Initial commit

AwaitGoodFixation.m

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+function [exp_params, hadToRecalibrate] = AwaitGoodFixation(exp_params, ...
+    window, windowRect, fixationScreen, getKeyInput)
+%AWAITGOODFIXATION wait for good fixation and recalibrate if necessary
+goodFixation = false;
+while(~goodFixation)
+    goodFixation = fixationPoint(window, fixationScreen, ...
+        windowRect(3) / 2, windowRect(4) / 2, ...
+        exp_params.fixation_threshold, exp_params.fixation_time, ...
+        exp_params.fixation_timeout);
+
+    if ~goodFixation
+        hadToRecalibrate = true;
+        DrawCenteredText(window, ...
+            {'Unable to detect fixation. Recalibrate [y/n]?'}, 0);
+        Screen('flip', window);
+        keyCode = getKeyInput();
+        localEyelinkFile = getEyelinkFilepath(...
+            'eyemovements_OcclusionQT_', exp_params.subject_name);
+        c = clock;
+        expEyelinkFile = [...
+            exp_params.subject_name(end-2:end) ...
+            num2str(mod(c(3), 10), '%0.1d') num2str(c(4), '%0.2d') ...
+            num2str(c(5), '%0.2d') '.edf'];
+        if(find(keyCode) == KbName('y')) % recalibrate if 'y' is entered
+            status = Eyelink('closefile');
+            if status ~= 0
+                fprintf('closefile error, status: %d', status);
+            end
+            Eyelink('ReceiveFile', exp_params.eyelink_file, localEyelinkFile);
+            exp_params.eyelink_file = expEyelinkFile;
+            calibrateEyelink(window, windowRect, exp_params.eyelink_file);
+        elseif find(keyCode) == KbName('x')
+            % save existing eyelink data
+            status = Eyelink('closefile');
+            if status ~= 0
+                fprintf('closefile error, status: %d', status);
+            end
+            Eyelink('ReceiveFile', exp_params.eyelink_file, ...
+                localEyelinkFile);
+            exp_params.eyelink_file = expEyelinkFile;
+
+            % turn eyelink OFF
+            exp_params.eyelink = 0;
+            goodFixation = true;
+        end
+    end
+end
+end
+
+function resultcode = fixationPoint(window, fixationScreen, ...
+    fixX, fixY, fixAccuracy, fixTime, timeout)
+%should probably add in some keyboard awareness here, in case we need to
+%cancel or pause or something during fixation.
+Screen('DrawTexture',window,fixationScreen);
+Screen('flip',window);
+fixOnTime = GetSecs;
+
+resultcode = 0;
+firstGoodTime = -1;
+lastGoodTime = -1;
+while (GetSecs - fixOnTime < timeout) && (resultcode < 1)
+    fsample = eyelink('NewestFloatSample');
+    if isstruct(fsample)
+        gx = max(fsample.gx); %gaze position in pixels - I think whichever eye is not tracked is -32768, so this should pull out the useful position
+        gy = max(fsample.gy);
+        rx = fsample.rx; %pixels per degree
+        ry = fsample.ry;
+        fixError = sqrt(((fixX - gx)/rx)^2 + ((fixY - gy)/ry)^2);
+        if fixError <= fixAccuracy
+            lastGoodTime = GetSecs;
+            if firstGoodTime == -1
+                firstGoodTime = lastGoodTime;
+            end
+        else
+            lastGoodTime = -1;
+            firstGoodTime = -1;
+        end
+        if lastGoodTime - firstGoodTime > fixTime
+            resultcode = 1;
+        end
+    elseif GetSecs - lastGoodTime > .05
+        firstGoodTime = -1;
+        lastGoodTime = -1;
+    end
+end
+end

