Skip to content

Commit

Permalink
Updated documentation of BonFly3MPTracker.
Browse files Browse the repository at this point in the history
  • Loading branch information
hugo.marques committed Nov 4, 2024
1 parent d52313c commit e535cbf
Show file tree
Hide file tree
Showing 7 changed files with 1,169 additions and 0 deletions.
4 changes: 4 additions & 0 deletions Marta/BonFly3MPTracker/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,10 @@ These should only need to be installed once on a fresh new system, and are not r

You can download the latest release of tensorflow.dll [here](https://www.tensorflow.org/install/lang_c#download_and_extract) and copy it inside your Extensions folder. You can click [here](https://github.com/bonsai-rx/sleap) for further instructions on install sleap in Bonsai.


## Running the parallel code
Currently, to parallelise the workflows, you need to manually divide your files across different directories in a given parent directory. Each of working directory will run independently from the others. This can be improved in the future, but we should test whether this is a good strategy to handle the data.

## Acknowledgements

This code was modified from the original one created by Bruno Cruz.
Expand Down
142 changes: 142 additions & 0 deletions Vasconcelos/MatingIdentification-INDP2024/bonsai/Bonsai.config
Original file line number Diff line number Diff line change
@@ -0,0 +1,142 @@
<?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>
<Package id="AForge" version="2.2.5" />
<Package id="AForge.Video" version="2.2.5" />
<Package id="AForge.Video.DirectShow" version="2.2.5" />
<Package id="Bonsai" version="2.8.5" />
<Package id="Bonsai.Arduino" version="2.8.1" />
<Package id="Bonsai.Audio" version="2.8.0" />
<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" />
<Package id="Bonsai.Dsp" version="2.8.0" />
<Package id="Bonsai.Dsp.Design" version="2.8.0" />
<Package id="Bonsai.Editor" version="2.8.5" />
<Package id="Bonsai.Gui" version="0.1.0" />
<Package id="Bonsai.Osc" version="2.7.0" />
<Package id="Bonsai.PointGrey" version="2.3.1" />
<Package id="Bonsai.Scripting.Expressions" version="2.8.0" />
<Package id="Bonsai.Scripting.Expressions.Design" version="2.8.0" />
<Package id="Bonsai.Shaders" version="0.27.0" />
<Package id="Bonsai.Shaders.Design" version="0.27.0" />
<Package id="Bonsai.StarterPack" version="2.8.1" />
<Package id="Bonsai.System" version="2.8.1" />
<Package id="Bonsai.System.Design" version="2.8.0" />
<Package id="Bonsai.Video" version="2.4.0" />
<Package id="Bonsai.Video.Design" version="2.4.0" />
<Package id="Bonsai.Vision" version="2.8.0" />
<Package id="Bonsai.Vision.Design" version="2.8.1" />
<Package id="Bonsai.Windows.Input" version="2.7.0" />
<Package id="jacobslusser.ScintillaNET" version="3.6.3" />
<Package id="Markdig" version="0.18.1" />
<Package id="Microsoft.Web.WebView2" version="1.0.1823.32" />
<Package id="openal.redist" version="2.0.7" />
<Package id="OpenCV.Net" version="3.4.2" />
<Package id="OpenTK" version="3.1.0" />
<Package id="OpenTK.GLControl" version="3.1.0" />
<Package id="Rx-Core" version="2.2.5" />
<Package id="Rx-Interfaces" version="2.2.5" />
<Package id="Rx-Linq" version="2.2.5" />
<Package id="Rx-PlatformServices" version="2.2.5" />
<Package id="SvgNet" version="3.3.3" />
<Package id="System.Buffers" version="4.5.1" />
<Package id="System.Linq.Dynamic" version="1.0.7" />
<Package id="System.Memory" version="4.5.5" />
<Package id="System.Numerics.Vectors" version="4.5.0" />
<Package id="System.Resources.Extensions" version="8.0.0" />
<Package id="System.Runtime.CompilerServices.Unsafe" version="4.5.3" />
