Merge pull request #149 from SainsburyWellcomeCentre/gl-dev

Remove obsolete operators and update operator naming conventions
SainsburyWellcomeCentre · Sep 28, 2023 · 18c2b77 · 18c2b77
2 parents b9bf23e + f724217
commit 18c2b77
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Showing 12 changed files with 32 additions and 246 deletions.
diff --git a/src/Aeon.Acquisition/ActivityTracking.bonsai b/src/Aeon.Acquisition/ActivityTracking.bonsai
@@ -4,7 +4,7 @@
                  xmlns:cv="clr-namespace:Bonsai.Vision;assembly=Bonsai.Vision"
                  xmlns:dsp="clr-namespace:Bonsai.Dsp;assembly=Bonsai.Dsp"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
-                 xmlns:aeon="clr-namespace:Aeon.Acquisition;assembly=Aeon.Acquisition"
+                 xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Description>Measures pixel motion in the specified region of interest.</Description>
   <Workflow>
@@ -54,7 +54,7 @@
         <Combinator xsi:type="rx:Zip" />
       </Expression>
       <Expression xsi:type="Combinator">
-        <Combinator xsi:type="aeon:CreateTimestamped" />
+        <Combinator xsi:type="harp:CreateTimestamped" />
       </Expression>
       <Expression xsi:type="ExternalizedMapping">
         <Property Name="Name" DisplayName="TrackingEvents" />

diff --git a/src/Aeon.Acquisition/Aeon.Acquisition.csproj b/src/Aeon.Acquisition/Aeon.Acquisition.csproj
@@ -6,7 +6,7 @@
     <PackageTags>Bonsai Rx Project Aeon Acquisition</PackageTags>
     <TargetFramework>net472</TargetFramework>
     <VersionPrefix>0.5.0</VersionPrefix>
-    <VersionSuffix>build230923</VersionSuffix>
+    <VersionSuffix>build230924</VersionSuffix>
   </PropertyGroup>
 
   <ItemGroup>

diff --git a/src/Aeon.Acquisition/AeonWriter.cs b/src/Aeon.Acquisition/AeonWriter.cs
diff --git a/src/Aeon.Acquisition/CreateTimestamped.cs b/src/Aeon.Acquisition/CreateTimestamped.cs
diff --git a/src/Aeon.Acquisition/LogData.bonsai b/src/Aeon.Acquisition/LogData.bonsai
@@ -74,12 +74,11 @@
             <Expression xsi:type="ExternalizedMapping">
               <Property Name="Selector" />
             </Expression>
-            <Expression xsi:type="aeon:AeonWriter">
+            <Expression xsi:type="io:CsvWriter">
               <io:Append>false</io:Append>
               <io:Overwrite>false</io:Overwrite>
               <io:Suffix>None</io:Suffix>
               <io:IncludeHeader>true</io:IncludeHeader>
-              <aeon:FlushDuration>PT1M</aeon:FlushDuration>
             </Expression>
             <Expression xsi:type="WorkflowOutput" />
           </Nodes>

diff --git a/src/Aeon.Acquisition/TransformTimestamped.cs b/src/Aeon.Acquisition/TransformTimestamped.cs
diff --git a/src/Aeon.Environment/Aeon.Environment.csproj b/src/Aeon.Environment/Aeon.Environment.csproj
@@ -7,7 +7,7 @@
     <PackageTags>Bonsai Rx Project Aeon Environment</PackageTags>
     <TargetFramework>net472</TargetFramework>
     <VersionPrefix>0.1.0</VersionPrefix>
-    <VersionSuffix>build230926</VersionSuffix>
+    <VersionSuffix>build230927</VersionSuffix>
   </PropertyGroup>
 
