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Add support for grouping pose tracking by model
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@glopesdev
glopesdev committed Oct 12, 2023
1 parent c886090 commit 7419c01
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Showing 2 changed files with 181 additions and 115 deletions.
134 changes: 83 additions & 51 deletions src/Aeon.Acquisition/LogPoseTracking.bonsai
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.8.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:aeon="clr-namespace:Aeon.Acquisition;assembly=Aeon.Acquisition"
xmlns:sys="clr-namespace:System;assembly=mscorlib"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns="https://bonsai-rx.org/2018/workflow">
<Description>Chunks and logs a timestamped pose tracking stream into the base data log.</Description>
<Workflow>
Expand All @@ -14,63 +14,95 @@
<Expression xsi:type="ExternalizedMapping">
<Property Name="Address" />
<Property Name="IdentityIndex" />
<Property Name="LogName" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="aeon:FormatPose">
<aeon:Address>255</aeon:Address>
<aeon:IdentityIndex xsi:nil="true" />
</Combinator>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Value" DisplayName="LogName" />
</Expression>
<Expression xsi:type="PropertySource" TypeArguments="WorkflowProperty(sys:String),sys:String">
<MemberName>LogName</MemberName>
<Value>PoseTrackingData</Value>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" />
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>PoseTrackingMetadata</Name>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Zip" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Take">
<rx:Count>1</rx:Count>
</Combinator>
</Expression>
<Expression xsi:type="Format">
<Format>{0}_{1}</Format>
<Selector>Item1,Item2.LogName</Selector>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="LogName" />
</PropertyMappings>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Aeon.Acquisition:LogHarp.bonsai">
<Heartbeats xsi:nil="true" />
<ClosingDuration xsi:nil="true" />
<LogName>PoseTrackingData</LogName>
<Expression xsi:type="rx:SelectMany">
<Name>LogPoseModel</Name>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="rx:AsyncSubject">
<Name>TrackingGroup</Name>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>TrackingGroup</Name>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Merge" />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Address" />
<Property Name="IdentityIndex" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="aeon:FormatPose">
<aeon:Address>255</aeon:Address>
<aeon:IdentityIndex xsi:nil="true" />
</Combinator>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Value" DisplayName="LogName" />
</Expression>
<Expression xsi:type="PropertySource" TypeArguments="WorkflowProperty(sys:String),sys:String">
<MemberName>LogName</MemberName>
<Value>PoseTrackingData</Value>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>TrackingGroup</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Key</Selector>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Zip" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Take">
<rx:Count>1</rx:Count>
</Combinator>
</Expression>
<Expression xsi:type="Format">
<Format>{0}_{1}</Format>
<Selector>Item1,Item2.LogName</Selector>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="LogName" />
</PropertyMappings>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Aeon.Acquisition:LogHarp.bonsai">
<Heartbeats xsi:nil="true" />
<ClosingDuration xsi:nil="true" />
<LogName>PoseTrackingData</LogName>
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="3" To="5" Label="Source1" />
<Edge From="4" To="5" Label="Source2" />
<Edge From="5" To="14" Label="Source1" />
<Edge From="6" To="7" Label="Source1" />
<Edge From="7" To="10" Label="Source1" />
<Edge From="8" To="9" 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" />
</Edges>
</Workflow>
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="2" Label="Source1" />
<Edge From="1" To="2" Label="Source2" />
<Edge From="2" To="11" Label="Source1" />
<Edge From="3" To="4" Label="Source1" />
<Edge From="4" To="7" Label="Source1" />
<Edge From="5" To="6" Label="Source1" />
<Edge From="6" To="7" Label="Source2" />
<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="11" Label="Source2" />
<Edge From="11" To="12" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
</Edges>
</Workflow>
</WorkflowBuilder>
162 changes: 98 additions & 64 deletions src/Aeon.Acquisition/PoseTracking.bonsai
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.8.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:aeon="clr-namespace:Aeon.Acquisition;assembly=Aeon.Acquisition"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:aeon="clr-namespace:Aeon.Acquisition;assembly=Aeon.Acquisition"
xmlns:sleap="clr-namespace:Bonsai.Sleap;assembly=Bonsai.Sleap"
xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp"
xmlns="https://bonsai-rx.org/2018/workflow">
Expand All @@ -12,84 +12,118 @@