DrawCenteredText.m

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+function DrawCenteredText(window, text, color, shiftX)
+if ~exist('shiftX', 'var')
+    shiftX = 0;
+end
+
+% text has to be a cell array of lines
+
+if nargin < 3
+   color = 0;
+end
+win_rect=Screen('Rect', window);
+total_height=0;
+for ln=1:length(text);
+   bbox{ln} = Screen('TextBounds',window,text{ln});
+   total_height=total_height+bbox{ln}(RectBottom);
+   bbox{ln} = CenterRect(bbox{ln},win_rect);
+end
+y=win_rect(RectTop)+(win_rect(RectBottom)-win_rect(RectTop)-total_height)/2;
+for ln=1:length(text);
+   x=bbox{ln}(RectLeft) + shiftX;
+   Screen('DrawText',window,text{ln},x,y,color);
+   y=y+bbox{ln}(RectBottom)-bbox{ln}(RectTop);
+end

GKlab_ScreenGeometry.m

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+function [Geo] = GKlab_ScreenGeometry (ScrWdPix, ScrWdCm, DistToScrCm)
+
+% General screen considerations: 
+
+% Scanner Projection System Measurements:
+HalfScrWdCm = ScrWdCm/2;
+
+% Screen Size (Scanner Projector) in Pixels:
+% ScrWdPix = 1920; %1024
+HalfScrWdPix = ScrWdPix/2;
+
+CmPerPix = ScrWdCm/ScrWdPix; % = .035
+DistToScrPix = ceil(DistToScrCm/CmPerPix); % = 2429
+
+% For the Pixs nearest to the Fov: 
+PixFromFov = 1;
+
+Geo.FovDegPerPix = atand(PixFromFov/DistToScrPix);
+Geo.FovPixPerDeg = Geo.FovDegPerPix^(-1);
+
+% For the Pixs nearest to the Scr's edge:
+PixNearPeriph1 = HalfScrWdPix-1;
+PixNearPeriph2 = HalfScrWdPix;
+
+Geo.PeriphDegPerPix = atand(PixNearPeriph2/DistToScrPix) - atand(PixNearPeriph1/DistToScrPix);
+Geo.PeriphPixPerDeg = Geo.PeriphDegPerPix^(-1);
+
+Geo.GenPixPerDeg = pi * ScrWdPix / atan(ScrWdCm/DistToScrCm/2) / 360; % slightly different.

GenScreenSetup.m

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+function [win,ScrVars] = GenScreenSetup(BG,Res)
+
+% Based on mlScreenSetup
+% 
+% Function to set up all the usual screen values that Mark Lescroart uses:
+% Inputs: 
+%   BackGround - default [128 128 128]
+%       Text size = 18
+%       Text font = Arial
+%       Background = [128 128 128] (gray)
+% 
+
+% Inputs: 
+if ~exist('BG','var')
+    ScrVars.BG = [128 128 128];
+else
+    ScrVars.BG = BG;
+end
+AssertOpenGL;
+
+WarnStr = '\n\n\nmlScreenSetup currently has anti-aliasing turned on. This may decrease performance! \nPlease check code timing before proceeding with experiments!\n\n\n';
+warning([mfilename ':Anti-Alias Warning'],WarnStr)
+
+%%% Get screen number
+ScrVars.ScreenNumber = max(Screen('Screens'));
+try
+    if exist('Res','var')
+        Screen('Resolution', ScrVars.ScreenNumber, Res(1), Res(2));
+    end
+
+    ExtraParams = Screen('Resolution', ScrVars.ScreenNumber);
+    if (ExtraParams.width~=Res(1) || ExtraParams.height~=Res(2)) 
+        ScrVars.Xdimensions(1) = ExtraParams.height;
+        ScrVars.Xdimensions(2) = ExtraParams.width;
+        ScrVars.XframeRate     = ExtraParams.hz;
+        beep;
+        warning('DisplayError:DisplaySizeChangeFail','Failed to set indicated resolution.');
+        display('Saving current resolution to display structure (ScrVars)...');
+        pause(.5);
+    else
+        display('Resolution and refresh rate successfully set.');
+    end
+catch
+    ExtraParams = Screen('Resolution',ScrVars.ScreenNumber);
+    ScrVars.Xdimensions(1) = ExtraParams.height;
+    ScrVars.Xdimensions(2) = ExtraParams.width;
+    ScrVars.XframeRate     = ExtraParams.hz;
+    beep;
+    pause(.5);
+    warning('DisplayError:DisplaySizeChangeFail','Error occurred in Screen(''Resolution'') call.\n\tMay have failed to set indicated resolution and refresh rate.');
+    display('Saving current resolution and refresh rate to display structure...');
+end
+% Open full screen for experiment: 
+% Usage: [Window,Rect] = Screen('OpenWindow',windowPtrOrScreenNumber [,color] [,rect][,pixelSize][,numberOfBuffers][,stereomode][,multisample][,imagingmode]);
+[win, ScrVars.winRect] = Screen('OpenWindow',ScrVars.ScreenNumber, ScrVars.BG,[],32,2,[],6);
+
+%%% Getting inter-flip interval (ifi):
+Priority(MaxPriority(win));
+ScrVars.ifi = Screen('GetFlipInterval', win, 20);
+Priority(0);
+
+Screen('TextFont', win, 'Arial');
+Screen('TextSize', win, 18);
+
+%%% Establishing generally useful screen value variables in a struct array:
+ScrVars.x_min = ScrVars.winRect(1);
+ScrVars.x_max = ScrVars.winRect(3);
+ScrVars.y_min = ScrVars.winRect(2);
+ScrVars.y_max = ScrVars.winRect(4);
+
+ScrVars.AspectRatio = ScrVars.x_max/ScrVars.y_max;
+ScrVars.winWidth = ScrVars.x_max-ScrVars.x_min;
+ScrVars.winHeight = ScrVars.y_max-ScrVars.y_min;
+ScrVars.x_center = ScrVars.winWidth/2;
+ScrVars.y_center = ScrVars.winHeight/2;
+
+ScrVars.FixRect = [0 0 10 10];
+ScrVars.FixRectBig = [0 0 12 12];
+ScrVars.Fixation = CenterRectOnPoint (ScrVars.FixRect, ScrVars.x_center, ScrVars.y_center);
+ScrVars.FixationBig = CenterRectOnPoint (ScrVars.FixRectBig, ScrVars.x_center, ScrVars.y_center);
+
+%[ScrVars.ScreenGeo] = SkyraScreenGeometry;

