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runExperiment.m
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% ========================================================================
classdef runExperiment < optickaCore
%> @class runExperiment
%> @brief The main experiment manager.
%>
%> RUNEXPERIMENT accepts a variable sequence « taskSequence », stimulus set «
%> metaStimulus » and for behavioural tasks a « stateMachine » state machine
%> file, and runs the stimuli based on the task objects passed. This class uses
%> the fundamental configuration of the screen (calibration, size etc. via «
%> screenManager »), and manages communication to a DAQ systems using digital I/O
%> and communication over a TCP/UDP client⇄server socket (via «dataConnection»).
%> It also interfaces with hardware like eyetrackers
%>
%> There are 2 main experiment types:
%> 1) MOC (method of constants) tasks -- uses stimuli and task objects
%> directly to run standard randomised variable tasks. See optickatest.m
%> for an example. Does not use the «stateMachine».
%> 2) Behavioural tasks that use state machines for control logic. These
%> tasks still use stimuli and task objects to provide stimuli and
%> variable lists, but use a state machine to control the task
%> structure.
%>
%> Stimuli should be «metaStimulus» class, so for example:
%>
%> ```
%> myStim = metaStimulus;
%> myStim{1} = gratingStimulus('mask',true,'sf',1);
%> task = taskSequence; % this creates randomised variable lists
%> task.nVar = struct('name','angle','stimulus',1,'values',[-90 0 90]);
%> myExp = runExperiment('stimuli', myStim,'task', task);
%> runMOC(myExp); % run method of constants type experiment
%> ```
%>
%> will run a minimal experiment showing a 1c/d circularly masked grating.
%>
%> @todo refactor checkKey(): can we use a config for keyboard commands?
%>
%> Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
% ========================================================================
properties
%> subject name
subjectName char = 'Simulcra'
%> researcher name
researcherName char = 'Jane Doe'
%> a metaStimulus class instance holding our stimulus objects
stimuli metaStimulus
%> a taskSequence class instance determining our stimulus variables
task taskSequence
%> a screenManager class instance managing the PTB Screen
screen screenManager
%> filename for a stateMachine state info file
stateInfoFile char = ''
%> user functions file that can be passed to the state machine
userFunctionsFile char = ''
%> what strobe device to use
%> device = display++ | datapixx | labjackt | labjack | arduino
%> optional port = not needed for most of the interfaces
%> optional config = plain | plexon style strobe
%> optional stim OFF strobe value used for MOC tasks
strobe struct = struct('device','','port','',...
'mode','plain','stimOFFValue',255)
%> what reward device to use
reward struct = struct('device','','port','',...
'board','');
%> which eyetracker to use
eyetracker struct = struct('device','','dummy',true,...
'esettings',[],'tsettings',[])
%> use control commands to start / stop recording
%> device = intan | plexon | none
%> port = tcp port
control struct = struct('device','','port','127.0.0.1:5000')
%> Keyboard device, use -1 for all keyboards (slower) or [] for
%> default
keyboardDevice = [];
%> log all frame times?
logFrames logical = true
%> enable debugging? (poorer temporal fidelity)
debug logical = false
%> flip as fast as possible?
benchmark logical = false
%> verbose logging to command window?
verbose = false
end
properties (Transient = true)
%> structure for screenManager on initialisation and info from opticka
screenSettings struct = struct()
%> this lets the opticka UI leave commands to runExperiment
uiCommand char = ''
%> return if runExperiment is running (true) or not (false)
isRunning logical = false
end
properties (Hidden = true)
%> draw simple fixation cross during trial for MOC tasks?
drawFixation logical = false
%> shows the info text and position grid during stimulus presentation
visualDebug logical = false
%> used to select single stimulus in training mode
stimList = []
%> which stimulus is selected?
thisStim = []
%> tS is the runtime settings structure, saved here as a backup
tS struct
%> what mode to run the Display++ digital I/O in? Plexon requires
%> the use of a strobe trigger line, whereas most other equipment
%> just uses simple threshold reading
dPPMode char = 'plain'
%> which port is the arduino on?
arduinoPort char = ''
%> show a white square in the top-right corner to trigger a photodiode
%> attached to screen for MOC task. For stateMachine tasks you need
%> to pass in the drawing command for this to take effect.
photoDiode logical = false
%> turn diary on for runTask, saved to the same folder as the data
diaryMode logical = false
%> opticka version, passed on first use by opticka
optickaVersion char
%> do we record times for every function run by state machine?
