RealTimePunisherDisplay_CLOUD.m

function [blockData] = RealTimePunisherDisplay_CLOUD(toml_file, runNum)
%%%%%%% LOAD CONFIGURATIONS FROM TOML FILE
%Display_Cfg;
addpath(genpath('matlab-toml'));
raw_text = fileread(toml_file);
Cfg = toml.decode(raw_text);
subjectNum = Cfg.session.subjectNum;
subjectDay = Cfg.session.subjectDay;
subjectDayInt = floor(subjectDay); get the actual day number
useButtonBox = Cfg.session.useButtonBox;
rtData = Cfg.session.rtData;
debugMode = Cfg.session.debugMode;
usePyOutput = Cfg.session.usePyOutput;
%%%%%%% LOAD CONFIGURATIONS FROM TOML FILE


Screen('Preference', 'SkipSyncTests', 1);
fprintf('Running for subject %i, run% i, day %i\n', subjectNum,runNum,subjectDay);
fprintf('usebuttonbox: %i\nrealtimedata: %i\ndebug: %i\nusePyOutput: %i\n', useButtonBox,rtData,debugMode, usePyOutput);

seed = sum(100*clock); %get random seed
RandStream.setGlobalStream(RandStream('mt19937ar','seed',seed));%set seed
%%%%%%%

% function [blockData] = RealTimePunisherDisplay(dataDirHeader,subjectNum,subjectName,runNum,useButtonBox,fMRI,rtData,debug)
%
% Face/house attention experiment with real-time classifier feedback
%
%
% REQUIRED INPUTS:
% - dataDirHeader: where the volume files are being sent to
% - subjectNum:  participant number [any integer]
%                if subjectNum = 0, no information will be saved
% - subjecsubjectNametName: ntblab subject naming convention [MMDDYY#_REALTIME02]
% - matchNum:    if subject is yoked to a subject & which subject
% - runNum:      run number [any integer]
% - useButtonBox:whether using skyra realtime computer [1/0]
% - fMRI:        whether collecting fMRI data [scannumber if yes/0 if not]q5
% - rtData:  whether to give feedback in realtime [1/0]
% - debug:       whether debugging [1/0]
%
% OUTPUTS
% - testTiming: elapsed time for each iteration of SVM testing
% - blockData:
%
% Written by: Nick Turk-Browne
% Editied by: Megan deBettencourt
% Version: 2.0
% Last modified: 10/14/11

%% check inputs
KbName('UnifyKeyNames');
addpath(genpath('/opt/psychtoolbox/'))
Screen('Preference', 'SkipSyncTests', 1);

%check that there is a sufficient number of inputs

if ~isnumeric(subjectNum)
   error('subjectNum must be a number'); 
end


if ~isnumeric(runNum)
    error('runNum must be a number');
end

if (useButtonBox~=1) && (useButtonBox~=0)
    error('useButtonBox must be either 1 (if at scanner) or 0 (if not)')
end

if (rtData~=1) && (rtData~=0)
    error('rtData must be either 1 (if returning feedback) or 0 (if not)')
end

if (debugMode~=1) && (debugMode~=0)
    error('debugMode must be either 1 (if debugging) or 0 (if not)')
end


%% Boilerplate

if (~debugMode) %so that when debugging you can do other things
    %Screen('Preference', 'SkipSyncTests', 1);
   ListenChar(2);  %prevent command window output
   HideCursor;     %hide mouse cursor  
   
else
    Screen('Preference', 'SkipSyncTests', 2);
end



%initialize system time calls
seed = sum(100*clock); %get random seed
GetSecs;

%% Experimental Parameters

%stimulus number parameters
categStr = {'sc','fa'};
typeStr = {'stab','rtfd'};

% block timing
instructDur = 1;    % secs
instructTRnum = 1;  % TRs
%fixationOn = TR-.3; % secs

% trial timing
stimDur = 1;        % secs
respWindow = .85;   % secs
deltat = .1;        % secs
allowance = .05;    % secs

% display parameters
textColor = 0;
textFont = 'Arial';
textSize = 35;
textSpacing = 25;
fixColor = 0;
respColor = 255;
backColor = 127;
imageSize = 256; % assumed square %MdB check image size
destSize = 518; % size that we want image
fixationSize = 4;% pixels
progWidth = 400; % image loading progress bar
progHeight = 20;
minimumDisplay = 0.25;

% how to average the faces and scenes
attImgPropPhase1 = .5;
attImgPropPhase2 = .5;
% new: to use during the stable trials
faceProp = 0.6;
sceneProp = 1-faceProp;
% function mapping classifier output to attended image proportion
% this has the constraints built in
%gain = 2.75;
gain = 2.3;
x_shift = .2;
%y_shift = .05;
y_shift = 0.12;
steepness = .9;

ScreenResX = 1280;
ScreenResY = 720;


