Neural decoder example

README.md

@@ -12,9 +12,11 @@ All of the datasets used in these examples can be found by going to: [https://do
 
 ZebrafishExampleVid.avi - provided by Nicholas Guilbeault in the Thiele lab at the University of Toronto. If you would like to refer to this data, please cite Guilbeault, N.C., Guerguiev, J., Martin, M. et al. (2021). BonZeb: open-source, modular software tools for high-resolution zebrafish tracking and analysis. *Scientific Reports* *11*, 8148, [https://doi.org/10.1038/s41598-021-85896-x](https://doi.org/10.1038/s41598-021-85896-x).
 
-ForagingMouseExampleVid.avi - provided by the Sainsbury Wellcome Centre Foraging Behaviour Working Group. (2023). Aeon: An open-source platform to study the neural basis of ethological behaviours over naturalistic timescales, [https://doi.org/10.5281/zenodo.8413142](https://doi.org/10.5281/zenodo.8413142)
+ForagingMouseExampleVid.avi - provided by the Sainsbury Wellcome Centre Foraging Behaviour Working Group. (2023). Aeon: An open-source platform to study the neural basis of ethological behaviours over naturalistic timescales, [https://doi.org/10.5281/zenodo.8413142](https://doi.org/10.5281/zenodo.8413142).
 
-ReceptiveFieldSimpleCell.zip - provided by the authors of "Touryan, J., Felsen, G., & Dan, Y. (2005). Spatial structure of complex cell receptive fields measured with natural images. Neuron, 45(5), 781-791." [https://doi.org/10.1016/j.neuron.2005.01.029](https://doi.org/10.1016/j.neuron.2005.01.029)
+ReceptiveFieldSimpleCell.zip - provided by the authors of "Touryan, J., Felsen, G., & Dan, Y. (2005). Spatial structure of complex cell receptive fields measured with natural images. Neuron, 45(5), 781-791." [https://doi.org/10.1016/j.neuron.2005.01.029](https://doi.org/10.1016/j.neuron.2005.01.029).
+
+HippocampalTetrodeRecording.zip - provided by the authors of Joshi, A., Denovellis, E.L., Mankili, A. et al. (2023). Dynamic synchronization between hippocampal representations and stepping. Nature 617, 125–131. [https://doi.org/10.1038/s41586-023-05928-6](https://doi.org/10.1038/s41586-023-05928-6).
 
 ### Acknowledgements
 

examples/NeuralDecoding/PositionDecodingFromHippocampus/.bonsai/Bonsai.config

@@ -0,0 +1,116 @@
+<?xml version="1.0" encoding="utf-8"?>
+<PackageConfiguration xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <Packages>
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+    <Package id="Bonsai.Core" version="2.8.5" />
+    <Package id="Bonsai.Design" version="2.8.5" />
+    <Package id="Bonsai.Design.Visualizers" version="2.8.0" />
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+    <Package id="Bonsai.Gui.ZedGraph" version="0.1.0" />
+    <Package id="Bonsai.ML" version="0.4.0" />
+    <Package id="Bonsai.ML.Design" version="0.4.0" />
+    <Package id="Bonsai.ML.NeuralDecoder" version="0.4.0" />
+    <Package id="Bonsai.ML.NeuralDecoder.Design" version="0.4.0" />
+    <Package id="Bonsai.ML.Python" version="0.4.0" />
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+    <AssemblyReference assemblyName="Bonsai.ML.Design" />
+    <AssemblyReference assemblyName="Bonsai.ML.NeuralDecoder" />
+    <AssemblyReference assemblyName="Bonsai.ML.NeuralDecoder.Design" />
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+    <AssemblyLocation assemblyName="Bonsai.ML.NeuralDecoder" processorArchitecture="MSIL" location="Packages/Bonsai.ML.NeuralDecoder.0.4.0/lib/net472/Bonsai.ML.NeuralDecoder.dll" />
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+  </AssemblyLocations>
+  <LibraryFolders>
+    <LibraryFolder path="Packages/Microsoft.Web.WebView2.1.0.1823.32/runtimes/win-arm64/native" platform="arm64" />
+    <LibraryFolder path="Packages/Microsoft.Web.WebView2.1.0.1823.32/runtimes/win-arm64/native_uap" platform="arm64" />
+    <LibraryFolder path="Packages/Microsoft.Web.WebView2.1.0.1823.32/runtimes/win-x64/native" platform="x64" />
+    <LibraryFolder path="Packages/Microsoft.Web.WebView2.1.0.1823.32/runtimes/win-x64/native_uap" platform="x64" />
+    <LibraryFolder path="Packages/Microsoft.Web.WebView2.1.0.1823.32/runtimes/win-x86/native" platform="x86" />
+    <LibraryFolder path="Packages/Microsoft.Web.WebView2.1.0.1823.32/runtimes/win-x86/native_uap" platform="x86" />
+  </LibraryFolders>
+</PackageConfiguration>

