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Implement OperantLogic.stop_duration as a distribution instead of scalar value #450

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Merged
bruno-f-cruz merged 1 commit into from
Nov 14, 2025
Merged

Implement OperantLogic.stop_duration as a distribution instead of scalar value #450

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16 changes: 11 additions & 5 deletions src/DataSchemas/aind_behavior_vr_foraging.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3013,11 +3013,17 @@
"type": "boolean"
},
"stop_duration": {
"default": 0,
"description": "Duration (s) the animal must stop for to lock its choice",
"minimum": 0,
"title": "Stop Duration",
"type": "number"
"$ref": "#/$defs/Distribution",
"default": {
"family": "Scalar",
"distribution_parameters": {
"family": "Scalar",
"value": 0.0
},
"truncation_parameters": null,
"scaling_parameters": null
},
"description": "Duration (s) the animal must stop for to lock its choice"
},
"time_to_collect_reward": {
"default": 100000,
Expand Down
79 changes: 6 additions & 73 deletions src/Extensions/AddRewardSite.bonsai
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Expand Up @@ -121,64 +121,11 @@
<Expression xsi:type="SubscribeSubject">
<Name>ActivePatch</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>RewardSpecification</Selector>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="Delay" Selector="Delay" />
</PropertyMappings>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>ActivePatch</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>RewardSpecification</Selector>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>OperantLogic</Selector>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="IsOperant" Selector="IsOperant" />
<Property Name="TimeToCollectReward" Selector="TimeToCollectReward" />
<Property Name="GraceDistanceThreshold" Selector="GraceDistanceThreshold" />
</PropertyMappings>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>ActivePatch</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>RewardSpecification.OperantLogic.StopDuration</Selector>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>StopDurationOffset</Name>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:CombineLatest" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Take">
<rx:Count>1</rx:Count>
</Combinator>
</Expression>
<Expression xsi:type="Add" />
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="StopDuration" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p1:OperantLogic">
<p1:IsOperant>true</p1:IsOperant>
<p1:StopDuration>0</p1:StopDuration>
<p1:TimeToCollectReward>100000</p1:TimeToCollectReward>
<p1:GraceDistanceThreshold>10</p1:GraceDistanceThreshold>
</Combinator>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="OperantLogic" />
<Property Name="OperantLogic" Selector="RewardSpecification.OperantLogic" />
<Property Name="Delay" Selector="RewardSpecification.Delay" />
<Property Name="RewardFunction" Selector="RewardSpecification.RewardFunction" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
Expand All @@ -198,24 +145,10 @@
</Nodes>
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="1" To="2" Label="Source1" />
<Edge From="2" To="18" Label="Source1" />
<Edge From="3" To="4" Label="Source1" />
<Edge From="1" To="4" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="3" To="4" Label="Source2" />
<Edge From="4" To="5" Label="Source1" />
<Edge From="5" To="6" Label="Source1" />
<Edge From="6" To="14" Label="Source1" />
<Edge From="7" To="8" Label="Source1" />
<Edge From="8" To="10" Label="Source1" />
<Edge From="9" To="10" Label="Source2" />
<Edge From="10" To="11" Label="Source1" />
<Edge From="11" To="12" Label="Source1" />
<Edge From="12" To="13" Label="Source1" />
<Edge From="13" To="14" Label="Source2" />
<Edge From="14" To="15" Label="Source1" />
<Edge From="15" To="18" Label="Source2" />
<Edge From="16" To="17" Label="Source1" />
<Edge From="17" To="18" Label="Source3" />
<Edge From="18" To="19" Label="Source1" />
</Edges>
</Workflow>
</Expression>
Expand Down
97 changes: 94 additions & 3 deletions src/Extensions/AindBehaviorVrForaging.Generated.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -8336,7 +8336,7 @@ public partial class OperantLogic

private bool _isOperant;

private double _stopDuration;
private Distribution _stopDuration;

private double _timeToCollectReward;

Expand All @@ -8345,7 +8345,7 @@ public partial class OperantLogic
public OperantLogic()
{
_isOperant = true;
_stopDuration = 0D;
_stopDuration = new Distribution();
_timeToCollectReward = 100000D;
_graceDistanceThreshold = 10D;
}
Expand Down Expand Up @@ -8378,9 +8378,10 @@ public bool IsOperant
/// <summary>
/// Duration (s) the animal must stop for to lock its choice
/// </summary>
[System.Xml.Serialization.XmlIgnoreAttribute()]
[Newtonsoft.Json.JsonPropertyAttribute("stop_duration")]
[System.ComponentModel.DescriptionAttribute("Duration (s) the animal must stop for to lock its choice")]
public double StopDuration
public Distribution StopDuration
{
get
{
Expand Down Expand Up @@ -15277,6 +15278,51 @@ public override string ToString()
}


[System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
[Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "family")]
[Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
[Bonsai.CombinatorAttribute(MethodName="Generate")]
public partial class Delay
{

public Delay()
{
}

protected Delay(Delay other)
{
}

public System.IObservable<Delay> Generate()
{
return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Delay(this)));
}

public System.IObservable<Delay> Generate<TSource>(System.IObservable<TSource> source)
{
return System.Reactive.Linq.Observable.Select(source, _ => new Delay(this));
}

protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
{
return false;
}

public override string ToString()
{
System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder();
stringBuilder.Append(GetType().Name);
stringBuilder.Append(" { ");
if (PrintMembers(stringBuilder))
{
stringBuilder.Append(" ");
}
stringBuilder.Append("}");
return stringBuilder.ToString();
}
}


