detection.m

function a = detection(devicesFolder)

% loads parameters that were set in the ToneBoxGui
load([devicesFolder 'PiParams.mat'])

% makes sure that a folder exists for the device that is running, if a
% folder doesn't exist then one is created
checkFolder = exist([devicesFolder,cageID]);
if checkFolder == 0
    mkdir(devicesFolder,cageID)
end

%removes parameters file from the Devices folder into the folder
%corresponding to the device that is running, this prevents the ToneBoxGui from
%overwriting the parameters before a device is done downloading the file.
%Once this file is moved, another device can be selected and set up back in
%the ToneBoxGui
movefile([devicesFolder 'PiParams.mat'],[devicesFolder, cageID '/PiParams.mat'])

%sets variables for certain loop stoppages to zero, quit changes to 1 when 
%the Stop buton on the ToneBoxGui is pressed and it stops the entire phase, 
%intervalStop does the same as quit except it can be accessed during an 
%inter-block interval, pauseProgram becomes 1 when all the devices are
%paused through the ToneBoxGui.
quit = 0;
intervalStop = 0;
pauseProgram = 0;

%the variables are saved to a file to be accessed later, the program will
%check the status of these variables throughout the loop to see if the Stop
%button or Pause button has been pressed on the ToneBoxGui
save([devicesFolder,cageID,'\stopButton.mat'],'quit','intervalStop','pauseProgram')

% checks to see if a general performance (data) file already exists in the
% folder that is associated with the device. If the file already exists, then
% that file is renamed with a message that indicates there was an error. 
% This is a failsafe, the only way this file would exist at the beginning 
% of the function is if the function had stopped unexpectedly or 
% erroneously. Otherwise, this file is deleted at the end of the function 
% and the data is saved to a separate file that is time stamped.
checkFile = exist([devicesFolder, cageID '/performance.mat'])
if checkFile == 2
    try
        load([devicesFolder, cageID '/performance.mat'])
        movefile ([devicesFolder, cageID '/performance.mat'], [devicesFolder, cageID '/performance' datestr(now,'dd-mm-yyyy_HH.MM') '_stop_error.mat'])
    
    %if the performance file exists but matlab can't load it, i.e. it is
    %corrupted, the backup file will be renamed and saved with an error
    %message
    catch
        load([devicesFolder,cageID '/performance_backup.mat'])
        movefile([devicesFolder,cageID '/performance_backup.mat'],[devicesFolder, cageID '/performance' datestr(now,'dd-mm-yyyy_HH.MM') '_stop_error.mat'])
    end
end

%variable to determine whether the phase is running trials or on an
%inter-block interval
blockInterval = 0;

%these variables indicate which phase is running, used for data analysis
phaseChoice = 3;
phaseName = 'detection';

%records of the number of each responses, respectively hit, early, miss,
%and false alarm
hitCount = 0;
earlyCount = 0;
missCount = 0;
falseAlarmCount = 0;

%records of the number of trials
totalTrials = 0;

%records of the time each trial starts
timeStamp = {};

%Compiles the licks from each trial into a matrix, each row is another 
%trial of recorded licks
lickTotal = {};

%variable used to find when the first lick occurred
lickData = [];

% nbins can be adjusted based depending on if the sampling rate of
% the sensor is too fast or too slow, this value was picked based on
% observing how fast a mouse can lick and react to the stimulus, the bins
% are used to break up the lick response data
nbins = 75;

% Compiles all the separate lick histograms into one big data set
totalData = [];

%sets the x axis based on the nbins variable for plotting histograms later
%in data analysis
xaxis = linspace(0,4,nbins);

% records the first lick for all trials
lickResponse = zeros(1,nbins);

% saves target tone selections from gui to this function
target = targetChoice;

% saves tone level selections from ToneBoxGui
toneLevel = toneLevelChoice;

%records which tone played during that trial
toneVec = [];

%records whether the response was a hit 'H', early 'E', a miss 'M', or a 
%false alarm 'F'
responseVec = [];

%records which level the tone was played at
levelVec = [];

