Merge pull request #25 from bonsai-rx/lds-refactor

Refactor LDS Package
bonsai-rx · Sep 23, 2024 · 6d3ccfa · 6d3ccfa
2 parents 3a3bc3b + 32555e8
commit 6d3ccfa
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Showing 24 changed files with 66 additions and 514 deletions.
diff --git a/src/Bonsai.ML.Design/MultidimensionalArrayVisualizer.cs b/src/Bonsai.ML.Design/MultidimensionalArrayVisualizer.cs
@@ -1,13 +1,16 @@
 using System;
 using System.Windows.Forms;
+using Bonsai;
 using Bonsai.Design;
 
+[assembly: TypeVisualizer(typeof(Bonsai.ML.Design.MultidimensionalArrayVisualizer),
+    Target = typeof(double[,]))]
+
 namespace Bonsai.ML.Design
 {
     /// <summary>
     /// Provides a type visualizer to display multi dimensional array data as a heatmap.
     /// </summary>
-    [TypeVisualizer(typeof(MultidimensionalArrayVisualizer), Target = typeof(double[,]))]
     public class MultidimensionalArrayVisualizer : DialogTypeVisualizer
     {
         /// <summary>

diff --git a/src/Bonsai.ML.HiddenMarkovModels/Bonsai.ML.HiddenMarkovModels.csproj b/src/Bonsai.ML.HiddenMarkovModels/Bonsai.ML.HiddenMarkovModels.csproj
@@ -6,7 +6,6 @@
     <TargetFrameworks>net472;netstandard2.0</TargetFrameworks>
   </PropertyGroup>
   <ItemGroup>
-    <PackageReference Include="Bonsai.Core" Version="2.8.1" />
     <PackageReference Include="Bonsai.Scripting.Expressions" Version="2.8.0" />
     <PackageReference Include="Bonsai.Scripting.Python" Version="0.2.1" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/Bonsai.ML.LinearDynamicalSystems.csproj b/src/Bonsai.ML.LinearDynamicalSystems/Bonsai.ML.LinearDynamicalSystems.csproj
@@ -5,13 +5,13 @@
     <PackageTags>Bonsai Rx ML KalmanFilter LinearDynamicalSystems</PackageTags>
     <TargetFrameworks>net472;netstandard2.0</TargetFrameworks>
   </PropertyGroup>
-  <ItemGroup>
-    <PackageReference Include="Bonsai.Core" Version="2.8.1" />
-    <PackageReference Include="Bonsai.Scripting.Python" Version="0.2.1" />
-    <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
-  </ItemGroup>
   <ItemGroup>
     <EmbeddedResource Include="*.py" />
     <EmbeddedResource Include="**\*.bonsai" />
   </ItemGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\Bonsai.ML\Bonsai.ML.csproj" />
+    <ProjectReference Include="..\Bonsai.ML.Python\Bonsai.ML.Python.csproj" />
+    <ProjectReference Include="..\Bonsai.ML.Data\Bonsai.ML.Data.csproj" />
+  </ItemGroup>
 </Project>
diff --git a/src/Bonsai.ML.LinearDynamicalSystems/CreateModelReference.cs b/src/Bonsai.ML.LinearDynamicalSystems/CreateModelReference.cs
diff --git a/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/CreateKFModel.bonsai b/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/CreateKFModel.bonsai
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <WorkflowBuilder Version="2.8.1"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-                 xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
+                 xmlns:p1="clr-namespace:Bonsai.ML;assembly=Bonsai.ML"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                  xmlns:p2="clr-namespace:Bonsai.ML.LinearDynamicalSystems.Kinematics;assembly=Bonsai.ML.LinearDynamicalSystems"
                  xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
@@ -12,9 +12,7 @@
         <Property Name="Name" Category="ModelReference" />
       </Expression>
       <Expression xsi:type="Combinator">
-        <Combinator xsi:type="p1:CreateModelReference">
-          <p1:Name>model</p1:Name>
-        </Combinator>
+        <Combinator xsi:type="p1:CreateModelReference" />
       </Expression>
       <Expression xsi:type="rx:BehaviorSubject">
         <Name>model</Name>