[System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
[Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "family")]
[Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
Expand Down Expand Up @@ -16217,6 +16263,45 @@ private static System.IObservable<TResult> Process<TResult>(System.IObservable<V
}


[System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
[System.ComponentModel.DefaultPropertyAttribute("Type")]
[Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Combinator)]
public partial class MatchDelay : Bonsai.Expressions.SingleArgumentExpressionBuilder
{

public Bonsai.Expressions.TypeMapping Type { get; set; }

public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable<System.Linq.Expressions.Expression> arguments)
{
var typeMapping = Type;
var returnType = typeMapping != null ? typeMapping.GetType().GetGenericArguments()[0] : typeof(Delay);
return System.Linq.Expressions.Expression.Call(
typeof(MatchDelay),
"Process",
new System.Type[] { returnType },
System.Linq.Enumerable.Single(arguments));
}


private static System.IObservable<TResult> Process<TResult>(System.IObservable<Delay> source)
where TResult : Delay
{
return System.Reactive.Linq.Observable.Create<TResult>(observer =>
{
var sourceObserver = System.Reactive.Observer.Create<Delay>(
value =>
{
var match = value as TResult;
if (match != null) observer.OnNext(match);
},
observer.OnError,
observer.OnCompleted);
return System.ObservableExtensions.SubscribeSafe(source, sourceObserver);
});
}
}


[System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
[System.ComponentModel.DefaultPropertyAttribute("Type")]
[Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Combinator)]
Expand Down Expand Up @@ -17093,6 +17178,11 @@ public System.IObservable<string> Process(System.IObservable<AindBehaviorVrForag
return Process<AindBehaviorVrForagingTaskLogicVector3>(source);
}

public System.IObservable<string> Process(System.IObservable<Delay> source)
{
return Process<Delay>(source);
}

public System.IObservable<string> Process(System.IObservable<Amount> source)
{
return Process<Amount>(source);
Expand Down Expand Up @@ -17264,6 +17354,7 @@ public System.IObservable<string> Process(System.IObservable<ScalingParameters2>
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<WebCamera>))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<AindBehaviorServicesRigVisualStimulationVector3>))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<AindBehaviorVrForagingTaskLogicVector3>))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<Delay>))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<Amount>))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<Probability>))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping<Available>))]
Expand Down
37 changes: 30 additions & 7 deletions src/Extensions/InstantiateSite.bonsai
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Expand Up @@ -3,11 +3,11 @@
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions"
xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders"
xmlns:p1="clr-namespace:AindVrForagingDataSchema;assembly=Extensions"
xmlns:p2="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core"
xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders"
xmlns:dsp="clr-namespace:Bonsai.Dsp;assembly=Bonsai.Dsp"
xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp"
xmlns:p2="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core"
xmlns:p3="clr-namespace:Bonsai.Numerics.Distributions;assembly=Bonsai.Numerics"
xmlns:bv="clr-namespace:BonVision;assembly=BonVision"
xmlns="https://bonsai-rx.org/2018/workflow">
Expand Down Expand Up @@ -151,8 +151,25 @@
<Expression xsi:type="MemberSelector">
<Selector>OperantLogic.StopDuration</Selector>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p1:SampleDistribution" />
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>StopDurationOffset</Name>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:FirstOrDefault" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:WithLatestFrom" />
</Expression>
<Expression xsi:type="Add" />
<Expression xsi:type="scr:ExpressionTransform">
<scr:Expression>TimeSpan.FromSeconds(it)</scr:Expression>
<scr:Name>Math.Max(0, it)</scr:Name>
<scr:Expression>Math.Max(0, it)</scr:Expression>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p2:TimeSpanFromSeconds" />
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
Expand All @@ -161,7 +178,7 @@
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="gl:Timer">
<gl:DueTime>PT0.0000001S</gl:DueTime>
<gl:DueTime>PT0S</gl:DueTime>
</Combinator>
</Expression>
<Expression xsi:type="WorkflowInput">
Expand All @@ -178,12 +195,18 @@
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="1" To="2" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="2" To="5" Label="Source1" />
<Edge From="3" To="4" Label="Source1" />
<Edge From="4" To="6" Label="Source1" />
<Edge From="5" To="6" Label="Source2" />
<Edge From="4" To="5" Label="Source2" />
<Edge From="5" To="6" Label="Source1" />
<Edge From="6" To="7" Label="Source1" />
<Edge From="7" To="8" Label="Source1" />
<Edge From="8" To="9" Label="Source1" />
<Edge From="9" To="10" Label="Source1" />
<Edge From="10" To="12" Label="Source1" />
<Edge From="11" To="12" Label="Source2" />
<Edge From="12" To="13" Label="Source1" />
<Edge From="13" To="14" Label="Source1" />
</Edges>
</Workflow>
</Expression>
Expand Down
6 changes: 4 additions & 2 deletions src/aind_behavior_vr_foraging/task_logic.py
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Expand Up @@ -228,8 +228,10 @@ class OperantLogic(BaseModel):
"""

is_operant: bool = Field(default=True, description="Will the trial implement operant logic")
stop_duration: float = Field(
default=0, ge=0, description="Duration (s) the animal must stop for to lock its choice"
stop_duration: distributions.Distribution = Field(
default=scalar_value(0),
validate_default=True,
description="Duration (s) the animal must stop for to lock its choice",
)
time_to_collect_reward: float = Field(
default=100000, ge=0, description="Time(s) the animal has to collect the reward"
Expand Down