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maskedAIDuration.m
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maskedAIDuration.m
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function maskedAIDuration(ana)
%----------compatibility for windows
%if ispc; PsychJavaTrouble(); end
KbName('UnifyKeyNames');
%===================Initiate out metadata===================
ana.date = datestr(datetime);
ana.version = Screen('Version');
ana.computer = Screen('Computer');
%===================experiment parameters===================
if ana.debug
ana.screenID = 0;
else
ana.screenID = max(Screen('Screens'));%-1;
end
%===================Make a name for this run===================
cd(ana.ResultDir)
if ~isempty(ana.subject)
if ana.useStaircase; type = 'AISTAIR'; else; type = 'AIMOC'; end %#ok<*UNRCH>
nameExp = [type '_' ana.subject];
c = sprintf(' %i',fix(clock()));
nameExp = [nameExp c];
ana.nameExp = regexprep(nameExp,' ','_');
else
ana.nameExp = 'debug';
end
cla(ana.plotAxis1);
cla(ana.plotAxis2);
cla(ana.plotAxis3);
useEyeLink = ana.useEyelink;
nBlocks = ana.nBlocks;
nBlocksOverall = nBlocks * length(ana.pedestalRange);
pedestalBlack = ana.pedestalRange;
pedestalBlackLinear = pedestalBlack;
pedestalWhite = ana.pedestalRange;
pedestalWhiteLinear = pedestalWhite;
%-------------------response values, linked to left, up, down
DISAPPEAR = 1; UNSURE = 2; BREAKFIX = -1;
%-----------------------Positions to move stimuli
XPos1 = [3 1.5 -1.5 -1.5 1.5 -3] * 3 / 3;
YPos1 = [0 2.598 2.598 -2.598 -2.598 0] * 3 / 3;
XPos =XPos1; YPos = YPos1;
saveMetaData();
%======================================================stimulus objects
%---------------------main disc (stimulus and pedestal).
st = discStimulus();
st.name = ['STIM_' ana.nameExp];
st.xPosition = XPos1(1);
st.colour = [1 1 1 1];
st.size = ana.discSize;
st.sigma = ana.sigma;
%-----mask stimulus
m = dotsStimulus();
m.mask = true;
m.density = 1000;
m.coherence = 0;
m.size = st.size+1;
m.speed=0.5;
m.name = ['MASK_' ana.nameExp];
m.xPosition = st.xPosition;
m.size = st.size;
%----------combine them into a single meta stimulus------------------
stimuli = metaStimulus();
stimuli.name = ana.nameExp;
sidx = 1;
maskidx = 1;
stimuli{sidx} = st;
stimuli.maskStimuli{maskidx} = m;
stimuli.showMask = false;
%======================================================stimulus objects
%-----------------------open the PTB screens------------------------
PsychDefaultSetup(2);
Screen('Preference', 'SkipSyncTests', 0);
%===================open our screen====================
sM = screenManager();
sM.screen = ana.screenID;
sM.windowed = ana.windowed;
sM.pixelsPerCm = ana.pixelsPerCm;
sM.distance = ana.distance;
sM.debug = ana.debug;
sM.blend = true;
sM.bitDepth = 'FloatingPoint32Bit';
if exist(ana.gammaTable, 'file')
load(ana.gammaTable);
if isa(c,'calibrateLuminance')
sM.gammaTable = c;
end
clear c;
if ana.debug
sM.gammaTable.plot
end
end
sM.backgroundColour = ana.backgroundColor;
screenVals = sM.open; % OPEN THE SCREEN
fprintf('\n--->>> AIContrast Opened Screen %i : %s\n', sM.win, sM.fullName);
setup(stimuli,sM); %setup our stimulus object
%==============================setup eyelink==========================
if useEyeLink == true
ana.strictFixation = true;
eL = eyelinkManager('IP',[]);
fprintf('--->>> eL setup starting: %s\n', eL.fullName);
eL.isDummy = ana.isDummy; %use dummy or real eyelink?
eL.name = ana.nameExp;
eL.saveFile = [ana.nameExp '.edf'];
eL.recordData = true; %save EDF file
eL.sampleRate = ana.sampleRate;
eL.remoteCalibration = false; % manual calibration?
