Skip to content
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

Jump to bottom

Add support for grouping pose tracking by model #152

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Add support for grouping pose tracking by model #152

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
134 changes: 83 additions & 51 deletions src/Aeon.Acquisition/LogPoseTracking.bonsai
View file
Open in desktop
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
View file
Open in desktop
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>
Loading