examples/NeuralDecoding/PositionDecodingFromHippocampus/.bonsai/NuGet.config

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="utf-8"?>
+<configuration>
+  <packageSources>
+    <add key="Gallery" value="Gallery" />
+    <add key="Bonsai Packages" value="https://www.myget.org/F/bonsai/api/v3/index.json" />
+    <add key="Community Packages" value="https://www.myget.org/F/bonsai-community/api/v3/index.json" />
+  </packageSources>
+</configuration>

examples/NeuralDecoding/PositionDecodingFromHippocampus/.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

examples/NeuralDecoding/PositionDecodingFromHippocampus/.bonsai/Setup.sh

@@ -0,0 +1,41 @@
+#! /bin/bash
+
+SETUP_SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)"
+
+DEFAULT_VERSION="latest"
+VERSION="$DEFAULT_VERSION"
+
+while [[ "$#" -gt 0 ]]; do
+    case $1 in
+        --version) VERSION="$2"; shift ;;
+        *) echo "Unknown parameter passed: $1"; exit 1 ;;
+    esac
+    shift
+done
+
+echo "Setting up Bonsai v=$VERSION environment..."
+
+if [ ! -f "$SETUP_SCRIPT_DIR/Bonsai.exe" ]; then
+    CONFIG="$SETUP_SCRIPT_DIR/Bonsai.config"
+    if [ -f "$CONFIG" ]; then
+        DETECTED=$(xmllint --xpath '//PackageConfiguration/Packages/Package[@id="Bonsai"]/@version' "$CONFIG" | sed -e 's/^[^"]*"//' -e 's/"$//')
+        echo "Version detected v=$DETECTED."
+        RELEASE="https://github.com/bonsai-rx/bonsai/releases/download/$DETECTED/Bonsai.zip"
+    else
+        if [ $VERSION = "latest" ]; then
+            RELEASE="https://github.com/bonsai-rx/bonsai/releases/latest/download/Bonsai.zip"
+        else
+            RELEASE="https://github.com/bonsai-rx/bonsai/releases/download/$VERSION/Bonsai.zip"
+        fi
+    fi
+    echo "Download URL: $RELEASE"
+    wget $RELEASE -O "$SETUP_SCRIPT_DIR/temp.zip"
+    mv -f "$SETUP_SCRIPT_DIR/NuGet.config" "$SETUP_SCRIPT_DIR/temp.config"
+    unzip -d "$SETUP_SCRIPT_DIR" -o "$SETUP_SCRIPT_DIR/temp.zip"
+    mv -f "$SETUP_SCRIPT_DIR/temp.config" "$SETUP_SCRIPT_DIR/NuGet.config"
+    rm -rf "$SETUP_SCRIPT_DIR/temp.zip"
+    rm -rf "$SETUP_SCRIPT_DIR/Bonsai32.exe"
+fi
+
+source "$SETUP_SCRIPT_DIR/activate"
+source "$SETUP_SCRIPT_DIR/run" --no-editor

examples/NeuralDecoding/PositionDecodingFromHippocampus/.bonsai/activate

@@ -0,0 +1,15 @@
+#!/bin/bash
+# activate.sh
+if [[ -v BONSAI_EXE_PATH ]]; then
+    echo "Error! Cannot have multiple bonsai environments activated at the same time. Please deactivate the current environment before activating the new one."
+    return
+fi
+BONSAI_ENV_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)"
+export BONSAI_ENV_DIR
+export BONSAI_EXE_PATH="$BONSAI_ENV_DIR/Bonsai.exe"
+export ORIGINAL_PS1="$PS1"
+export PS1="($(basename "$BONSAI_ENV_DIR")) $PS1"
+alias bonsai='source "$BONSAI_ENV_DIR"/run'
+alias bonsai-clean='GTK_DATA_PREFIX= source "$BONSAI_ENV_DIR"/run'
+alias deactivate='source "$BONSAI_ENV_DIR"/deactivate'
+echo "Activated bonsai environment in $BONSAI_ENV_DIR"

examples/NeuralDecoding/PositionDecodingFromHippocampus/.bonsai/deactivate

@@ -0,0 +1,8 @@
+#!/bin/bash
+unset BONSAI_EXE_PATH
+export PS1="$ORIGINAL_PS1"
+unset ORIGINAL_PS1
+unalias bonsai
+unalias bonsai-clean
+unalias deactivate
+echo "Deactivated bonsai environment."