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/Forecast.cs b/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/Forecast.cs
@@ -1,12 +1,11 @@
 using System;
-using System.Reactive;
 using System.Reactive.Linq;
-using System.Collections.ObjectModel;
 using System.Xml.Serialization;
 using System.ComponentModel;
 using Newtonsoft.Json;
 using Python.Runtime;
 using System.Collections.Generic;
+using Bonsai.ML.Python;
 
 namespace Bonsai.ML.LinearDynamicalSystems.Kinematics
 {

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/KFModelParameters.cs b/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/KFModelParameters.cs
@@ -3,6 +3,7 @@
 using System.Reactive.Linq;
 using Python.Runtime;
 using Newtonsoft.Json;
+using Bonsai.ML.Python;
 
 namespace Bonsai.ML.LinearDynamicalSystems.Kinematics
 {

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/PerformForecasting.bonsai b/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/PerformForecasting.bonsai
@@ -2,7 +2,7 @@
 <WorkflowBuilder Version="2.8.1"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                  xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
-                 xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
+                 xmlns:p1="clr-namespace:Bonsai.ML;assembly=Bonsai.ML"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                  xmlns:p2="clr-namespace:Bonsai.ML.LinearDynamicalSystems.Kinematics;assembly=Bonsai.ML.LinearDynamicalSystems"
                  xmlns="https://bonsai-rx.org/2018/workflow">

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/PerformInference.bonsai b/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/PerformInference.bonsai
@@ -2,9 +2,10 @@
 <WorkflowBuilder Version="2.8.1"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                  xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
-                 xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
+                 xmlns:p1="clr-namespace:Bonsai.ML;assembly=Bonsai.ML"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
-                 xmlns:p2="clr-namespace:Bonsai.ML.LinearDynamicalSystems.Kinematics;assembly=Bonsai.ML.LinearDynamicalSystems"
+                 xmlns:p2="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
+                 xmlns:p3="clr-namespace:Bonsai.ML.LinearDynamicalSystems.Kinematics;assembly=Bonsai.ML.LinearDynamicalSystems"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Workflow>
     <Nodes>
@@ -127,10 +128,10 @@
         </Combinator>
       </Expression>
       <Expression xsi:type="Combinator">
-        <Combinator xsi:type="p1:State" />
+        <Combinator xsi:type="p2:State" />
       </Expression>
       <Expression xsi:type="Combinator">
-        <Combinator xsi:type="p2:KinematicState" />
+        <Combinator xsi:type="p3:KinematicState" />
       </Expression>
       <Expression xsi:type="WorkflowOutput" />
     </Nodes>

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/Learning/RunOptimizationAsync.bonsai b/src/Bonsai.ML.LinearDynamicalSystems/Learning/RunOptimizationAsync.bonsai
@@ -3,7 +3,7 @@
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                  xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
-                 xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
+                 xmlns:p1="clr-namespace:Bonsai.ML;assembly=Bonsai.ML"
                  xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Workflow>

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/CreateKFModel.bonsai b/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/CreateKFModel.bonsai
@@ -2,7 +2,7 @@
 <WorkflowBuilder Version="2.8.1"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                  xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems.LinearRegression;assembly=Bonsai.ML.LinearDynamicalSystems"
-                 xmlns:p2="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
+                 xmlns:p2="clr-namespace:Bonsai.ML;assembly=Bonsai.ML"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                  xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
                  xmlns="https://bonsai-rx.org/2018/workflow">
@@ -31,9 +31,7 @@
         <Property Name="Name" Category="ModelReference" />
       </Expression>
       <Expression xsi:type="Combinator">
-        <Combinator xsi:type="p2:CreateModelReference">
-          <p2:Name>model</p2:Name>
-        </Combinator>
+        <Combinator xsi:type="p2:CreateModelReference" />
       </Expression>
       <Expression xsi:type="rx:BehaviorSubject">
         <Name>model</Name>