%% Response Mapping and Counterbalancing

% skyra: use current design button box (keys 1,2,3,4)
KbName('UnifyKeyNames');
LEFT = KbName('1!');
subj_keycode = LEFT;
DEVICENAME = 'Current Designs, Inc. 932';
if useButtonBox && (~debugMode)
    [index devName] = GetKeyboardIndices;
    for device = 1:length(index)
        if strcmp(devName(device),DEVICENAME)
            DEVICE = index(device);
        end
    end
else
    % let's set it to look for the Dell keyboard instead
    %DEVICENAME = 'Dell KB216 Wired Keyboard';
    DEVICENAME = 'DELL Dell QuietKey Keyboard';
    [index devName] = GetKeyboardIndices;
    for device = 1:length(index)
        if strcmp(devName(device),DEVICENAME)
            DEVICE = index(device);
        end
    end
    %DEVICE = -1;
end
TRIGGER = '5%';
%TRIGGER ='=+' put in for Princeton scanner
TRIGGER_keycode = getKeys(TRIGGER);
% counterbalancing response mapping based on subject assignment
% correctResp spells out the responses for {INDOOR,OUTDOOR,MALE,FEMALE}
respMap = mod(subjectNum-1,4)+1;
switch (respMap)
    case 1
        sceneInstruct = 'Places: respond if it is an indoor place. DO NOT respond if it is an outdoor place';
        faceInstruct = 'Faces: respond if it is a male face. DO NOT respond if it is a female face';
        sceneShorterInstruct = 'indoor places';
        faceShorterInstruct = 'male faces';
    case 2
        sceneInstruct = 'Places: respond if it is an outdoor place. DO NOT respond if it is an indoor place';
        faceInstruct = 'Faces: respond if it is a female face. DO NOT respond if it is a male face';
        sceneShorterInstruct = 'outdoor places';
        faceShorterInstruct = 'female faces';
    case 3
        sceneInstruct = 'Places: respond if it is an outdoor place. DO NOT respond if it is an indoor place';
        faceInstruct = 'Faces: respond if it is a male face. DO NOT respond if it is a female face';
        sceneShorterInstruct = 'outdoor places';
        faceShorterInstruct = 'male faces';
    case 4
        sceneInstruct = 'Places: respond if it is an indoor place. DO NOT respond if it is an outdoor place';
        faceInstruct = 'Faces: respond if it is a female face. DO NOT respond if it is a male face';
        sceneShorterInstruct = 'indoor places';
        faceShorterInstruct = 'female faces';
    otherwise
        error('Impossible response mapping!');
end

%% Initialize Screens

screenNumbers = Screen('Screens');

% show full screen if real, otherwise part of screen
if debugMode
    screenNum = 0;
else
    screenNum = screenNumbers(end);
end

%retrieve the size of the display screen
if debugMode
    screenX = 800;
    screenY = 800;
else
    % first just make the screen tiny
    
    [screenX screenY] = Screen('WindowSize',screenNum);
    % put this back in!!!
    windowSize.degrees = [51 30];
    resolution = Screen('Resolution', screenNum);
    %resolution = Screen('Resolution', 0); % REMOVE THIS AFTERWARDS!!
    %windowSize.pixels = [resolution.width/2 resolution.height];
    %screenX = windowSize.pixels(1);
    %screenY = windowSize.pixels(2);
    % new: setting resolution manually
    % for Penn
     screenX = 1920;
     screenY = 1080;
     % for Princeton
     %screenX = 1280;
     %screenY =  720;
%     %to ensure that the images are standardized (they take up the same degrees of the visual field) for all subjects
%     if (screenX ~= ScreenResX) || (screenY ~= ScreenResY)
%         fprintf('The screen dimensions may be incorrect. For screenNum = %d,screenX = %d (not 1152) and screenY = %d (not 864)',screenNum, screenX, screenY);
%     end
end

%create main window
% ACM: took out if statement because specifying top doesn't work on penn
% comp
%if (useButtonBox)%scanner display monitor has error with inputs of screen size
%    mainWindow = Screen(screenNum,'OpenWindow',backColor);
%else
mainWindow = Screen(screenNum,'OpenWindow',backColor,[0 0 screenX screenY]);
%end
ifi = Screen('GetFlipInterval', mainWindow);
slack  = ifi/2;
% details of main window
centerX = screenX/2; centerY = screenY/2;
Screen(mainWindow,'TextFont',textFont);
Screen(mainWindow,'TextSize',textSize);

% placeholder for images
imageRect = [0,0,imageSize,imageSize];

% position of images
%centerRect = [centerX-imageSize/2,centerY-imageSize/2,centerX+imageSize/2,centerY+imageSize/2];
centerRect = [centerX-destSize/2,centerY-destSize/2,centerX+destSize/2,centerY+destSize/2];

% position of fixation dot
fixDotRect = [centerX-fixationSize,centerY-fixationSize,centerX+fixationSize,centerY+fixationSize];

% image loading progress bar
progRect = [centerX-progWidth/2,centerY-progHeight/2,centerX+progWidth/2,centerY+progHeight/2];


%% Load or Initialize Real-Time Data & Staircasing Parameters
dataDirHeader = pwd;
dataHeader = fullfile(dataDirHeader,[ 'data/subject' num2str(subjectNum)]);
dayHeader = [dataHeader '/day' num2str(subjectDay)];
runHeader = [dayHeader '/run' num2str(runNum)];
classOutputDir = [runHeader '/classoutput'];
fname = findNewestFile(runHeader, fullfile(runHeader, ['blockdatadesign_' num2str(runNum) '*.mat']));
%fn = ls([runHeader '/blockdatadesign_' num2str(runNum) '_*']);
load(fname);

if any([blockData.type]==2) %#ok<NODEF>
    restInstruct = 'The feedback blocks will start soon';
else
    restInstruct = 'The next blocks will start soon';
end
restDur = 3; % seconds to keep that display on
stimFix = 6; % seconds to keep the middle on before starting the block 5
%% Load Images

cd images;
% 1/25: updating to _new image categories where luminance isn't made to
% have the same mean--instead the luminance is scaled by the maximum
% luminance that it is to see if that makes things more equal in luminance
for categ=1:nSubCategs
    
    % move into the right folder
    if (categ == INDOOR)
        cd indoor_NEW;
    elseif (categ == OUTDOOR)
        cd outdoor_NEW;
    elseif (categ == MALE)
        cd male_neut_NEW;
    elseif (categ == FEMALE)
        cd female_neut_NEW;
    elseif (categ == MALESAD)
        cd male_sad_NEW;
    elseif (categ == FEMALESAD)
        cd female_sad_NEW;
    elseif (categ == MALEHAPPY)
        cd male_happy_NEW;
    elseif (categ == FEMALEHAPPY)
        cd female_happy_NEW;
    else
        error('Impossible category!');
    end
    