% saves all these variables to a performance file to be saved at the end of
% each loop. this file is used for data analysis in the DataGraph GUI
save([devicesFolder, cageID '/performance.mat'],'phaseName','hitCount','missCount','earlyCount','falseAlarmCount',...
    'xaxis','totalTrials','lickResponse','totalData','target','phaseChoice','cageID','timeStamp','blockInterval','toneVec','levelVec','responseVec')

%starts a timer that, once it reaches 60 minutes, will indicate the end of
%a block and the beginning of an inter-block interval
ibi = tic;

%quit becomes 1 when the Stop button is pressed on the ToneBoxGui
while quit == 0
    
    %creates a backup file for the data
    copyfile([devicesFolder, cageID '/performance.mat'],[devicesFolder, cageID '/performance_backup.mat'])
    
    %if an error occurs, then the value will become 1 and the data for that
    %trial will be voided. The raspberry pi sometimes will drop connection
    %and the few commands that get sent to the pi will cause the program to
    %pause and error. There are try-catch loops for each command sent to
    %the raspberry pi. If an error occurs, the raspberry pi connection will
    %be deleted and reloaded from the parameters file.
    error = 0;
    
    % checks the quit variable at the beginning of each loop, if quit is 1
    % then the loop will run once more and then stop
    load([devicesFolder, cageID '/stopButton.mat']);
    
    %records the number of trials
    totalTrials = totalTrials + 1;
    
    % this records the time of each trial
    timeStamp = [timeStamp; {totalTrials datestr(now,'mm/dd/yyyy HH:MM:SS')}];
    
    save([devicesFolder, cageID '/performance.mat'],'phaseName','hitCount','missCount','earlyCount','falseAlarmCount',...
    'xaxis','totalTrials','lickResponse','totalData','target','phaseChoice','cageID','timeStamp','blockInterval','toneVec','levelVec','responseVec')
    
    %resets delay value
    delay = 0;
    
    %if the trial results in the corresponding response, the variable will
    %equal 1
    hit = 0;
    early = 0;
    falseAlarm = 0;
    
    %records the licks of the current trial, then resets each loop
    lickTrial = [];
    
    %if the silent trials option is selected in the ToneBoxGui, then sielnt
    %trials will occur in 30 percent of the trials
    percent = 30;
    if silentTrials == 1
        randomNumber = randi(100);
    else
        randomNumber = 100;
    end
    
    
    % this tests to make sure the raspberry pi is connected
    try
        system(rpi,'hostname');
    catch
        disp('connection error 1')
        datestr(now,'mm/dd/yyyy HH:MM:SS')
        clear rpi
        load([devicesFolder, cageID '/PiParams.mat'],'rpi')
        error = 1;
    end
    
    % this delay ensures that a new trial doesn't start until that the
    % animal hasn't licked for 5 consecutive seconds
    C = tic;
    lickPin = 0;
    noresp = randsample(5:5:25,1);
    while toc(C) < noresp && intervalStop == 0
        try
            lickPin = readDigitalPin(rpi, 5);
        catch
            disp('connection error 6')
            datestr(now,'mm/dd/yyyy HH:MM:SS')
            clear rpi
            load([devicesFolder, cageID '/PiParams.mat'],'rpi')
            pause(5)
        end
        if lickPin == 1
            C = tic;
        end
        w = toc(C);
    end
    
    %starts a timer to help align the sound file with the trial time
    V = tic;
    %30 percent of trials randomNumber will be smaller than percent so if
    %silent trials were selected then on 30 percent of trials there will be
    %no sound
    if randomNumber > percent
        % sound files are stored as Tone_XkHz_YdB.wav, and the different values
        % of X are the different tone frequencies. The sound variable selects a
        % random value from the specific tones that were selected in the
        % ToneBoxGui. The different values of Y are different tone levels and
        % the randLevel variable selects a random value from the specific tone
        % levels what were selected in the ToneBoxGui
        sound = num2str(target(randi(length(target))));
        randLevel = num2str(toneLevel(randi(length(toneLevel))));
        
