Split visualizers package into separate projects for individual proje…

…cts within the Bonsai.ML collection
bonsai-rx · Jul 16, 2024 · f10087a · f10087a
1 parent 05007b9
commit f10087a
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Showing 20 changed files with 167 additions and 84 deletions.
diff --git a/Bonsai.ML.sln b/Bonsai.ML.sln
@@ -1,4 +1,4 @@
-
+
 Microsoft Visual Studio Solution File, Format Version 12.00
 # Visual Studio Version 17
 VisualStudioVersion = 17.0.31903.59
@@ -22,6 +22,10 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution
 EndProject
 Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Bonsai.ML.HiddenMarkovModels", "src\Bonsai.ML.HiddenMarkovModels\Bonsai.ML.HiddenMarkovModels.csproj", "{BAD0A733-8EFB-4EAF-9648-9851656AF7FF}"
 EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Bonsai.ML.Visualizers.LinearDynamicalSystems", "src\Bonsai.ML.Visualizers.LinearDynamicalSystems\Bonsai.ML.Visualizers.LinearDynamicalSystems.csproj", "{17DF50BE-F481-4904-A4C8-5DF9725B2CA1}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Bonsai.ML.Visualizers.HiddenMarkovModels", "src\Bonsai.ML.Visualizers.HiddenMarkovModels\Bonsai.ML.Visualizers.HiddenMarkovModels.csproj", "{FC395DDC-62A4-4E14-A198-272AB05B33C7}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -48,16 +52,26 @@ Global
 		{BAD0A733-8EFB-4EAF-9648-9851656AF7FF}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{BAD0A733-8EFB-4EAF-9648-9851656AF7FF}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{BAD0A733-8EFB-4EAF-9648-9851656AF7FF}.Release|Any CPU.Build.0 = Release|Any CPU
+		{17DF50BE-F481-4904-A4C8-5DF9725B2CA1}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{17DF50BE-F481-4904-A4C8-5DF9725B2CA1}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{17DF50BE-F481-4904-A4C8-5DF9725B2CA1}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{17DF50BE-F481-4904-A4C8-5DF9725B2CA1}.Release|Any CPU.Build.0 = Release|Any CPU
+		{FC395DDC-62A4-4E14-A198-272AB05B33C7}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{FC395DDC-62A4-4E14-A198-272AB05B33C7}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{FC395DDC-62A4-4E14-A198-272AB05B33C7}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{FC395DDC-62A4-4E14-A198-272AB05B33C7}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
 	EndGlobalSection
 	GlobalSection(NestedProjects) = preSolution
+		{FC395DDC-62A4-4E14-A198-272AB05B33C7} = {12312384-8828-4786-AE19-EFCEDF968290}
 		{AA6BE73F-1E15-49A5-AC3C-CD069035C940} = {12312384-8828-4786-AE19-EFCEDF968290}
 		{17AABD18-E275-4409-9E33-3D755B809FF6} = {12312384-8828-4786-AE19-EFCEDF968290}
 		{196AA5C7-AE8A-477B-B01A-B94676EC60EE} = {12312384-8828-4786-AE19-EFCEDF968290}
 		{81DB65B3-EA65-4947-8CF1-0E777324C082} = {461FE3E2-21C4-47F9-8405-DF72326AAB2B}
 		{BAD0A733-8EFB-4EAF-9648-9851656AF7FF} = {12312384-8828-4786-AE19-EFCEDF968290}
+		{17DF50BE-F481-4904-A4C8-5DF9725B2CA1} = {12312384-8828-4786-AE19-EFCEDF968290}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		SolutionGuid = {B6468F13-97CD-45E0-9E1E-C122D7F1E09F}

diff --git a/src/Bonsai.ML.Visualizers.HiddenMarkovModels/Bonsai.ML.Visualizers.HiddenMarkovModels.csproj b/src/Bonsai.ML.Visualizers.HiddenMarkovModels/Bonsai.ML.Visualizers.HiddenMarkovModels.csproj
@@ -0,0 +1,20 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <Title>Bonsai.ML.Visualizers.HiddenMarkovModels</Title>
+    <Description>A package for visualizing data from the Bonsai.ML.HiddenMarkovModels package.</Description>
+    <PackageTags>Bonsai Rx ML Machine Learning Visualizers Hidden Markov Models</PackageTags>
+    <TargetFramework>net472</TargetFramework>
+    <UseWindowsForms>true</UseWindowsForms>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <PackageReference Include="Bonsai.Core" Version="2.8.2" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\Bonsai.ML.Visualizers\Bonsai.ML.Visualizers.csproj" />
+    <ProjectReference Include="..\Bonsai.ML.HiddenMarkovModels\Bonsai.ML.HiddenMarkovModels.csproj" />
+  </ItemGroup>
+
+</Project>
diff --git a/...GaussianObservationsClustersVisualizer.cs → ...GaussianObservationsClustersVisualizer.cs b/...GaussianObservationsClustersVisualizer.cs → ...GaussianObservationsClustersVisualizer.cs
@@ -9,7 +9,6 @@
 using OxyPlot.Series;
 using OxyPlot.Axes;
 using OxyPlot.WindowsForms;
-using MathNet.Numerics.LinearAlgebra;
 