    % get filenames
    dirList{categ} = dir; %#ok<AGROW>
    dirList{categ} = dirList{categ}(3:end); %#ok<AGROW>  skip . & ..
    if (~isempty(dirList{categ}))
        if (strcmp(dirList{categ}(1).name,'.DS_Store')==1)
            dirList{categ} = dirList{categ}(2:end); %#ok<AGROW>
        end
        
        if (strcmp(dirList{categ}(end).name,'Thumbs.db')==1)
            dirList{categ} = dirList{categ}(1:(end-1)); %#ok<AGROW>
        end
        
        numImages(categ) = length(dirList{categ}); %#ok<AGROW>
        
        if (numImages(categ)>0)
            
            % get images
            for img=1:numImages(categ)
                
                % update progress bar
                Screen('FrameRect',mainWindow,0,progRect,10);
                Screen('FillRect',mainWindow,0,progRect);
                Screen('FillRect',mainWindow,[255 0 0],progRect-[0 0 round((1-img/numImages(categ))*progWidth) 0]);
                Screen('Flip',mainWindow);
                
                % read images
                images{categ,img} = imread(dirList{categ}(img).name); %#ok<AGROW>
                tempFFT = fft2(images{categ,img});
                imagePower{categ,img} = abs(tempFFT); %#ok<AGROW>
                imagePhase{categ,img} = angle(tempFFT); %#ok<AGROW>
            end
            
            cd ..;
        end
    else
        error('Need at least one image per directory!');
    end
end
cd ..;
Screen('Flip',mainWindow);


%% Output Files Setup

% open and set-up output file
dataFile = fopen([runHeader '/behavior.txt'],'a');
fprintf(dataFile,'\n*********************************************\n');
fprintf(dataFile,'* rtAttenPenn v.1.0\n');
fprintf(dataFile,['* Date/Time: ' datestr(now,0) '\n']);
fprintf(dataFile,['* Seed: ' num2str(seed) '\n']);
fprintf(dataFile,['* Subject Number: ' num2str(subjectNum) '\n']);
fprintf(dataFile,['* Run Number: ' num2str(runNum) '\n']);
fprintf(dataFile,['* Use Button Box: ' num2str(useButtonBox) '\n']);
fprintf(dataFile,['* rtData: ' num2str(rtData) '\n']);
fprintf(dataFile,['* debugMode: ' num2str(debugMode) '\n']);
fprintf(dataFile,'*********************************************\n\n');

% print header to command window
fprintf('\n*********************************************\n');
fprintf('* rtAttenPenn v.1.0\n');
fprintf(['* Date/Time: ' datestr(now,0) '\n']);
fprintf(['* Seed: ' num2str(seed) '\n']);
fprintf(['* Subject Number: ' num2str(subjectNum) '\n']);
fprintf(['* Run Number: ' num2str(runNum) '\n']);
fprintf(['* Use Button Box: ' num2str(useButtonBox) '\n']);
fprintf(['* rtData: ' num2str(rtData) '\n']);
fprintf(['* debugMode: ' num2str(debugMode) '\n']);
fprintf('*********************************************\n\n');


%% Show Instructions

% clear screen
Screen(mainWindow,'FillRect',backColor);
Screen('Flip',mainWindow);
FlushEvents('keyDown');

% show instructions
if (blockData(1).type == 1)
    runInstruct{1} = sceneInstruct;
    runInstruct{2} = faceInstruct;
else
    runInstruct{1} = faceInstruct;
    runInstruct{2} = sceneInstruct;
end
runInstruct{3} = '-- Please press to begin once you understand these instructions. --';
for instruct=1:length(runInstruct)
    tempBounds = Screen('TextBounds',mainWindow,runInstruct{instruct});
    if instruct==3
        textSpacing = textSpacing*3;
    end
    Screen('drawtext',mainWindow,runInstruct{instruct},centerX-tempBounds(3)/2,centerY-tempBounds(4)/5+textSpacing*(instruct-1),textColor);
    clear tempBounds;
end
Screen('Flip',mainWindow);
waitForKeyboard(subj_keycode,DEVICE);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% now here we're adding to say waiting for scanner, hold tight!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
waitMessage = 'Waiting for scanner start, hold tight!';
tempBounds = Screen('TextBounds', mainWindow, waitMessage);
Screen('drawtext',mainWindow,waitMessage,centerX-tempBounds(3)/2,centerY-tempBounds(4)/2,textColor);
Screen('Flip', mainWindow);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% now here we're going to say to stay still once the triggers start coming
% in
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% Start Experiment
STILLREMINDER = ['The scan is now starting.\n\nMoving your head even a little blurs the image, so '...
    'please try to keep your head totally still until the scanning noise stops.\n\n Do it for science!'];
STILLDURATION = 6;

% wait for initial trigger
Priority(MaxPriority(screenNum));

if (rtData && ~debugMode )
   % if strcmp(computer,'MACI') % taking out because we're running on a linux!
        %runStart = WaitTRPulsePTB3_skyra(1);
        timing.trig.wait = WaitTRPulse(TRIGGER_keycode,DEVICE);
        runStart = timing.trig.wait;
        DrawFormattedText(mainWindow,STILLREMINDER,'center','center',textColor,70)
        %tempBounds = Screen('TextBounds', mainWindow, STILLREMINDER);
        %Screen('drawtext',mainWindow,STILLREMINDER,centerX-tempBounds(3)/2,centerY-tempBounds(4)/2,textColor);
        startTime = Screen('Flip',mainWindow);
        elapsedTime = 0;
        while (elapsedTime < STILLDURATION)
            pause(0.005)
            elapsedTime = GetSecs()-startTime;
        end
        % else
   %     WaitSecs(.5);
   %     runStart = KbWait;
   % end
else
    runStart = GetSecs;
    %timing = -1;
end
Screen(mainWindow,'FillRect',backColor);
Screen(mainWindow,'FillOval',fixColor,fixDotRect);
Screen('Flip',mainWindow);
Priority(0);