calibrateEyelink.m

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+function result = calibrateEyelink(window, screenRect, edfFile)
+
+try
+   Eyelink('Shutdown')
+end
+
+el=EyelinkInitDefaults(window);
+% Disable key output to Matlab window:
+%ListenChar(2);
+
+% STEP 3
+% Initialization of the connection with the Eyelink Gazetracker.
+% exit program if this fails.
+if ~EyelinkInit(0, 1)
+    fprintf('Eyelink Init aborted.\n');
+    cleanup;  % cleanup function
+    return;
+end
+
+[v vs]=Eyelink('GetTrackerVersion');
+fprintf('Running experiment on a ''%s'' tracker.\n', vs );
+
+Eyelink('command', 'calibration_type = HV9');
+
+% set the eyetracker commands
+Eyelink('Command', 'screen_pixel_coords = %d %d %d %d', screenRect(1),screenRect(2),screenRect(3)-1,screenRect(4)-1);
+
+Eyelink('Message', 'DISPLAY_COORDS %d %d %d %d', screenRect(1),screenRect(2),screenRect(3)-1,screenRect(4)-1);
+
+Eyelink('Command', 'file_event_filter = LEFT,RIGHT,FIXATION,SACCADE,BLINK,MESSAGE,BUTTON,INPUT');
+
+Eyelink('Command', 'link_event_filter = LEFT,RIGHT,FIXATION,BUTTON');
+
+% make sure that we get gaze data from the Eyelink
+Eyelink('Command', 'link_sample_data = LEFT,RIGHT,GAZE,AREA');
+
+% open file to record data to
+Eyelink('Openfile', edfFile);
+
+% STEP 4
+% Calibrate the eye tracker
+result = EyelinkDoTrackerSetup(el);
+
+% do a final check of calibration using driftcorrection
+EyelinkDoDriftCorrection(el);
+
+% STEP 5
+% start recording eye position
+Eyelink('StartRecording');
+% record a few samples before we actually start displaying
+WaitSecs(0.1);
+% mark zero-plot time in data file
+Eyelink('Message', 'DISPLAY_ON');	% message for RT recording in analysis
+Eyelink('Message', 'SYNCTIME');
+
+fprintf('Eyelink set up complete...\n');
+end

