SimpleITK-Notebooks/Python

• SimpleITK Python Notebooks
• • Setting Up a Python Environment
  • • Anaconda
    • Plain Python
  • Downloading Data

SimpleITK Python Notebooks

As of this writing, SimpleITK version >=2.2.0 or newer is required to run these notebooks. This version is available from PyPi and Anaconda Cloud.

Setting Up a Python Environment

We recommend setting up a separate Python virtual environment to run through these notebooks as a tutorial. Use either the Anaconda Python distribution or a plain Python distribution.

Anaconda

With Anaconda you can set up a virtual environment, named sitkpy, and install all dependencies including SimpleITK using a single command:

conda env create -f environment.yml

Run the notebooks

To launch:

conda activate sitkpy
jupyter notebook

To deactivate the conda environment:

conda deactivate

Plain Python

Create the virtual environment called sitkpy.

python -m venv sitkpy

Activate the virtual environment:
On windows: sitkpy\Scripts\activate.bat
On linux/osx: source sitkpy/bin/activate

Install all of the required packages and activate the ipywidgets notebook extension.

pip install -r Python/requirements.txt
jupyter nbextension enable --py --sys-prefix widgetsnbextension

The requirements.txt file lists the required packages (see here).

Run the notebooks

To launch:
Activate the virtual environment as above and:

jupyter notebook

Downloading Data

The data is automatically downloaded to the "Data" directory when you execute the notebooks.

In some situations, such as a tutorial session, you may not have internet access. This requires that you download all the data before hand:

cd SimpleITK-Notebooks
Utilities/downloaddata.py Data/ Data/manifest.json