudio('Open',[],[],1,freq,2);
-%PsychPortAudio('FillBuffer',phandle,soundData_static);
-%fprintf('\nstatic wav file loaded. \n')
-
-%% PTB Setup
-screenNumber = max(Screen('Screens'));
-%screenNumber = 0;
-%Screen('Preference', 'SkipSyncTests', 2);
-[w, winRect, xMid, yMid] = startPTB(screenNumber, 1, [128 128 128]);
-HideCursor;
-
-%% Color indeces, and Screen parameters and inter-flip interval.  
-% Color indices
-white = WhiteIndex(screenNumber);                        
-black = BlackIndex(screenNumber);
-grey = ceil((white+black)/2);
-
-% Flip interval and screen size
-ifi = Screen('GetFlipInterval', w);                                            % Get the flip interval
-[tw, th] = Screen('WindowSize', w);
-
-%nframes  = floor(blockDur/ifi);
-% while mod(nframes,2)~=0                                                % make sure the nframes are even number
-%     nframes = nframes-1;                                                       % to be able to re-assign dots in the static condition (to perform divison calculation)
-% end
-
-%% Welcome screen
-Screen('TextFont',w, 'Courier New');
-Screen('TextSize',w, 20);
-Screen('TextStyle', w, 1);
-DrawFormattedText(w,'Press for FASTER sound \n\n\n(static or motion)',...
-            'center', 'center', black);
-Screen('Flip', w);
-[~, ~, ~]=KbCheck;
-KbWait;
-Screen('Flip', w);
-
-WaitSecs(0.25);
-
-% DrawFormattedText(w,'The experiment is about to begin','center', 'center', black);
-% Screen('Flip', w);
-% [KeyIsDown, pend, KeyCode]=KbCheck;
-% 
-% KbWait;
-% Screen('Flip', w);
-
 %% FUNCTION
 if strcmp(device,'PC')
     DrawFormattedText(w,'Waiting For Trigger',...
         'center', 'center', black);
     Screen('Flip', w);
-    
+
     % press key
     KbWait();
     KeyIsDown=1;
     while KeyIsDown>0
         [KeyIsDown, ~, ~]=KbCheck;
     end
-    
+
 % open Serial Port "SerPor" - COM1 (BAUD RATE: 11520)
 elseif strcmp(device,'Scanner')
     DrawFormattedText(w,'Waiting For Trigger','center', 'center', black);
@@ -159,19 +64,19 @@
 playTime = zeros(numBlocks,1);
 
 for blocks = 1:numBlocks
-    
+
     timeLogger.block(blocks).startTime = GetSecs - experimentStartTime;        % Get the start time of the block
     timeLogger.block(blocks).condition = condition(blocks);                    % Get the condition of the block (motion or static)
-    timeLogger.block(blocks).names = names(blocks);                            % Get the name of the block 
-    
+    timeLogger.block(blocks).names = names(blocks);                            % Get the name of the block
+
     responseCount=0;
-    
+
     for iEvent = 1: numEventsPerBlock
-        
+
         Sound=[];
-        
+
         if isTarget(blocks,iEvent)==0
-            
+
             if strcmp(directions(blocks,iEvent),'S')
                 Sound= soundData.S;
             elseif strcmp(directions(blocks,iEvent),'U')
@@ -183,9 +88,9 @@
             elseif strcmp(directions(blocks,iEvent),'L')
                 Sound= soundData.L;
             end
-        
+
         elseif isTarget(blocks,iEvent)==1
-            
+
             if strcmp(directions(blocks,iEvent),'S')
                 Sound= soundData.S_T;
             elseif strcmp(directions(blocks,iEvent),'U')
@@ -197,72 +102,72 @@
             elseif strcmp(directions(blocks,iEvent),'L')
                 Sound= soundData.L_T;
             end
-            
+
         end
-        
+
         eventOnsets(blocks,iEvent)=GetSecs-experimentStartTime;
-        
+
         PsychPortAudio('FillBuffer',phandle,Sound);
         playTime(blocks,1) = PsychPortAudio('Start',phandle);
-         
+
          %length(playedAudio)/freq
-         
+
          while GetSecs() <= eventOnsets(blocks,iEvent)+ experimentStartTime + (length(Sound)/freq)
-             
+
              if strcmp(device,'Scanner')
                  [sbutton,secs] = TakeSerialButton(SerPor);
                  %[sbutton,secs] = MT_TakeSerialButtonPerFrame(SerPor);
                  %responseKey(end+1)= sbutton;
                  if sbutton~= 0
                      responseTime(end+1)= secs - experimentStartTime;
-                     
+
                      %%%%%%%%%%%%%%%%%%%%%
                      % while you are pressing, wait till it is
                             % released
                             while  sbutton ~= 0
                                 [sbutton,secs]= TakeSerialButton(Cfg.SerPor);
                             end
                      %%%%%%%%%%%%%%%%%%%%%
-                            
+
                      responseCount = responseCount + 1;
                  end
-                 
-                 
-                 
+
+
+
              elseif  strcmp(device,'PC')
-                 
+
                  [keyIsDown, secs, ~ ] = KbCheck();
-                 
+
                  if keyIsDown
                      responseTime(end+1)= secs - experimentStartTime;
                      while keyIsDown ==1
                          [keyIsDown , ~] = KbCheck();
                      end
-                     
+
                      responseCount = responseCount + 1;
                  end
              end
-             
+
          end
-         
+
          eventEnds(blocks,iEvent)=GetSecs-experimentStartTime;
          eventDurations(blocks,iEvent)=eventEnds(blocks,iEvent)-eventOnsets(blocks,iEvent);
-         
+
          WaitSecs(ISI);
-         
+
     end
-    
+
     responsesPerBlock (blocks,1) = responseCount ;
-    
+
     %% Get Block end and duration
     timeLogger.block(blocks).endTime = GetSecs - experimentStartTime;            % Get the time for the block end
     timeLogger.block(blocks).length  = timeLogger.block(blocks).endTime - timeLogger.block(blocks).startTime;  %Get the block duration
-    
+
     %% Fixation cross and inter-block interval
     Screen('FillOval', w, uint8(white), fix_cord);	                             % draw fixation dot (flip erases it)
     blank_onset=Screen('Flip', w);
     WaitSecs('UntilTime', blank_onset + ibi);                                    % wait for the inter-block interval
-    
+
 end;
 
