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. If you are intrested to install c3d on MacOS or Windows, you can dowanlod it from this link.

Installing package and dependencies for iCVMapp3r locally

1. Clone repository

    git clone https://github.com/AICONSlab/iCVMapp3r.git iCVMapp3r
   
    (or install zip file and uncompress)
   
    cd iCVMapp3r
   

   If you want to create a virtual environment where iCVMapp3r can be run,

    conda create -n icvmapper python=3.6 anaconda
    conda activate icvmapper
   

   To end the session,

    conda deactivate
   

   To remove the environment

    conda env remove --name icvmapper
   

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 .[icvmapper_gpu]
   

   If not:

    pip install -e .[icvmapper]
   

3. Test the installation by running

    icvmapper --help
   

   To confirm that the command line function works, and

    icvmapper
   

   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 iCVMapp3r

To update iCVMapp3r, navigate to the directory where iCVMapp3r 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)