Skip to content

Implement refractory period during quiescence #153

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
micahwoodard merged 4 commits into from
Aug 25, 2026
Merged

Implement refractory period during quiescence #153

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
85dc4fd
Implement refractory period during quiescence
bruno-f-cruz Aug 20, 2026
5b47ef4
Protect against negative values
bruno-f-cruz Aug 22, 2026
d9a6fd0
Fix Rng object creation
bruno-f-cruz Aug 22, 2026
7cf384c
adds take after trial to close refractory period
micahwoodard Aug 25, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 12 additions & 0 deletions schema/aind_behavior_dynamic_foraging.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3526,6 +3526,18 @@
"title": "Quiescence Period Duration",
"type": "number"
},
"quiescence_period_refractory_duration": {
"default": null,
"description": "Duration of the refractory period after a lick is detected during the quiescence period (in seconds).",
"oneOf": [
{
"$ref": "#/$defs/Distribution"
},
{
"type": "null"
}
]
},
"inter_trial_interval_duration": {
"default": 5.0,
"description": "Duration of the inter-trial interval (in seconds).",
Expand Down
23 changes: 23 additions & 0 deletions src/Extensions/AindBehaviorDynamicForaging.Generated.cs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6278,6 +6278,8 @@ public partial class Trial

private double _quiescencePeriodDuration;

private AllenNeuralDynamics.AindBehaviorServices.Distributions.Distribution _quiescencePeriodRefractoryDuration;

private double _interTrialIntervalDuration;

private bool? _isAutoRewardRight;
Expand Down Expand Up @@ -6310,6 +6312,7 @@ protected Trial(Trial other)
_responseDeadlineDuration = other._responseDeadlineDuration;
_quickRetractSettings = other._quickRetractSettings;
_quiescencePeriodDuration = other._quiescencePeriodDuration;
_quiescencePeriodRefractoryDuration = other._quiescencePeriodRefractoryDuration;
_interTrialIntervalDuration = other._interTrialIntervalDuration;
_isAutoRewardRight = other._isAutoRewardRight;
_lickspoutOffsetDelta = other._lickspoutOffsetDelta;
Expand Down Expand Up @@ -6474,6 +6477,25 @@ public double QuiescencePeriodDuration
}
}

/// <summary>
/// Duration of the refractory period after a lick is detected during the quiescence period (in seconds).
/// </summary>
[System.Xml.Serialization.XmlIgnoreAttribute()]
[Newtonsoft.Json.JsonPropertyAttribute("quiescence_period_refractory_duration")]
[System.ComponentModel.DescriptionAttribute("Duration of the refractory period after a lick is detected during the quiescence " +
"period (in seconds).")]
public AllenNeuralDynamics.AindBehaviorServices.Distributions.Distribution QuiescencePeriodRefractoryDuration
{
get
{
return _quiescencePeriodRefractoryDuration;
}
set
{
_quiescencePeriodRefractoryDuration = value;
}
}

