From dc53b91dd2ec4b0abe1ef394999025e29cd7d565 Mon Sep 17 00:00:00 2001 From: ncguilbeault Date: Fri, 10 Oct 2025 14:42:09 +0100 Subject: [PATCH] Updated files and workflows to use new names of packages and namespaces --- .../.bonsai/Bonsai.config | 6 ++--- .../LoadModelConfig.bonsai | 6 ++--- .../SaveModelConfig.bonsai | 10 ++++---- .../.bonsai/Bonsai.config | 24 +++++++++---------- .../InferringBehavioralState.bonsai | 18 +++++++------- .../README.md | 2 +- .../SimulatedData/.bonsai/Bonsai.config | 18 +++++++------- .../SimulatedData/SimulatedData.bonsai | 10 ++++---- .../ForagingMouse/.bonsai/Bonsai.config | 12 +++++----- .../ForagingMouse/ForagingMouse.bonsai | 8 +++---- .../.bonsai/Bonsai.config | 12 +++++----- .../ForecastingForagingMouse.bonsai | 10 ++++---- .../.bonsai/Bonsai.config | 12 +++++----- .../ModelOptimizationForagingMouse.bonsai | 10 ++++---- .../SimulatedData/.bonsai/Bonsai.config | 12 +++++----- .../SimulatedData/Simulation.bonsai | 8 +++---- .../.bonsai/Bonsai.config | 12 +++++----- .../ZebrafishTracking.bonsai | 8 +++---- .../.bonsai/Bonsai.config | 12 +++++----- .../ReceptiveFieldSimpleCell.bonsai | 8 +++---- .../SimulatedData/.bonsai/Bonsai.config | 12 +++++----- .../SimulatedData/Simulation.bonsai | 8 +++---- 22 files changed, 119 insertions(+), 119 deletions(-) diff --git a/examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/Bonsai.config b/examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/Bonsai.config index 44c0693..a735886 100644 --- a/examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/Bonsai.config +++ b/examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/Bonsai.config @@ -7,7 +7,7 @@ - + @@ -41,7 +41,7 @@ - + @@ -54,7 +54,7 @@ - + diff --git a/examples/HiddenMarkovModels/ExtendedModelConfiguration/LoadModelConfig.bonsai b/examples/HiddenMarkovModels/ExtendedModelConfiguration/LoadModelConfig.bonsai index 71e43ce..4acb6ea 100644 --- a/examples/HiddenMarkovModels/ExtendedModelConfiguration/LoadModelConfig.bonsai +++ b/examples/HiddenMarkovModels/ExtendedModelConfiguration/LoadModelConfig.bonsai @@ -4,7 +4,7 @@ xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python" xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core" xmlns:io="clr-namespace:Bonsai.IO;assembly=Bonsai.System" - xmlns:p1="clr-namespace:Bonsai.ML.HiddenMarkovModels;assembly=Bonsai.ML.HiddenMarkovModels" + xmlns:p1="clr-namespace:Bonsai.ML.Hmm.Python;assembly=Bonsai.ML.Hmm.Python" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -14,7 +14,7 @@ - + @@ -49,7 +49,7 @@ - + hmm 2 2 diff --git a/examples/HiddenMarkovModels/ExtendedModelConfiguration/SaveModelConfig.bonsai b/examples/HiddenMarkovModels/ExtendedModelConfiguration/SaveModelConfig.bonsai index 526fbb1..8465aeb 100644 --- a/examples/HiddenMarkovModels/ExtendedModelConfiguration/SaveModelConfig.bonsai +++ b/examples/HiddenMarkovModels/ExtendedModelConfiguration/SaveModelConfig.bonsai @@ -2,9 +2,9 @@ @@ -16,7 +16,7 @@ - + @@ -64,7 +64,7 @@ - + hmm 2 2 diff --git a/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/Bonsai.config b/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/Bonsai.config index 9dbd6bf..c3a352c 100644 --- a/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/Bonsai.config +++ b/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/Bonsai.config @@ -11,10 +11,10 @@ - - - - + + + + @@ -61,10 +61,10 @@ - - - - + + + + @@ -83,10 +83,10 @@ - - - - + + + + diff --git a/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/InferringBehavioralState.bonsai b/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/InferringBehavioralState.bonsai index 1ec5ecd..ec90f17 100644 --- a/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/InferringBehavioralState.bonsai +++ b/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/InferringBehavioralState.bonsai @@ -19,8 +19,8 @@ - - + + MouseTracking @@ -307,7 +307,7 @@ - + Centroid @@ -325,7 +325,7 @@ - + KFmodel 60 668.08917236328125 @@ -342,7 +342,7 @@ KFParameters - + hmm 6 2 @@ -359,7 +359,7 @@ Centroid - + KFmodel @@ -434,7 +434,7 @@ 1 - + hmm @@ -464,7 +464,7 @@ HMMObservation - + 1000 hmm 50 @@ -473,7 +473,7 @@ true true - + hmm PT1S diff --git a/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/README.md b/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/README.md index c843c1c..7e87739 100644 --- a/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/README.md +++ b/examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/README.md @@ -27,7 +27,7 @@ If you used