% prepare for trial sequence
fprintf(dataFile,'run\tblock\tbltyp\tblcat\ttrial\tonsdif\tpulse\tscat\tfcat\tsimg\tfimg\tcorresp\tresp\tacc\trt\tfile\tload\tcatsep\tattProp\tsmoothProp\n');
fprintf('run\tblock\tbltyp\tblcat\ttrial\tonsdif\tpulse\tscat\tfcat\tsimg\tfimg\tcorresp\tresp\tacc\trt\tfile\tload\tcatsep\tattProp\tsmoothProp\n');

%% set up

for iBlock = 1:numel(blockData)
    %block instructions
    if (blockData(iBlock).attCateg==SCENE)
        blockInstruct{1} = sceneShorterInstruct; %#ok<AGROW>
    elseif (blockData(iBlock).attCateg==FACE)
        blockInstruct{2} = faceShorterInstruct; %#ok<AGROW>
    end
    
    %timing
    blockDur(iBlock+1) = TR*(instructLen+blockData(iBlock).trialsPerBlock/nTrialsPerTR+IBI); %#ok<AGROW>
    blockOnsets(iBlock) = disdaqs + sum(blockDur(1:iBlock)); %#ok<AGROW>
end
blockOnsets((numel(blockOnsets)/2+1):end) = blockOnsets((numel(blockOnsets)/2+1):end)+stimFix; % account for the rest in between

typeOrder = [blockData.type];
indBlocksPhase1 = 1:(numel(typeOrder)/2);
indBlocksPhase2 = (numel(typeOrder)/2+1):numel(typeOrder);

%% Block Sequence - Phase 1

trialCounter = 0;
volCounter = 1+disdaqs/TR-1;
for iBlock=1:numel(indBlocksPhase1)
    
    % timing
    blockData(iBlock).actualblockonset = GetSecs; %#ok<AGROW>
    blockData(iBlock).plannedinstructonset = blockOnsets(iBlock)+runStart; %#ok<AGROW>
    blockData(iBlock).plannedinstructoffset = blockData(iBlock).plannedinstructonset + instructDur;
    blockData(iBlock).plannedtrialonsets = blockData(iBlock).plannedinstructonset + TR*instructTRnum + [0 cumsum(repmat(TR/nTrialsPerTR,1,blockData(iBlock).trialsPerBlock))]; % so this says start on the next TR
    blockData(iBlock).plannedIBI = blockData(iBlock).plannedtrialonsets(blockData(iBlock).trialsPerBlock) + stimDur;
    % show instructions
    tempBounds = Screen('TextBounds',mainWindow,blockInstruct{blockData(iBlock).attCateg});
    Screen('drawtext',mainWindow,blockInstruct{blockData(iBlock).attCateg},centerX-tempBounds(3)/2,centerY-tempBounds(4)/5,textColor);
    clear tempBounds;
    timespec = blockData(iBlock).plannedinstructonset - slack;
    if rtData
        [timing.trig.instructpulses(iBlock),blockData(iBlock).instructpulses] = WaitTRPulse(TRIGGER_keycode,DEVICE,blockData(iBlock).plannedinstructonset);
    end
    blockData(iBlock).actualinstructonset = Screen('Flip',mainWindow,timespec); %#ok<AGROW> % turn on
    fprintf('Flip time error = %.4f\n', blockData(iBlock).actualinstructonset-blockData(iBlock).plannedinstructonset)
    % show fixation
    timespec = blockData(iBlock).plannedinstructoffset - slack;
    Screen(mainWindow,'FillOval',fixColor,fixDotRect);
    blockData(iBlock).actualinstructoffset = Screen('Flip',mainWindow,timespec); %turn off
    % start trial sequence
    for iTrial=1:(blockData(iBlock).trialsPerBlock)
        
        trialCounter = trialCounter+1;
            
        % prep images
        for half=[SCENE FACE]
            % get current images
            tempPower{half} = imagePower{blockData(iBlock).categs{half}(iTrial),blockData(iBlock).images{half}(iTrial)}; %#ok<AGROW>
            tempImagePhase{half} = imagePhase{blockData(iBlock).categs{half}(iTrial),blockData(iBlock).images{half}(iTrial)}; %#ok<AGROW>
            tempImage{half} = real(ifft2(tempPower{half}.*exp(sqrt(-1)*tempImagePhase{half}))); %#ok<AGROW>
        end
       
        %update imgProp value
        blockData(iBlock).attImgProp(iTrial)=attImgPropPhase1; 
        
        % generate image
        %fullImage = uint8((1-blockData(iBlock).attImgProp(iTrial))*tempImage{SCENE}+blockData(iBlock).attImgProp(iTrial)*tempImage{FACE});
        % new: have it always be 60% face, 40% scene
        fullImage = uint8(tempImage{SCENE}*sceneProp+tempImage{FACE}*faceProp);
        
        % make textures
        imageTex = Screen('MakeTexture',mainWindow,fullImage);
        Screen('PreloadTextures',mainWindow,imageTex);
        
        % wait for trigger and show image
        FlushEvents('keyDown');
        Priority(MaxPriority(screenNum));
        Screen('FillRect',mainWindow,backColor);
        Screen('DrawTexture',mainWindow,imageTex,imageRect,centerRect);
        Screen(mainWindow,'FillOval',fixColor,fixDotRect);
        tRespTimeout = blockData(iBlock).plannedtrialonsets(iTrial)+respWindow; %response timeout
        