 [assembly: TypeVisualizer(typeof(GaussianObservationsClustersVisualizer), Target = typeof(GaussianObservationsStatistics))]
 
@@ -245,40 +244,20 @@ public override void Show(object value)
                     var yVar = gaussianObservationsStatistics.CovarianceMatrices[i, dimension2SelectedIndex, dimension2SelectedIndex];
                     var xyCov = gaussianObservationsStatistics.CovarianceMatrices[i, dimension2SelectedIndex, dimension1SelectedIndex];
 
-                    var covariance = Matrix<double>.Build.DenseOfArray(new double[,] {
-                        {
-                            xVar,
-                            xyCov
-                        },
-                        {
-                            xyCov,
-                            yVar
-                        },
-                    });
-
-                    var evd = covariance.Evd();
-                    var evals = evd.EigenValues.Real();
-                    evals = evals.PointwiseAbsoluteMaximum(0);
-                    var evecs = evd.EigenVectors;
-
-                    double angle = Math.Atan2(evecs[1, 0], evecs[0, 0]);
+                    var ellipseParameters = EllipseHelper.GetEllipseParameters(xVar, yVar, xyCov);
 
                     for (int j = 1; j < 4; j++)
                     {
-
-                        var majorAxis = j * Math.Sqrt(evals[0]);
-                        var minorAxis = j * Math.Sqrt(evals[1]);
-
                         var points = new List<DataPoint>();
                         int numPoints = 100;
                         for (int k = 0; k < numPoints + 1; k++)
                         {
                             double theta = 2 * Math.PI * k / numPoints;
-                            double x = majorAxis * Math.Cos(theta);
-                            double y = minorAxis * Math.Sin(theta);
+                            double x = j * ellipseParameters.MajorAxis * Math.Cos(theta);
+                            double y = j * ellipseParameters.MinorAxis * Math.Sin(theta);
 
-                            double xRot = x * Math.Cos(angle) - y * Math.Sin(angle);
-                            double yRot = x * Math.Sin(angle) + y * Math.Cos(angle);
+                            double xRot = x * Math.Cos(ellipseParameters.Angle) - y * Math.Sin(ellipseParameters.Angle);
+                            double yRot = x * Math.Sin(ellipseParameters.Angle) + y * Math.Cos(ellipseParameters.Angle);
 
                             points.Add(new DataPoint(xMean + xRot, yMean + yRot));
                         }

diff --git a/...ussianObservationsStatisticsVisualizer.cs → ...ussianObservationsStatisticsVisualizer.cs b/...ussianObservationsStatisticsVisualizer.cs → ...ussianObservationsStatisticsVisualizer.cs
diff --git a/src/Bonsai.ML.Visualizers.HiddenMarkovModels/Properties/launchSettings.json b/src/Bonsai.ML.Visualizers.HiddenMarkovModels/Properties/launchSettings.json
@@ -0,0 +1,10 @@
+{
+  "profiles": {
+    "Bonsai": {
+      "commandName": "Executable",
+      "executablePath": "$(registry:HKEY_CURRENT_USER\\Software\\Bonsai Foundation\\Bonsai@InstallDir)Bonsai.exe",
+      "commandLineArgs": "--lib:\"$(TargetDir).\"",
+      "nativeDebugging": true
+    }
+  }
+}
diff --git a/...Visualizers/StateProbabilityVisualizer.cs → ...arkovModels/StateProbabilityVisualizer.cs b/...Visualizers/StateProbabilityVisualizer.cs → ...arkovModels/StateProbabilityVisualizer.cs
@@ -67,7 +67,7 @@ public override void Show(object value)
                 var paddingPercentage = 0.05;
 