logStateTimers logical = false
%> do we ask for comments for runMOC
comments logical = true
%> our old stimulus structure used to be a simple cell, now we use metaStimulus
stimulus
%> audio device
audioDevice = []
end
properties (Transient = true, Hidden = true)
%> keep track of several task values during runTask()
lastXPosition = 0
lastYPosition = 0
lastXExclusion = []
lastYExclusion = []
lastSize = 1
lastIndex = 0
end
properties (SetAccess = private, GetAccess = public)
%> log of timings for MOC tasks
runLog
%> log of timings for state machine tasks
taskLog
%> behavioural responses log
behaviouralRecord
%> stateMachine object
stateMachine
%> eyetracker manager object
eyeTracker
%> generic IO manager
io
%> DataPixx control object
dPixx
%> Display++ control object
dPP
%> LabJack control object
lJack
%> Arduino control object
arduino
%> user functions object
userFunctions
%> data connection
dC
%> state machine control cell array
stateInfo cell = {}
%> general computer info retrieved using PTB Screen('computer')
computer
%> PTB version information: Screen('version')
ptb
%> copy of screen settings from screenManager
screenVals struct
%> previous info populated during load of a saved object
previousInfo struct = struct()
end
properties (SetAccess = private, GetAccess = private)
pauseToggle = 0
%> general info on current run
currentInfo
%> variable info on the current run
variableInfo
%> send a strobe on next flip?
sendStrobe logical = false
%> need an eyetracker sample on next flip?
needSample logical = false
%> send an eyetracker SYNCTIME on next flip?
sendSyncTime logical = false
%> do we flip the screen or not?
doFlip logical = true
%> do we flip the eyetracker window? 0=no 1=yes 2=yes+clear
doTrackerFlip double = 0;
%> is it MOC run (false) or stateMachine runTask (true)?
isRunTask logical = true
%> are we using taskSequeence or not?
isTask logical = true
%> should we stop the task?
stopTask logical = false
%> prestimuli
stimShown = false
%> properties allowed to be modified during construction
allowedProperties = {'reward','strobe','eyetracker','control',...
'logFrames','logStateTimers','subjectName','researcherName'...
'stateInfoFile','userFunctionFile','dummyMode','stimuli','task',...
'screen','visualDebug','debug','verbose','screenSettings','benchmark',...
'comments','arduinoPort','photoDiode'}
end
%=======================================================================
methods %------------------PUBLIC METHODS
%=======================================================================
% ===================================================================
function me = runExperiment(varargin)
%> @fn runExperiment
%>
%> runExperiment CONSTRUCTOR
%>
%> @param varargin can be passed as a structure or name,arg pairs
%> @return instance of the class.
% ===================================================================
args = optickaCore.addDefaults(varargin,struct('name','Run Experiment'));
me=me@optickaCore(args); %superclass constructor
me.parseArgs(args,me.allowedProperties);
end
% ===================================================================
function runMOC(me, tS)
%> @fn runMOC
%>
%> runMOC uses built-in loop for experiment control and runs a
%> methods-of-constants (MOC) experiment with the settings passed to
%> it (stimuli,task and screen). This is different to the runTask
%> method as it doesn't use a stateMachine for experimental logic,
%> just a minimal deterministic trial+block loop.
%>
%> @todo currently we can only record eye positions with the
%> eyelink, add other tracker support
%>
%> @param me required class object
%> @param tS structure with some options to pass
% ===================================================================
%------initialise the rewardManager global object
[rM] = initialiseGlobals(me);
if rM.isOpen
try rM.close; rM.reset; end
end
try
if isfield(me.reward,'port') && ~isempty(me.reward.port); rM.port = me.reward.port; end
if isfield(me.reward,'board') && ~isempty(me.reward.board); rM.board = me.reward.board; end
end
refreshScreen(me);
initialiseSaveFile(me); %generate a savePrefix for this run
me.name = [me.subjectName '-' me.savePrefix]; %give us a run name
if isempty(me.screen) || isempty(me.task)
me.initialise; %we set up screenManager and taskSequence objects
end
if me.screen.isPTB == false %NEED PTB!
errordlg('There is no working PTB available!')
error('There is no working PTB available!')
