Bpod Protocol

SP_Phase3_CSUS.m

function SP_Phase3_CSUS
% 
% Hyun-Jae Pi, June2016
% This protocol has been modified by other contributors.
% This protocol will deliver a stimulation followed by water
% delivery after the CS (the animal controls the delivery by triggering deliver reward. 
% The initial delay will be shuffled between 2 and 3.

global BpodSystem


%% ******************************************

TrialTypeProbs = [1 0] % First probability being Go or NOGO.

%% Define parameters
S = BpodSystem.ProtocolSettings; % Load settings chosen in launch manager into current workspace as a struct called S
if isempty(fieldnames(S))  % If settings file was an empty struct, populate struct with default settings

    S.GUI.RewardAmount = 10; % amount of reward delivered to the mouse in microliters
    S.GUI.InitialDelay = 2;
    S.GUI.ITI = 0.7;
    S.GUI.WaitForLickDur = 1;
    S.StimulusDuration = 0.3; 
    S.InitialDelayMean = [2 3];
    S.TrialTypeProbs = TrialTypeProbs;
    S.RewardValveCode =1;
    S.Timeout = 1.5;

     
end


%% Define trial types

 maxTrials = 5000;
 for x = 1:maxTrials
    P = rand;
    Cutoffs = cumsum(S.TrialTypeProbs);
    Found = 0;
    for y = 1:length(S.TrialTypeProbs)
        if P<Cutoffs(y) && Found == 0
            Found = 1;
            S.TrialTypes(x) = y;
        end
    end
 end

%randomises delay
for i = 1:ceil(maxTrials / length(S.InitialDelayMean)) %adjust divisor based on no. test frequencies
   delay(i,:) = Shuffle(S.InitialDelayMean);
end

initdel = reshape(delay',[1, maxTrials]);
S.InitdelTypes = initdel;
clear new i delay

S.InitdelTypes = initdel(randperm(length(initdel)));

BpodSystem.Data.TrialTypes = []; % The trial type of each trial completed will be added here.
%% Initialize parameter GUI plugin
BpodParameterGUI('init', S);
TotalRewardDisplay('init', S);

%% Initialize plots
% BpodSystem.ProtocolFigures.OutcomePlotFig =
figure('Position', [100 300 1000 300],'Name','Outcome plot','numbertitle','off', 'MenuBar', 'none', 'Resize', 'off');
BpodSystem.GUIHandles.OutcomePlot = axes('Position', [.075 .3 .89 .6]);
OutcomePlot_SP_Phase3_CSUS(BpodSystem.GUIHandles.OutcomePlot,'init',2-S.TrialTypes);

%% Main loop
maxTrials = 5000;
for currentTrial = 1:maxTrials
     fprintf(['Trial # ' num2str(currentTrial) ': trial type ' num2str(S.TrialTypes(currentTrial))  '\n']);
     S = BpodParameterGUI('sync', S); % Sync parameters with BpodParameterGUI plugin    
     % Backgroud_noise = {'WireState', 2};
    switch S.TrialTypes(currentTrial)
        case 1
            StimOutputAction = {'WireState',1}; % {'SoftCode',1,'BNCState',0, 'WireState',2}
            Offsettime = 0;
            RewardOutputAction = {'ValveState',1}; % {'BNCState',2, 'WireState',2};
        case 2
            StimOutputAction = {'BNCState', 1}; % {'SoftCode', 2, 'BNCState', 1, 'WireState',2};
            Offsettime = 0;            
            RewardOutputAction = {}; 
  
    end
        
  
    WaterTime =  GetValveTimes(S.GUI.RewardAmount, [1]);
    
    %     Assemble state matrix
    sma = NewStateMatrix();
    sma = AddState(sma, 'Name', 'InitialDelay', ...
        'Timer', S.InitdelTypes(currentTrial), ...
        'StateChangeConditions',{'Tup', 'StartTrial'},...
        'OutputActions', {});
    sma = AddState(sma, 'Name', 'StartTrial', ...
        'Timer', 0,...
        'StateChangeConditions',{'Tup','DeliverStimulus'},...
        'OutputActions', {});  % Send a TTL on BNC output 2 of Bpod for syncing with imaging system ; WireState 1 for initiating �maging system
    sma = AddState(sma, 'Name', 'DeliverStimulus', ...
           'Timer', S.StimulusDuration,...
           'StateChangeConditions', {'Tup','WaitForLick'},...
           'OutputActions', StimOutputAction);       

