Merge pull request #139 from SainsburyWellcomeCentre/gl-dev

Refactor embedded operators to use latest workflow modules
SainsburyWellcomeCentre · Aug 18, 2023 · 29a51cf · 29a51cf
2 parents ef7e3af + bcd446d
commit 29a51cf
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Showing 32 changed files with 352 additions and 383 deletions.
diff --git a/src/Aeon.Acquisition/ActivityTracking.bonsai b/src/Aeon.Acquisition/ActivityTracking.bonsai
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<WorkflowBuilder Version="2.6.2"
+<WorkflowBuilder Version="2.8.0"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                  xmlns:cv="clr-namespace:Bonsai.Vision;assembly=Bonsai.Vision"
                  xmlns:dsp="clr-namespace:Bonsai.Dsp;assembly=Bonsai.Dsp"
@@ -15,12 +15,6 @@
       <Expression xsi:type="MemberSelector">
         <Selector>Value.Image</Selector>
       </Expression>
-      <Expression xsi:type="ExternalizedMapping">
-        <Property Name="ThresholdValue" />
-      </Expression>
-      <Expression xsi:type="ExternalizedMapping">
-        <Property Name="Name" DisplayName="TrackingEvents" />
-      </Expression>
       <Expression xsi:type="ExternalizedMapping">
         <Property Name="Regions" />
       </Expression>
@@ -35,6 +29,9 @@
           </cv:FillValue>
         </Combinator>
       </Expression>
+      <Expression xsi:type="ExternalizedMapping">
+        <Property Name="ThresholdValue" />
+      </Expression>
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="cv:BackgroundSubtraction">
           <cv:BackgroundFrames>1</cv:BackgroundFrames>
@@ -59,25 +56,28 @@
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="aeon:CreateTimestamped" />
       </Expression>
-      <Expression xsi:type="PublishSubject">
+      <Expression xsi:type="ExternalizedMapping">
+        <Property Name="Name" DisplayName="TrackingEvents" />
+      </Expression>
+      <Expression xsi:type="rx:PublishSubject">
         <Name>ActivityEvents</Name>
       </Expression>
       <Expression xsi:type="WorkflowOutput" />
     </Nodes>
     <Edges>
       <Edge From="0" To="1" Label="Source1" />
-      <Edge From="0" To="9" Label="Source1" />
-      <Edge From="1" To="5" Label="Source1" />
-      <Edge From="2" To="6" Label="Source2" />
-      <Edge From="3" To="12" Label="Source2" />
+      <Edge From="0" To="8" Label="Source1" />
+      <Edge From="1" To="3" Label="Source1" />
+      <Edge From="2" To="3" Label="Source2" />
+      <Edge From="3" To="5" Label="Source1" />
       <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="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="7" To="9" Label="Source1" />
+      <Edge From="8" To="9" Label="Source2" />
+      <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" />
     </Edges>
   </Workflow>

diff --git a/src/Aeon.Acquisition/Aeon.Acquisition.csproj b/src/Aeon.Acquisition/Aeon.Acquisition.csproj
@@ -7,7 +7,7 @@
     <PackageTags>Bonsai Rx Project Aeon Acquisition</PackageTags>
     <TargetFramework>net472</TargetFramework>
     <VersionPrefix>0.4.0</VersionPrefix>
-    <VersionSuffix>build230818</VersionSuffix>
+    <VersionSuffix>build230821</VersionSuffix>
   </PropertyGroup>
 
   <ItemGroup>
@@ -18,6 +18,7 @@
     <PackageReference Include="Bonsai.Core" Version="2.8.1" />
     <PackageReference Include="Bonsai.Audio" Version="2.8.0" />
     <PackageReference Include="Bonsai.Harp" Version="3.5.0" />
+    <PackageReference Include="Harp.CameraControllerGen2" Version="0.1.0" />
     <PackageReference Include="Harp.OutputExpander" Version="0.2.0-build230803" />
     <PackageReference Include="Bonsai.Osc" Version="2.7.0" />
     <PackageReference Include="Bonsai.Pylon" Version="0.3.0" />
@@ -27,6 +28,7 @@
     <PackageReference Include="Bonsai.System" Version="2.8.0" />
     <PackageReference Include="Bonsai.Scripting.Expressions" Version="2.8.0" />
     <PackageReference Include="Bonsai.ZeroMQ" Version="0.2.0" />
+    <PackageReference Include="Harp.Synchronizer" Version="0.1.0" />
     <PackageReference Include="LibGit2Sharp" Version="0.25.4" />
     <PackageReference Include="Bonsai.Vision" Version="2.8.0" />
     <PackageReference Include="MathNet.Numerics" Version="4.5.1" />

diff --git a/src/Aeon.Acquisition/AeonAudio.cs b/src/Aeon.Acquisition/AeonAudio.cs
@@ -13,21 +13,20 @@ namespace Aeon.Acquisition
     [Description("Configures and initializes a software timestamped audio capture.")]
     public class AeonAudio : AudioCapture
     {
-        IEnumerable<Timestamped<Mat>> TimestampBuffers(IEnumerable<Mat> buffers, HarpMessage message)
+        IEnumerable<Timestamped<Mat>> TimestampBuffers(IEnumerable<Mat> buffers, double timestamp)
         {
-            var timestamp = message.GetTimestamp();
             foreach (var buffer in buffers)
             {
                 yield return Timestamped.Create(buffer, timestamp);
             }
         }
 
-        public IObservable<Timestamped<Mat>> Generate(IObservable<HarpMessage> source)
+        public IObservable<Timestamped<Mat>> Generate<TPayload>(IObservable<Timestamped<TPayload>> source)
         {
             var data = Generate();
             return source.Publish(triggers =>
                 data.Buffer(triggers)
-                    .Zip(triggers, (list, trigger) => TimestampBuffers(list, trigger))
+                    .Zip(triggers, (list, trigger) => TimestampBuffers(list, trigger.Seconds))
                     .SelectMany(x => x));
         }
     }

diff --git a/src/Aeon.Acquisition/AudioSource.bonsai b/src/Aeon.Acquisition/AudioSource.bonsai
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<WorkflowBuilder Version="2.7.0"
+<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"