end
%===============================enable diary logging if requested
if me.diaryMode
diary off
diary([me.paths.savedData filesep me.name '.log']);
end
%===============================enable diary logging if requested
if me.diaryMode
diary off
diary([me.paths.savedData filesep me.name '.log']);
end
%===============================initialise runLog for this run
me.previousInfo.runLog = [];
me.runLog = [];
me.taskLog = []; clear timeLogger;
me.runLog = timeLogger();
tL = me.runLog;
tL.name = me.name;
if me.logFrames
tL.preAllocate(me.screenVals.fps*60*15);
end
%===============================make a short handle to the screenManager and metaStimulus objects
me.stimuli.screen = me.screen;
s = me.screen;
stims = me.stimuli;
if ~exist('tS','var') || isempty(tS)
tS.controlPlexon = false;
tS.askForComments = true;
end
if ~isfield(tS,'controlPlexon'); tS.controlPlexon = false; end
if ~isfield(tS,'askForComments'); tS.askForComments = true; end
%===============================initialise task
task = me.task;
initialise(task, true);
%-----------------------------------------------------------
try%======This is our main TRY CATCH experiment display loop
%-----------------------------------------------------------
me.lastIndex = 0;
me.isRunning = true;
me.isRunTask = false;
%================================get pre-run comments for this data collection
if tS.askForComments && ~me.debug
comment = inputdlg({'CHECK Recording system!!! Initial Comment for this Run?'},['Run Comment for ' me.name]);
if ~isempty(comment)
comment = comment{1};
me.comment = [me.name ':' comment];
bR.comment = me.comment; eT.comment = me.comment; sM.comment = me.comment; io.comment = me.comment; tL.comment = me.comment; tS.comment = me.comment;
end
end
%=============================Premptive save in case of crash or error: SAVES IN /TMP
rE = me;
tS.tmpFile = [tempdir filesep me.name '.mat'];
fprintf('===>>> Save initial state: %s\n',tS.tmpFile);
save(tS.tmpFile,'rE','tS');
%================================open the PTB screen and setup stimuli
me.screenVals = s.open(me.debug,tL);
stims.verbose = me.verbose;
task.fps = me.screenVals.fps;
setup(stims, s); %run setup() for each stimulus
if s.movieSettings.record; prepareMovie(s); end
%================================initialise and set up I/O
io = configureIO(me); %#ok<*PROPLC>
dC = dataConnection('protocol','tcp');
%========================================Start amplifier
%
if strcmp(me.control.device,'intan')
addr = strsplit(me.control.port,':');
dC.rAddress = addr{1};
dC.rPort = addr{2};
try
open(dC);
write(dC,uint8(['set Filename.BaseFilename ' me.name]));
write(dC,uint8(['set Filename.Path ' 'C:/OptickaFiles']));
write(dC,uint8('set runmode run'));
catch
warning('runTask cannot contact intan!!!')
me.control.device = '';
end
elseif strcmp(me.control.device,'plexon')
if strcmp(me.strobe.device,'datapixx') || strcmp(me.strobe.device,'display++')
startRecording(io);
WaitSecs(0.5);
resumeRecording(io);
elseif strcmp(me.strobe.device,'labjack')
% Trigger the omniplex (TTL on FIO1) into paused mode
io.setDIO([2,0,0]);WaitSecs(0.001);io.setDIO([0,0,0]);
WaitSecs(0.5);
io.setDIO([3,0,0],[3,0,0])%(Set HIGH FIO0->Pin 24), unpausing the omniplex
end
end
%=========================================================
% lets draw 2 seconds worth of the stimuli we will be using
% covered by a blank. Primes the GPU and other components with the sorts
% of stimuli/tasks used and this does appear to minimise
% some of the frames lost on first presentation for very complex
% stimuli using 32bit computation buffers...
fprintf('\n===>>> Warming up the GPU and I/O systems... <<<===\n')
show(stims);
for i = 1:s.screenVals.fps*2
draw(stims);
drawBackground(s);
drawText(s,'Warming up the GPU, Eyetracker and I/O systems...');
s.drawPhotoDiodeSquare([0 0 0 1]);
finishDrawing(s);
animate(stims);
if ~mod(i,10); io.sendStrobe(me.strobe.stimOFFValue); end
flip(s);
optickaCore.getKeys();
end
update(stims); %make sure stimuli are set back to their start state
if ismethod(me,'resetLog'); resetLog(me); end
io.resetStrobe;flip(s);flip(s);
tL.screenLog.beforeDisplay = GetSecs();
%===========================double check the labJackT handle is still valid
if isa(io,'labJackT') && io.isOpen && ~io.isHandleValid
io.close;
io.open;
disp('We had to reopen the labJackT to ensure a stable connection...')