/// <summary>
/// Duration of the inter-trial interval (in seconds).
/// </summary>
Expand Down Expand Up @@ -6566,6 +6588,7 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
stringBuilder.Append("ResponseDeadlineDuration = " + _responseDeadlineDuration + ", ");
stringBuilder.Append("QuickRetractSettings = " + _quickRetractSettings + ", ");
stringBuilder.Append("QuiescencePeriodDuration = " + _quiescencePeriodDuration + ", ");
stringBuilder.Append("QuiescencePeriodRefractoryDuration = " + _quiescencePeriodRefractoryDuration + ", ");
stringBuilder.Append("InterTrialIntervalDuration = " + _interTrialIntervalDuration + ", ");
stringBuilder.Append("IsAutoRewardRight = " + _isAutoRewardRight + ", ");
stringBuilder.Append("LickspoutOffsetDelta = " + _lickspoutOffsetDelta + ", ");
Expand Down
184 changes: 138 additions & 46 deletions src/Extensions/TaskEngine.bonsai
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -260,59 +260,132 @@
<Name>QuiescentPeriod</Name>
<Workflow>
<Nodes>
<Expression xsi:type="Unit" />
<Expression xsi:type="SubscribeSubject">
<Name>ThisTrial</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>QuiescencePeriodDuration</Selector>
</Expression>
<Expression xsi:type="scr:ExpressionTransform">
<scr:Name>it &lt; 0 ? 0 : it</scr:Name>
<scr:Expression>it &lt; 0 ? 0 : it</scr:Expression>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p3:TimeSpanFromSeconds" />
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="DueTime" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Timer">
<rx:DueTime>PT1S</rx:DueTime>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="BooleanProperty">
<Value>true</Value>
</Combinator>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>IsRightLickEvent</Name>
</Expression>
<Expression xsi:type="Unit" />
<Expression xsi:type="rx:PublishSubject">
<Name>lickReset</Name>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="BooleanProperty">
<Value>false</Value>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Merge" />
</Expression>
<Expression xsi:type="rx:CreateObservable">
<Name>CreateTimer</Name>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Take">
<rx:Count>1</rx:Count>
</Combinator>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>ThisTrial</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>QuiescencePeriodRefractoryDuration</Selector>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>RngObject</Name>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="RandomSource" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p4:SampleDistribution" />
</Expression>
<Expression xsi:type="scr:ExpressionTransform">
<scr:Name>it &lt; 0 ? 0 : it</scr:Name>
<scr:Expression>it &lt; 0 ? 0 : it</scr:Expression>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p3:TimeSpanFromSeconds" />
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="DueTime" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Timer">
<rx:DueTime>PT3S</rx:DueTime>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="BooleanProperty">
<Value>false</Value>
</Combinator>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>ThisTrial</Name>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Take">
<rx:Count>1</rx:Count>
</Combinator>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>QuiescencePeriodRefractoryDuration</Selector>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="AllenNeuralDynamics.Core:FilterNotNull.bonsai" />
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:SubscribeWhen" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Concat" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Repeat" />
</Expression>
<Expression xsi:type="rx:Condition">
<Name>QuiescentCompleted</Name>
<Workflow>
<Nodes>
<Expression xsi:type="SubscribeSubject">
<Name>ThisTrial</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>QuiescencePeriodDuration</Selector>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p3:TimeSpanFromSeconds" />
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="DueTime" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Timer">
<rx:DueTime>PT0S</rx:DueTime>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Take">
<rx:Count>1</rx:Count>
</Combinator>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="1" To="2" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="3" To="4" Label="Source1" />
<Edge From="4" To="5" Label="Source1" />
<Edge From="5" To="6" Label="Source1" />
</Edges>
</Workflow>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Switch" />
<Combinator xsi:type="rx:Take">
<rx:Count>1</rx:Count>
</Combinator>
</Expression>
<Expression xsi:type="rx:SelectMany">
<Name>SolveSpoutPosition</Name>
Expand Down Expand Up @@ -340,11 +413,6 @@
</Edges>
</Workflow>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Take">
<rx:Count>1</rx:Count>
</Combinator>
</Expression>
<Expression xsi:type="WorkflowOutput" />
<Expression xsi:type="Unit" />
<Expression xsi:type="Combinator">
Expand Down Expand Up @@ -383,7 +451,7 @@
<Selector>TimeToResetDuringQuiescence</Selector>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>RngSeedValue</Name>
<Name>RngObject</Name>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
Expand Down Expand Up @@ -445,23 +513,47 @@
</Expression>
</Nodes>
<Edges>
<Edge From="0" To="4" Label="Source1" />
<Edge From="0" To="1" Label="Source1" />
<Edge From="1" To="2" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="3" To="4" Label="Source2" />
<Edge From="3" To="4" Label="Source1" />
<Edge From="4" To="5" Label="Source1" />
<Edge From="5" To="6" Label="Source1" />
<Edge From="6" To="7" Label="Source1" />
<Edge From="6" To="11" Label="Source1" />
<Edge From="7" To="8" Label="Source1" />
<Edge From="8" To="9" Label="Source1" />
<Edge From="10" To="11" Label="Source1" />
<Edge From="9" To="10" Label="Source1" />
<Edge From="10" To="11" Label="Source2" />
<Edge From="11" To="12" Label="Source1" />
<Edge From="12" To="28" Label="Source1" />
<Edge From="13" To="14" Label="Source1" />
<Edge From="14" To="15" Label="Source1" />
<Edge From="15" To="19" Label="Source1" />
<Edge From="16" To="17" Label="Source1" />
<Edge From="14" To="17" Label="Source1" />
<Edge From="15" To="16" Label="Source1" />
<Edge From="16" To="17" Label="Source2" />
<Edge From="17" To="18" Label="Source1" />
<Edge From="18" To="19" Label="Source2" />
<Edge From="18" To="19" Label="Source1" />
<Edge From="19" To="20" Label="Source1" />
<Edge From="20" To="21" Label="Source1" />
<Edge From="21" To="22" Label="Source1" />
<Edge From="22" To="27" Label="Source1" />
<Edge From="23" To="24" Label="Source1" />
<Edge From="24" To="25" Label="Source1" />
<Edge From="25" To="26" Label="Source1" />
<Edge From="26" To="27" Label="Source2" />
<Edge From="27" To="28" Label="Source2" />
<Edge From="28" To="29" Label="Source1" />
<Edge From="29" To="30" Label="Source1" />
<Edge From="30" To="31" Label="Source1" />
<Edge From="31" To="32" Label="Source1" />
<Edge From="32" To="33" Label="Source1" />
<Edge From="34" To="35" Label="Source1" />
<Edge From="35" To="36" Label="Source1" />
<Edge From="37" To="38" Label="Source1" />
<Edge From="38" To="39" Label="Source1" />
<Edge From="39" To="43" Label="Source1" />
<Edge From="40" To="41" Label="Source1" />
<Edge From="41" To="42" Label="Source1" />
<Edge From="42" To="43" Label="Source2" />
</Edges>
</Workflow>
</Expression>
Expand Down
4 changes: 4 additions & 0 deletions src/aind_behavior_dynamic_foraging/task_logic/trial_models.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,10 @@ class Trial(BaseModel):
ge=0,
description="Duration of the quiescence period before trial starts (in seconds). Each lick resets the timer.",
)
quiescence_period_refractory_duration: Optional[Distribution] = Field(
default=None,
description="Duration of the refractory period after a lick is detected during the quiescence period (in seconds).",
)
inter_trial_interval_duration: float = Field(
default=5.0, ge=0.5, description="Duration of the inter-trial interval (in seconds)."
)
Expand Down
Loading