the bootstrapping method, you don't have to worry about the package * Bonsai - Numerics v0.9.0 > [!WARNING] -> This example builds on the [LDS Kinematics Foraging Mouse example](../../LinearDynamicalSystems/Kinematics/ForagingMouse/README.md) and requires both the *Bonsai.ML.LinearDynamicalSystems* package and the *Bonsai.ML.HiddenMarkovModels* package. See the installation guide to ensure both packages are installed and working correctly. +> This example builds on the [LDS Kinematics Foraging Mouse example](../../LinearDynamicalSystems/Kinematics/ForagingMouse/README.md) and requires both the *Bonsai.ML.Lds.Python* package and the *Bonsai.ML.Hmm.Python* package. See the installation guide to ensure both packages are installed and working correctly. ### Workflow diff --git a/examples/HiddenMarkovModels/SimulatedData/.bonsai/Bonsai.config b/examples/HiddenMarkovModels/SimulatedData/.bonsai/Bonsai.config index ee3ff2a..1d14a7b 100644 --- a/examples/HiddenMarkovModels/SimulatedData/.bonsai/Bonsai.config +++ b/examples/HiddenMarkovModels/SimulatedData/.bonsai/Bonsai.config @@ -12,9 +12,9 @@ - - - + + + @@ -63,9 +63,9 @@ - - - + + + @@ -86,9 +86,9 @@ - - - + + + diff --git a/examples/HiddenMarkovModels/SimulatedData/SimulatedData.bonsai b/examples/HiddenMarkovModels/SimulatedData/SimulatedData.bonsai index 9f483e5..462206f 100644 --- a/examples/HiddenMarkovModels/SimulatedData/SimulatedData.bonsai +++ b/examples/HiddenMarkovModels/SimulatedData/SimulatedData.bonsai @@ -18,11 +18,11 @@ - + - + hmm 2 2 @@ -292,7 +292,7 @@ Observation - + 80 hmm 50 @@ -301,7 +301,7 @@ true true - + hmm PT1S @@ -317,7 +317,7 @@ Observation - + hmm diff --git a/examples/LinearDynamicalSystems/Kinematics/ForagingMouse/.bonsai/Bonsai.config b/examples/LinearDynamicalSystems/Kinematics/ForagingMouse/.bonsai/Bonsai.config index db732e2..1e820a4 100644 --- a/examples/LinearDynamicalSystems/Kinematics/ForagingMouse/.bonsai/Bonsai.config +++ b/examples/LinearDynamicalSystems/Kinematics/ForagingMouse/.bonsai/Bonsai.config @@ -11,8 +11,8 @@ - - + + @@ -65,8 +65,8 @@ - - + + @@ -88,8 +88,8 @@ - - + + diff --git a/examples/LinearDynamicalSystems/Kinematics/ForagingMouse/ForagingMouse.bonsai b/examples/LinearDynamicalSystems/Kinematics/ForagingMouse/ForagingMouse.bonsai index 2d1c46f..22e26b0 100644 --- a/examples/LinearDynamicalSystems/Kinematics/ForagingMouse/ForagingMouse.bonsai +++ b/examples/LinearDynamicalSystems/Kinematics/ForagingMouse/ForagingMouse.bonsai @@ -309,11 +309,11 @@ RuntimeEngine - + Centroid - + Observation @@ -358,7 +358,7 @@ - + model 50 640.20025634765625 @@ -384,7 +384,7 @@ - + model diff --git a/examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/.bonsai/Bonsai.config b/examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/.bonsai/Bonsai.config index e7c50d3..0eb5c9c 100644 --- a/examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/.bonsai/Bonsai.config +++ b/examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/.bonsai/Bonsai.config @@ -11,8 +11,8 @@ - - + + @@ -61,8 +61,8 @@ - - + + @@ -82,8 +82,8 @@ - - + + diff --git a/examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/ForecastingForagingMouse.bonsai b/examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/ForecastingForagingMouse.bonsai index ea26b98..fa0e755 100644 --- a/examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/ForecastingForagingMouse.bonsai +++ b/examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/ForecastingForagingMouse.bonsai @@ -307,11 +307,11 @@ RuntimeEngine - + Centroid - + Observation @@ -356,7 +356,7 @@ - + model 50 640.20025634765625 @@ -382,13 +382,13 @@ - + model InferredKinematics - + model 30 diff --git a/examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/.bonsai/Bonsai.config b/examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/.bonsai/Bonsai.config index 3e51b05..378d520 100644 --- a/examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/.bonsai/Bonsai.config +++ b/examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/.bonsai/Bonsai.config @@ -11,8 +11,8 @@ - - + + @@ -64,8 +64,8 @@ - - + + @@ -87,8 +87,8 @@ - - + + diff --git a/examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/ModelOptimizationForagingMouse.bonsai b/examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/ModelOptimizationForagingMouse.bonsai index 6b505f4..cdcdf3b 100644 --- a/examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/ModelOptimizationForagingMouse.bonsai +++ b/examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/ModelOptimizationForagingMouse.bonsai @@ -309,11 +309,11 @@ RuntimeEngine - + Centroid - + Observation @@ -358,7 +358,7 @@ - + model 50 640.20025634765625 @@ -384,7 +384,7 @@ - + 200 model true @@ -403,7 +403,7 @@ - + model diff --git a/examples/LinearDynamicalSystems/Kinematics/SimulatedData/.bonsai/Bonsai.config b/examples/LinearDynamicalSystems/Kinematics/SimulatedData/.bonsai/Bonsai.config index 6251c80..9623a4d 100644 --- a/examples/LinearDynamicalSystems/Kinematics/SimulatedData/.bonsai/Bonsai.config +++ b/examples/LinearDynamicalSystems/Kinematics/SimulatedData/.bonsai/Bonsai.config @@ -11,8 +11,8 @@ - - + + @@ -66,8 +66,8 @@ - - + + @@ -90,8 +90,8 @@ - - + + diff --git a/examples/LinearDynamicalSystems/Kinematics/SimulatedData/Simulation.bonsai b/examples/LinearDynamicalSystems/Kinematics/SimulatedData/Simulation.bonsai index 7437c8f..02d5312 100644 --- a/examples/LinearDynamicalSystems/Kinematics/SimulatedData/Simulation.bonsai +++ b/examples/LinearDynamicalSystems/Kinematics/SimulatedData/Simulation.bonsai @@ -33,7 +33,7 @@ RuntimeEngine - + Fps @@ -217,7 +217,7 @@ - + Observation @@ -243,7 +243,7 @@ - + model 20 391.51131518877759 @@ -269,7 +269,7 @@ - + model diff --git a/examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/.bonsai/Bonsai.config b/examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/.bonsai/Bonsai.config index db732e2..1e820a4 100644 --- a/examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/.bonsai/Bonsai.config +++ b/examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/.bonsai/Bonsai.config @@ -11,8 +11,8 @@ - - + + @@ -65,8 +65,8 @@ - - + + @@ -88,8 +88,8 @@ - - + + diff --git a/examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/ZebrafishTracking.bonsai b/examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/ZebrafishTracking.bonsai index 02041d5..fe6632b 100644 --- a/examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/ZebrafishTracking.bonsai +++ b/examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/ZebrafishTracking.bonsai @@ -91,11 +91,11 @@ RuntimeEngine - + Centroid - + Observation @@ -140,7 +140,7 @@ - + model 200 86.041664123535156 @@ -166,7 +166,7 @@ - + model diff --git a/examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/.bonsai/Bonsai.config b/examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/.bonsai/Bonsai.config index 67d7be6..9367173 100644 --- a/examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/.bonsai/Bonsai.config +++ b/examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/.bonsai/Bonsai.config @@ -10,8 +10,8 @@ - - + + @@ -55,8 +55,8 @@ - - + + @@ -73,8 +73,8 @@ - - + + diff --git a/examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/ReceptiveFieldSimpleCell.bonsai b/examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/ReceptiveFieldSimpleCell.bonsai index 99408d6..7ef83c6 100644 --- a/examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/ReceptiveFieldSimpleCell.bonsai +++ b/examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/ReceptiveFieldSimpleCell.bonsai @@ -4,7 +4,7 @@ xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python" xmlns:io="clr-namespace:Bonsai.IO;assembly=Bonsai.System" xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core" - xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems" + xmlns:p1="clr-namespace:Bonsai.ML.Lds.Python;assembly=Bonsai.ML.Lds.Python" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -14,7 +14,7 @@ - + LoadData @@ -63,7 +63,7 @@ - + 25 2 145 @@ -81,7 +81,7 @@ - + model diff --git a/examples/LinearDynamicalSystems/LinearRegression/SimulatedData/.bonsai/Bonsai.config b/examples/LinearDynamicalSystems/LinearRegression/SimulatedData/.bonsai/Bonsai.config index f65445c..69d9e22 100644 --- a/examples/LinearDynamicalSystems/LinearRegression/SimulatedData/.bonsai/Bonsai.config +++ b/examples/LinearDynamicalSystems/LinearRegression/SimulatedData/.bonsai/Bonsai.config @@ -10,8 +10,8 @@ - - + + @@ -59,8 +59,8 @@ - - + + @@ -80,8 +80,8 @@ - - + + diff --git a/examples/LinearDynamicalSystems/LinearRegression/SimulatedData/Simulation.bonsai b/examples/LinearDynamicalSystems/LinearRegression/SimulatedData/Simulation.bonsai index e2e7863..7786219 100644 --- a/examples/LinearDynamicalSystems/LinearRegression/SimulatedData/Simulation.bonsai +++ b/examples/LinearDynamicalSystems/LinearRegression/SimulatedData/Simulation.bonsai @@ -15,7 +15,7 @@ - + SyntheticDataset @@ -237,7 +237,7 @@ - + 25 2 2 @@ -255,10 +255,10 @@ - + model - + model -1 1