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Improve documentation of IncludeWorkflows #40

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a4f707b
Add scripts for bonsai linux environment
ncguilbeault Nov 20, 2024
8527c39
Added description to the include workflow and description to the Name…
ncguilbeault Nov 20, 2024
bca290c
Added descriptions to include workflows and properties
ncguilbeault Nov 20, 2024
240b094
Added periods to the end of descriptions.
ncguilbeault Nov 20, 2024
3b87503
Added descriptions to workflows and properties
ncguilbeault Nov 20, 2024
13dec06
Improved documentation strings
ncguilbeault Nov 20, 2024
614de1c
Removed unused parameters
ncguilbeault Nov 20, 2024
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Added descriptions to workflows and properties
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@ncguilbeault
ncguilbeault committed Jan 20, 2025
commit 3b875036a02e35709a54224cc10be2d198daacbd
4 changes: 2 additions & 2 deletions src/Bonsai.ML.HiddenMarkovModels/CheckFitFinished.bonsai
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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">
<Description>Periodically evaluates the `get_fit_finished` function of the HMM. Returns a boolean value representing the objects `fit_finished` attribute. This should onle be used in a state after the `RunFitAsync` function has already been started.</Description>
<Description>Periodically evaluates the `get_fit_finished` function of the HMM. Returns whether the `fit_finished` attribute is true. This should only be used after the `RunFitAsync` function has already been started.</Description>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="Name" Description="The name of the python variable referencing the model object." Category="ModelReference" />
<Property Name="Name" DisplayName="Name" Description="The name of the Python variable referencing the model object." Category="ModelReference" />
<Property Name="TimerFrequency" DisplayName="TimerFrequency" Description="The frequency with which to check if the asynchronous fit loop is complete." Category="Polling" />
</Expression>
<Expression xsi:type="rx:SelectMany">
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14 changes: 7 additions & 7 deletions src/Bonsai.ML.HiddenMarkovModels/CreateHMM.bonsai
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xmlns:p2="clr-namespace:Bonsai.ML.HiddenMarkovModels;assembly=Bonsai.ML.HiddenMarkovModels"
xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
xmlns="https://bonsai-rx.org/2018/workflow">
<Description>Creates a new HMM python object inside of the HMM module and assigns it to a named python variable.</Description>
<Description>Creates a new HMM Python object inside of the HMM module and assigns it to a named Python variable.</Description>
<Workflow>
<Nodes>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="Name" Description="The name of the python variable referencing the model object." Category="ModelReference" />
<Property Name="Name" DisplayName="Name" Description="The name of the Python variable referencing the model object." Category="ModelReference" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p1:CreateModelReference">
Expand All @@ -27,11 +27,11 @@
<Name>Source1</Name>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="NumStates" Description="The number of discrete latent states of the HMM model." />
<Property Name="Dimensions" Description="The dimensionality of the observations into the HMM model." />
<Property Name="ObservationsModelType" Description="The type of distribution that the HMM will use to model the emission of data observations." />
<Property Name="StateParameters" Description="The optional state parameters of the HMM model. If an observations model or transitions model is defined within the state parameters, they will override the values set in the observations model type and transitions model type properties, respectively." />
<Property Name="TransitionsModelType" Description="The type of transition model that the HMM will use to calculate the probabilities of transitioning between states."/>
<Property Name="NumStates" Description="The number of discrete latent states in the HMM." />
<Property Name="Dimensions" Description="The dimensionality of the observations going into the HMM." />
<Property Name="ObservationModelType" Description="The type of distribution that the HMM will use to model the emission of data observations." />
<Property Name="StateParameters" Description="The optional state parameters of the HMM. If an observation model or transition model is defined within the state parameters, these will override the values set in the observation model type and transition model type properties, respectively." />
<Property Name="TransitionModelType" Description="The type of model that the HMM will use to calculate the probabilities of transitioning between states."/>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p2:ModelParameters">
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4 changes: 2 additions & 2 deletions src/Bonsai.ML.HiddenMarkovModels/GetGaussianObservationsStatistics.bonsai
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xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:p2="clr-namespace:Bonsai.ML.HiddenMarkovModels.Observations;assembly=Bonsai.ML.HiddenMarkovModels"
xmlns="https://bonsai-rx.org/2018/workflow">
<Description>Computes the statistics of the Gaussian observations in the HMM model. Only works for models with Gaussian observations.</Description>
