Beneuro Pose Estimation

Tools to centralize and run 3d pose estimation from data recorded in the lab. Eventually this tool will be integrated into bnd, our main data organization tool found here.

Installation

Installing the dependencies of this project is not a straighforward task at all. This is the main reason why we are opting to make it a standalone project hosted in its own environment and separate from bnd.

Build the environment

1. Install python 3.7
2. Install Miniforge or Miniconda if you don't have it already:

   # Miniforge (recommended)
   $ Invoke-WebRequest -Uri "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Windows-x86_64.exe" -OutFile "$env:UserProfile/Downloads/Miniforge3-Windows-x86_64.exe"; Start-Process -FilePath "$env:UserProfile/Downloads/Miniforge3-Windows-x86_64.exe" -ArgumentList "/InstallationType=JustMe /RegisterPython=1 /S" -Wait; Remove-Item -Path "$env:UserProfile/Downloads/Miniforge3-Windows-x86_64.exe"

   # Miniconda
   $ curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe -o miniconda.exe; Start-Process -FilePath ".\miniconda.exe" -ArgumentList "/S" -Wait; del miniconda.exe

3. Clone repo and navigate to folder:

   git clone [email protected]:BeNeuroLab/beneuro_pose_estimation.git
   cd ./beneuro_pose_estimation

4. Creating the conda environment

conda create -y -n bnp -c conda-forge -c nvidia -c sleap/label/dev -c sleap -c anaconda sleap=1.4.1

# Activate the Conda environment
conda activate bnp

# Remove opencv pypi version to avoid conflicts
pip uninstall -y opencv-python-headless

# Install the required version of OpenCV
pip install "opencv-contrib-python<4.7.0"

# Install sleap_anipose and the required version of anipose
pip install sleap_anipose
pip install "anipose<1.1"

# Upgrade apptools to the latest version
pip install --upgrade apptools

# Install package in editable form
pip install -e .\  # Windows

The key package versions are:

# Name                    Version                   Build  Channel
anipose                   1.0.1                    pypi_0    pypi
aniposelib                0.5.1                    pypi_0    pypi
sleap-anipose             0.1.8                    pypi_0    pypi
opencv-contrib-python     4.6.0.66                 pypi_0    pypi
opencv-python             4.10.0.84                pypi_0    pypi