eL.calibrationStyle = ana.calibrationStyle; % calibration style
eL.modify.calibrationtargetcolour = [1 1 1];
eL.modify.calibrationtargetsize = 1;
eL.modify.calibrationtargetwidth = 0.05;
eL.modify.waitformodereadytime = 500;
eL.modify.devicenumber = -1; % -1 = use any keyboard
% X, Y, FixInitTime, FixTime, Radius, StrictFix
updateFixationValues(eL, ana.fixX, ana.fixY, ana.firstFixInit,...
ana.firstFixTime, ana.firstFixDiameter, ana.strictFixation);
%sM.verbose = true; eL.verbose = true; sM.verbosityLevel = 10; eL.verbosityLevel = 4; %force lots of log output
initialise(eL, sM); %use sM to pass screen values to eyelink
setup(eL); % do setup and calibration
fprintf('--->>> eL setup complete: %s\n', eL.fullName);
WaitSecs('YieldSecs',0.5);
getSample(eL); %make sure everything is in memory etc.
end
%---------------------------Set up task variables----------------------
task = stimulusSequence();
task.name = ana.nameExp;
task.nBlocks = nBlocksOverall;
task.nVar(1).name = 'colour';
task.nVar(1).stimulus = 1;
task.nVar(1).values = [0.5-ana.stimulusCon 0.5+ana.stimulusCon];
randomiseStimuli(task);
initialiseTask(task);
staircaseB = []; staircaseW = [];
taskW = stimulusSequence();
taskW.name = ana.nameExp;
taskW.nBlocks = nBlocks;
taskW.nVar(1).name = 'pedestalWhite';
taskW.nVar(1).stimulus = 1;
taskW.nVar(1).values = pedestalWhite;
randomiseStimuli(taskW);
initialiseTask(taskW);
taskB = stimulusSequence();
taskB.name = ana.nameExp;
taskB.nBlocks = nBlocks;
taskB.nVar(1).name = 'pedestalBlack';
taskB.nVar(1).stimulus = 1;
taskB.nVar(1).values = pedestalBlack;
randomiseStimuli(taskB);
initialiseTask(taskB);
clc
%=====================================================================
try %our main experimental try catch loop
%=====================================================================
loop = 1;
posloop = 1;
breakloop = false;
fixated = 'no';
response = NaN;
responseRedo = 0; %number of trials the subject was unsure and redid (left arrow)
while ~breakloop && task.thisRun <= task.nRuns
%-----setup our values and print some info for the trial
hide(stimuli);
response = NaN;
stimuli.showMask = false;
colourOut = task.outValues{task.thisRun,1};
stimuli{1}.colourOut = colourOut;
if colourOut == 0.5 - ana.stimulusCon
pedestal = taskB.outValues{taskB.thisRun,1};
else
pedestal = taskW.outValues{taskW.thisRun,1};
end
stimuli{1}.sizeOut = pedestal;
stimuli{1}.sigmaOut = ana.sigma;
% if pedestal <= 1; XPos = 2/3*XPos1; YPos = 2/3*YPos1; end
% if pedestal >= 4; XPos = 4/3*XPos1; YPos = 4/3*YPos1; end
if posloop > 6; posloop = 1; end
stimuli{1}.xPositionOut = XPos(posloop);
stimuli{1}.yPositionOut = YPos(posloop);
stimuli.maskStimuli{1}.xPositionOut = XPos(posloop);
stimuli.maskStimuli{1}.yPositionOut = YPos(posloop);
ts.x = XPos(posloop);
ts.y = YPos(posloop);
ts.size = stimuli{1}.size;
ts.selected = true;