                 var nStates = stateProbability.Probabilities.Length;
-                CategoryAxis categoryAxis = (CategoryAxis)Plot.xAxis;
+                CategoryAxis categoryAxis = (CategoryAxis)Plot.XAxis;
                 categoryAxis.ItemsSource = Enumerable.Range(0, nStates);
 
                 for (int i = 0; i < nStates; i++)

diff --git a/...ML.Visualizers.LinearDynamicalSystems/Bonsai.ML.Visualizers.LinearDynamicalSystems.csproj b/...ML.Visualizers.LinearDynamicalSystems/Bonsai.ML.Visualizers.LinearDynamicalSystems.csproj
@@ -0,0 +1,20 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <Title>Bonsai.ML.Visualizers.LinearDynamicalSystems</Title>
+    <Description>A package for the Bonsai visual programming language.</Description>
+    <PackageTags>Bonsai Rx ML Machine Learning Visualizers LinearDynamicalSystems</PackageTags>
+    <TargetFramework>net472</TargetFramework>
+    <UseWindowsForms>true</UseWindowsForms>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\Bonsai.ML.Visualizers\Bonsai.ML.Visualizers.csproj" />
+    <ProjectReference Include="..\Bonsai.ML.LinearDynamicalSystems\Bonsai.ML.LinearDynamicalSystems.csproj" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <PackageReference Include="Bonsai.Vision.Design" Version="2.8.1" />
+  </ItemGroup>
+
+</Project>
diff --git a/...ai.ML.Visualizers/ForecastImageOverlay.cs → ...rDynamicalSystems/ForecastImageOverlay.cs b/...ai.ML.Visualizers/ForecastImageOverlay.cs → ...rDynamicalSystems/ForecastImageOverlay.cs
@@ -1,7 +1,7 @@
 using Bonsai.Design;
 using Bonsai.Vision.Design;
 using Bonsai;
-using Bonsai.ML.Visualizers;
+using Bonsai.ML.Visualizers.LinearDynamicalSystems;
 using Bonsai.ML.LinearDynamicalSystems.Kinematics;
 using System;
 using System.Collections.Generic;
@@ -11,7 +11,7 @@
 
 [assembly: TypeVisualizer(typeof(ForecastImageOverlay), Target = typeof(MashupSource<ImageMashupVisualizer, ForecastVisualizer>))]
 
-namespace Bonsai.ML.Visualizers
+namespace Bonsai.ML.Visualizers.LinearDynamicalSystems
 {
     /// <summary>
     /// Provides a mashup visualizer to display the forecast of a Kalman Filter kinematics model overtime of an ImageMashupVisualizer.
@@ -50,26 +50,17 @@ public override void Show(object value)
                 double yVar = kinematicState.Position.Y.Variance;
                 double xyCov = kinematicState.Position.Covariance;
 
-                var covariance = Matrix<double>.Build.DenseOfArray(new double[,] {
-                    { xVar, xyCov },
-                    { xyCov, yVar }
-                });
-
-                var evd = covariance.Evd();
-                var evals = evd.EigenValues.Real();
-                var evecs = evd.EigenVectors;
-
-                double angle = Math.Atan2(evecs[1, 0], evecs[0, 0]) * 180 / Math.PI;
+                EllipseParameters ellipseParameters = EllipseHelper.GetEllipseParameters(xVar, yVar, xyCov);
 
                 Size axes = new Size
                 {
-                    Width = (int)(2 * Math.Sqrt(evals[0])),
-                    Height = (int)(2 * Math.Sqrt(evals[1]))
+                    Width = (int)(2 * ellipseParameters.MajorAxis),
+                    Height = (int)(2 * ellipseParameters.MinorAxis)
                 };
 
                 OxyColor color = OxyColors.Yellow;
 
-                CV.Ellipse(overlay, center, axes, angle, 0, 360, new Scalar(color.B, color.G, color.R, color.A), -1);
+                CV.Ellipse(overlay, center, axes, ellipseParameters.Angle, 0, 360, new Scalar(color.B, color.G, color.R, color.A), -1);
             }
 
             CV.AddWeighted(image, 1 - alpha, overlay, alpha, 1, image);

diff --git a/...sai.ML.Visualizers/ForecastPlotOverlay.cs → ...arDynamicalSystems/ForecastPlotOverlay.cs b/...sai.ML.Visualizers/ForecastPlotOverlay.cs → ...arDynamicalSystems/ForecastPlotOverlay.cs
@@ -1,6 +1,6 @@
 using Bonsai.Design;
 using Bonsai;
-using Bonsai.ML.Visualizers;
+using Bonsai.ML.Visualizers.LinearDynamicalSystems;
 using Bonsai.ML.LinearDynamicalSystems;
 using Bonsai.ML.LinearDynamicalSystems.Kinematics;
 using System;
@@ -10,10 +10,10 @@
 