end
%=============================profiling starts here if uncommented
%profile clear; profile on;
%===========================take over the keyboard + max priority
KbReleaseWait; %make sure keyboard keys are all released
if me.debug == false
%warning('off'); %#ok<*WNOFF>
ListenChar(-1); %2=capture all keystrokes
end
if ~isdeployed
try commandwindow; end
end
Priority(MaxPriority(s.win)); %bump our priority to maximum allowed
%================================Set state for first trial
me.updateMOCVars(1,1); %------set the variables for the very first run
task.isBlank = true;
task.tick = 1;
task.switched = 1;
task.totalRuns = 1;
tL.t.miss(1) = 0;
tL.t.stimTime(1) = 0;
tL.t.vbl(1) = Screen('Flip', s.win);
tL.lastvbl = tL.vbl(1);
tL.startTime = tL.lastvbl;
tL.screenLog.beforeDisplay = tL.lastvbl;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% DISPLAY LOOP
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
while ~task.taskFinished
if task.isBlank
if me.photoDiode;s.drawPhotoDiodeSquare([0 0 0 1]); end
else
draw(stims);
if me.photoDiode;s.drawPhotoDiodeSquare([1 1 1 1]); end
end
if s.visualDebug; s.drawGrid; me.infoTextScreen; end
Screen('DrawingFinished', s.win); % Tell PTB that no further drawing commands will follow before Screen('Flip')
%========= check for keyboard if in blank ========%
if task.isBlank
if strcmpi(me.uiCommand,'stop');break; end
[~,name,~] = optickaCore.getKeys(me.keyboardDevice);
if strcmpi(name,'q'); break; end
end
%================= UPDATE TASK ===================%
updateMOCTask(me,tL.lastvbl); %update our task structure
%=======Display++ or DataPixx: I/O send strobe
% command for this screen flip needs to be sent
% PRIOR to the flip! Also remember DPP will be
% delayed by one flip
if me.sendStrobe && matches(me.strobe.device,'display++')
sendStrobe(io); me.sendStrobe = false;
elseif me.sendStrobe && matches(me.strobe.device,'datapixx')
triggerStrobe(io); me.sendStrobe = false;
end
%======= FLIP: Show it at correct retrace: ========%
nextvbl = tL.lastvbl + me.screenVals.halfisi;
if me.logFrames == true
[tL.t.vbl(task.tick),tL.t.show(task.tick), ...
tL.t.flip(task.tick),tL.t.miss(task.tick)] ...
= Screen('Flip', s.win, nextvbl);
tL.lastvbl = tL.t.vbl(task.tick);
elseif ~me.benchmark
[tL.t.vbl, tL.t.show, tL.t.flip, tL.t.miss] ...
= Screen('Flip', s.win, nextvbl);
tL.lastvbl = tL.t.vbl;
else
tL.t.vbl = Screen('Flip', s.win, 0, 2, 2);
tL.lastvbl = tL.t.vbl;
end
%======LabJack: I/O needs to send strobe immediately after screen flip -----%
if me.sendStrobe && matches(me.strobe.device,'labjackt')
sendStrobe(io); me.sendStrobe = false;
end
%===================Logging=======================%
if task.tick == 1 && ~me.benchmark
tL.startTime = tL.t.vbl(1); %respecify this with actual stimulus vbl
task.startTime = tL.startTime; %respecify this with actual stimulus vbl
end
if me.logFrames
if ~task.isBlank
tL.t.stimTime(task.tick)=1+task.switched;
else
tL.t.stimTime(task.tick)=0-task.switched;
end
end
if s.movieSettings.record ...
&& ~task.isBlank ...
