Merge pull request #9 from marcobarilari/marco_update-main-script

update the main script and other subfun to the elder brother (visual loc) state of the art

Author: marcobarilari

audioLocTranslational.m

@@ -1,9 +1,14 @@
 %% 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
+% by Mohamed Rezk 2018
+% adapted by MarcoB and RemiG 2020
+
+%%
+
+getOnlyPress = 1;
+
+more off;
 
 % Clear all the previous stuff
 % clc; clear;
@@ -12,13 +17,10 @@
     clear Screen;
 end
 
-getOnlyPress = 1;
-
-more off;
-
 % make sure we got access to all the required functions and inputs
 initEnv();
 
+% set and load all the parameters to run the experiment
 cfg = setParameters;
 cfg = userInputs(cfg);
 cfg = createFilename(cfg);
@@ -28,27 +30,30 @@
 % Safety loop: close the screen if code crashes
 try
 
-    % % % REFACTOR THIS FUNCTION
-    [cfg] = loadAudioFiles(cfg);
-
     %% Init the experiment
     [cfg] = initPTB(cfg);
 
-    % % Convert some values from degrees to pixels
-    % cfg = deg2Pix('diameterAperture', cfg, cfg);
-    % expParameters = deg2Pix('dotSize', expParameters, cfg);
+    % % % REFACTOR THIS FUNCTION % % %
+
+    [cfg] = loadAudioFiles(cfg);
+
+    % % % REFACTOR THIS FUNCTION % % %
 
     [el] = eyeTracker('Calibration', cfg);
 
-    % % % REFACTOR THIS FUNCTION
+    % % % REFACTOR THIS FUNCTION % % %
+
     [cfg] = expDesign(cfg);
 
+    % % % REFACTOR THIS FUNCTION % % %
+
     % Prepare for the output logfiles with all
-    logFile = saveEventsFile('open', cfg, [], ...
-        'direction', 'speed', 'target', 'event', 'block');
+    logFile.extraColumns = cfg.extraColumns;
+    logFile = saveEventsFile('open', cfg, logFile);
 
-    %     disp(cfg);
+    disp(cfg);
 
+    % Show experiment instruction
     standByScreen(cfg);
 
     % prepare the KbQueue to collect responses
@@ -79,25 +84,30 @@
             checkAbort(cfg, cfg.keyboard.keyboard);
 
             % set direction, speed of that event and if it is a target
-            thisEvent.trial_type = 'dummy';
-            thisEvent.direction = cfg.designDirections(iBlock, iEvent);
-            thisEvent.speed = cfg.designSpeeds(iBlock, iEvent);
-            thisEvent.target = cfg.designFixationTargets(iBlock, iEvent);
+            thisEvent.trial_type = cfg.design.blockNames{iBlock};
+            thisEvent.direction = cfg.design.directions(iBlock, iEvent);
+            % thisEvent.speed = cfg.design.speeds(iBlock, iEvent);
+            thisEvent.target = cfg.design.fixationTargets(iBlock, iEvent);
+
+            % % % REFACTOR THIS FUNCTION % % %
 
             % play the sounds and collect onset and duration of the event
-            [onset, duration] = doAudMot(cfg, thisEvent, cfg.audio.pahandle);
+            [onset, duration] = doAudMot(cfg, thisEvent);
+
+            % % % REFACTOR THIS FUNCTION % % %
 
             thisEvent.event = iEvent;
             thisEvent.block = iBlock;
+            thisEvent.keyName = 'n/a';
             thisEvent.duration = duration;
             thisEvent.onset = onset - cfg.experimentStart;
 
             % Save the events txt logfile
             % we save event by event so we clear this variable every loop
             thisEvent.fileID = logFile.fileID;
+            thisEvent.extraColumns = logFile.extraColumns;
 
-            saveEventsFile('save', cfg, thisEvent, ...
-                'direction', 'speed', 'target', 'event', 'block');
+            saveEventsFile('save', cfg, thisEvent);
 
             clear thisEvent;
 
@@ -106,7 +116,7 @@
             responseEvents = getResponse('check', cfg.keyboard.responseBox, cfg, ...
                 getOnlyPress);
 
-            triggerString = ['trigger'];
+            triggerString = ['trigger_' cfg.design.blockNames{iBlock}];
             saveResponsesAndTriggers(responseEvents, cfg, logFile, triggerString);
 
             % wait for the inter-stimulus interval
@@ -118,28 +128,31 @@
 
         WaitSecs(cfg.timing.IBI);
 
+        % trigger monitoring
+        triggerEvents = getResponse('check', cfg.keyboard.responseBox, cfg, ...
+            getOnlyPress);
+
+        triggerString = 'trigger_baseline';
+        saveResponsesAndTriggers(triggerEvents, cfg, logFile, triggerString);
+
     end
 