<Description>Computes the statistics of the Gaussian observations in the HMM. Only works for models with Gaussian observations.</Description>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
Expand All @@ -17,7 +17,7 @@
<Combinator xsi:type="py:ObserveOnGIL" />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="Name" Description="The name of the python variable referencing the model object." Category="ModelReference" />
<Property Name="Name" DisplayName="Name" Description="The name of the Python variable referencing the model object." Category="ModelReference" />
</Expression>
<Expression xsi:type="SubscribeSubject" TypeArguments="p1:ModelReference">
<Name>hmm</Name>
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4 changes: 2 additions & 2 deletions src/Bonsai.ML.HiddenMarkovModels/InferState.bonsai
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xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:p2="clr-namespace:Bonsai.ML.HiddenMarkovModels;assembly=Bonsai.ML.HiddenMarkovModels"
xmlns="https://bonsai-rx.org/2018/workflow">
<Description>Infers the state of the HMM model given the observations.</Description>
<Description>Infers the state of the HMM given the observations.</Description>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
Expand All @@ -16,7 +16,7 @@
<Combinator xsi:type="py:ObserveOnGIL" />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="Name" Description="The name of the python variable referencing the model object." Category="ModelReference" />
<Property Name="Name" DisplayName="Name" Description="The name of the Python variable referencing the model object." Category="ModelReference" />
</Expression>
<Expression xsi:type="SubscribeSubject" TypeArguments="p1:ModelReference">
<Name>hmm</Name>
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8 changes: 4 additions & 4 deletions src/Bonsai.ML.HiddenMarkovModels/ModelParameters.cs
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Expand Up @@ -29,9 +29,9 @@ public class ModelParameters : PythonStringBuilder
private StateParameters stateParameters = null;

/// <summary>
/// The number of states of the HMM model.
/// The number of discrete latent states in the HMM model.
/// </summary>
[Description("The number of discrete latent states of the HMM model.")]
[Description("The number of discrete latent states in the HMM.")]
[Category("ModelSpecification")]
public int NumStates
{
Expand All @@ -44,9 +44,9 @@ public int NumStates
}

/// <summary>
/// The dimensionality of the observations into the HMM model.
/// The dimensionality of the observations going into the HMM.
/// </summary>
[Description("The dimensionality of the observations into the HMM model.")]
[Description("The dimensionality of the observations going into the HMM.")]
[Category("ModelSpecification")]
public int Dimensions
{
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8 changes: 4 additions & 4 deletions src/Bonsai.ML.HiddenMarkovModels/RunFitAsync.bonsai
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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">
<Description>Runs the asynchronous fit loop of the HMM model.</Description>
<Description>Runs the asynchronous fit loop of the HMM.</Description>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Value" DisplayName="BatchSize" Description="The size of the batch of data to use for fitting the model." Category="TrainingData" />
<Property Name="Value" DisplayName="BatchSize" Description="The size of the batch used for fitting the model." Category="TrainingData" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="IntProperty">
Expand Down Expand Up @@ -48,7 +48,7 @@
<Combinator xsi:type="py:ObserveOnGIL" />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="Name" Description="The name of the python variable referencing the model object." Category="ModelReference" />
<Property Name="Name" DisplayName="Name" Description="The name of the Python variable referencing the model object." Category="ModelReference" />
</Expression>
<Expression xsi:type="SubscribeSubject" TypeArguments="p1:ModelReference">
<Name>hmm</Name>
Expand All @@ -65,7 +65,7 @@
</Combinator>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Value" DisplayName="NumIterations" Description="The number of iterations to use for fitting the model to a single batch of data." Category="Hyperparameters" />
<Property Name="Value" DisplayName="NumIterations" Description="The number of iterations used for fitting the model to a single batch of data." Category="Hyperparameters" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="IntProperty">
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25 changes: 13 additions & 12 deletions src/Bonsai.ML.LinearDynamicalSystems/Kinematics/CreateKFModel.bonsai
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xmlns:p2="clr-namespace:Bonsai.ML.LinearDynamicalSystems.Kinematics;assembly=Bonsai.ML.LinearDynamicalSystems"
xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
xmlns="https://bonsai-rx.org/2018/workflow">
<Description>Creates a Kalman filter model for kinematics estimation based on the discrete Weiner process acceleration model.</Description>
<Workflow>
<Nodes>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" Category="ModelReference" />
<Property Name="Name" DisplayName="Name" Description="The name of the Python variable referencing the model object." Category="ModelReference" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p1:CreateModelReference" />
Expand All @@ -24,17 +25,17 @@
<Name>Source1</Name>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Fps" Category="ModelParams" />