 [assembly: TypeVisualizer(typeof(ForecastPlotOverlay), Target = typeof(MashupSource<KinematicStateVisualizer, ForecastVisualizer>))]
 
-namespace Bonsai.ML.Visualizers
+namespace Bonsai.ML.Visualizers.LinearDynamicalSystems
 {
     /// <summary>
-    /// Provides a mashup visualizer to display the forecast of a Kalman Filter kinematics model overtime of a KinematicStateVisualizer.
+    /// Provides a mashup visualizer to display the forecast of a Kalman Filter kinematics model alongside the kinematic state.
     /// </summary>
     public class ForecastPlotOverlay : DialogTypeVisualizer
     {

diff --git a/...nsai.ML.Visualizers/ForecastVisualizer.cs → ...earDynamicalSystems/ForecastVisualizer.cs b/...nsai.ML.Visualizers/ForecastVisualizer.cs → ...earDynamicalSystems/ForecastVisualizer.cs
@@ -3,7 +3,7 @@
 using System.Collections.Generic;
 using Bonsai;
 using Bonsai.Design;
-using Bonsai.ML.Visualizers;
+using Bonsai.ML.Visualizers.LinearDynamicalSystems;
 using Bonsai.ML.LinearDynamicalSystems.Kinematics;
 using OxyPlot;
 using System.Reactive;
@@ -12,7 +12,7 @@
 
 [assembly: TypeVisualizer(typeof(ForecastVisualizer), Target = typeof(Forecast))]
 
-namespace Bonsai.ML.Visualizers
+namespace Bonsai.ML.Visualizers.LinearDynamicalSystems
 {
     /// <summary>
     /// Provides a type visualizer to display the forecast of a Kalman Filter kinematics model.

diff --git a/...L.Visualizers/KinematicStateVisualizer.cs → ...amicalSystems/KinematicStateVisualizer.cs b/...L.Visualizers/KinematicStateVisualizer.cs → ...amicalSystems/KinematicStateVisualizer.cs
@@ -1,7 +1,7 @@
 using Bonsai.Design;
 using Bonsai;
 using Bonsai.ML.LinearDynamicalSystems.Kinematics;
-using Bonsai.ML.Visualizers;
+using Bonsai.ML.Visualizers.LinearDynamicalSystems;
 using System.Collections.Generic;
 using System;
 using System.Windows.Forms;
@@ -11,7 +11,7 @@
 
 [assembly: TypeVisualizer(typeof(KinematicStateVisualizer), Target = typeof(KinematicState))]
 
-namespace Bonsai.ML.Visualizers
+namespace Bonsai.ML.Visualizers.LinearDynamicalSystems
 {
 
     /// <summary>
@@ -20,7 +20,7 @@ namespace Bonsai.ML.Visualizers
     public class KinematicStateVisualizer : MashupVisualizer
     {
         private TableLayoutPanel container;
-        private int updateFrequency = 1000 / 50;
+        private int updateFrequency = 20;
         private bool resetAxes = true;
         private int rowCount = 3;
         private int columnCount = 2;

diff --git a/....Visualizers/MultivariatePDFVisualizer.cs → ...micalSystems/MultivariatePDFVisualizer.cs b/....Visualizers/MultivariatePDFVisualizer.cs → ...micalSystems/MultivariatePDFVisualizer.cs
@@ -1,23 +1,17 @@
 using System;
 using System.Windows.Forms;
-using System.Collections.Generic;
-using System.Reflection;
 using Bonsai;
 using Bonsai.Design;
-using Bonsai.ML.Visualizers;
-using Bonsai.ML.LinearDynamicalSystems;
+using Bonsai.ML.Visualizers.LinearDynamicalSystems;
 using Bonsai.ML.LinearDynamicalSystems.LinearRegression;
-using System.Drawing;
-using System.Reactive;
-using Bonsai.Reactive;
 
 [assembly: TypeVisualizer(typeof(MultivariatePDFVisualizer), Target = typeof(MultivariatePDF))]
 
-namespace Bonsai.ML.Visualizers
+namespace Bonsai.ML.Visualizers.LinearDynamicalSystems
 {
 
