Merge pull request #16 from Remi-Gau/remi-update_to_other_CPP_repos

Update to new cfg structure

Author: Remi-Gau

lib/CPP_BIDS

@@ -1,95 +1,95 @@
-function [cfg, expParameters] = setParameters();
+function [cfg] = setParameters()
 
     % Initialize the parameters and general configuration variables
-    expParameters = struct();
     cfg = struct();
 
-    
-
     % by default the data will be stored in an output folder created where the
     % setParamters.m file is
     % change that if you want the data to be saved somewhere else
-    expParameters.outputDir = fullfile( ...
+    cfg.dir.output = fullfile( ...
         fileparts(mfilename('fullpath')), '..', ...
         'output');
 
     %% Debug mode settings
-    cfg.debug = true; % To test the script out of the scanner, skip PTB sync
-    cfg.testingSmallScreen = false; % To test on a part of the screen, change to 1
-    cfg.testingTranspScreen = true; % To test with trasparent full size screen
+    cfg.debug.do = true; % To test the script out of the scanner, skip PTB sync
+    cfg.debug.smallWin = false; % To test on a part of the screen, change to 1
+    cfg.debug.transpWin = true; % To test with trasparent full size screen
 
-    expParameters.verbose = true;
+    cfg.verbose = false;
 
     %% Engine parameters
 
     cfg.testingDevice = 'pc';
-    cfg.eyeTracker = false;
-    cfg.initAudio = false;
+    cfg.eyeTracker.do = false;
+    cfg.audio.do = false;
 
-    [cfg, expParameters] = setMonitor(cfg, expParameters);
+    cfg = setMonitor(cfg, cfg);
 
     % Keyboards
-    [cfg, expParameters] = setKeyboards(cfg, expParameters);
+    cfg = setKeyboards(cfg, cfg);
 
     % MRI settings
-    [cfg, expParameters] = setMRI(cfg, expParameters);
+    cfg = setMRI(cfg, cfg);
 
     %% Experiment Design
-    expParameters.names = {'static', 'motion'};
-    expParameters.possibleDirections = [-1 1]; % 1 motion , -1 static
-    expParameters.numBlocks = size(expParameters.possibleDirections, 2);
-    expParameters.numRepetitions = 1; % AT THE MOMENT IT IS NOT SET IN THE MAIN SCRIPT
-    expParameters.IBI = 0; % 8;
+    cfg.names = {'static', 'motion'};
+    cfg.possibleDirections = [-1 1]; % 1 motion , -1 static
+    cfg.numBlocks = size(cfg.possibleDirections, 2);
+    cfg.numRepetitions = 1; % AT THE MOMENT IT IS NOT SET IN THE MAIN SCRIPT
+    cfg.IBI = 0; % 8;
     % Time between events in secs
-    expParameters.ISI = 0.1;
+    cfg.ISI = 0.1;
     % Number of seconds before the motion stimuli are presented
-    expParameters.onsetDelay = 5;
+    cfg.onsetDelay = 5;
     % Number of seconds after the end all the stimuli before ending the run
-    expParameters.endDelay = 1;
+    cfg.endDelay = 1;
 
     %% Visual Stimulation
-    % speed in visual angles
-    expParameters.speedEvent = 8;
+
     % Number of events per block (should not be changed)
-    expParameters.numEventsPerBlock = 12;
-    expParameters.eventDuration = 1;
+    cfg.numEventsPerBlock = 12;
+    cfg.eventDuration = 1; % second
+
+    % speed in visual angles
+    cfg.dot.speed = 8;
     % Coherence Level (0-1)
-    expParameters.coh = 1;
+    cfg.dot.coh = 1;
     % Maximum number dots per frame
-    expParameters.maxDotsPerFrame = 300;
+    cfg.dot.maxNbPerFrame = 300;
     % Dot life time in seconds
-    expParameters.dotLifeTime = 1;
+    cfg.dot.lifeTime = 1;
     % Dot Size (dot width) in visual angles.
-    expParameters.dotSize = 0.1;
-    expParameters.dotColor = cfg.white;
-    expParameters.dontClear = 0;
+    cfg.dot.size = 0.1;
+    cfg.dot.color = cfg.color.white;
+    cfg.dot.dontClear = 0;
+
     % Diameter/length of side of aperture in Visual angles
     cfg.diameterAperture = 8;
 