        % command to raspberry pi to play random sound selection
        system(rpi,['sudo mplayer /home/tonebox/Tone_' sound 'kHz_' randLevel 'dB.wav </dev/null >/dev/null 2>&1 &']);
        disp(['sudo mplayer /home/tonebox/Tone_' sound 'kHz_' randLevel 'dB.wav </dev/null >/dev/null 2>&1 &'])
    else
        %this trial will be silent
        disp('silent trial')
        sound = '0';
        randLevel = 'X';
    end
    
    %records which sound and which tone level were played, sound = 0 and
    %randLevel = X for silent trials
    toneVec = [toneVec,{num2str(sound)}];
    levelVec = [levelVec,{num2str(randLevel)}];
    
    % ensures that the sound begins at 1 second in the trial, there is a
    % delay between calling the command and executing the command
    while toc(V) < .66
        A = 0;
    end
    
    % timer for the beginning of each trial
    A = tic;
    
    % time of a trial is 4 seconds, the response window is between 1 and 3
    % seconds
    while toc(A) < 4
        
        % tells the raspberry pi to read the capacitive touch sensor
        try 
           lickPin = readDigitalPin(rpi, 5);
        catch
            disp('connection error 2')
            datestr(now,'mm/dd/yyyy HH:MM:SS')
            clear rpi
            load([devicesFolder, cageID '/PiParams.mat'],'rpi')
            pause(5)
            error = 1;
        end
        
        % lickTrial will be timestamped every time the capacitive touch
        % sensor is triggered, this is how licks are recorded each trial
        if lickPin == 1
            lickTrial = [lickTrial; toc(A)];
        end
        
        % these conditions indicate a "hit" or a "alarm", if the trial is
        % not a silent trial then the solenoid will be triggered, the last
        % condition ensures that the solenoid will only get triggered once
        if toc(A) >= 1 && toc(A) <=3 && lickPin == 1 && early == 0 && length(lickTrial) == 1
            
            %if there is a response in this window during a silent trial,
            %the response is considered a "false alarm"
            if sound == '0'
                falseAlarm = 1;
            else
                hit = 1;
                % the reward is 2 seconds of water so the second timer keeps
                % track to turn the solenoid on for 2 seconds
                B = tic;
                while toc(B) <= 2
                    
                    % tells the raspberry pi to turn on the solenoid to 
                    % deliver water
                    try
                        writeDigitalPin(rpi, 13, 1)
                        disp('solenoid on')
                    catch
                        disp('connection error 3')
                        datestr(now,'mm/dd/yyyy HH:MM:SS')
                        clear rpi
                        load([devicesFolder, cageID '/PiParams.mat'],'rpi')
                        pause(5)
                        error = 1;
                    end
                    
                    % tells the raspberry pi to read the capacitive touch
                    % sensor so the licks during this period are still 
                    % recorded
                    try
                        lickPin = readDigitalPin(rpi, 5);
                    catch
                        disp('connection error 4')
                        datestr(now,'mm/dd/yyyy HH:MM:SS')
                        clear rpi
                        load([devicesFolder, cageID '/PiParams.mat'],'rpi')
                        pause(5)
                        error = 1;
                    end
                    if lickPin == 1
                        lickTrial = [lickTrial; toc(A)];
                    end
                end
                
                %tells the raspberry pi to turn off the solenoid after 2s
                try
                    writeDigitalPin(rpi,13,0)
                catch
                    disp('connection error 5')
                    datestr(now,'mm/dd/yyyy HH:MM:SS')
                    clear rpi
                    load([devicesFolder, cageID '/PiParams.mat'],'rpi')
                    pause(5)
                    error = 1;
                    writeDigitalPin(rpi,13,0)
                end
            end
            

        end
        
        % if a lick is detected before the response window (<1s) then the
        % response is considered "early", punishment for this response is 
        % a longer delay time in between trials, delay is set to 20 seconds
        if toc(A) < 1 && lickPin == 1
            early = 1;
        end
    end
    