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Value.Image</Selector>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="PathPrefix" Description="The optional root folder containing all pretrained models." />
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="PathPrefix" />
<Property Name="ModelPath" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="aeon:CreatePoseTrackingMetadata">
<aeon:ModelPath />
</Combinator>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="PoseTrackingMetadata" Description="The name of the subject storing model metadata." />
</Expression>
<Expression xsi:type="rx:AsyncSubject">
<Name>PoseTrackingMetadata</Name>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="ModelFileName" Selector="ModelFileName" />
<Property Name="TrainingConfig" Selector="TrainingConfig" />
</PropertyMappings>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="CentroidMinConfidence" />
<Property Name="IdentityMinConfidence" />
<Property Name="PartMinConfidence" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="sleap:PredictPoseIdentities">
<sleap:CentroidMinConfidence xsi:nil="true" />
<sleap:IdentityMinConfidence xsi:nil="true" />
<sleap:PartMinConfidence xsi:nil="true" />
<sleap:ScaleFactor xsi:nil="true" />
<sleap:ColorConversion xsi:nil="true" />
</Combinator>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Seconds</Selector>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Zip" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="harp:CreateTimestamped" />
<Expression xsi:type="rx:Defer">
<Workflow>
<Nodes>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="PathPrefix" Description="The optional root folder containing all pretrained models." />
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="ModelPath" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="aeon:CreatePoseTrackingMetadata">
<aeon:ModelPath />
</Combinator>
</Expression>
<Expression xsi:type="rx:AsyncSubject">
<Name>PoseTrackingMetadata</Name>
</Expression>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Value.Image</Selector>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>PoseTrackingMetadata</Name>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="ModelFileName" Selector="ModelFileName" />
<Property Name="TrainingConfig" Selector="TrainingConfig" />
</PropertyMappings>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="CentroidMinConfidence" />
<Property Name="IdentityMinConfidence" />
<Property Name="PartMinConfidence" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="sleap:PredictPoseIdentities">
<sleap:CentroidMinConfidence xsi:nil="true" />
<sleap:IdentityMinConfidence xsi:nil="true" />
<sleap:PartMinConfidence xsi:nil="true" />
<sleap:ScaleFactor xsi:nil="true" />
<sleap:ColorConversion xsi:nil="true" />
</Combinator>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Seconds</Selector>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Zip" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="harp:CreateTimestamped" />
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>PoseTrackingMetadata</Name>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:CombineLatest" />
</Expression>
<Expression xsi:type="rx:GroupBy">
<rx:KeySelector>Item2</rx:KeySelector>
<rx:ElementSelector>Item1</rx:ElementSelector>
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="1" To="3" Label="Source1" />
<Edge From="2" To="3" Label="Source2" />
<Edge From="3" To="4" Label="Source1" />
<Edge From="5" To="6" Label="Source1" />
<Edge From="5" To="11" Label="Source1" />
<Edge From="6" To="10" Label="Source1" />
<Edge From="7" To="8" Label="Source1" />
<Edge From="8" To="10" Label="Source2" />
<Edge From="9" To="10" Label="Source3" />
<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="15" Label="Source1" />
<Edge From="14" To="15" Label="Source2" />
<Edge From="15" To="16" Label="Source1" />
<Edge From="16" To="17" Label="Source1" />
</Edges>
</Workflow>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="PoseTrackingEvents" Description="The name of the output sequence containing all pose tracking data." />
</Expression>
<Expression xsi:type="rx:PublishSubject">
<Expression xsi:type="rx:BehaviorSubject">
<Name>PoseTrackingEvents</Name>
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="0" To="11" Label="Source1" />
<Edge From="1" To="10" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="3" To="5" Label="Source1" />
<Edge From="4" To="5" Label="Source2" />
<Edge From="5" To="7" Label="Source1" />
<Edge From="6" To="7" Label="Source2" />
<Edge From="7" To="8" Label="Source1" />
<Edge From="8" To="10" Label="Source2" />
<Edge From="9" To="10" Label="Source3" />
<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="15" Label="Source1" />
<Edge From="14" To="15" Label="Source2" />
<Edge From="15" To="16" Label="Source1" />
<Edge From="0" To="2" Label="Source1" />
<Edge From="1" To="2" Label="Source2" />
<Edge From="2" To="4" Label="Source1" />
<Edge From="3" To="4" Label="Source2" />
<Edge From="4" To="5" Label="Source1" />
</Edges>
</Workflow>
</WorkflowBuilder>

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