<Package id="YamlDotNet" version="13.1.1" />
<Package id="ZedGraph" version="5.1.7" />
</Packages>
<AssemblyReferences>
<AssemblyReference assemblyName="Bonsai" />
<AssemblyReference assemblyName="Bonsai.Arduino" />
<AssemblyReference assemblyName="Bonsai.Audio" />
<AssemblyReference assemblyName="Bonsai.Core" />
<AssemblyReference assemblyName="Bonsai.Design" />
<AssemblyReference assemblyName="Bonsai.Design.Visualizers" />
<AssemblyReference assemblyName="Bonsai.Dsp" />
<AssemblyReference assemblyName="Bonsai.Dsp.Design" />
<AssemblyReference assemblyName="Bonsai.Editor" />
<AssemblyReference assemblyName="Bonsai.Gui" />
<AssemblyReference assemblyName="Bonsai.Osc" />
<AssemblyReference assemblyName="Bonsai.PointGrey" />
<AssemblyReference assemblyName="Bonsai.Scripting.Expressions" />
<AssemblyReference assemblyName="Bonsai.Scripting.Expressions.Design" />
<AssemblyReference assemblyName="Bonsai.Shaders" />
<AssemblyReference assemblyName="Bonsai.Shaders.Design" />
<AssemblyReference assemblyName="Bonsai.System" />
<AssemblyReference assemblyName="Bonsai.System.Design" />
<AssemblyReference assemblyName="Bonsai.Video" />
<AssemblyReference assemblyName="Bonsai.Video.Design" />
<AssemblyReference assemblyName="Bonsai.Vision" />
<AssemblyReference assemblyName="Bonsai.Vision.Design" />
<AssemblyReference assemblyName="Bonsai.Windows.Input" />
</AssemblyReferences>
<AssemblyLocations>
<AssemblyLocation assemblyName="AForge" processorArchitecture="MSIL" location="Packages/AForge.2.2.5/lib/AForge.dll" />
<AssemblyLocation assemblyName="AForge.Video" processorArchitecture="MSIL" location="Packages/AForge.Video.2.2.5/lib/AForge.Video.dll" />
<AssemblyLocation assemblyName="AForge.Video.DirectShow" processorArchitecture="MSIL" location="Packages/AForge.Video.DirectShow.2.2.5/lib/AForge.Video.DirectShow.dll" />
<AssemblyLocation assemblyName="Bonsai" processorArchitecture="MSIL" location="Packages/Bonsai.2.8.5/lib/net48/Bonsai.exe" />
<AssemblyLocation assemblyName="Bonsai.Arduino" processorArchitecture="MSIL" location="Packages/Bonsai.Arduino.2.8.1/lib/net462/Bonsai.Arduino.dll" />
<AssemblyLocation assemblyName="Bonsai.Audio" processorArchitecture="MSIL" location="Packages/Bonsai.Audio.2.8.0/lib/net462/Bonsai.Audio.dll" />
<AssemblyLocation assemblyName="Bonsai.Core" processorArchitecture="MSIL" location="Packages/Bonsai.Core.2.8.5/lib/net462/Bonsai.Core.dll" />
<AssemblyLocation assemblyName="Bonsai.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Design.2.8.5/lib/net462/Bonsai.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.Design.Visualizers" processorArchitecture="MSIL" location="Packages/Bonsai.Design.Visualizers.2.8.0/lib/net462/Bonsai.Design.Visualizers.dll" />
<AssemblyLocation assemblyName="Bonsai.Dsp" processorArchitecture="MSIL" location="Packages/Bonsai.Dsp.2.8.0/lib/net462/Bonsai.Dsp.dll" />
<AssemblyLocation assemblyName="Bonsai.Dsp.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Dsp.Design.2.8.0/lib/net462/Bonsai.Dsp.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.Editor" processorArchitecture="MSIL" location="Packages/Bonsai.Editor.2.8.5/lib/net472/Bonsai.Editor.dll" />
<AssemblyLocation assemblyName="Bonsai.Gui" processorArchitecture="MSIL" location="Packages/Bonsai.Gui.0.1.0/lib/net472/Bonsai.Gui.dll" />
<AssemblyLocation assemblyName="Bonsai.Osc" processorArchitecture="MSIL" location="Packages/Bonsai.Osc.2.7.0/lib/net462/Bonsai.Osc.dll" />
<AssemblyLocation assemblyName="Bonsai.PointGrey" processorArchitecture="MSIL" location="Packages/Bonsai.PointGrey.2.3.1/lib/net45/Bonsai.PointGrey.dll" />