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/CreateMultivariatePDF.bonsai b/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/CreateMultivariatePDF.bonsai
@@ -2,7 +2,7 @@
 <WorkflowBuilder Version="2.8.1"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                  xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
-                 xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
+                 xmlns:p1="clr-namespace:Bonsai.ML;assembly=Bonsai.ML"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                  xmlns:p2="clr-namespace:Bonsai.ML.LinearDynamicalSystems.LinearRegression;assembly=Bonsai.ML.LinearDynamicalSystems"
                  xmlns="https://bonsai-rx.org/2018/workflow">

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/GridParameters.cs b/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/GridParameters.cs
@@ -3,6 +3,7 @@
 using System.Reactive.Linq;
 using Newtonsoft.Json;
 using Python.Runtime;
+using Bonsai.ML.Python;
 
 namespace Bonsai.ML.LinearDynamicalSystems.LinearRegression
 {

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/KFModelParameters.cs b/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/KFModelParameters.cs
@@ -2,6 +2,7 @@
 using Newtonsoft.Json;
 using System;
 using System.Reactive.Linq;
+using Bonsai.ML.Python;
 using Python.Runtime;
 using System.Xml.Serialization;
 
@@ -105,7 +106,7 @@ public int NumFeatures
             set
             {
                 _x = value;
-                _xString = _x == null ? "None" : NumpyHelper.NumpyParser.ParseArray(_x);
+                _xString = _x == null ? "None" : StringFormatter.FormatToPython(_x);
             }
         }
 
@@ -125,7 +126,7 @@ public int NumFeatures
             set
             {
                 _p = value;
-                _pString = _p == null ? "None" : NumpyHelper.NumpyParser.ParseArray(_p);
+                _pString = _p == null ? "None" : StringFormatter.FormatToPython(_p);
             }
         }
 
@@ -188,10 +189,10 @@ public IObservable<KFModelParameters> Process<TSource>(IObservable<TSource> sour
                     P = _p
                 });
         }
-
+
+        /// <inheritdoc/>
         public override string ToString()
         {
-
             return $"likelihood_precision_coef={_likelihood_precision_coefString}, prior_precision_coef={_prior_precision_coefString}, n_features={_n_featuresString}, x={_xString}, P={_pString}";
         }
     }

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/MultivariatePDF.cs b/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/MultivariatePDF.cs
@@ -3,6 +3,7 @@
 using System.Reactive.Linq;
 using Python.Runtime;
 using System.Xml.Serialization;
+using Bonsai.ML.Python;
 
 namespace Bonsai.ML.LinearDynamicalSystems.LinearRegression
 {
@@ -35,7 +36,7 @@ public IObservable<MultivariatePDF> Process(IObservable<PyObject> source)
             return Observable.Select(source, pyObject =>
             {
                 var gridParameters = GridParameters.ConvertPyObject(pyObject);
-                var values = (double[,])pyObject.GetArrayAttribute("pdf_values");
+                var values = (double[,])pyObject.GetArrayAttr("pdf_values");
                 return new MultivariatePDF {
                     GridParameters = gridParameters,
                     Values = values

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/PerformInference.bonsai b/src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/PerformInference.bonsai
@@ -1,9 +1,10 @@
 <?xml version="1.0" encoding="utf-8"?>
-<WorkflowBuilder Version="2.8.1"
+<WorkflowBuilder Version="2.8.2"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                  xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
-                 xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
+                 xmlns:p1="clr-namespace:Bonsai.ML;assembly=Bonsai.ML"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
+                 xmlns:p2="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Workflow>
     <Nodes>
@@ -126,7 +127,7 @@
         </Combinator>
       </Expression>
       <Expression xsi:type="Combinator">
-        <Combinator xsi:type="p1:State" />
+        <Combinator xsi:type="p2:State" />
       </Expression>
       <Expression xsi:type="WorkflowOutput" />
     </Nodes>

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/ModelReference.cs b/src/Bonsai.ML.LinearDynamicalSystems/ModelReference.cs