     /// <summary>
-    /// Provides a type visualizer to display the state components of a Kalman Filter kinematics model.
+    /// Provides a type visualizer to display a multivariate probability distribution as a heatmap.
     /// </summary>
     public class MultivariatePDFVisualizer : DialogTypeVisualizer
     {

diff --git a/src/Bonsai.ML.Visualizers.LinearDynamicalSystems/Properties/launchSettings.json b/src/Bonsai.ML.Visualizers.LinearDynamicalSystems/Properties/launchSettings.json
@@ -0,0 +1,10 @@
+{
+  "profiles": {
+    "Bonsai": {
+      "commandName": "Executable",
+      "executablePath": "$(registry:HKEY_CURRENT_USER\\Software\\Bonsai Foundation\\Bonsai@InstallDir)Bonsai.exe",
+      "commandLineArgs": "--lib:\"$(TargetDir).\"",
+      "nativeDebugging": true
+    }
+  }
+}
diff --git a/...L.Visualizers/StateComponentVisualizer.cs → ...amicalSystems/StateComponentVisualizer.cs b/...L.Visualizers/StateComponentVisualizer.cs → ...amicalSystems/StateComponentVisualizer.cs
@@ -3,7 +3,7 @@
 using System.Collections.Generic;
 using Bonsai;
 using Bonsai.Design;
-using Bonsai.ML.Visualizers;
+using Bonsai.ML.Visualizers.LinearDynamicalSystems;
 using Bonsai.ML.LinearDynamicalSystems;
 using OxyPlot;
 using System.Reactive;
@@ -12,7 +12,7 @@
 
 [assembly: TypeVisualizer(typeof(StateComponentVisualizer), Target = typeof(StateComponent))]
 
-namespace Bonsai.ML.Visualizers
+namespace Bonsai.ML.Visualizers.LinearDynamicalSystems
 {
     /// <summary>
     /// Provides a type visualizer to display the state components of a Kalman Filter kinematics model.

diff --git a/src/Bonsai.ML.Visualizers/BarSeriesOxyPlotBase.cs b/src/Bonsai.ML.Visualizers/BarSeriesOxyPlotBase.cs
@@ -3,19 +3,20 @@
 using OxyPlot.Series;
 using OxyPlot.WindowsForms;
 using System.Drawing;
-using System;
 using OxyPlot.Axes;
-using System.Collections;
 
 namespace Bonsai.ML.Visualizers
 {
-    internal class BarSeriesOxyPlotBase : UserControl
+    /// <summary>
+    /// Provides a user control to display data as a bar plot using OxyPlot.
+    /// </summary>
+    public class BarSeriesOxyPlotBase : UserControl
     {
         private PlotView view;
         private PlotModel model;
         private OxyColor defaultBarSeriesColor = OxyColors.Automatic;
 
-        internal Axis xAxis;
+        private Axis xAxis;
         private Axis yAxis;
 
         private StatusStrip statusStrip;
@@ -30,6 +31,16 @@ internal class BarSeriesOxyPlotBase : UserControl
         /// </summary>
         public StatusStrip StatusStrip => statusStrip;
 
+        /// <summary>
+        /// Gets the X Axis.
+        /// </summary>
+        public Axis XAxis => xAxis;
+
+        /// <summary>
+        /// Gets the Y Axis.
+        /// </summary>
+        public Axis YAxis => yAxis;
+
         /// <summary>
         /// Initializes a new instance of the <see cref="BarSeriesOxyPlotBase"/> class
         /// </summary>

diff --git a/src/Bonsai.ML.Visualizers/Bonsai.ML.Visualizers.csproj b/src/Bonsai.ML.Visualizers/Bonsai.ML.Visualizers.csproj
@@ -7,15 +7,9 @@
     <UseWindowsForms>true</UseWindowsForms>
   </PropertyGroup>
   <ItemGroup>
-    <PackageReference Include="Bonsai.Core" Version="2.8.1" />
     <PackageReference Include="Bonsai.Design" Version="2.8.0" />
-    <PackageReference Include="Bonsai.Vision.Design" Version="2.8.1" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
     <PackageReference Include="OxyPlot.Core" Version="2.1.2" />
     <PackageReference Include="OxyPlot.WindowsForms" Version="2.1.2" />
   </ItemGroup>
-  <ItemGroup>
-    <ProjectReference Include="..\Bonsai.ML.LinearDynamicalSystems\Bonsai.ML.LinearDynamicalSystems.csproj" />
-    <ProjectReference Include="..\Bonsai.ML.HiddenMarkovModels\Bonsai.ML.HiddenMarkovModels.csproj" />
-  </ItemGroup>
 </Project>