     % End of the run for the BOLD to go down
     WaitSecs(cfg.timing.endDelay);
 
+    cfg = getExperimentEnd(cfg);
+
     % Close the logfiles
     saveEventsFile('close', cfg, logFile);
 
     getResponse('stop', cfg.keyboard.responseBox);
     getResponse('release', cfg.keyboard.responseBox);
 
-    totalExperimentTime = GetSecs - cfg.experimentStart;
-
     eyeTracker('Shutdown', cfg);
 
-    % save the whole workspace
-    matFile = fullfile(cfg.dir.output, strrep(cfg.fileName.events, 'tsv', 'mat'));
-    if IsOctave
-        save(matFile, '-mat7-binary');
-    else
-        save(matFile, '-v7.3');
-    end
+    createBoldJson(cfg, cfg);
+
+    farewellScreen(cfg);
 
     cleanUp();
 

subfun/expDesign.m

@@ -22,16 +22,16 @@
     %   matrix of the design
     %
     % Output:
-    %   - ExpParameters.designBlockNames      = cell array (nr_blocks, 1) with the
+    %   - ExpParameters.design.blockNames      = cell array (nr_blocks, 1) with the
     %    name for each block
     %
-    %   - ExpParameters.designDirections      = array (nr_blocks, nbEventsPerBlock)
+    %   - ExpParameters.design.directions      = array (nr_blocks, nbEventsPerBlock)
     %    with the direction to present in a given block
     %       - 0 90 180 270 indicate the angle
     %       - -1 indicates static
     %
     %
-    %   - ExpParameters.designFixationTargets = array (nr_blocks, nbEventsPerBlock)
+    %   - ExpParameters.design.fixationTargets = array (nr_blocks, nbEventsPerBlock)
     %   showing for each event if it should be accompanied by a target
     %
 
@@ -48,8 +48,8 @@
 
     % Set variables here for a dummy test of this function
     if nargin < 1 || isempty(cfg)
-        cfg.design.names             = {'static', 'motion'};
-        cfg.design.nbRepetitions    = 4;
+        cfg.design.names = {'static', 'motion'};
+        cfg.design.nbRepetitions = 4;
         cfg.design.nbEventsPerBlock = 12;
         cfg.target.maxNbPerBlock = 2;
     end
@@ -93,14 +93,14 @@
 
     %% Give the blocks the names with condition
 
-    cfg.designBlockNames      = cell(nrBlocks, 1);
-    cfg.designDirections      = zeros(nrBlocks, nbEventsPerBlock);
-    cfg.designFixationTargets = zeros(nrBlocks, nbEventsPerBlock);
+    cfg.design.blockNames      = cell(nrBlocks, 1);
+    cfg.design.directions      = zeros(nrBlocks, nbEventsPerBlock);
+    cfg.design.fixationTargets = zeros(nrBlocks, nbEventsPerBlock);
 
     for iMotionBlock = 1:nbRepetitions
 
-        cfg.designDirections(motionIndex(iMotionBlock), :) = Shuffle(motionDirections);
-        cfg.designDirections(staticIndex(iMotionBlock), :) = Shuffle(staticDirections);
+        cfg.design.directions(motionIndex(iMotionBlock), :) = Shuffle(motionDirections);
+        cfg.design.directions(staticIndex(iMotionBlock), :) = Shuffle(staticDirections);
 
     end
 
@@ -113,7 +113,7 @@
             case 'motion'
                 thisBlockName = {'motion'};
         end
-        cfg.designBlockNames(iBlock) = thisBlockName;
+        cfg.design.blockNames(iBlock) = thisBlockName;
 
         % set target
         % if there are 2 targets per block we make sure that they are at least
@@ -141,19 +141,19 @@
 
         end
 
-        cfg.designFixationTargets(iBlock, chosenTarget) = 1;
+        cfg.design.fixationTargets(iBlock, chosenTarget) = 1;
 
     end
 
     %% Visualize the design matrix
     if displayFigs
 
-        uniqueNames = unique(cfg.designBlockNames) ;
+        uniqueNames = unique(cfg.design.blockNames) ;
 
-        Ind = zeros(length(cfg.designBlockNames), length(uniqueNames)) ;
+        Ind = zeros(length(cfg.design.blockNames), length(uniqueNames)) ;
 
         for i = 1:length(uniqueNames)
-            CondInd(:, i) = find(strcmp(cfg.designBlockNames, uniqueNames{i})) ; %#ok<*AGROW>
+            CondInd(:, i) = find(strcmp(cfg.design.blockNames, uniqueNames{i})) ; %#ok<*AGROW>
             Ind(CondInd(:, i), i) = 1 ;
         end