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

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

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]

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)