Added XML documentation

src/Bonsai.ML.HiddenMarkovModels/ModelParameters.cs

@@ -12,8 +12,11 @@
 
 namespace Bonsai.ML.HiddenMarkovModels
 {
+    /// <summary>
+    /// Represents the model parameters of a Hidden Markov Model (HMM).
+    /// </summary>
     [Combinator]
-    [Description("")]
+    [Description("Model parameters of a Hidden Markov Model (HMM).")]
     [WorkflowElementCategory(ElementCategory.Source)]
     public class ModelParameters : PythonStringBuilder
     {
@@ -28,15 +31,15 @@ public class ModelParameters : PythonStringBuilder
         /// </summary>
         [JsonProperty("num_states")]
         [Description("The number of discrete latent states of the HMM model")]
-        [Category("InitialParameters")]
+        [Category("ModelSpecification")]
         public int NumStates { get => numStates; set { numStates = value; UpdateString(); } }
 
         /// <summary>
         /// The dimensionality of the observations into the HMM model.
         /// </summary>
         [JsonProperty("dimensions")]
         [Description("The dimensionality of the observations into the HMM model")]
-        [Category("InitialParameters")]
+        [Category("ModelSpecification")]
         public int Dimensions { get => dimensions; set { dimensions = value; UpdateString(); } }
 
         /// <summary>
@@ -45,7 +48,7 @@ public class ModelParameters : PythonStringBuilder
         [JsonProperty("observation_type")]
         [JsonConverter(typeof(ObservationsTypeJsonConverter))]
         [Description("The type of distribution that the HMM will use to model the emission of data observations.")]
-        [Category("InitialParameters")]
+        [Category("ModelSpecification")]
         public ObservationsType ObservationsType { get => observationsType; set { observationsType = value; UpdateString(); } }
 
         /// <summary>
@@ -60,7 +63,10 @@ public StateParameters StateParameters
             set
             {
                 stateParameters = value;
-                ObservationsType = stateParameters.Observations.ObservationsType;
+                if (value != null) 
+                {
+                    ObservationsType = stateParameters.Observations.ObservationsType;
+                }
                 UpdateString();
             }
         }
@@ -75,6 +81,9 @@ public ModelParameters()
             ObservationsType = ObservationsType.Gaussian;
         }
 
+        /// <summary>
+        /// Returns an observable sequence of <see cref="ModelParameters"/> objects.
+        /// </summary>
         public IObservable<ModelParameters> Process()
         {
             return Observable.Return(
@@ -87,6 +96,10 @@ public IObservable<ModelParameters> Process()
                 });
         }
 
+        /// <summary>
+        /// Takes an observable seqence and returns an observable sequence of <see cref="ModelParameters"/> 
+        /// objects that are emitted every time the input sequence emits a new element.
+        /// </summary>
         public IObservable<ModelParameters> Process<TSource>(IObservable<TSource> source)
         {
             return Observable.Select(source, item =>
@@ -101,17 +114,21 @@ public IObservable<ModelParameters> Process<TSource>(IObservable<TSource> source
             });
         }
 
+        /// <summary>
+        /// Transforms an observable sequence of <see cref="PyObject"/> into an observable sequence 
+        /// of <see cref="ModelParameters"/> objects by accessing internal attributes of the <see cref="PyObject"/>.
+        /// </summary>
         public IObservable<ModelParameters> Process(IObservable<PyObject> source)
         {
             var sharedSource = source.Publish().RefCount();
             var stateParametersObservable = new StateParameters().Process(sharedSource);
             return sharedSource.Select(pyObject =>
             {
-                NumStates = pyObject.GetAttr<int>("num_states");
-                Dimensions = pyObject.GetAttr<int>("dimensions");
+                numStates = pyObject.GetAttr<int>("num_states");
+                dimensions = pyObject.GetAttr<int>("dimensions");
                 var observationsTypeStrPyObj = pyObject.GetAttr<string>("observation_type");
 