&& (s.movieSettings.loop <= s.movieSettings.nFrames)
s.addMovieFrame();
end
%===================Tick tock!=======================%
task.tick=task.tick+1; tL.tick = task.tick;
end
%==================================================================%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Finished display loop
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%==================================================================%
ListenChar(0);
drawBackground(s);
vbl=Screen('Flip', s.win);
tL.screenLog.afterDisplay=vbl;
%================================Amplifier control
if strcmp(me.control.device,'intan')
write(dC,uint8('set runmode stop'));
elseif strcmp(me.control.device,'plexon')
if strcmp(me.strobe.device,'datapixx') || strcmp(me.strobe.device,'display++')
pauseRecording(io);
WaitSecs(0.25)
stopRecording(io);
elseif strcmp(me.strobe.device,'labjack')
io.setDIO([0,0,0],[1,0,0]); %this is RSTOP, pausing the omniplex
io.setDIO([2,0,0]);WaitSecs(0.05);io.setDIO([0,0,0]); %we stop recording mode completely
end
end
%-----get our profiling report for our task loop
%profile off; profile report; profile clear
tL.screenLog.deltaDispay=tL.screenLog.afterDisplay - tL.screenLog.beforeDisplay;
tL.screenLog.deltaUntilDisplay=tL.startTime - tL.screenLog.beforeDisplay;
tL.screenLog.deltaToFirstVBL=tL.vbl(1) - tL.screenLog.beforeDisplay;
if me.benchmark == true
tL.screenLog.benchmark = task.tick / (tL.screenLog.afterDisplay - tL.startTime);
fprintf('\n---> BENCHMARK FPS = %g\n', tL.screenLog.benchmark);
end
s.screenVals.info = Screen('GetWindowInfo', s.win);
try resetScreenGamma(s); end
if matches(me.eyetracker.device,'eyelink')
try close(me.eyeTracker); end
me.eyeTracker = [];
end
try finaliseMovie(s,false); end
try reset(stims); end
try close(s); end
try close(io); end
removeEmptyValues(tL);
me.tS = tS; %store our tS structure for backup
if tS.askForComments && ~me.debug
comment = inputdlg('Final Comment for this Run?','Run Comment');
if ~isempty(comment)
comment = comment{1};
me.comment = [me.comment ' | Final Comment: ' comment];
bR.comment = me.comment;
eT.comment = me.comment;
sM.comment = me.comment;
io.comment = me.comment;
tL.comment = me.comment;
tS.comment = me.comment;
end
end
%------SAVE the DATA
sname = [me.paths.savedData filesep me.name '.mat'];
rE = me;
save(sname,'rE','tS');
fprintf('\n\n#####################\n===>>> SAVED DATA to: %s\n#####################\n\n',sname)
tL.calculateMisses;
if tL.nMissed > 0
fprintf('\n!!!>>> >>> >>> There were %i MISSED FRAMES <<< <<< <<<!!!\n',tL.nMissed);
end
if s.movieSettings.record; playMovie(s); end
me.isRunning = false;
me.visualDebug = false;
catch ME
me.isRunning = false;
fprintf('\n\n---!!! ERROR in runExperiment.runMOC()\n');
if strcmp(me.control.device,'plexon')
pauseRecording(io); %pause plexon
WaitSecs(0.25)
stopRecording(io);
close(io);
end
%profile off; profile clear
warning('on');
Priority(0);
ListenChar(0);
ShowCursor;
resetScreenGamma(s);
try close(s); end
try close(me.eyeTracker); end
me.eyeTracker = [];
me.behaviouralRecord = [];
try close(rM); end
me.lJack=[];
me.io = [];
clear tL s tS bR rM eT io sM
rethrow(ME);
end
end %==============END runMOC
% ===================================================================
function runTask(me)
%> @fn runTask
%>
%> runTask runs a state machine (behaviourally) driven task.
%>
%> Uses a StateInfo.m file to control the behavioural paradigm. The
%> state machine controls the logic of the experiment, and this
%> method manages the display loop.
%>
% ===================================================================
if exist(me.stateInfoFile,'file') && contains(me.stateInfoFile, 'DefaultStateInfo') && me.stimuli.n == 0
warning('You are trying to start a Default behavioural task without stimuli!');
return
end
refreshScreen(me);
initialiseSaveFile(me); %generate a savePrefix for this run
me.comment = [me.comment ' ' me.name];
me.name = [me.subjectName '-' me.savePrefix]; %give us a run name
if isempty(me.screen) || isempty(me.task)
me.initialise; %we set up screenManager and taskSequence objects
end
if me.screen.isPTB == false %NEED PTB!
errordlg('There is no working PTB available!')
error('There is no working PTB available!')
end
%------enable diary logging if requested
if me.diaryMode
diary off
diary([me.paths.savedData filesep me.name '.log']);
end
%------make sure we reset any state machine functions to not cause
% problems when they are reassigned below. For example, io interfaces
% can be reset unless we clear this before we open the io.
me.stateInfo = {};
if isa(me.stateMachine,'stateMachine'); me.stateMachine.reset; me.stateMachine = []; end
%------initialise the rewardManager global object
[rM, aM] = initialiseGlobals(me);
if rM.isOpen
try rM.close; rM.reset; end
end
try
if isfield(me.reward,'port') && ~isempty(me.reward.port); rM.port = me.reward.port; end
if isfield(me.reward,'board') && ~isempty(me.reward.board); rM.board = me.reward.board; end
end
%------initialise an audioManager for beeps,playing sounds etc.
