uflcod/endophenotype-study-analysis

Endophenotype Study Analyis

Repository for exploring how anyalyze results produced by the endophenotype study.

The image files may be either 2D or 3D.

Virtual environment setup

• To create a virtual environment run the command python -m venv venv. This will create a virtual environment in the venv directory. You can specify a different directory name if you wish.
• Run source venv/bin/activate to activate (i.e., run) the virtual environment.
• After activating the environment, install the project libraries using the command pip install -r requirements.txt -U.

Jupyter hack for virtual environments

Jupyter notebooks won't necessarily have access to the libraries installed in the virtual environment.
One hack to get around this is to create a softlink to the Jupyter binary created in the virtual environment like so ln -s venv/bin/jupyter.

You can then start Jupyter within the virtual environment using the softlink. E.g., ./jupyter lab.
The allows the Jupyter notebook to access the libraries in the virtual environment.

Another option is create a Jupyter kernel from the virtual environment. See here for details.