Examples using the new Bonsai.ML.Lds.Torch package for estimating neural latents

docs/toc.yml

@@ -2,55 +2,66 @@
   href: ../README.md
 
 - name: Linear Dynamical Systems
-- name: Getting Started
-  href: ../examples/LinearDynamicalSystems/README.md
-- name: Kinematics
-- name: Simulated Data
-  href: ../examples/LinearDynamicalSystems/Kinematics/SimulatedData/README.md
-- name: Zebrafish Centroid Tracking
-  href: ../examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/README.md
-- name: Foraging Mouse
-  href: ../examples/LinearDynamicalSystems/Kinematics/ForagingMouse/README.md
-- name: Optimizing Model Parameters for Foraging Mouse
-  href: ../examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/README.md
-- name: Forecasting Foraging Mouse Kinematics
-  href: ../examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/README.md
-- name: Linear Regression
-- name: Simulated Data
-  href: ../examples/LinearDynamicalSystems/LinearRegression/SimulatedData/README.md
-- name: Receptive Field Simple Cell
-  href: ../examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/README.md
-
+  items:
+  - name: Kinematics
+    items:
+    - name: Simulated Data
+      href: ../examples/LinearDynamicalSystems/Kinematics/SimulatedData/README.md
+    - name: Zebrafish Centroid Tracking
+      href: ../examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/README.md
+    - name: Foraging Mouse
+      href: ../examples/LinearDynamicalSystems/Kinematics/ForagingMouse/README.md
+    - name: Optimizing Model Parameters for Foraging Mouse
+      href: ../examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/README.md
+    - name: Forecasting Foraging Mouse Kinematics
+      href: ../examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/README.md
+  - name: Linear Regression
+    items:
+    - name: Simulated Data
+      href: ../examples/LinearDynamicalSystems/LinearRegression/SimulatedData/README.md
+    - name: Receptive Field Simple Cell
+      href: ../examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/README.md
+  - name: Neural Latents
+    items:
+    - name: Estimating Parameters of LDS
+      href: ../examples/LinearDynamicalSystems/NeuralLatents/EstimatingParameters/README.md
+    - name: Online Filtering
+      href: ../examples/LinearDynamicalSystems/NeuralLatents/OnlineFiltering/README.md
+
 - name: Hidden Markov Models
-- name: Getting Started
-  href: ../examples/HiddenMarkovModels/README.md
-- name: Simulated Data
-  href: ../examples/HiddenMarkovModels/SimulatedData/README.md
-- name: Inferring Behavioral State from Kinematics
-  href: ../examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/README.md
-- name: Extended Model Configuration
-  href: ../examples/HiddenMarkovModels/ExtendedModelConfiguration/README.md
+  items:
+  - name: Getting Started
+    href: ../examples/HiddenMarkovModels/README.md
+  - name: Simulated Data
+    href: ../examples/HiddenMarkovModels/SimulatedData/README.md
+  - name: Inferring Behavioral State from Kinematics
+    href: ../examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/README.md
+  - name: Extended Model Configuration
+    href: ../examples/HiddenMarkovModels/ExtendedModelConfiguration/README.md
 
 - name: Torch
-- name: Linear Regression
-  href: ../examples/Torch/LinearRegression/README.md
+  items:
+  - name: Linear Regression
+    href: ../examples/Torch/LinearRegression/README.md
 
-- name: Torch Models
-- name: Custom PyTorch Model
-  href: ../examples/Torch/CustomPyTorchModel/README.md
-- name: Pretrained Neural Network for Image Classification
-  href: ../examples/Torch/NeuralNetsPretrainedModel/README.md
-- name: Downloading and Running a TorchHub Model
-  href: ../examples/Torch/NeuralNetsTorchHub/README.md
-- name: Training a Neural Network Online
-  href: ../examples/Torch/NeuralNetsTrainedOnline/README.md
+  - name: Neural Networks
+    items:
+    - name: Exporting a PyTorch Model
+      href: ../examples/Torch/CustomPyTorchModel/README.md
+    - name: Running a Pretrained Neural Network for Image Classification
+      href: ../examples/Torch/NeuralNetsPretrainedModel/README.md
+    - name: Downloading and Running a TorchHub Model
+      href: ../examples/Torch/NeuralNetsTorchHub/README.md
+    - name: Training a Neural Network Online
+      href: ../examples/Torch/NeuralNetsTrainedOnline/README.md
 
 - name: Point Process Decoder
-- name: Decode Position from Hippocampus using Sorted Spikes
-  href: ../examples/PointProcessDecoder/DecodePositionFromHippocampusSortedUnits/README.md
-- name: Decode Position from Hippocampus using Clusterless Marks
-  href: ../examples/PointProcessDecoder/DecodePositionFromHippocampusClusterless/README.md
-- name: Decode Position from Striatum using Sorted Spikes
-  href: ../examples/PointProcessDecoder/DecodePositionFromStriatumSortedUnits/README.md
-- name: Classify Dynamics and Decode Position from Hippocampal Sorted Units 
-  href: ../examples/PointProcessDecoder/ClassifyPositionFromHippocampusSortedUnits/README.md
+  items:
+  - name: Decode Position from Hippocampus using Sorted Spikes
+    href: ../examples/PointProcessDecoder/DecodePositionFromHippocampusSortedUnits/README.md
+  - name: Decode Position from Hippocampus using Clusterless Marks
+    href: ../examples/PointProcessDecoder/DecodePositionFromHippocampusClusterless/README.md
+  - name: Decode Position from Striatum using Sorted Spikes
+    href: ../examples/PointProcessDecoder/DecodePositionFromStriatumSortedUnits/README.md
+  - name: Classify Dynamics and Decode Position from Hippocampal Sorted Units 
+    href: ../examples/PointProcessDecoder/ClassifyPositionFromHippocampusSortedUnits/README.md

examples/LinearDynamicalSystems/NeuralLatents/EstimatingParameters/.bonsai/Bonsai.config

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examples/LinearDynamicalSystems/NeuralLatents/EstimatingParameters/.bonsai/NuGet.config

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+<?xml version="1.0" encoding="utf-8"?>
+<configuration>
+  <packageSources>
+  </packageSources>
+</configuration>

examples/LinearDynamicalSystems/NeuralLatents/EstimatingParameters/.bonsai/Setup.ps1

@@ -0,0 +1,21 @@
+Push-Location $PSScriptRoot
+if (!(Test-Path "./Bonsai.exe")) {
+    $release = "https://github.com/bonsai-rx/bonsai/releases/latest/download/Bonsai.zip"
+    $configPath = "./Bonsai.config"
+    if (Test-Path $configPath) {
+        [xml]$config = Get-Content $configPath
+        $bootstrapper = $config.PackageConfiguration.Packages.Package.where{$_.id -eq 'Bonsai'}
+        if ($bootstrapper) {
+            $version = $bootstrapper.version
+            $release = "https://github.com/bonsai-rx/bonsai/releases/download/$version/Bonsai.zip"
+        }
+    }
+    Invoke-WebRequest $release -OutFile "temp.zip"
+    Move-Item -Path "NuGet.config" "temp.config" -ErrorAction SilentlyContinue
+    Expand-Archive "temp.zip" -DestinationPath "." -Force
+    Move-Item -Path "temp.config" "NuGet.config" -Force -ErrorAction SilentlyContinue
+    Remove-Item -Path "temp.zip"
+	Remove-Item -Path "Bonsai32.exe"
+}
+& .\Bonsai.exe --no-editor
+Pop-Location