 % At the end of the blocks wait ... secs before ending the experiment.
@@ -291,13 +196,13 @@
 %         responseTime(i)=0;                                                       % this way, we remove the additional 1s for the same button response
 %     end                                                                          % - The same concept for the responseTime
 % end
-% 
+%
 % for i=length(targetTime):-1:2                                                   % The same concept as responseKey adn responseTime.
 %     if targetTime(i-1)~=0                                                       % Our Targets lasts 3 frames, to remove the TargetTime for the 2nd and 3rd frame
 %         targetTime(i)=0;                                                        % we remove targets that are preceeded by a non-zero value
 %     end                                                                          % that way, we have the time of the first frame only of the target
 % end
-% 
+%
 % responseKey  = responseKey(responseKey > 0);                                       % Remove zero elements from responseKey, responseTime, & targetTime
 % responseTime = responseTime(responseTime > 0);
 % targetTime   = targetTime(targetTime > 0);
@@ -327,5 +232,5 @@
     if strcmp(Cfg.device,'Scanner')
         CloseSerialPort(Cfg.SerPor);
     end
-    
-end
+
+end
diff --git a/audioLocTranslational.m b/audioLocTranslational.m
@@ -0,0 +1,76 @@
+%% Auditory hMT localizer using translational motion in four directions
+%  (up- down- left and right-ward)
+
+% Original Script Written by Sam Weiller to localize MT+/V5
+% adapted by M.Rezk to localize MT/MST (Huk,2002)
+% re-adapted by MarcoB and RemiG 2020
+
+%%
+
+% Clear all the previous stuff
+% clc; clear;
+if ~ismac
+    close all;
+    clear Screen;
+end
+
+% make sure we got access to all the required functions and inputs
+addpath(genpath(fullfile(pwd, 'subfun')))
+
+[expParameters, cfg] = setParameters;
+
+% set and load all the parameters to run the experiment
+expParameters = userInputs(cfg, expParameters);
+expParameters = createFilename(expParameters, cfg);
+
+expParameters %#ok<NOPTS>
+
+%%  Experiment
+
+% Safety loop: close the screen if code crashes
+try
+
+    %% Init the experiment
+    [cfg] = initPTB(cfg);
+
+    % % Convert some values from degrees to pixels
+    % cfg = deg2Pix('diameterAperture', cfg, cfg);
+    % expParameters = deg2Pix('dotSize', expParameters, cfg);
+    %
+    %
+    [el] = eyeTracker('Calibration', cfg, expParameters);
+
+    % % % REFACTOR THIS FUNCTION
+    [expParameters] = expDesign(expParameters);
+    % % %
+
+    % Prepare for the output logfiles with all
+    logFile = saveEventsFile('open', expParameters, [], ...
+    'direction', 'speed', 'target', 'event', 'block');
+
+    % % % REFACTOR THIS FUNCTION
+    [soundData, freq] = loadAudioFiles(SubjName);
+    phandle = PsychPortAudio('Open',[],[],1,freq,2);
+    % % %
+
+    % Prepare for fixation Cross
+    if expParameters.Task1
+
+        cfg.xCoords = [-expParameters.fixCrossDimPix expParameters.fixCrossDimPix 0 0] ...
+            + expParameters.xDisplacementFixCross;
+
+        cfg.yCoords = [0 0 -expParameters.fixCrossDimPix expParameters.fixCrossDimPix] ...
+            + expParameters.yDisplacementFixCross;
+
+        cfg.allCoords = [cfg.xCoords; cfg.yCoords];
+
+    end
+
+
+
+catch
+
+  cleanUp()
+  psychrethrow(psychlasterror);
+
+end
diff --git a/setParameters.m b/setParameters.m
@@ -30,7 +30,7 @@
 %% Engine parameters
 
 % Monitor parameters
-cfg.monitorWidth  	  = 42;  % Monitor Width in cm
+cfg.monitorWidth  	  = 42;  % Monitor Width in cm (x-axis)
 cfg.screenDistance    = 134; % Distance from the screen in cm
 cfg.diameterAperture  = 8;   % Diameter/length of side of aperture in Visual angles
 
@@ -158,6 +158,8 @@
     expParameters.yDisplacementFixCross        = 0;    % Manual displacement of the fixation cross
     expParameters.fixationCrossColor           = cfg.white;
     expParameters.fixationCrossColorTarget     = cfg.red;
+    expParameters.fixationRadius               = 0.15; % Radius of fixation point (deg)
+
 end
 
 if cfg.debug