%save([tempdir filesep nameExp '.mat'],'task','taskB','taskW');
fprintf('\n==>># %i: Pedestal = %.3g | Colour = %.3g | ',task.thisRun,pedestal,colourOut);
Priority(MaxPriority(sM.win));
posloop = posloop + 1;
stimuli.update();
stimuli.maskStimuli{1}.update();
%-----initialise eyelink and draw fix spot
if useEyeLink
resetFixation(eL);
trackerClearScreen(eL);
trackerDrawStimuli(eL,ts);
trackerDrawFixation(eL); %draw fixation window on eyelink computer
edfMessage(eL,'V_RT MESSAGE END_FIX END_RT'); ... %this 3 lines set the trial info for the eyelink
edfMessage(eL,['TRIALID ' num2str(task.thisRun)]); ... %obj.getTaskIndex gives us which trial we're at
edfMessage(eL,['MSG:PEDESTAL ' num2str(pedestal)]); ... %add in the pedestal of the current state for good measure
edfMessage(eL,['MSG:CONTRAST ' num2str(colourOut)]); ... %add in the pedestal of the current state for good measure
startRecording(eL);
statusMessage(eL,'INITIATE FIXATION...');
fixated = '';
syncTime(eL);
while ~strcmpi(fixated,'fix') && ~strcmpi(fixated,'breakfix')
drawCross(sM,0.4,[0 0 0 0],ana.fixX,ana.fixY);
Screen('DrawingFinished', sM.win); %tell PTB/GPU to draw
tFix = Screen('Flip',sM.win); %flip the buffer
getSample(eL);
fixated=testSearchHoldFixation(eL,'fix','breakfix');
end
if strcmpi(fixated,'breakfix')
fprintf(' BREAK INIT FIXATION');
response = BREAKFIX;
end
else
drawCross(sM,0.4,[0 0 0 0],ana.fixX,ana.fixY);%[0.5 0.5 0.5 0.5]
tFix = Screen('Flip',sM.win); %flip the buffer
WaitSecs(0.5);
fixated = 'fix';
end
%------Our main stimulus drawing loop
finishLoop = false;
while strcmp(fixated, 'fix') && finishLoop == false
if useEyeLink; edfMessage(eL,'END_FIX'); statusMessage(eL,'Show Stimulus...'); end
%=====================STIMULUS
stimuli.show();
tStim = GetSecs; vbl = tStim;
while vbl <= tStim + ana.stimulusTime
draw(stimuli); %draw stimulus
drawCross(sM,0.4,[0 0 0 0],ana.fixX,ana.fixY);
Screen('DrawingFinished', sM.win); %tell PTB/GPU to draw
if useEyeLink
getSample(eL); %drawEyePosition(eL);
isfix = isFixated(eL);
if ~isfix
fixated = 'breakfix';
break
end
end
animate(stimuli); %animate stimulus, will be seen on next draw
vbl = Screen('Flip',sM.win, vbl + screenVals.halfisi); %flip the buffer
end
tPedestal = GetSecs;
tMask = 0;
if useEyeLink && ~strcmpi(fixated,'fix')
response = BREAKFIX; finishLoop = true;
statusMessage(eL,'Subject Broke Fixation!');
edfMessage(eL,'MSG:BreakFix')
break
end
%=====================RESPONSE
drawBackground(sM);
Screen('DrawText',sM.win,['When you see nothing, press: [DOWN]=DISAPPEAR [RIGHT]=SHOW AGAIN'],0,0);
drawCross(sM,0.4,[0 0 0 0],ana.fixX,ana.fixY);
Screen('DrawingFinished', sM.win); %tell PTB/GPU to draw
tMaskOff = Screen('Flip',sM.win);
if useEyeLink
statusMessage(eL,'Waiting for Subject Response!');
edfMessage(eL,'Subject Responding')
edfMessage(eL,'END_RT'); ...