     %% Task(s)
-    
-    expParameters.task = 'visualLocalizer';
+
+    cfg.task.name = 'visual localizer';
 
     % Instruction
-    expParameters.taskInstruction = '1-Detect the RED fixation cross\n \n\n';
+    cfg.task.instruction = '1-Detect the RED fixation cross\n \n\n';
 
     % Fixation cross (in pixels)
     % Set the length of the lines of the fixation cross
-    expParameters.fixCrossDimPix = 10;
+    cfg.fixation.dimensionPix = 10;
     % Set the line width for our fixation cross
-    expParameters.lineWidthPix = 4;
-    expParameters.maxNumFixationTargetPerBlock = 2;
-    expParameters.targetDuration = 0.15; % In secs
-
-    expParameters.xDisplacementFixCross = 0; % Manual displacement of the fixation cross
-    expParameters.yDisplacementFixCross = 0; % Manual displacement of the fixation cross
-    expParameters.fixationCrossColor = cfg.white;
-    expParameters.fixationCrossColorTarget = cfg.red;
-    
-    expParameters.extraColumns = {'direction', 'speed', 'target', 'event', 'block'};
+    cfg.fixation.lineWidthPix = 4;
+    cfg.fixation.xDisplacement = 0; % Manual displacement of the fixation cross
+    cfg.fixation.yDisplacement = 0; % Manual displacement of the fixation cross
+    cfg.fixation.color = cfg.color.white;
+    cfg.fixation.colorTarget = cfg.color.red;
+
+    cfg.target.maxNbPerBlock = 2;
+    cfg.target.duration = 0.15; % In secs
+
+    cfg.extraColumns = {'direction', 'speed', 'target', 'event', 'block'};
 end
 
-function [cfg, expParameters] = setKeyboards(cfg, expParameters)
+function cfg = setKeyboards(cfg)
     cfg.keyboard.escapeKey = 'ESCAPE';
     cfg.keyboard.responseKey = {'space'};
     cfg.keyboard.keyboard = [];
@@ -101,34 +101,34 @@
     end
 end
 
-function [cfg, expParameters] = setMRI(cfg, expParameters)
+function cfg = setMRI(cfg)
     % letter sent by the trigger to sync stimulation and volume acquisition
-    cfg.triggerKey = 't';
-    cfg.numTriggers = 4;
+    cfg.mri.triggerKey = 't';
+    cfg.mri.triggerNb = 4;
 
-    expParameters.bids.MRI.RepetitionTime = 2;
+    cfg.mri.repetitionTime = 2;
 
-    expParameters.bids.MRI.Instructions = 'Detect the RED fixation cross';
-    expParameters.bids.MRI.TaskDescription = [];
+    cfg.bids.MRI.Instructions = 'Detect the RED fixation cross';
+    cfg.bids.MRI.TaskDescription = [];
 
 end
 
-function [cfg, expParameters] = setMonitor(cfg, expParameters)
+function cfg = setMonitor(cfg)
 
     % Monitor parameters for PTB
-    cfg.white = [255 255 255];
-    cfg.black = [0 0 0];
-    cfg.red = [255 0 0];
-    cfg.grey = mean([cfg.black; cfg.white]);
-    cfg.backgroundColor = cfg.black;
-    cfg.textColor = cfg.white;
+    cfg.color.white = [255 255 255];
+    cfg.color.black = [0 0 0];
+    cfg.color.red = [255 0 0];
+    cfg.color.grey = mean([cfg.color.black; cfg.color.white]);
+    cfg.color.background = cfg.color.black;
+    cfg.text.color = cfg.color.white;
 
     % Monitor parameters
-    cfg.monitorWidth = 42; % in cm
-    cfg.screenDistance = 134; % distance from the screen in cm
+    cfg.screen.monitorWidth = 42; % in cm
+    cfg.screen.monitorDistance = 134; % distance from the screen in cm
 
     if strcmpi(cfg.testingDevice, 'mri')
-        cfg.monitorWidth = 42;
-        cfg.screenDistance = 134;
+        cfg.screen.monitorWidth = 42;
+        cfg.screen.monitorDistance = 134;
     end
 end

lib/CPP_PTB

@@ -1,4 +1,4 @@
-function [onset, duration] = doDotMo(cfg, expParameters, thisEvent)
+function [onset, duration] = doDotMo(cfg, thisEvent)
     % Draws the stimulation of static/moving in 4 directions dots or static
     %
     % DIRECTIONS
@@ -18,19 +18,19 @@
     % smaller number (nDots / Area of aperture) on average.
 
