Installation Guide¶

This note briefly describes how to install and use EasyReg. Unfortunately, it is currently not available on Conda, but it is fairly simple to instally manually. It is recommended to use virtual environment to avoid conflicts.

Requirements¶

Our framework needs the following:

python == 3.6

pytorch >= 1.0

It runs both on Mac OS and Linux, it is not tested in Windows.

Step 0: Installing Anaconda¶

This step mostly skipped, but we rely on Anaconda to install the package, if you are missing Anaconda, their installation manual can be found in this link: https://docs.anaconda.com/anaconda/install/

Step 1: Creating virtual environment¶

As suggested, the virtual environment can be initiliazed with the following command:

conda create -n easyreg python=3.6
conda activate easyreg

If at any point, it can be deleted via following:

conda remove --name easyreg --all

Step2: Downloading the files¶

As our package is not available at PyPI, it is best to refer our repository to download the package files from our repository.

git clone https://github.com/uncbiag/easyreg.git

We further need to download .. _Mermaid: https://mermaid.readthedocs.io/ as our framework heavily depends on the primitives built in Mermaid library.

cd easyreg
git clone https://github.com/uncbiag/mermaid.git

Step3: Installing dependencies¶

Other dependencies, such as ITK, can be installed from our requirements.txt.

pip install -r requirements.txt

Step4: Installing Mermaid¶

Mermaid framework needs to be installed seperately, it can be done with two simple steps:

cd mermaid
python setup.py develop