end
finishLoop = true;
end
%-----check keyboard
if response ~= BREAKFIX
ListenChar(2);
[secs, keyCode] = KbWait(-1);
rchar = KbName(keyCode);
tEnd = GetSecs;
if iscell(rchar);rchar=rchar{1};end
switch lower(rchar)
case {'downarrow','down'} %darker than
response = DISAPPEAR;
updateResponse();
if useEyeLink
trackerDrawText(eL,'Subject Pressed RIGHT!');
edfMessage(eL,'Subject Pressed RIGHT')
end
doPlot();
case {'righttarrow','right'}
response = UNSURE;
updateResponse();
if useEyeLink
trackerDrawText(eL,'Subject UNSURE!');
edfMessage(eL,'Subject UNSURE')
end
% doPlot();
case {'backspace','delete'}
response = -10;
updateResponse();
if useEyeLink
trackerDrawText(eL,'Subject UNDO!');
edfMessage(eL,'Subject UNDO')
end
% doPlot();
case {'c'} %calibrate
response = BREAKFIX;
stopRecording(eL);
setOffline(eL);
trackerSetup(eL);
WaitSecs(2);
case {'d'}
response = BREAKFIX;
stopRecording(eL);
setOffline(eL);
success = driftCorrection(eL);
WaitSecs(2);
case {'q'} %quit
response = BREAKFIX;
fprintf('\n!!!QUIT!!!\n');
breakloop = true;
otherwise
response = UNSURE;
updateResponse();
if useEyeLink
statusMessage(eL,'Subject UNSURE!');
edfMessage(eL,'Subject UNSURE')
end
end
end
ListenChar(0);
if useEyeLink
resetFixation(eL); trackerClearScreen(eL);
stopRecording(eL);
edfMessage(eL,['TRIAL_RESULT ' num2str(response)]);
setOffline(eL);
end
drawBackground(sM);
Screen('Flip',sM.win); %flip the buffer
WaitSecs(0.5);
end
%-----Cleanup
Screen('Flip',sM.win);
Priority(0); ListenChar(0); ShowCursor;
close(sM); %close screen
p=uigetdir(pwd,'Select Directory to Save Data, CANCEL to not save.');
if ischar(p)
cd(p);
response = task.response;
responseInfo = task.responseInfo;
if ~useEyeLink; eL = []; end
save([ana.nameExp '.mat'], 'ana', 'response', 'responseInfo', 'task',...
'taskB', 'taskW', 'staircaseB', 'staircaseW', 'sM',...
'stimuli', 'eL');
disp(['=====SAVE, saved current data to: ' pwd]);
else
if useEyeLink; eL.saveFile = ''; end %blank save file so it doesn't save
end
if useEyeLink == true; close(eL); end
reset(stimuli); %reset our stimulus ready for use again
catch ME
ple(ME)
close(sM); %close screen
Priority(0); ListenChar(0); ShowCursor;
disp(['!!!!!!!!=====CRASH, save current data to: ' pwd]);
if ~useEyeLink; eL = []; end
save([ana.nameExp 'CRASH.mat'], 'task', 'taskB', 'taskW',...
'ana', 'sM', 'stimuli', 'eL', 'ME')
if useEyeLink == true; eL.saveFile = [ana.nameExp 'CRASH.edf']; close(eL); end
reset(stimuli);
clear stimuli task taskB taskW md eL s
rethrow(ME);
end
function updateResponse()
% tEnd = GetSecs;
ListenChar(0);
if response == DISAPPEAR %subject responded
responseInfo.response = response;
responseInfo.duration = tEnd - tPedestal;
responseInfo.N = task.thisRun;
responseInfo.times = [tFix tStim tPedestal tMask tMaskOff tEnd];
responseInfo.contrastOut = colourOut;
responseInfo.pedestal = pedestal;
responseInfo.pedestalGamma = pedestal;
responseInfo.blackN = taskB.thisRun;
responseInfo.whiteN = taskW.thisRun;
responseInfo.redo = responseRedo;
updateTask(task,response,tEnd,responseInfo)
task.thisRun = taskB.thisRun+taskW.thisRun;
ana.duration (1,task.thisRun-1 )= responseInfo.duration;