createFixationMatrix.m

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+function fixationMatrix = createFixationMatrix(...
+    fixationSize, fixationWidth, backgroundColor, fixationColor)
+fixationMatrix = backgroundColor * ...
+    ones(fixationSize + fixationWidth);
+fixationMatrix(ceil(fixationSize / 2 - fixationWidth / 2) + ...
+    1:floor(fixationSize / 2 + fixationWidth / 2 + 1), :) = fixationColor;
+fixationMatrix(:, ceil(fixationSize / 2 - fixationWidth / 2) + ...
+    1:floor(fixationSize / 2 + fixationWidth / 2 + 1)) = fixationColor;
+end

createGratingImage.m

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+function gratingImage = createGratingImage(targetDegrees, degreesPerPixel, ...
+    background, foreground)
+pixels = round(targetDegrees / degreesPerPixel);
+gratingImage = background * ones(pixels, pixels);
+numBars = 5;
+gratingWidth = (targetDegrees / numBars) / degreesPerPixel;
+for x = 1:gratingWidth * 2:pixels
+    gratingImage(:, x:x + gratingWidth) = foreground;
+end
+end

drawScoreScreen.m

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+function drawScoreScreen(window, blockIndex, ...
+    performance, performanceMessages, color)
+if performance > 0.9
+    markstr = performanceMessages{5};
+elseif performance > 0.8
+    markstr = performanceMessages{4};
+elseif performance > 0.7
+    markstr = performanceMessages{3};
+elseif performance > 0.6
+    markstr = performanceMessages{2};
+else
+    markstr = performanceMessages{1};
+end
+fprintf('%s\n', markstr);
+DrawCenteredText(window, ...
+    {['Block ', num2str(blockIndex) ':  ', markstr]}, color);
+Screen('flip',window);
+WaitSecs(1);
+end
+

getEyelinkFilepath.m

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+function filepath = getEyelinkFilepath(prefix, subjectName)
+c = clock;
+filepath = fullfile('subjects', subjectName, ...
+    [prefix subjectName ...
+	'-' num2str(c(1)) '_' num2str(c(2),'%0.2d') '_' ...
+    num2str(c(3), '%0.2d') '-' num2str(c(4),'%0.2d') '_' ...
+    num2str(c(5), '%0.2d') '_' num2str(round(c(6)), '%0.2d') ...
+    '.edf']);
+end

initPMD1208FS.m

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+function d=initPMD1208FS();
+
+% initPMD1208FS
+% usage:
+% d=initPMD1208FS
+% 
+% last modified: Itamar Khan / Hesehng Liu
+
+daq=DaqDeviceIndex;
+switch length(daq)
+    case 0,
+        fprintf('Sorry. Couldn''t find a PMD-1208FS box connected to your computer.\n');
+        d = -1;
+        return;
+    case 1,
+        fprintf('Yay. You have a PMD-1208FS daq: \n');
+    case 2,
+        fprintf('Yay. You have two PMD-1208FS daqs: \n');
+    otherwise,
+        fprintf('Yay. You have %d PMD-1208FS daqs: \n',length(daq));
+end
+devices=PsychHID('Devices');
+for i=1:length(daq)
+    d=devices(daq(i));
+    fprintf('device %d, serialNumber %s\n',d.index,d.serialNumber);
+end

parseArgs.m

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+function exp_params = parseArgs(exp_params, varargin)
+for a = 1:2:length(varargin)
+    argument = lower(cell2mat(varargin(a)));
+    value = lower(cell2mat(varargin(a + 1)));
+    if strcmp(value, 'yes') || strcmp(value, 'on')
+        value = true;
+    elseif strcmp(value, 'no') || strcmp(value, 'off')
+        value = false;
+    end
+    % assign the value to a variable with the same name as the argument
+    if isfield(exp_params, argument)
+        exp_params = setfield(exp_params, argument, value);
+    else
+        error('unknown parameter: %s', argument);
+    end
+end
+end