        %wait for pulse
        if (rtData) && mod(iTrial,nTrialsPerTR)==1
            %[~,blockData(iBlock).pulses(iTrial)] = WaitTRPulsePTB3_skyra(1,blockData(iBlock).plannedtrialonsets(iTrial)+allowance); %#ok<AGROW>
            [timing.trig.pulses(iBlock,iTrial),blockData(iBlock).pulses(iTrial)] = WaitTRPulse(TRIGGER_keycode,DEVICE,blockData(iBlock).plannedtrialonsets(iTrial));
            timespec = blockData(iBlock).plannedtrialonsets(iTrial) - slack;
            blockData(iBlock).actualtrialonsets(iTrial) = Screen('Flip',mainWindow,timespec); %#ok<AGROW> % turn on
        else
            blockData(iBlock).pulses(iTrial) = 0; %#ok<AGROW>
            timespec = blockData(iBlock).plannedtrialonsets(iTrial) - slack;
            blockData(iBlock).actualtrialonsets(iTrial) = Screen('Flip',mainWindow,timespec); %#ok<AGROW>
        end
        stimOn = 1;
        FlushEvents('keyDown');
        while(GetSecs < tRespTimeout)
            
            % check for responses if none received yet
            if isnan(blockData(iBlock).rts(iTrial))
                [keyIsDown, secs, keyCode] = KbCheck(DEVICE); % -1 checks all keyboards
                if keyIsDown
                    if (keyCode(LEFT))
                        blockData(iBlock).rts(iTrial) = secs-blockData(iBlock).actualtrialonsets(iTrial); %#ok<AGROW> NTB: deltasecs is timed to last KbCheck call
                        blockData(iBlock).resps(iTrial) = find(keyCode,1); %#ok<AGROW>
                        Screen('FillRect',mainWindow,backColor);
                        if (stimOn) % leave image up if response before image duration
                            Screen('DrawTexture',mainWindow,imageTex,imageRect,centerRect);
                        end
                        Screen(mainWindow,'FillOval',respColor,fixDotRect);
                        Screen('Flip',mainWindow);
                    end
                end
            end
        end
        
        %accuracy
        if ~isnan(blockData(iBlock).corrresps(iTrial)) %go trial
            if (blockData(iBlock).resps(iTrial)==blockData(iBlock).corrresps(iTrial)) %made correct response
                blockData(iBlock).accs(iTrial) = 1; %#ok<AGROW>
            else
                blockData(iBlock).accs(iTrial) = 0; %#ok<AGROW>
            end
        else %nogo trial
            if isnan(blockData(iBlock).resps(iTrial)) %correctly did NOT make a response
                blockData(iBlock).accs(iTrial) = 2; %#ok<AGROW>
            else %made a response
                blockData(iBlock).accs(iTrial) = 0; %#ok<AGROW>
            end
        end
        
        
        % print trial results
        fprintf(dataFile,'%d\t%d\t%s\t%s\t%d\t%.3f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n',runNum,iBlock,typeStr{blockData(iBlock).type},categStr{blockData(iBlock).attCateg},iTrial,blockData(iBlock).actualtrialonsets(iTrial)-blockData(iBlock).plannedtrialonsets(iTrial),blockData(iBlock).pulses(iTrial),blockData(iBlock).categs{SCENE}(iTrial),blockData(iBlock).categs{FACE}(iTrial),blockData(iBlock).images{SCENE}(iTrial),blockData(iBlock).images{FACE}(iTrial),blockData(iBlock).corrresps(iTrial),blockData(iBlock).resps(iTrial),blockData(iBlock).accs(iTrial),blockData(iBlock).rts(iTrial),NaN,NaN,NaN,blockData(iBlock).attImgProp(iTrial),NaN);
        fprintf('%d\t%d\t%s\t%s\t%d\t%.3f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n',runNum,iBlock,typeStr{blockData(iBlock).type},categStr{blockData(iBlock).attCateg},iTrial,blockData(iBlock).actualtrialonsets(iTrial)-blockData(iBlock).plannedtrialonsets(iTrial),blockData(iBlock).pulses(iTrial),blockData(iBlock).categs{SCENE}(iTrial),blockData(iBlock).categs{FACE}(iTrial),blockData(iBlock).images{SCENE}(iTrial),blockData(iBlock).images{FACE}(iTrial),blockData(iBlock).corrresps(iTrial),blockData(iBlock).resps(iTrial),blockData(iBlock).accs(iTrial),blockData(iBlock).rts(iTrial),NaN,NaN,NaN,blockData(iBlock).attImgProp(iTrial),NaN);
        
    end % trial loop

    Screen('FillRect',mainWindow,backColor);
    Screen(mainWindow,'FillOval',fixColor,fixDotRect);
    % the IBI goes here!
    if rtData
        [timing.trig.IBIpulses(iBlock),blockData(iBlock).IBIpulses] = WaitTRPulse(TRIGGER_keycode,DEVICE,blockData(iBlock).plannedIBI);
    end
    timespec = blockData(iBlock).plannedIBI -slack;
    blockData(iBlock).actualIBI = Screen('Flip',mainWindow,timespec);
    fprintf('Flip time error = %.4f\n', blockData(iBlock).actualIBI-blockData(iBlock).plannedIBI)
end % end phase 1 block loop


%% pause & wait for model to be trained
timing.plannedreston = blockData(iBlock).plannedIBI + TR*IBI;
timing.plannedrestoff = timing.plannedreston + restDur;

% show instructions-wait for first trigger
if rtData
[timing.trig.pulserest,timing.pulsereston] = WaitTRPulse(TRIGGER_keycode,DEVICE,timing.plannedreston);
end
tempBounds = Screen('TextBounds',mainWindow,restInstruct);
Screen('drawtext',mainWindow,restInstruct,centerX-tempBounds(3)/2,centerY-tempBounds(4)/5,textColor);
clear tempBounds;
timespec = timing.plannedreston - slack;
timing.actualreston = Screen('Flip',mainWindow,timespec); % show instructions
fprintf('Flip time error = %.4f\n', timing.actualreston-timing.plannedreston)