if colourOut == 0.5 - ana.stimulusCon
taskB.thisRun = taskB.thisRun + 1;
else
taskW.thisRun = taskW.thisRun + 1;
end
elseif response == -10
if task.totalRuns > 1
if task.responseInfo(end) == 0
taskB.rewindRun;
else
taskW.rewindRun;
end
task.rewindRun
fprintf('new trial = %i\n', task.thisRun);
end
elseif response == UNSURE
responseRedo = responseRedo + 1;
fprintf('Subject is trying stimulus again, overall = %.2g %\n',responseRedo);
end
end
function doPlot()
ListenChar(0);
info = cell2mat(task.responseInfo);
ped = [info.pedestal];%responseInfo.pedestal;
dura = ana.duration;
for i = 1:length(dura);
x(1,i) = find(ana.pedestalRange == ped(1,i));
end
idxW = [info.contrastOut] == 0.5 + ana.stimulusCon;
idxB = [info.contrastOut] == 0.5 - ana.stimulusCon;
cla(ana.plotAxis1);
plot(ana.plotAxis1, x(idxB), dura(idxB),'ro','MarkerFaceColor','r','MarkerSize',8); hold(ana.plotAxis1,'on')
plot(ana.plotAxis1, x(idxW), dura(idxW),'bo','MarkerFaceColor','b','MarkerSize',8);
drawnow;
end
function setupStairCase()
priorAlphaB = linspace(min(pedestalBlack), max(pedestalBlack),ana.alphaGrain);
priorAlphaW = linspace(min(pedestalWhite), max(pedestalWhite),ana.alphaGrain);
if ana.logSlope
s = log10(0.01); e = log10(ana.betaMax);
else
s = 0.01; e = ana.betaMax;
end
priorBetaB = linspace(s, e, ana.betaGrain); %our slope
priorBetaW = linspace(s, e, ana.betaGrain); %our slope
priorGammaRange = ana.gamma; %fixed value (using vector here would make it a free parameter)
priorLambdaRange = ana.lambda; %ditto
staircaseB = PAL_AMPM_setupPM('stimRange',pedestalBlack,'PF',ana.PF,...
'priorAlphaRange', priorAlphaB, 'priorBetaRange', priorBetaB,...
'priorGammaRange',priorGammaRange, 'priorLambdaRange',priorLambdaRange,...
'numTrials', stopRule,'marginalize',ana.marginalize);
staircaseW = PAL_AMPM_setupPM('stimRange',pedestalWhite,'PF',ana.PF,...
'priorAlphaRange', priorAlphaW, 'priorBetaRange', priorBetaW,...
'priorGammaRange',priorGammaRange, 'priorLambdaRange',priorLambdaRange,...
'numTrials', stopRule,'marginalize',ana.marginalize);
if usePriors
if ana.logSlope
bP = log10(ana.betaPrior);
bSD = log10(ana.betaSD);
else
bP = ana.betaPrior;
bSD = ana.betaSD;
end
priorB = PAL_pdfNormal(staircaseB.priorAlphas,ana.alphaPriorB,ana.alphaSD).*PAL_pdfNormal(staircaseB.priorBetas,bP,bSD);
priorW = PAL_pdfNormal(staircaseW.priorAlphas,ana.alphaPriorW,ana.alphaSD).*PAL_pdfNormal(staircaseW.priorBetas,bP,bSD);
staircaseB = PAL_AMPM_setupPM(staircaseB,'prior',priorB);
staircaseW = PAL_AMPM_setupPM(staircaseW,'prior',priorW);
figure;
if ana.logSlope
subplot(1,2,1);imagesc(10.^staircaseB.priorBetaRange,staircaseB.priorAlphaRange,staircaseB.prior);axis square
else
subplot(1,2,1);imagesc(staircaseB.priorBetaRange,staircaseB.priorAlphaRange,staircaseB.prior);axis square
end
ylabel('Threshold');xlabel('Slope');title('Initial Bayesian Priors BLACK')
if ana.logSlope
subplot(1,2,2);imagesc(10.^staircaseW.priorBetaRange,staircaseW.priorAlphaRange,staircaseW.prior); axis square
else
subplot(1,2,2);imagesc(staircaseW.priorBetaRange,staircaseW.priorAlphaRange,staircaseW.prior); axis square
end
ylabel('Threshold');xlabel('Slope');title('Initial Bayesian Priors WHITE')
