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Refactor LDS Package #25

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merged 13 commits into from
Sep 23, 2024
Merged

Refactor LDS Package #25

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8eb97f5
Change from class attribute to assembly attribute
ncguilbeault Sep 23, 2024
d03fd86
Removed bonsai.core package reference
ncguilbeault Sep 23, 2024
0e93825
Rmoeved bonsai.core pkg reference and added bonsai.ml
ncguilbeault Sep 23, 2024
106fb3a
Removed model reference
ncguilbeault Sep 23, 2024
925bdb1
Removed dependencies in favor of bonsai.ml and python scripting pkgs
ncguilbeault Sep 23, 2024
49a3ffe
Removed numpy and python helpers, added correct package references
ncguilbeault Sep 23, 2024
f2a6e0d
Added bonsai.ml pkg ref
ncguilbeault Sep 23, 2024
c5df24a
Update to use python string formatter
ncguilbeault Sep 23, 2024
bbba751
Remove unused pkg imports
ncguilbeault Sep 23, 2024
a219b59
Added XML comment to process overload
ncguilbeault Sep 23, 2024
3c69800
Updated to use bonsai.ml
ncguilbeault Sep 23, 2024
c5e20f9
Added XML comments
ncguilbeault Sep 23, 2024
32555e8
Updated workflows
ncguilbeault Sep 23, 2024
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5 changes: 4 additions & 1 deletion src/Bonsai.ML.Design/MultidimensionalArrayVisualizer.cs
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@@ -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>
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1 change: 0 additions & 1 deletion src/Bonsai.ML.HiddenMarkovModels/Bonsai.ML.HiddenMarkovModels.csproj
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Expand Up @@ -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" />
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10 changes: 5 additions & 5 deletions src/Bonsai.ML.LinearDynamicalSystems/Bonsai.ML.LinearDynamicalSystems.csproj
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Expand Up @@ -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>
33 changes: 0 additions & 33 deletions src/Bonsai.ML.LinearDynamicalSystems/CreateModelReference.cs
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6 changes: 2 additions & 4 deletions src/Bonsai.ML.LinearDynamicalSystems/Kinematics/CreateKFModel.bonsai
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@@ -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"
Expand All @@ -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>
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3 changes: 1 addition & 2 deletions src/Bonsai.ML.LinearDynamicalSystems/Kinematics/Forecast.cs
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@@ -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
{
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1 change: 1 addition & 0 deletions src/Bonsai.ML.LinearDynamicalSystems/Kinematics/KFModelParameters.cs
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Expand Up @@ -3,6 +3,7 @@
using System.Reactive.Linq;
using Python.Runtime;
using Newtonsoft.Json;
using Bonsai.ML.Python;

namespace Bonsai.ML.LinearDynamicalSystems.Kinematics
{
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2 changes: 1 addition & 1 deletion src/Bonsai.ML.LinearDynamicalSystems/Kinematics/PerformForecasting.bonsai
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Expand Up @@ -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">
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9 changes: 5 additions & 4 deletions src/Bonsai.ML.LinearDynamicalSystems/Kinematics/PerformInference.bonsai
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Expand Up @@ -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>
Expand Down Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion src/Bonsai.ML.LinearDynamicalSystems/Learning/RunOptimizationAsync.bonsai
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Expand Up @@ -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>
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6 changes: 2 additions & 4 deletions src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/CreateKFModel.bonsai
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Expand Up @@ -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">
Expand Down Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/CreateMultivariatePDF.bonsai
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Expand Up @@ -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">
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1 change: 1 addition & 0 deletions src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/GridParameters.cs
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Expand Up @@ -3,6 +3,7 @@
using System.Reactive.Linq;
using Newtonsoft.Json;
using Python.Runtime;
using Bonsai.ML.Python;

namespace Bonsai.ML.LinearDynamicalSystems.LinearRegression
{
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9 changes: 5 additions & 4 deletions src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/KFModelParameters.cs
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using Newtonsoft.Json;
using System;
using System.Reactive.Linq;
using Bonsai.ML.Python;
using Python.Runtime;
using System.Xml.Serialization;

Expand Down Expand Up @@ -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);
}
}

Expand All @@ -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);
}
}

Expand Down Expand Up @@ -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}";
}
}
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3 changes: 2 additions & 1 deletion src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/MultivariatePDF.cs
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Expand Up @@ -3,6 +3,7 @@
using System.Reactive.Linq;
using Python.Runtime;
using System.Xml.Serialization;
using Bonsai.ML.Python;

namespace Bonsai.ML.LinearDynamicalSystems.LinearRegression
{
Expand Down Expand Up @@ -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
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7 changes: 4 additions & 3 deletions src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/PerformInference.bonsai
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<?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>
Expand Down Expand Up @@ -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>
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26 changes: 0 additions & 26 deletions src/Bonsai.ML.LinearDynamicalSystems/ModelReference.cs
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