   <ItemGroup>

diff --git a/src/Aeon.Environment/LightController.bonsai b/src/Aeon.Environment/LightController.bonsai
@@ -5,7 +5,7 @@
                  xmlns:osc="clr-namespace:Bonsai.Osc;assembly=Bonsai.Osc"
                  xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
-                 xmlns:aeon="clr-namespace:Aeon.Acquisition;assembly=Aeon.Acquisition"
+                 xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp"
                  xmlns:sys="clr-namespace:System;assembly=mscorlib"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Description>Provides control and acquisition functionality for automated room lighting.</Description>
@@ -33,16 +33,13 @@ Item1 as Channel,
 Item2 as Value)</scr:Expression>
       </Expression>
       <Expression xsi:type="SubscribeSubject">
-        <Name>GlobalTrigger</Name>
-      </Expression>
-      <Expression xsi:type="MemberSelector">
-        <Selector>Seconds</Selector>
+        <Name>SynchronizerEvents</Name>
       </Expression>
       <Expression xsi:type="Combinator">
         <Combinator xsi:type="rx:WithLatestFrom" />
       </Expression>
       <Expression xsi:type="Combinator">
-        <Combinator xsi:type="aeon:CreateTimestamped" />
+        <Combinator xsi:type="harp:CreateTimestamped" />
       </Expression>
       <Expression xsi:type="ExternalizedMapping">
         <Property Name="Name" DisplayName="LightEvents" Description="The name of the output sequence containing all timestamped light events." />
@@ -90,22 +87,21 @@ Item2 as Value)</scr:Expression>
       <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="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="10" Label="Source1" />
-      <Edge From="9" To="10" Label="Source2" />
-      <Edge From="10" To="11" Label="Source1" />
-      <Edge From="12" To="13" Label="Source1" />
-      <Edge From="13" To="18" Label="Source1" />
-      <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" />
-      <Edge From="19" To="21" Label="Source1" />
-      <Edge From="20" To="21" Label="Source2" />
+      <Edge From="4" To="6" Label="Source1" />
+      <Edge From="5" To="6" Label="Source2" />
+      <Edge From="6" To="7" 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="11" To="12" Label="Source1" />
+      <Edge From="12" To="17" Label="Source1" />
+      <Edge From="13" To="14" Label="Source1" />
+      <Edge From="14" To="17" Label="Source2" />
+      <Edge From="15" To="16" Label="Source1" />
+      <Edge From="16" To="17" Label="Source3" />
+      <Edge From="17" To="18" Label="Source1" />
+      <Edge From="18" To="20" Label="Source1" />
+      <Edge From="19" To="20" Label="Source2" />
     </Edges>
   </Workflow>
 </WorkflowBuilder>
diff --git a/src/Aeon.Environment/RoomLightController.cs → src/Aeon.Environment/RoomLightDevice.cs b/src/Aeon.Environment/RoomLightController.cs → src/Aeon.Environment/RoomLightDevice.cs
@@ -13,9 +13,8 @@
 namespace Aeon.Environment
 {
     [Combinator]
-    [WorkflowElementCategory(ElementCategory.Source)]
     [Description("Creates and configures a connection to the room light controller over Brainboxes Ethernet to Serial.")]
-    public class RoomLightController
+    public class RoomLightDevice
     {
         readonly CreateSerialPort serialPort = new();
 

diff --git a/src/Aeon.Environment/WeightScale.bonsai b/src/Aeon.Environment/WeightScale.bonsai
@@ -4,7 +4,7 @@
                  xmlns:port="clr-namespace:Bonsai.IO.Ports;assembly=Bonsai.System"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                  xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions"
-                 xmlns:aeon="clr-namespace:Aeon.Acquisition;assembly=Aeon.Acquisition"
+                 xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp"
                  xmlns:sys="clr-namespace:System;assembly=mscorlib"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Description>Contains acquisition functionality for automated arena weighing scales.</Description>
@@ -62,7 +62,7 @@ Item2.Contains("?") ? 0.0 : 1.0 as Confidence)</scr:Expression>
         <Combinator xsi:type="rx:WithLatestFrom" />
       </Expression>
       <Expression xsi:type="Combinator">
-        <Combinator xsi:type="aeon:CreateTimestamped" />
+        <Combinator xsi:type="harp:CreateTimestamped" />
       </Expression>
       <Expression xsi:type="ExternalizedMapping">
         <Property Name="Name" DisplayName="WeightEvents" Description="The name of the output sequence containing all weight events." />
@@ -100,7 +100,7 @@ Item2.Contains("?") ? 0.0 : 1.0 as Confidence)</scr:Expression>
         <Combinator xsi:type="rx:WithLatestFrom" />
       </Expression>
       <Expression xsi:type="Combinator">
-        <Combinator xsi:type="aeon:CreateTimestamped" />
+        <Combinator xsi:type="harp:CreateTimestamped" />
       </Expression>
       <Expression xsi:type="ExternalizedMapping">
         <Property Name="Name" DisplayName="TareEvents" Description="The name of the output sequence containing all timestamped tare events." />

diff --git a/src/Aeon.Tests/AssertWorkflow.cs b/src/Aeon.Tests/AssertWorkflow.cs
@@ -33,7 +33,10 @@ public static void CanBuildEmbeddedResources(Assembly assembly)
                             workflowElement.GetType().Name != nameof(AeonCapture))
 #pragma warning restore CS0612 // Type or member is obsolete
                         {
-                            Assert.IsNotInstanceOfType(workflowElement, typeof(UnknownTypeBuilder));
+                            Assert.IsNotInstanceOfType(
+                                workflowElement,
+                                typeof(UnknownTypeBuilder),
+                                $"Embedded workflow: {name}.");
                         }
                         return builder;
                     }, recurse: true);

diff --git a/src/Aeon.Tests/OperatorTests.cs b/src/Aeon.Tests/OperatorTests.cs
@@ -11,7 +11,7 @@ public class OperatorTests
         [TestMethod]
         public void Build_Workflows()
         {
-            var acquisition = typeof(CreateTimestamped).Assembly;
+            var acquisition = typeof(GroupByTime).Assembly;
             var environment = typeof(EnvironmentState).Assembly;
             var foraging = typeof(WheelDisplacement).Assembly;
             AssertWorkflow.CanBuildEmbeddedResources(acquisition);