-                ObservationsType = GetFromString(observationsTypeStrPyObj);
+                observationsType = GetFromString(observationsTypeStrPyObj);
 
                 return new ModelParameters()
                 {
@@ -126,12 +143,12 @@ public IObservable<ModelParameters> Process(IObservable<PyObject> source)
             });
         }
 
+        /// <inheritdoc/>
         protected override string BuildString()
         {
             StringBuilder.Clear();
             StringBuilder.Append($"num_states={numStates},")
                 .Append($"dimensions={dimensions},");
-
             if (stateParameters == null)
             {
                 StringBuilder.Append($"observation_type=\"{GetString(observationsType)}\"");

src/Bonsai.ML.HiddenMarkovModels/Observations/AutoRegressiveObservations.cs

@@ -1,9 +1,13 @@
 using System.ComponentModel;
 using System.Collections.Generic;
 using Newtonsoft.Json;
+using System;
 
 namespace Bonsai.ML.HiddenMarkovModels.Observations
 {
+    /// <summary>
+    /// Represents an autoregressive observations model.
+    /// </summary>
     [JsonObject(MemberSerialization.OptIn)]
     public class AutoRegressiveObservations : ObservationsModel
     {
@@ -43,6 +47,7 @@ public class AutoRegressiveObservations : ObservationsModel
 
         /// <inheritdoc/>
         [JsonProperty]
+        [JsonConverter(typeof(ObservationsTypeJsonConverter))]
         public override ObservationsType ObservationsType => ObservationsType.AutoRegressive;
 
         /// <inheritdoc/>
@@ -67,9 +72,12 @@ public override object[] Params
             ["lags"] = Lags,
         };
 
+        /// <summary>
+        /// Initializes a new instance of the <see cref="AutoRegressiveObservations"/> class.
+        /// </summary>
         public AutoRegressiveObservations (params object[] args)
         {
-            Lags = (int)args[0];
+            Lags = Convert.ToInt32(args[0]);
             UpdateString();
         }
     }

src/Bonsai.ML.HiddenMarkovModels/Observations/AutoRegressiveObservationsModel.cs

@@ -7,8 +7,12 @@
 
 namespace Bonsai.ML.HiddenMarkovModels.Observations
 {
+    /// <summary>
+    /// Represents an operator that is used to create and transform an observable sequence
+    /// of <see cref="AutoRegressiveObservations"/> objects.
+    /// </summary>
     [Combinator]
-    [Description("")]
+    [Description("Creates an observable sequence of AutoRegressiveObservations objects.")]
     [WorkflowElementCategory(ElementCategory.Source)]
     [JsonObject(MemberSerialization.OptIn)]
     public class AutoRegressiveObservationsModel
@@ -48,6 +52,9 @@ public class AutoRegressiveObservationsModel
         [Description("The square root sigmas of the observations for each state.")]
         public double[,,] SqrtSigmas { get; private set; } = null;
 
+        /// <summary>
+        /// Returns an observable sequence of <see cref="AutoRegressiveObservations"/> objects.
+        /// </summary>
         public IObservable<AutoRegressiveObservations> Process()
         {
             return Observable.Return(
@@ -56,6 +63,10 @@ public IObservable<AutoRegressiveObservations> Process()
                 });
         }
 
+        /// <summary>
+        /// Transforms an observable sequence of <see cref="PyObject"/> into an observable sequence 
+        /// of <see cref="AutoRegressiveObservations"/> objects by accessing internal attributes of the <see cref="PyObject"/>.
+        /// </summary>
         public IObservable<AutoRegressiveObservations> Process(IObservable<PyObject> source)
         {
             return Observable.Select(source, pyObject =>

src/Bonsai.ML.HiddenMarkovModels/Observations/BernoulliObservations.cs

@@ -1,9 +1,11 @@
 using System.ComponentModel;
 using Newtonsoft.Json;
-using static Bonsai.ML.HiddenMarkovModels.Observations.ObservationsLookup;
 
 namespace Bonsai.ML.HiddenMarkovModels.Observations
 {
+    /// <summary>
+    /// Represents an bernoulli observations model.
+    /// </summary>
     [JsonObject(MemberSerialization.OptIn)]
     public class BernoulliObservations : ObservationsModel
     {
@@ -15,6 +17,7 @@ public class BernoulliObservations : ObservationsModel
 