aM.device = me.audioDevice;
if isempty(me.audioDevice) || me.audioDevice >= 0
aM.silentMode = false;
reset(aM);
if ~aM.isSetup; try setup(aM); end; end
aM.beep(2000,0.1,0.1);
else
reset(aM);
aM.silentMode = true;
end
if isempty(regexpi(me.comment, '^Protocol','once'))
me.comment = '';
end
fprintf('\n\n\n===>>>>>> Start task: %s <<<<<<===\n\n\n',me.name);
%--------------------------------------------------------------
% tS is a general structure to hold various parameters will be saved
% after the run; prefer structure over class to keep it light. These
% defaults can be overwritten by the StateFile.m
tS = struct();
tS.runName = me.name; %==name of this run
tS.name = 'generic';%==name of this protocol
tS.useTask = false; %==use taskSequence (randomised variable task object)
tS.includeErrors = false; %==do error trials count to move taskSequence forward
tS.keyExclusionPattern = ["fixate","stimulus"]; %==which states skip keyboard check
tS.enableTrainingKeys = false; %==enable keys useful during task training, but not for data recording
tS.recordEyePosition = false; %==record eye position within PTB, **in addition** to the eyetracker?
tS.askForComments = false; %==little UI requestor asks for comments before/after run
tS.saveData = false; %==save behavioural and eye movement data?
tS.showBehaviourPlot = true; %==open the behaviourPlot figure? Can cause more memory use
tS.rewardTime = 250; %==TTL time in milliseconds
tS.rewardPin = 2; %==Output pin, 2 by default with Arduino.
tS.tOut = 5; %==if wrong response, how long to time out before next trial
tS.correctSound = [2000, 0.1, 0.1]; %==freq,length,volume
tS.errorSound = [300, 1, 1]; %==freq,length,volume
%------initialise time logs for this run
me.taskLog = []; clear timeLogger;
me.taskLog = timeLogger();
tL = me.taskLog; %short handle to log
tL.name = me.name;
if me.logFrames
tL.preAllocate(me.screenVals.fps*60*15);
end
%-----behavioural record
me.behaviouralRecord = behaviouralRecord('name',me.name); %#ok<*CPROP>
bR = me.behaviouralRecord; %short handle
%------make a short handle to the screenManager and metaStimulus objects
me.stimuli.screen = me.screen;
s = me.screen;
stims = me.stimuli;
%------initialise task
task = me.task;
initialise(task, true);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
try %================This is our main TASK setup=====================
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
me.lastIndex = 0;
me.isRunning = true;
me.isRunTask = true;
%================================open the PTB screen and setup stimuli
me.screenVals = s.open(me.debug,tL);
stims.verbose = me.verbose;
task.fps = s.screenVals.fps;
setup(stims, s);
%================================initialise and set up I/O
io = configureIO(me);
dC = me.dC;
%================================set up the eyetracker interface
configureEyetracker(me, s);
eT = me.eyeTracker;
%================================initialise the user functions object
if ~exist(me.userFunctionsFile,'file')
me.userFunctionsFile = [me.paths.root filesep 'userFunctions.m'];
end
[p,f] = fileparts(me.userFunctionsFile);
if matches(p,me.paths.root); p = me.paths.protocols; end
if ~matches(f,"userFunctions")
copyfile(me.userFunctionsFile,[p filesep 'userFunctions.m']);
run([p filesep 'userFunctions.m']);
else
run(me.userFunctionsFile)
end
me.userFunctions = ans; %#ok<NOANS>
uF = me.userFunctions;
uF.rE = me; uF.s = s; uF.task = task; uF.eT = eT;
uF.stims = stims; uF.io = io; uF.rM = rM; uF.verbose = me.verbose;
%================================initialise the state machine
me.stateMachine = [];
clear stateMachine; % this seems to improve performance with logging!!!
me.stateMachine = stateMachine('verbose', me.verbose,...