<Property Name="Pos_x0" Category="ModelParams" />
<Property Name="Pos_y0" Category="ModelParams" />
<Property Name="Vel_x0" Category="ModelParams" />
<Property Name="Vel_y0" Category="ModelParams" />
<Property Name="Acc_x0" Category="ModelParams" />
<Property Name="Acc_y0" Category="ModelParams" />
<Property Name="Sigma_a" Category="ModelParams" />
<Property Name="Sigma_x" Category="ModelParams" />
<Property Name="Sigma_y" Category="ModelParams" />
<Property Name="Sqrt_diag_V0_value" Category="ModelParams" />
<Property Name="Fps" Description="The frames per second of the observations." Category="ModelParams" />
<Property Name="Pos_x0" Description="The initial x position." Category="ModelParams" />
<Property Name="Pos_y0" Description="The initial y position." Category="ModelParams" />
<Property Name="Vel_x0" Description="The initial x velocity." Category="ModelParams" />
<Property Name="Vel_y0" Description="The initial y velocity." Category="ModelParams" />
<Property Name="Acc_x0" Description="The initial x acceleration." Category="ModelParams" />
<Property Name="Acc_y0" Description="The initial y acceleration." Category="ModelParams" />
<Property Name="Sigma_a" Description="A scalar value representing the measurement noise." Category="ModelParams" />
<Property Name="Sigma_x" Description="A scalar value representing the prediction noise along the x axis." Category="ModelParams" />
<Property Name="Sigma_y" Description="A scalar value representing the prediction noise along the y axis." Category="ModelParams" />
<Property Name="Sqrt_diag_V0_value" Description="The initial value of the diagonal of the state covariance matrix." Category="ModelParams" />
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In general in Bonsai / C# we would use Pascal casing rather than snake case, but no need to change anything now, this is just a general comment for us to think about regarding casing of properties coming from Python.

</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p2:KFModelParameters">
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1 change: 1 addition & 0 deletions src/Bonsai.ML.LinearDynamicalSystems/Kinematics/CreateObservation2D.bonsai
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems.Kinematics;assembly=Bonsai.ML.LinearDynamicalSystems"
xmlns="https://bonsai-rx.org/2018/workflow">
<Description>Creates a 2 dimensional object with the properties X and Y from the input.</Description>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
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5 changes: 3 additions & 2 deletions src/Bonsai.ML.LinearDynamicalSystems/Kinematics/PerformForecasting.bonsai
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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">
<Description>Performs forecasting on the LDS kinematics model.</Description>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
Expand All @@ -15,7 +16,7 @@
<Combinator xsi:type="py:ObserveOnGIL" />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" />
<Property Name="Name" DisplayName="Name" Description="The name of the Python variable referencing the model object." Category="ModelReference" />
</Expression>
<Expression xsi:type="SubscribeSubject" TypeArguments="p1:ModelReference">
<Name>model</Name>
Expand All @@ -24,7 +25,7 @@
<Selector>Name</Selector>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Value" DisplayName="Timesteps" />
<Property Name="Value" DisplayName="Timesteps" Description="The number of timesteps to forecast into the future." Category="ForecastParameters"/>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="IntProperty">
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3 changes: 2 additions & 1 deletion src/Bonsai.ML.LinearDynamicalSystems/Kinematics/PerformInference.bonsai
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Expand Up @@ -7,6 +7,7 @@
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">
<Description>Performs inference on the LDS kinematics model.</Description>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
Expand All @@ -16,7 +17,7 @@
<Combinator xsi:type="py:ObserveOnGIL" />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="Name" Category="ModelReference" />
<Property Name="Name" DisplayName="Name" Description="The name of the Python variable referencing the model object." Category="ModelReference" />
</Expression>
<Expression xsi:type="SubscribeSubject" TypeArguments="p1:ModelReference">
<Name>model</Name>
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3 changes: 2 additions & 1 deletion src/Bonsai.ML.LinearDynamicalSystems/Learning/CheckOptimizationFinished.bonsai
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xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions"
xmlns="https://bonsai-rx.org/2018/workflow">
<Description>Periodically evaluates the `get_optimization_finished` function of the LDS model. Returns whether the `optimization_finished` attribute is true. This should only be used after the `RunOptimizationAsync` function has already been started.</Description>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
Expand All @@ -15,7 +16,7 @@
<Combinator xsi:type="py:ObserveOnGIL" />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="Name" Category="ModelReference" />
<Property Name="Name" DisplayName="Name" Description="The name of the python variable referencing the model object." Category="ModelReference" />
</Expression>
<Expression xsi:type="SubscribeSubject" TypeArguments="p1:ModelReference">
<Name>model</Name>
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