       if S.TrialTypes(currentTrial) == 1       
        sma = AddState(sma, 'Name', 'WaitForLick', ...
            'Timer',S.GUI.WaitForLickDur,...
            'StateChangeConditions', {'Tup', 'ITI', 'Port1In', 'DeliverReward'},... 
            'OutputActions', {});       
    end
    
    if S.TrialTypes(currentTrial) == 2
        sma = AddState(sma, 'Name', 'WaitForLick', ...
            'Timer',S.GUI.WaitForLickDur,...
            'StateChangeConditions', {'Tup', 'ITI', 'Port1In', 'Timeout'},... 
            'OutputActions', {});          
    end
    
   
    sma = AddState(sma,'Name', 'DeliverReward', ...
         'Timer',WaterTime, ...
         'StateChangeConditions',{'Tup', 'ITI', 'Port1In', 'StillDrinking'},...
         'OutputActions', RewardOutputAction); 
    sma = AddState(sma,'Name', 'Timeout', ...
         'Timer',S.Timeout, ...
         'StateChangeConditions',{'Tup', 'ITI', 'Port1In', 'Timeout'},...
         'OutputActions', {});        
    sma = AddState(sma, 'Name', 'ITI', ...
        'Timer',S.GUI.ITI,...
        'StateChangeConditions', {'Tup', 'exit', 'Port1In','ResetTimerForDrinking'}, ...
        'OutputActions', {});            
    sma = AddState(sma,'Name', 'StillDrinking', ...
        'Timer', 0.5, ...
        'StateChangeConditions', {'Tup', 'ITI','Port1In','ResetTimerForDrinking'},...
        'OutputActions', {});
    sma = AddState(sma,'Name', 'ResetTimerForDrinking', ...
        'Timer', 0.5, ...
        'StateChangeConditions', {'Tup', 'StillDrinking',},...
        'OutputActions', {});
    
    BpodSystem.Data.TrialSettings(currentTrial) = S; % Adds the settings used for the current trial to the Data struct (to be saved after the trial ends)
    SendStateMatrix(sma);
    RawEvents = RunStateMatrix;
    BpodSystem.Data = AddTrialEvents(BpodSystem.Data,RawEvents);
    %BpodSystem.Data = BpodNotebook(BpodSystem.Data);
    BpodSystem.Data.TrialSettings(currentTrial) = S; % Adds the settings used for the current trial to the Data struct (to be saved after the trial ends)
    BpodSystem.Data.TrialTypes(currentTrial) = S.TrialTypes(currentTrial); % Adds the trial type of the current trial to data
    BpodSystem.Data.InitDelayTypes(currentTrial) = S.InitdelTypes(currentTrial); % Adds the trial type of the current trial to data
    UpdateTotalRewardDisplay(S.GUI.RewardAmount, currentTrial);
    Outcomes = UpdateOutcomePlot(S.TrialTypes, BpodSystem.Data);
    BpodSystem.Data.TrialOutcome(currentTrial) = Outcomes(currentTrial);
    SaveBpodSessionData; % Saves the field BpodSystem.Data to the current data file
    
end
end

%---------------------------------------- /MAIN LOOP

%% sub-functions
function Outcomes = UpdateOutcomePlot(TrialTypes, Data)
global BpodSystem
Outcomes = zeros(1,Data.nTrials);
for x = 1:Data.nTrials
    if ~isnan(Data.RawEvents.Trial{x}.States.DeliverReward(1))
        Outcomes(x) = 1;
%     elseif ~isnan(Data.RawEvents.Trial{x}.States.DeliverPunish(1))
%         Outcomes(x) = 0;
    else
        Outcomes(x) = 3;
    end
end
OutcomePlot_SP_Phase3_CSUS(BpodSystem.GUIHandles.OutcomePlot,'update',Data.nTrials+1,2-TrialTypes,Outcomes)
end

function UpdateTotalRewardDisplay(RewardAmount, currentTrial)
% If rewarded based on the state data, update the TotalRewardDisplay
global BpodSystem
    if ~isnan(BpodSystem.Data.RawEvents.Trial{currentTrial}.States.DeliverReward(1))
        TotalRewardDisplay('add', RewardAmount);
    end
end