examples/NeuralDecoding/PositionDecodingFromHippocampus/.bonsai/run

@@ -0,0 +1,58 @@
+#!/bin/bash
+# run.sh
+
+SETUP_SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)"
+CONFIG="$SETUP_SCRIPT_DIR/Bonsai.config"
+
+cleanup() {
+    update_paths_to_windows
+}
+
+update_paths_to_linux() {
+    ASSEMBLYLOCATIONS=$(xmllint --xpath '//PackageConfiguration/AssemblyLocations/AssemblyLocation/@location' "$CONFIG" | sed -e 's/^[^"]*"//' -e 's/"$//')
+    for ASSEMBLYLOCATION in $ASSEMBLYLOCATIONS; do
+        NEWASSEMBLYLOCATION="${ASSEMBLYLOCATION//\\/\/}"
+        xmlstarlet edit --inplace --update "/PackageConfiguration/AssemblyLocations/AssemblyLocation[@location='$ASSEMBLYLOCATION']/@location" --value "$NEWASSEMBLYLOCATION" "$CONFIG"
+    done
+
+    LIBRARYFOLDERS=$(xmllint --xpath '//PackageConfiguration/LibraryFolders/LibraryFolder/@path' "$CONFIG" | sed -e 's/^[^"]*"//' -e 's/"$//')
+    for LIBRARYFOLDER in $LIBRARYFOLDERS; do
+        NEWLIBRARYFOLDER="${LIBRARYFOLDER//\\/\/}"
+        xmlstarlet edit --inplace --update "//PackageConfiguration/LibraryFolders/LibraryFolder[@path='$LIBRARYFOLDER']/@path" --value "$NEWLIBRARYFOLDER" "$CONFIG"
+    done
+}
+
+update_paths_to_windows() {
+    ASSEMBLYLOCATIONS=$(xmllint --xpath '//PackageConfiguration/AssemblyLocations/AssemblyLocation/@location' "$CONFIG" | sed -e 's/^[^"]*"//' -e 's/"$//')
+    for ASSEMBLYLOCATION in $ASSEMBLYLOCATIONS; do
+        NEWASSEMBLYLOCATION="${ASSEMBLYLOCATION//\//\\}"
+        xmlstarlet edit --inplace --update "/PackageConfiguration/AssemblyLocations/AssemblyLocation[@location='$ASSEMBLYLOCATION']/@location" --value "$NEWASSEMBLYLOCATION" "$CONFIG"
+    done
+
+    LIBRARYFOLDERS=$(xmllint --xpath '//PackageConfiguration/LibraryFolders/LibraryFolder/@path' "$CONFIG" | sed -e 's/^[^"]*"//' -e 's/"$//')
+    for LIBRARYFOLDER in $LIBRARYFOLDERS; do
+        NEWLIBRARYFOLDER="${LIBRARYFOLDER//\//\\}"
+        xmlstarlet edit --inplace --update "//PackageConfiguration/LibraryFolders/LibraryFolder[@path='$LIBRARYFOLDER']/@path" --value "$NEWLIBRARYFOLDER" "$CONFIG"
+    done
+}
+
+if [[ -v BONSAI_EXE_PATH ]]; then
+    if [ ! -f "$BONSAI_EXE_PATH" ]; then
+        bash "$BONSAI_ENV_DIR"/Setup.sh
+        bash "$BONSAI_ENV_DIR"/run "$@"
+    else
+        BONSAI_VERSION=$(xmllint --xpath "//PackageConfiguration/Packages/Package[@id='Bonsai']/@version" "$CONFIG" | sed -e 's/^[^"]*"//' -e 's/"$//')       
+        if [[ -z ${BONSAI_VERSION+x} ]] && [ "$BONSAI_VERSION" \< "2.8.4" ]; then
+            echo "Updating paths to Linux format..."
+            trap cleanup EXIT INT TERM
+            update_paths_to_linux
+            mono "$BONSAI_EXE_PATH" "$@"
+            cleanup
+        else
+            mono "$BONSAI_EXE_PATH" "$@"
+        fi
+    fi
+else
+    echo "BONSAI_EXE_PATH is not set. Please set the path to the Bonsai executable."
+    return
+fi