'realTime', task.realTime, 'name', me.name);
sM = me.stateMachine;
if task.realTime; sM.timeDelta = 0; else; sM.timeDelta=s.screenVals.ifi; end
sM.fnTimers = me.logStateTimers; %record fn evaluations?
if isempty(me.stateInfoFile) || ~exist(me.stateInfoFile,'file') || contains(me.stateInfoFile, ['opticka' filesep 'DefaultStateInfo.m'])
me.stateInfoFile = [me.paths.root filesep 'DefaultStateInfo.m'];
me.paths.stateInfoFile = me.stateInfoFile;
end
if ~exist(me.stateInfoFile,'file')
errordlg('runExperiment.runTask(): Please specify a valid State Machine file!!!')
else
me.stateInfoFile = regexprep(me.stateInfoFile,'\s+','\\ ');
disp(['======>>> Loading State File: ' me.stateInfoFile]);
clear(me.stateInfoFile);
if ~isdeployed
run(me.stateInfoFile);
else
runDeployed(me.stateInfoFile);
end
me.stateInfo = stateInfoTmp;
addStates(sM, me.stateInfo);
me.paths.stateInfoFile = me.stateInfoFile;
clear stateInfoTmp
end
uF.sM = sM;
me.lastXPosition = tS.fixX;
me.lastYPosition = tS.fixY;
me.lastXExclusion = [];
me.lastYExclusion = [];
me.eyetracker.name = tS.name;
if me.eyetracker.dummy; eT.isDummy = true; end %===use dummy or real eyetracker?
if tS.saveData; eT.recordData = true; end %===save Eyetracker data?
if isfield(tS,'rewardTime'); bR.rewardTime = tS.rewardTime; end
%================================get pre-run comments for this data collection
if tS.askForComments
comment = inputdlg({'CHECK Recording system!!! Initial Comment for this Run?'},['Run Comment for ' me.name]);
if ~isempty(comment)
comment = comment{1};
me.comment = [me.name ':' comment];
bR.comment = me.comment; eT.comment = me.comment; sM.comment = me.comment; io.comment = me.comment; tL.comment = me.comment; tS.comment = me.comment;
end
end
%================================raise priority
fprintf('===>>> Increasing Priority...\n');
op = Screen('Preference', 'Verbosity',4);
Priority(MaxPriority(s.win)); %bump our priority to maximum allowed
Screen('Preference', 'Verbosity',op);
%============================================================WARMUP
% lets draw ~1 seconds worth of the stimuli we will be using
% covered by a blank. This primes the GPU, eyetracker, IO
% and other components with the same stimuli/task code used later...
fprintf('\n===>>> Warming up the GPU, Eyetracker and I/O systems... <<<===\n')
t = GetSecs();
WaitSecs('UntilTime',t+0.01);
tSM = stateMachine();
tSM.warmUp(); clear tSM;
show(stims); % allows all child stimuli to be drawn
getStimulusPositions(stims);
if ~isempty(me.eyetracker.device); resetAll(eT); end % blank eyelink screen
for i = 1:s.screenVals.fps*1
draw(stims); % draw all child stimuli
drawBackground(s); % draw our blank background
drawPhotoDiodeSquare(s, [mod(i,2) mod(i,2) mod(i,2) 1]); % set our photodiode square white
drawText(s,'Warming up GPU, Eyetracker and I/O systems...');
finishDrawing(s);
animate(stims); % run our stimulus animation routines to the next frame
if ~mod(i,10); sendStrobe(io, 255); end % send a strobed word
if ~isempty(me.eyetracker.device)
getSample(eT); % get an eyetracker sample
if i == 1
trackerMessage(eT,sprintf('WARMUP_TEST %i',getTaskIndex(me)));
trackerDrawStatus(eT,'Warming Up System',stims.stimulusPositions);
end
trackerDrawEyePosition(eT);
end
[pressed, name, ~] = optickaCore.getKeys(me.keyboardDevice);
flip(s);
if eT.secondScreen; trackerFlip(eT, 1, false); end
end
update(stims); %make sure all stimuli are set back to their start state
resetLog(stims);
if ~isempty(me.eyetracker.device)
resetAll(eT);
trackerClearScreen(eT);
if eT.secondScreen; trackerFlip(eT, 0, true); end
end
resetStrobe(io); flip(s); flip(s); % reset the strobe system
%=============================Preemptive save in case of crash or error: SAVES IN /TMP
rE = me;
tS.tmpFile = [tempdir filesep me.name '.mat'];
fprintf('\n===>>> Save initial state: %s ...\n',tS.tmpFile);
save(tS.tmpFile,'rE','tS');
fprintf('\t ... Saved!\n');
%=============================Ensure we open the reward manager
if matches(me.reward.device,'arduino') && isa(rM,'arduinoManager') && ~rM.isOpen
fprintf('===>>> Opening Arduino for sending reward TTLs\n');
open(rM);
elseif matches(me.reward.device,'labjack') && isa(rM,'labJack')
fprintf('===>>> Opening LabJack for sending reward TTLs\n');
open(rM);
end
%===========================Start amplifier
if strcmp(me.control.device,'intan')
try
if ~dC.isOpen; open(dC); end
write(dC,uint8(['set Filename.BaseFilename ' me.name]));
write(dC,uint8(['set Filename.Path ' me.paths.savedData]));
write(dC,uint8(['set Note1 ' me.name]));
write(dC,uint8(['set Note2 ' me.comment]));
write(dC,uint8('set runmode record'));
WaitSecs(0.5);
catch
warning('runTask cannot contact intan!!!')
