Local Install

Python

For the main required Python packages (numpy, scipy, etc.) we recommend using Anaconda for Python 3.6

ANTs & Convert3D (c3d)

If either ANTs or c3d are not installed on your machine, run install_depends.sh, located in the project directory. The required software will be installed in the depends directory

Installing package and dependencies for HippMapp3r locally

1. Clone repository

    git clone https://github.com/mgoubran/HippMapp3r.git HippMapp3r
   
    (or install zip file and uncompress)
   
    cd HippMapp3r
   

   If you want to create a virtual environment where HippMapp3r can be run,

    conda create -n hippmapper python=3.6 anaconda
    source activate hippmapper
   

   To end the session, deactivate the environment

    source deactivate
   

   To delete the environment,

    conda env remove --name hippmapper
   

2. Install dependencies

    pip install git+https://www.github.com/keras-team/keras-contrib.git
   

   If the computer you are using has a GPU:

    pip install -e .[hippmapper_gpu]
   

   If not:

    pip install -e .[hippmapper]
   

3. Test the installation by running

    hippmapper --help
   

   To confirm that the command line function works, and

    hippmapper
   

   To launch the interactive GUI.

Download deep models

Download the models from this link and place them in the models directory

For tab completion

pip3 install argcomplete
activate-global-python-argcomplete

Updating HippMapp3r

To update HippMapp3r, navigate to the directory where HippMapp3r was cloned and run

git pull
pip install -e .[{option}] -process-dependency-links

where “option” is dependent on whether or not you have a GPU (see package installation steps above)