% show fixation
Screen(mainWindow,'FillRect',backColor);
Screen(mainWindow,'FillOval',fixColor,fixDotRect);
timespec = timing.plannedrestoff - slack;
timing.actualrestoff = Screen('Flip',mainWindow,timespec); %turn off

%% Block Sequence - Phase2

% prepare for trial sequence
fprintf(dataFile,'run\tblock\tloadsep\tblcat\ttrial\tonsdif\tscat\tfcat\tsimg\tfimg\tcorresp\tresp\tacc\trt\tfile\tload\tcatsep\tattProp\tsmoothProp\n');
fprintf('run\tblock\tloadsep\tblcat\ttrial\tonsdif\tscat\tfcat\tsimg\tfimg\tcorresp\tresp\tacc\trt\tfile\tload\tcatsep\tattProp\tsmoothProp\n');

trialCounter = 0;
volCounter = firstVolPhase2+disdaqs/TR-1;

for iBlock=indBlocksPhase2

    if ~isfield(blockData,'categsep')
        blockData(iBlock).categsep = NaN(1,blockData(iBlock).trialsPerBlock); %#ok<AGROW>
    end
    
    volCounter = volCounter+1;
    
    % timing
    blockData(iBlock).actualblockonset = GetSecs; %#ok<AGROW>
    blockData(iBlock).plannedinstructonset = blockOnsets(iBlock)+runStart; %#ok<AGROW>
    blockData(iBlock).plannedinstructoffset = blockData(iBlock).plannedinstructonset + instructDur;
    blockData(iBlock).plannedtrialonsets = blockData(iBlock).plannedinstructonset + TR*instructTRnum + [0 cumsum(repmat(TR/nTrialsPerTR,1,blockData(iBlock).trialsPerBlock))]; % so this says start on the next TR
    blockData(iBlock).plannedIBI = blockData(iBlock).plannedtrialonsets(blockData(iBlock).trialsPerBlock) + stimDur;
    % show instructions
    tempBounds = Screen('TextBounds',mainWindow,blockInstruct{blockData(iBlock).attCateg});
    Screen('drawtext',mainWindow,blockInstruct{blockData(iBlock).attCateg},centerX-tempBounds(3)/2,centerY-tempBounds(4)/5,textColor);
    clear tempBounds;
    timespec = blockData(iBlock).plannedinstructonset - slack;
    if rtData
        [timing.trig.instructpulses(iBlock),blockData(iBlock).instructpulses] = WaitTRPulse(TRIGGER_keycode,DEVICE,blockData(iBlock).plannedinstructonset);
    end
    blockData(iBlock).actualinstructonset = Screen('Flip',mainWindow,timespec); %#ok<AGROW> % turn on
    fprintf('Flip time error = %.4f\n', blockData(iBlock).actualinstructonset-blockData(iBlock).plannedinstructonset)
    % show fixation
    timespec = blockData(iBlock).plannedinstructoffset - slack;
    Screen(mainWindow,'FillOval',fixColor,fixDotRect);
    blockData(iBlock).actualinstructoffset = Screen('Flip',mainWindow,timespec); %turn off
    
    % start trial sequence
    for iTrial=1:(blockData(iBlock).trialsPerBlock)
        
        blockData(iBlock).tr1(iTrial) = GetSecs;
        trialCounter = trialCounter+1;
        if (mod(iTrial,nTrialsPerTR)==1) 
            volCounter = volCounter+1;
        end
        blockData(iBlock).volCounter(iTrial) = volCounter; %#ok<AGROW>
        
        % prep images
        for half=[SCENE FACE]
            % get current images
            tempPower{half} = imagePower{blockData(iBlock).categs{half}(iTrial),blockData(iBlock).images{half}(iTrial)}; %#ok<AGROW>
            tempImagePhase{half} = imagePhase{blockData(iBlock).categs{half}(iTrial),blockData(iBlock).images{half}(iTrial)}; %#ok<AGROW>
            tempImage{half} = real(ifft2(tempPower{half}.*exp(sqrt(-1)*tempImagePhase{half}))); %#ok<AGROW>
        end
        
        if iTrial <= nTrialsPerTR %initialize attImgProp for first 2 trials
            if iTrial == 1
                if blockData(iBlock).attCateg == FACE
                    attImgPropPhase2 = faceProp;
                else % attend to scene
                    attImgPropPhase2 = sceneProp;
                end
                blockData(iBlock).attImgProp(iTrial) = attImgPropPhase2; %#ok<AGROW>
                blockData(iBlock).smoothAttImgProp(iTrial) = attImgPropPhase2; %#ok<AGROW>
            end
            blockData(iBlock).attImgProp(iTrial+1) = attImgPropPhase2; %#ok<AGROW>
            blockData(iBlock).smoothAttImgProp(iTrial+1) = attImgPropPhase2; %#ok<AGROW>
        end
        
        % generate image
        fullImage = uint8((1-blockData(iBlock).smoothAttImgProp(iTrial))*tempImage{blockData(iBlock).inattCateg}+blockData(iBlock).smoothAttImgProp(iTrial)*tempImage{blockData(iBlock).attCateg});
        
        % make textures
        imageTex = Screen('MakeTexture',mainWindow,fullImage);
        Screen('PreloadTextures',mainWindow,imageTex);
        
        % wait for trigger and show image
        FlushEvents('keyDown');
        Priority(MaxPriority(screenNum));
        Screen('FillRect',mainWindow,backColor);
        Screen('DrawTexture',mainWindow,imageTex,imageRect,centerRect);
        Screen(mainWindow,'FillOval',fixColor,fixDotRect);
        
        blockData(iBlock).tprep(iTrial) = GetSecs;
        tRespTimeout = blockData(iBlock).plannedtrialonsets(iTrial)+respWindow;
        