<AssemblyLocation assemblyName="Bonsai.Scripting.Expressions" processorArchitecture="MSIL" location="Packages/Bonsai.Scripting.Expressions.2.8.0/lib/net462/Bonsai.Scripting.Expressions.dll" />
<AssemblyLocation assemblyName="Bonsai.Scripting.Expressions.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Scripting.Expressions.Design.2.8.0/lib/net462/Bonsai.Scripting.Expressions.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.Shaders" processorArchitecture="MSIL" location="Packages/Bonsai.Shaders.0.27.0/lib/net462/Bonsai.Shaders.dll" />
<AssemblyLocation assemblyName="Bonsai.Shaders.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Shaders.Design.0.27.0/lib/net462/Bonsai.Shaders.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.System" processorArchitecture="MSIL" location="Packages/Bonsai.System.2.8.1/lib/net462/Bonsai.System.dll" />
<AssemblyLocation assemblyName="Bonsai.System.Design" processorArchitecture="MSIL" location="Packages/Bonsai.System.Design.2.8.0/lib/net462/Bonsai.System.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.Video" processorArchitecture="MSIL" location="Packages/Bonsai.Video.2.4.0/lib/net462/Bonsai.Video.dll" />
<AssemblyLocation assemblyName="Bonsai.Video.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Video.Design.2.4.0/lib/net462/Bonsai.Video.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.Vision" processorArchitecture="MSIL" location="Packages/Bonsai.Vision.2.8.0/lib/net462/Bonsai.Vision.dll" />
<AssemblyLocation assemblyName="Bonsai.Vision.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Vision.Design.2.8.1/lib/net462/Bonsai.Vision.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.Windows.Input" processorArchitecture="MSIL" location="Packages/Bonsai.Windows.Input.2.7.0/lib/net462/Bonsai.Windows.Input.dll" />
<AssemblyLocation assemblyName="FlyCapture2Managed_v100" processorArchitecture="X86" location="Packages/Bonsai.PointGrey.2.3.1/build/net45/bin/x86/FlyCapture2Managed_v100.dll" />
<AssemblyLocation assemblyName="FlyCapture2Managed_v100" processorArchitecture="Amd64" location="Packages/Bonsai.PointGrey.2.3.1/build/net45/bin/x64/FlyCapture2Managed_v100.dll" />
<AssemblyLocation assemblyName="Markdig" processorArchitecture="MSIL" location="Packages/Markdig.0.18.1/lib/net40/Markdig.dll" />
<AssemblyLocation assemblyName="Microsoft.Web.WebView2.Core" processorArchitecture="MSIL" location="Packages/Microsoft.Web.WebView2.1.0.1823.32/lib/net45/Microsoft.Web.WebView2.Core.dll" />
<AssemblyLocation assemblyName="Microsoft.Web.WebView2.WinForms" processorArchitecture="MSIL" location="Packages/Microsoft.Web.WebView2.1.0.1823.32/lib/net45/Microsoft.Web.WebView2.WinForms.dll" />
<AssemblyLocation assemblyName="Microsoft.Web.WebView2.Wpf" processorArchitecture="MSIL" location="Packages/Microsoft.Web.WebView2.1.0.1823.32/lib/net45/Microsoft.Web.WebView2.Wpf.dll" />
<AssemblyLocation assemblyName="OpenCV.Net" processorArchitecture="MSIL" location="Packages/OpenCV.Net.3.4.2/lib/net462/OpenCV.Net.dll" />
<AssemblyLocation assemblyName="OpenTK" processorArchitecture="MSIL" location="Packages/OpenTK.3.1.0/lib/net20/OpenTK.dll" />
<AssemblyLocation assemblyName="OpenTK.GLControl" processorArchitecture="MSIL" location="Packages/OpenTK.GLControl.3.1.0/lib/net20/OpenTK.GLControl.dll" />
<AssemblyLocation assemblyName="ScintillaNET" processorArchitecture="MSIL" location="Packages/jacobslusser.ScintillaNET.3.6.3/lib/net40/ScintillaNET.dll" />
<AssemblyLocation assemblyName="SVG" processorArchitecture="MSIL" location="Packages/SvgNet.3.3.3/lib/net462/SVG.dll" />
<AssemblyLocation assemblyName="System.Buffers" processorArchitecture="MSIL" location="Packages/System.Buffers.4.5.1/lib/net461/System.Buffers.dll" />