drawnow;
end
end
function saveMetaData()
ana.values.nBlocksOverall = nBlocksOverall;
ana.values.pedestalBlackLinear = pedestalBlackLinear;
ana.values.pedestalWhiteLinear = pedestalWhiteLinear;
ana.values.pedestalBlack = pedestalBlack;
ana.values.pedestalWhite = pedestalWhite;
ana.values.DISAPPEAR = DISAPPEAR;
ana.values.UNSURE = UNSURE;
ana.values.BREAKFIX = BREAKFIX;
ana.values.XPos = XPos;
ana.values.yPos = YPos;
end
function [avg,error] = stderr(data,type,onlyerror)
if nargin<3; onlyerror=0; end
if nargin<2; type='SE'; end
if size(type,1)>1; type=reshape(type,1,size(type,1)); end
if size(data,1) > 1 && size(data,2) > 1; nvals = size(data,1);
else nvals = length(data); end
avg=nanmean(data);
switch(type)
case 'SE'
err=nanstd(data);
error=sqrt(err.^2/nvals);
case '2SE'
err=nanstd(data);
error=sqrt(err.^2/nvals);
error = error*2;
case 'CIMEAN'
[error, raw] = bootci(1000,{@nanmean,data},'alpha',0.01);
avg = nanmean(raw);
case 'CIMEDIAN'
[error, raw] = bootci(1000,{@nanmedian,data},'alpha',0.01);
avg = nanmedian(raw);
case 'SD'
error=nanstd(data);
case '2SD'
error=(nanstd(data))*2;
case '3SD'
error=(nanstd(data))*3;
case 'V'
error=nanstd(data).^2;
case 'F'
if max(data)==0
error=0;
else
error=nanvar(data)/nanmean(data);
end
case 'C'
if max(data)==0
error=0;
else
error=nanstd(data)/nanmean(data);
end
case 'A'
if max(data)==0
error=0;
else
error=nanvar(diff(data))/(2*nanmean(data));
end
end
if onlyerror==1
avg=error;
end
end
end
% vbl = Screen('Flip',s.win);
% Screen('DrawText',s.win,['Mask Time: ' num2str(maskTime) ' | Match: B=' num2str(blackMatch) ' W=' num2str(whiteMatch) ],0,0);
% drawSpot(s,0.1,[1 1 0],ana.fixX,ana.fixY);
% if stimuli{1}.contrastOut > 0
% t.colourOut = (0.5/7)*0; t.xPositionOut = -6; t.yPositionOut = -7; update(t); draw(t);
% t.colourOut = (0.5/7)*1; t.xPositionOut = -2; t.yPositionOut = -7; update(t); draw(t);
% t.colourOut = (0.5/7)*2; t.xPositionOut = 2; t.yPositionOut = -7; update(t); draw(t);
% t.colourOut = (0.5/7)*3; t.xPositionOut = 6; t.yPositionOut = -7; update(t); draw(t);
% t.colourOut = (0.5/7)*4; t.xPositionOut = -6; t.yPositionOut = -3; update(t); draw(t);
% t.colourOut = (0.5/7)*5; t.xPositionOut = -2; t.yPositionOut = -3; update(t); draw(t);
% t.colourOut = (0.5/7)*6; t.xPositionOut = 2; t.yPositionOut = -3; update(t); draw(t);
% t.colourOut = (0.5/7)*7; t.xPositionOut = 6; t.yPositionOut = -3; update(t); draw(t);
% else
% t.colourOut = (0.5/7)*7; t.xPositionOut = -6; t.yPositionOut = -7; update(t); draw(t);
% t.colourOut = (0.5/7)*8; t.xPositionOut = -2; t.yPositionOut = -7; update(t); draw(t);
% t.colourOut = (0.5/7)*9; t.xPositionOut = 2; t.yPositionOut = -7; update(t); draw(t);
% t.colourOut = (0.5/7)*10; t.xPositionOut = 6; t.yPositionOut = -7; update(t); draw(t);
% t.colourOut = (0.5/7)*11; t.xPositionOut = -6; t.yPositionOut = -3; update(t); draw(t);
% t.colourOut = (0.5/7)*12; t.xPositionOut = -2; t.yPositionOut = -3; update(t); draw(t);
% t.colourOut = (0.5/7)*13; t.xPositionOut = 2; t.yPositionOut = -3; update(t); draw(t);
% t.colourOut = (0.5/7)*14; t.xPositionOut = 6; t.yPositionOut = -3; update(t); draw(t);
% end
% Screen('flip',s.win);