me.control.device = '';
end
elseif strcmp(me.control.device,'plexon')
if strcmp(me.strobe.device,'datapixx') || strcmp(me.strobe.device,'display++')
startRecording(io);
WaitSecs(0.5);
resumeRecording(io);
elseif strcmp(me.strobe.device,'labjack')
% Trigger the omniplex (TTL on FIO1) into paused mode
io.setDIO([2,0,0]);WaitSecs(0.001);io.setDIO([0,0,0]);
WaitSecs(0.5);
io.setDIO([3,0,0],[3,0,0])%(Set HIGH FIO0->Pin 24), unpausing the omniplex
end
end
%===========================Initialise our various counters
task.tick = 1;
task.switched = 1;
task.totalRuns = 1;
me.isTask = tS.useTask;
if me.isTask
updateVariables(me, task.totalRuns, true, false); % set to first variable
update(stims); %update our stimuli ready for display
else
updateVariables(me, 1, false, false); % set to first variable
update(stims); %update our stimuli ready for display
end
tS.totalTicks = 1; % a tick counter
me.pauseToggle = 1; %toggle pause/unpause
tS.eyePos = []; %locally record eye position
tS.initialTaskIdx.comment = 'This is the task index before the task starts, it may be modified by resetRun() during task...';
tS.initialTaskIdx.index = task.outIndex;
tS.initialTaskIdx.vars = task.outValues;
%===========================double check the labJackT handle is still valid
if isa(io,'labJackT') && ~io.isHandleValid
io.close;
io.open;
disp('===>>> We had to reopen the labJackT to ensure a stable connection...')
end
%===========================set up our behavioural plot
if tS.showBehaviourPlot
fprintf('===>>> Creating Behavioural Record Plot Window...\n');
createPlot(bR, eT);
WaitSecs(0.01); drawnow;
end
%===========================take over the keyboard + max priority
KbReleaseWait; %make sure keyboard keys are all released
if me.debug == false
ListenChar(-1); %2=capture all keystrokes
end
if ~isdeployed
try commandwindow; end
end
%=============================profiling starts here if uncommented
%profile clear; profile on;
%=============================initialise our log times and vbl's
me.needSample = false;
me.stopTask = false;
me.doFlip = false;
me.doTrackerFlip = false;
me.sendStrobe = false;
tL.t.vbl(1) = Screen('Flip', s.win);
tL.lastvbl = tL.vbl(1);
tL.t.miss(1) = 0;
tL.t.stimTime(1) = 0;
tL.startTime = tL.lastvbl;
tL.screenLog.beforeDisplay = tL.lastvbl;
tL.screenLog.trackerStartTime = getTrackerTime(eT);
tL.screenLog.trackerStartOffset = getTimeOffset(eT);
%==============================IGNITE the stateMachine!
fprintf('\n===>>> Igniting the State Machine... <<<===\n');
start(sM);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Display + task loop
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
while me.stopTask == false
%------ Check eye position manually. -----%
if me.needSample; getSample(eT); end
%------ Run stateMachine one step forward -----%
update(sM);
%------ Extra bits if we will flip -----%
if me.doFlip
if s.visualDebug; drawGrid(s); infoTextScreen(me); end
finishDrawing(s);
end
%------ Check keyboard for commands (remember we can turn
% this off using either tS.keyExclusionPattern
% [per-state toggle] or tS.checkKeysDuringStimulus).
if isempty(tS.keyExclusionPattern) || ~matches(sM.currentName,tS.keyExclusionPattern)
checkKeys(me);
end
%----- FLIP: Show it at correct retrace: -----%
if me.doFlip
%------ Display++ or DataPixx: I/O send strobe
% command for this screen flip needs to be sent
% PRIOR to the flip! Also remember DPP will be
% delayed by one flip.
if me.sendStrobe
if strcmpi(me.strobe.device,'display++')
sendStrobe(io); me.sendStrobe = false;
elseif strcmpi(me.strobe.device,'datapixx')
triggerStrobe(io); me.sendStrobe = false;
end