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Bpod Protocol
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
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