        %wait for pulse
        if (rtData) && mod(iTrial,nTrialsPerTR) % this will be true for every other then
            %[~,blockData(iBlock).pulses(iTrial)] = WaitTRPulsePTB3_skyra(1,blockData(iBlock).plannedtrialonsets(iTrial)+allowance); %#ok<AGROW>
            [timing.trig.pulses(iBlock,iTrial),blockData(iBlock).pulses(iTrial)] = WaitTRPulse(TRIGGER_keycode,DEVICE,blockData(iBlock).plannedtrialonsets(iTrial));
            timespec = blockData(iBlock).plannedtrialonsets(iTrial) - slack;
            blockData(iBlock).actualtrialonsets(iTrial) = Screen('Flip',mainWindow,timespec); %#ok<AGROW> % turn on
        else
            blockData(iBlock).pulses(iTrial) = 0; %#ok<AGROW>
            timespec = blockData(iBlock).plannedtrialonsets(iTrial) - slack;
            blockData(iBlock).actualtrialonsets(iTrial) = Screen('Flip',mainWindow,timespec); %#ok<AGROW>
        end
        
        stimOn = 1;
        FlushEvents('keyDown');
        while(GetSecs < tRespTimeout)
            
            % check for responses if none received yet
            if isnan(blockData(iBlock).rts(iTrial))
                [keyIsDown, secs, keyCode] = KbCheck(DEVICE); % -1 checks all keyboards
                if keyIsDown
                    if (keyCode(LEFT))
                        blockData(iBlock).rts(iTrial) = secs-blockData(iBlock).actualtrialonsets(iTrial); %#ok<AGROW> NTB: deltasecs is timed to last KbCheck call
                        blockData(iBlock).resps(iTrial) = find(keyCode,1); %#ok<AGROW>
                        Screen('FillRect',mainWindow,backColor);
                        if (stimOn) % leave image up if response before image duration
                            Screen('DrawTexture',mainWindow,imageTex,imageRect,centerRect);
                        end
                        Screen(mainWindow,'FillOval',respColor,fixDotRect);
                        Screen('Flip',mainWindow);
                    end
                end
            end
        end
        
        %accuracy
        if ~isnan(blockData(iBlock).corrresps(iTrial)) %go trial
            if (blockData(iBlock).resps(iTrial)==blockData(iBlock).corrresps(iTrial)) %made correct response
                blockData(iBlock).accs(iTrial) = 1; %#ok<AGROW>
            else
                blockData(iBlock).accs(iTrial) = 0; %#ok<AGROW>
            end
        else %nogo trial
            if isnan(blockData(iBlock).resps(iTrial)) %correctly did NOT make a response
                blockData(iBlock).accs(iTrial) = 2; %#ok<AGROW>
            else %made a response
                blockData(iBlock).accs(iTrial) = 0; %#ok<AGROW>
            end
        end
        blockData(iBlock).tr2(iTrial) = GetSecs;

        %load rtfeedback values once per TR
        blockData(iBlock).RT1(iTrial) = GetSecs;
        FILEFOUND = 'NOSEP';
        if rtfeedback
            % will start looking at the odd TR numbers on 
            if (mod(iTrial,nTrialsPerTR)==1) && (iTrial>nTrialsPerTR)
                %number of odd trials - paired with TRs
                iTrialOdd = ceil(iTrial/2);
                
                %preset the file load to 0 and the timeout
                blockData(iBlock).classOutputFileLoad(iTrial) = 0; %#ok<AGROW>
                tClassOutputFileTimeout = GetSecs + deltat;
                
                %check for classifier output file
                timing.classifierLoadStart(iBlock,iTrial)=GetSecs;
                while (~blockData(iBlock).classOutputFileLoad(iTrial) && (GetSecs < tClassOutputFileTimeout))
                    [blockData(iBlock).classOutputFileLoad(iTrial) blockData(iBlock).classOutputFile{iTrial}] = GetSpecificClassOutputFile(classOutputDir,volCounter-2,usePyOutput); %#ok<AGROW>
                end
               timing.classifierLoadEnd(iBlock,iTrial)=GetSecs; 
                % get newest file in that TR
                blockData(iBlock).fileList{iTrial} = ls(classOutputDir);
                if ~usePyOutput
                    allFn = dir([classOutputDir '/vol' '*.mat']);
                else
                    allFn = dir([classOutputDir '/vol' '*_py.txt']);
                end
                dates = [allFn.datenum];
                names = {allFn.name};
                [~,newestIndex] = max(dates);
                if ~isempty(ls(classOutputDir))
                    blockData(iBlock).newestFile{iTrial} = names{newestIndex};
                end
                %load classifier output file
                if blockData(iBlock).classOutputFileLoad(iTrial)
                    tempStruct = load([classOutputDir '/' blockData(iBlock).classOutputFile{iTrial}]);
                    if ~usePyOutput
                        blockData(iBlock).categsep(iTrial) = tempStruct.classOutput; %#ok<AGROW>
                    else
                        blockData(iBlock).categsep(iTrial) = tempStruct;
                    end
                    FILEFOUND = 'FSEP';
                else
                    blockData(iBlock).classOutputFile{iTrial} = 'notload'; %#ok<AGROW>
                end
                
                %constrain the proportion of attended image
                if isnan(blockData(iBlock).categsep(iTrial)) %attImgProp for that trial for some reason was NaN
                    tempLastClassOutput = find(~isnan(blockData(iBlock).categsep),1,'last');
                    if ~isempty(tempLastClassOutput)
                        blockData(iBlock).attImgProp(iTrial+1) = blockData(iBlock).attImgProp(tempLastClassOutput); %#ok<AGROW>
                    else
                        blockData(iBlock).attImgProp(iTrial+1) = attImgPropPhase2; %#ok<AGROW>
                    end
%                      %******* SET DEMO AMOUNTS--DELETE THIS AFTERWARDS!!! ****
%                     vals = linspace(0,.8,25);
%                     blockData(iBlock).attImgProp(iTrial+1) = vals(iTrialOdd);
%                      %******* SET DEMO AMOUNTS--DELETE THIS AFTERWARDS!!! ****
                else
                    blockData(iBlock).attImgProp(iTrial+1) = steepness./(1+exp(-gain*(blockData(iBlock).categsep(iTrial)-x_shift)))+y_shift; %#ok<AGROW>
                    
                end
                
                %set for next trial
                if ((iTrial+2)<blockData(iBlock).trialsPerBlock)
                    blockData(iBlock).attImgProp(iTrial+2) = blockData(iBlock).attImgProp(iTrial+1); %#ok<AGROW>
                end
                