     %% Get parameters
-    dontClear  = expParameters.dontClear;
+    dontClear  = cfg.dot.dontClear;
 
     direction = thisEvent.direction(1);
     isTarget = thisEvent.target(1);
     speed = thisEvent.speed(1);
 
-    coh = expParameters.coh;
-    ndots = expParameters.maxDotsPerFrame;
-    dotSizePix = expParameters.dotSizePix;
-    dotLifeTime = expParameters.dotLifeTime;
-    dotColor = expParameters.dotColor;
+    coh = cfg.dot.coh;
+    ndots = cfg.dot.maxNbPerFrame;
+    dotSizePix = cfg.dot.sizePix;
+    dotLifeTime = cfg.dot.lifeTime;
+    dotColor = cfg.dot.color;
 
-    targetDuration = expParameters.targetDuration;
+    targetDuration = cfg.target.duration;
 
     % thisEvent = deg2Pix('speed', thisEvent, cfg);
     % dotSpeedPix = logFile.iEventSpeedPix;
@@ -45,7 +45,7 @@
 
         speed = 0;
 
-        dotLifeTime = expParameters.eventDuration;
+        dotLifeTime = cfg.eventDuration;
     end
 
     %% initialize variables
@@ -59,7 +59,7 @@
     % 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) * ...
+        speed * 10 / (diamAperture * 10) * (3 / cfg.screen.monitorRefresh) * ...
         [cos(pi * direction / 180.0) -sin(pi * direction / 180.0)], ndots, 1);
 
     % dxdy = repmat(...
@@ -71,13 +71,13 @@
     dotTime = ones(size(xy, 1), 1);
 
     % Set for how many frames to show the dots
-    continueShow = floor(expParameters.eventDuration / cfg.ifi);
+    continueShow = floor(cfg.eventDuration / cfg.screen.ifi);
 
     % Covert the dotLifeTime from seconds to frames
-    dotLifeTime = ceil(dotLifeTime / cfg.ifi);
+    dotLifeTime = ceil(dotLifeTime / cfg.screen.ifi);
 
     %% Start the dots presentation
-    vbl = Screen('Flip', cfg.win, 0, dontClear);
+    vbl = Screen('Flip', cfg.screen.win, 0, dontClear);
     onset = vbl;
 
     while continueShow
@@ -124,19 +124,19 @@
         %% PTB draws the dots stimulation
 
         % Draw the fixation cross
-        color = expParameters.fixationCrossColor;
+        color = cfg.fixation.color;
         % If this frame shows a target we change the color
         if GetSecs < (onset + targetDuration) && isTarget == 1
-            color = expParameters.fixationCrossColorTarget;
+            color = cfg.fixation.colorTarget;
         end
-        drawFixationCross(cfg, expParameters, color);
+        drawFixationCross(cfg, color);
 
         % Draw the dots
-        Screen('DrawDots', cfg.win, xy_pix, dotSizePix, dotColor, cfg.center, 2);
+        Screen('DrawDots', cfg.screen.win, xy_pix, dotSizePix, dotColor, cfg.screen.center, 2);
 
-        Screen('DrawingFinished', cfg.win, dontClear);
+        Screen('DrawingFinished', cfg.screen.win, dontClear);
 
-        vbl = Screen('Flip', cfg.win, vbl + cfg.ifi, dontClear);
+        vbl = Screen('Flip', cfg.screen.win, vbl + cfg.screen.ifi, dontClear);
 
         %% Update counters
 
@@ -150,11 +150,11 @@
 
     %% Erase last dots
 
-    drawFixationCross(cfg, expParameters, expParameters.fixationCrossColor);
+    drawFixationCross(cfg, cfg.fixation.color);
 
-    Screen('DrawingFinished', cfg.win, dontClear);
+    Screen('DrawingFinished', cfg.screen.win, dontClear);
 
-    vbl = Screen('Flip', cfg.win, vbl + cfg.ifi, dontClear);
+    vbl = Screen('Flip', cfg.screen.win, vbl + cfg.screen.ifi, dontClear);
 
     duration = vbl - onset;