    if error == 0
        % these count variables are used for a histogram to show
        % quantitatively how the mouse responded. the responseVec vector
        % also saves the type of response with a corresponding letter
        % delays in between trials after hit and miss responses are between
        % 5 and 9 seconds, early  and false alarm trials result in 20 
        % second delays. 
        if hit == 0 && early == 0 && falseAlarm == 0
            disp('miss')
            delay = randi([5,9])
            pause(delay)
            missCount = missCount + 1;
            responseVec = [responseVec,'M'];
        end
        if hit == 1
            disp('hit')
            delay = randi([5,9])
            pause(delay)
            hitCount = hitCount + 1;
            responseVec = [responseVec,'H'];
        end
        if early == 1
            disp('early')
            delay = 20 + randi([5,9])
            pause(delay)
            earlyCount = earlyCount + 1;
            responseVec = [responseVec,'E'];
        end
        if falseAlarm == 1
            disp('false alarm')
            delay = 20 + randi([5,9])
            pause(delay)
            falseAlarmCount = falseAlarmCount + 1;
            responseVec = [responseVec,'F'];
        end
        
        % Compiles the licks from each trial into a matrix, each row is 
        % another trial of recorded licks
        lickTotal = [lickTotal; {lickTrial}];
        
        % The next three lines find where the first lick occurred in the 
        % most recent trial
        lickData = cell2mat(lickTotal(totalTrials));
        % This line specifically separates the recorded licks into a histogram
        [lickHistogram,edges] = histcounts(lickData,nbins,'BinLimit',[0 4]);
        firstLick = find(lickHistogram>0,1);
        
        % This logs the first lick into a histogram of all the first licks for
        % all trials
        lickResponse(1,firstLick) = lickResponse(1,firstLick) + 1;
        
        % Compiles all the separate lick histograms into one big data set
        totalData = [totalData; lickHistogram];
        
        save([devicesFolder, cageID '/performance.mat'],'phaseName','hitCount','missCount','earlyCount','falseAlarmCount',...
            'xaxis','totalTrials','lickResponse','totalData','target','phaseChoice','cageID','timeStamp','blockInterval','toneVec','levelVec','responseVec')
    end
    
    %voids data if an error occurred during the trial
    if error == 1
        if length(responseVec) == totalTrials
            responseVec(length(responseVec)) = [];
        end
        totalTrials = totalTrials - 1;
        toneVec(length(toneVec)) = [];
        levelVec(length(levelVec)) = [];
    end
    
    % inter-block interval, after 60 minutes of trials there is a 60 minute
    % break
    if toc(ibi) > 3600
        %keeps track of loops/time
        trialTime = 0;
        %saves a variable so that the DataGraph GUI knows that the device
        %is on a break
        blockInterval = 1;
        save([devicesFolder, cageID  '/performance.mat'],'blockInterval','-append')
        % loop runs 3600 times unless stop button on ToneBoxGui is pressed, if
        % stop button is pressed, interval loop stops and main loop also
        % stops as the varialbes intervalStop and quit are both changed to
        % equal 1
        while trialTime < 3600 && intervalStop == 0
            trialTime = trialTime + 1;
            load([devicesFolder, cageID '/stopButton.mat']);
            pause(1)
        end
        %restarts the inter-block interval timer
        ibi = tic;
        %resets this variable so the status of the device is no longer on a
        %break
        blockInterval = 0;
        save([devicesFolder, cageID  '/performance.mat'],'blockInterval','-append')
    end
    
    % pauses program when Pause All button is pressed on ToneBoxGui, stops
    % the loop when the Resume All button is pressed
    while pauseProgram == 1
        pause(10)
        load([devicesFolder, cageID '/stopButton.mat']);
    end
    
end

% the final data will be saved to a time stamped performance file
save([devicesFolder, cageID '/performance' datestr(now,'dd-mm-yyyy_HH.MM') '.mat'],'phaseName','hitCount','missCount','earlyCount','falseAlarmCount',...
    'xaxis','totalTrials','lickResponse','totalData','target','phaseChoice','cageID','timeStamp','blockInterval','toneVec','levelVec','responseVec')

% deletes the generic performance file
delete([devicesFolder, cageID '/performance.mat'])