                %smooth the trials
                if iTrialOdd == 2
                    blockData(iBlock).smoothAttImgProp(2,iTrialOdd) = .5*blockData(iBlock).attImgProp(2,iTrialOdd-1)+.5*blockData(iBlock).attImgProp(2,iTrialOdd); %#ok<AGROW>
                else
                    blockData(iBlock).smoothAttImgProp(2,iTrialOdd) = (1/3)*blockData(iBlock).attImgProp(2,iTrialOdd-2)+(1/3)*blockData(iBlock).attImgProp(2,iTrialOdd-1)+(1/3)*blockData(iBlock).attImgProp(2,iTrialOdd); %#ok<AGROW>
                end
                
                %set for next trial
                if ((iTrial+2)<=blockData(iBlock).trialsPerBlock)
                    blockData(iBlock).smoothAttImgProp(iTrial+2) = blockData(iBlock).smoothAttImgProp(iTrial+1); %#ok<AGROW>
                end
            else
                blockData(iBlock).classOutputFile{iTrial} = '12orev'; %#ok<AGROW>
            end
        else
            if ((iTrial+1)<=blockData(iBlock).trialsPerBlock)
                blockData(iBlock).attImgProp(iTrial+1) = attImgPropPhase2; %#ok<AGROW>
                blockData(iBlock).smoothAttImgProp(iTrial+1)= attImgPropPhase2; %#ok<AGROW>
            end
            if ((iTrial+2)<=blockData(iBlock).trialsPerBlock-2)
                blockData(iBlock).attImgProp(iTrial+2) = attImgPropPhase2; %#ok<AGROW>
                blockData(iBlock).smoothAttImgProp(iTrial+2)= attImgPropPhase2; %#ok<AGROW>
            end
          
            blockData(iBlock).classOutputFile{iTrial} = 'notrt'; %#ok<AGROW>
            blockData(iBlock).classOutputFile{iTrial} = NaN; %#ok<AGROW>
        end
        blockData(iBlock).RT2(iTrial) = GetSecs;  
        % print trial results
        fprintf(dataFile,'%d\t%d\t%s\t%s\t%d\t%.3f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%.3f\t%d\t%d\t%.3f\t%.3f\t%.3f\n',runNum,iBlock,FILEFOUND,categStr{blockData(iBlock).attCateg},iTrial,blockData(iBlock).actualtrialonsets(iTrial)-blockData(iBlock).plannedtrialonsets(iTrial),blockData(iBlock).categs{SCENE}(iTrial),blockData(iBlock).categs{FACE}(iTrial),blockData(iBlock).images{SCENE}(iTrial),blockData(iBlock).images{FACE}(iTrial),blockData(iBlock).corrresps(iTrial),blockData(iBlock).resps(iTrial),blockData(iBlock).accs(iTrial),blockData(iBlock).rts(iTrial),blockData(iBlock).volCounter(iTrial),blockData(iBlock).classOutputFileLoad(iTrial),blockData(iBlock).categsep(iTrial),blockData(iBlock).attImgProp(iTrial),blockData(iBlock).smoothAttImgProp(iTrial));
        fprintf('%d\t%d\t%s\t%s\t%d\t%.3f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%.3f\t%d\t%d\t%.3f\t%.3f\t%.3f\n',runNum,iBlock,FILEFOUND,categStr{blockData(iBlock).attCateg},iTrial,blockData(iBlock).actualtrialonsets(iTrial)-blockData(iBlock).plannedtrialonsets(iTrial),blockData(iBlock).categs{SCENE}(iTrial),blockData(iBlock).categs{FACE}(iTrial),blockData(iBlock).images{SCENE}(iTrial),blockData(iBlock).images{FACE}(iTrial),blockData(iBlock).corrresps(iTrial),blockData(iBlock).resps(iTrial),blockData(iBlock).accs(iTrial),blockData(iBlock).rts(iTrial),blockData(iBlock).volCounter(iTrial),blockData(iBlock).classOutputFileLoad(iTrial),blockData(iBlock).categsep(iTrial),blockData(iBlock).attImgProp(iTrial),blockData(iBlock).smoothAttImgProp(iTrial));

    end % trial loop
    
    volCounter = volCounter+2;
    
    
    Screen('FillRect',mainWindow,backColor);
    Screen(mainWindow,'FillOval',fixColor,fixDotRect);
    if rtData
        [timing.trig.IBIpulses(iBlock),blockData(iBlock).IBIpulses] = WaitTRPulse(TRIGGER_keycode,DEVICE,blockData(iBlock).plannedIBI);
    end
    timespec = blockData(iBlock).plannedIBI -slack;
    blockData(iBlock).actualIBI = Screen('Flip',mainWindow,timespec);
    fprintf('Flip time error = %.4f\n', blockData(iBlock).actualIBI-blockData(iBlock).plannedIBI)
end % phase 2 block loop
% want to wait 7 TRS--2 IBIs and then 5 more TRs
WaitSecs(14);

%% save
% question: do you want to save it to this computer's data or where you
% save the data folder???
save([runHeader '/blockdata_' num2str(runNum) '_' datestr(now,30)],'blockData','runStart', 'timing');

% clean up and go home
sca;
ListenChar(1);
fclose('all');
end