         /// <inheritdoc/>
         [JsonProperty]
+        [JsonConverter(typeof(ObservationsTypeJsonConverter))]
         public override ObservationsType ObservationsType => ObservationsType.Bernoulli;
 
         /// <inheritdoc/>

src/Bonsai.ML.HiddenMarkovModels/Observations/BernoulliObservationsModel.cs

@@ -7,8 +7,12 @@
 
 namespace Bonsai.ML.HiddenMarkovModels.Observations
 {
+    /// <summary>
+    /// Represents an operator that is used to create and transform an observable sequence
+    /// of <see cref="BernoulliObservations"/> objects.
+    /// </summary>
     [Combinator]
-    [Description("")]
+    [Description("Creates an observable sequence of BernoulliObservations objects.")]
     [WorkflowElementCategory(ElementCategory.Source)]
     [JsonObject(MemberSerialization.OptIn)]
     public class BernoulliObservationsModel
@@ -20,6 +24,9 @@ public class BernoulliObservationsModel
         [Description("The logit P of the observations for each state.")]
         public double[,] LogitPs { get; private set; } = null;
 
+        /// <summary>
+        /// Returns an observable sequence of <see cref="BernoulliObservations"/> objects.
+        /// </summary>
         public IObservable<BernoulliObservations> Process()
         {
             return Observable.Return(
@@ -28,6 +35,10 @@ public IObservable<BernoulliObservations> Process()
                 });
         }
 
+        /// <summary>
+        /// Transforms an observable sequence of <see cref="PyObject"/> into an observable sequence 
+        /// of <see cref="BernoulliObservations"/> objects by accessing internal attributes of the <see cref="PyObject"/>.
+        /// </summary>
         public IObservable<BernoulliObservations> Process(IObservable<PyObject> source)
         {
             return Observable.Select(source, pyObject =>

src/Bonsai.ML.HiddenMarkovModels/Observations/ExponentialObservations.cs

@@ -1,14 +1,14 @@
 using System.ComponentModel;
-using System.Text;
 using Newtonsoft.Json;
-using static Bonsai.ML.HiddenMarkovModels.Observations.ObservationsLookup;
 
 namespace Bonsai.ML.HiddenMarkovModels.Observations
 {
+    /// <summary>
+    /// Represents an exponential observations model.
+    /// </summary>
     [JsonObject(MemberSerialization.OptIn)]
     public class ExponentialObservations : ObservationsModel
     {
-
         /// <summary>
         /// The log lambdas of the observations for each state.
         /// </summary>
@@ -17,6 +17,7 @@ public class ExponentialObservations : ObservationsModel
 
         /// <inheritdoc/>
         [JsonProperty]
+        [JsonConverter(typeof(ObservationsTypeJsonConverter))]
         public override ObservationsType ObservationsType => ObservationsType.Exponential;
 
         /// <inheritdoc/>

src/Bonsai.ML.HiddenMarkovModels/Observations/ExponentialObservationsModel.cs

@@ -7,8 +7,12 @@
 
 namespace Bonsai.ML.HiddenMarkovModels.Observations
 {
+    /// <summary>
+    /// Represents an operator that is used to create and transform an observable sequence
+    /// of <see cref="ExponentialObservations"/> objects.
+    /// </summary>
     [Combinator]
-    [Description("")]
+    [Description("Creates an observable sequence of ExponentialObservations objects.")]
     [WorkflowElementCategory(ElementCategory.Source)]
     [JsonObject(MemberSerialization.OptIn)]
     public class ExponentialObservationsModel
@@ -21,6 +25,9 @@ public class ExponentialObservationsModel
         [Description("The log lambdas of the observations for each state.")]
         public double[,] LogLambdas { get; private set; } = null;
 