<AssemblyLocation assemblyName="System.Linq.Dynamic" processorArchitecture="MSIL" location="Packages/System.Linq.Dynamic.1.0.7/lib/net40/System.Linq.Dynamic.dll" />
<AssemblyLocation assemblyName="System.Memory" processorArchitecture="MSIL" location="Packages/System.Memory.4.5.5/lib/net461/System.Memory.dll" />
<AssemblyLocation assemblyName="System.Numerics.Vectors" processorArchitecture="MSIL" location="Packages/System.Numerics.Vectors.4.5.0/lib/net46/System.Numerics.Vectors.dll" />
<AssemblyLocation assemblyName="System.Reactive.Core" processorArchitecture="MSIL" location="Packages/Rx-Core.2.2.5/lib/net45/System.Reactive.Core.dll" />
<AssemblyLocation assemblyName="System.Reactive.Interfaces" processorArchitecture="MSIL" location="Packages/Rx-Interfaces.2.2.5/lib/net45/System.Reactive.Interfaces.dll" />
<AssemblyLocation assemblyName="System.Reactive.Linq" processorArchitecture="MSIL" location="Packages/Rx-Linq.2.2.5/lib/net45/System.Reactive.Linq.dll" />
<AssemblyLocation assemblyName="System.Reactive.PlatformServices" processorArchitecture="MSIL" location="Packages/Rx-PlatformServices.2.2.5/lib/net45/System.Reactive.PlatformServices.dll" />
<AssemblyLocation assemblyName="System.Resources.Extensions" processorArchitecture="MSIL" location="Packages/System.Resources.Extensions.8.0.0/lib/net462/System.Resources.Extensions.dll" />
<AssemblyLocation assemblyName="System.Runtime.CompilerServices.Unsafe" processorArchitecture="MSIL" location="Packages/System.Runtime.CompilerServices.Unsafe.4.5.3/lib/net461/System.Runtime.CompilerServices.Unsafe.dll" />
<AssemblyLocation assemblyName="YamlDotNet" processorArchitecture="MSIL" location="Packages/YamlDotNet.13.1.1/lib/net47/YamlDotNet.dll" />
<AssemblyLocation assemblyName="ZedGraph" processorArchitecture="MSIL" location="Packages/ZedGraph.5.1.7/lib/net35-Client/ZedGraph.dll" />
</AssemblyLocations>
<LibraryFolders>
<LibraryFolder path="Packages/Bonsai.PointGrey.2.3.1/build/native/bin/x64" platform="x64" />
<LibraryFolder path="Packages/Bonsai.PointGrey.2.3.1/build/native/bin/x86" platform="x86" />
<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" />
<LibraryFolder path="Packages/openal.redist.2.0.7.0/build/native/bin/x64" platform="x64" />
<LibraryFolder path="Packages/openal.redist.2.0.7.0/build/native/bin/x86" platform="x86" />
<LibraryFolder path="Packages/OpenCV.Net.3.4.2/runtimes/win-x64/native/vc14/bin" platform="x64" />
<LibraryFolder path="Packages/OpenCV.Net.3.4.2/runtimes/win-x86/native/vc14/bin" platform="x86" />
</LibraryFolders>
</PackageConfiguration>
8 changes: 8 additions & 0 deletions Vasconcelos/MatingIdentification-INDP2024/bonsai/NuGet.config
Original file line number Diff line number Diff line change
@@ -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>
1 change: 1 addition & 0 deletions Vasconcelos/MatingIdentification-INDP2024/bonsai/Setup.cmd
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
powershell -ExecutionPolicy Bypass -File .\SetupPS.ps1
9 changes: 9 additions & 0 deletions Vasconcelos/MatingIdentification-INDP2024/bonsai/SetupPS.ps1
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
if (!(Test-Path "./Bonsai.exe")) {
Invoke-WebRequest "https://github.com/bonsai-rx/bonsai/releases/download/2.8.5/Bonsai.zip" -OutFile "temp.zip"
Move-Item -Path "NuGet.config" "temp.config"
Expand-Archive "temp.zip" -DestinationPath "." -Force
Move-Item -Path "temp.config" "NuGet.config" -Force
Remove-Item -Path "temp.zip"
Remove-Item -Path "Bonsai32.exe"
}
& .\Bonsai.exe --no-editor
Loading

0 comments on commit e535cbf

Please sign in to comment.