+        /// <summary>
+        /// Returns an observable sequence of <see cref="ExponentialObservations"/> objects.
+        /// </summary>
         public IObservable<ExponentialObservations> Process()
         {
             return Observable.Return(
@@ -29,6 +36,10 @@ public IObservable<ExponentialObservations> Process()
                 });
         }
 
+        /// <summary>
+        /// Transforms an observable sequence of <see cref="PyObject"/> into an observable sequence 
+        /// of <see cref="ExponentialObservations"/> objects by accessing internal attributes of the <see cref="PyObject"/>.
+        /// </summary>
         public IObservable<ExponentialObservations> Process(IObservable<PyObject> source)
         {
             return Observable.Select(source, pyObject =>

src/Bonsai.ML.HiddenMarkovModels/Observations/GaussianObservations.cs

@@ -1,13 +1,11 @@
-using System;
-using Python.Runtime;
-using System.Reactive.Linq;
 using System.ComponentModel;
-using System.Xml.Serialization;
 using Newtonsoft.Json;
-using System.Linq;
 
 namespace Bonsai.ML.HiddenMarkovModels.Observations
 {
+    /// <summary>
+    /// Represents a gaussian observations model.
+    /// </summary>
     [JsonObject(MemberSerialization.OptIn)]
     public class GaussianObservations : ObservationsModel
     {
@@ -26,6 +24,7 @@ public class GaussianObservations : ObservationsModel
 
         /// <inheritdoc/>
         [JsonProperty]
+        [JsonConverter(typeof(ObservationsTypeJsonConverter))]
         public override ObservationsType ObservationsType => ObservationsType.Gaussian;
 
         /// <inheritdoc/>

src/Bonsai.ML.HiddenMarkovModels/Observations/GaussianObservationsModel.cs

@@ -4,12 +4,15 @@
 using System.ComponentModel;
 using System.Xml.Serialization;
 using Newtonsoft.Json;
-using System.Linq;
 
 namespace Bonsai.ML.HiddenMarkovModels.Observations
 {
+    /// <summary>
+    /// Represents an operator that is used to create and transform an observable sequence
+    /// of <see cref="GaussianObservations"/> objects.
+    /// </summary>
     [Combinator]
-    [Description("")]
+    [Description("Creates an observable sequence of GaussianObservations objects.")]
     [WorkflowElementCategory(ElementCategory.Source)]
     [JsonObject(MemberSerialization.OptIn)]
     public class GaussianObservationsModel
@@ -29,6 +32,9 @@ public class GaussianObservationsModel
         [Description("The standard deviations of the observations for each state.")]
         public double[,,] SqrtSigmas { get; private set; } = null;
 
+        /// <summary>
+        /// Returns an observable sequence of <see cref="GaussianObservations"/> objects.
+        /// </summary>
         public IObservable<GaussianObservations> Process()
         {
             return Observable.Return(
@@ -37,6 +43,10 @@ public IObservable<GaussianObservations> Process()
                 });
         }
 
+        /// <summary>
+        /// Transforms an observable sequence of <see cref="PyObject"/> into an observable sequence 
+        /// of <see cref="GaussianObservations"/> objects by accessing internal attributes of the <see cref="PyObject"/>.
+        /// </summary>
         public IObservable<GaussianObservations> Process(IObservable<PyObject> source)
         {
             return Observable.Select(source, pyObject =>

src/Bonsai.ML.HiddenMarkovModels/Observations/GaussianObservationsStatistics.cs

@@ -1,12 +1,10 @@
-using Bonsai;
-using System;
 using System.ComponentModel;
-using System.Reactive.Linq;
-using Python.Runtime;
-using System.Xml.Serialization;
 
 namespace Bonsai.ML.HiddenMarkovModels.Observations
 {
+    /// <summary>
+    /// Represents summary statistics and related data of an HMM model with gaussian observations.
+    /// </summary>
     public class GaussianObservationsStatistics
     {
         /// <summary>