SimpleITK Notebook Answers

SimpleITK is an abstraction layer and wrapper around the Insight Toolkit for many languages including python.

This is a collection of IPython Notebooks, that have been written to quickly answer questions, such as that from the ITK mailing lists. While these have been written with python and use ITK via SimpelITK, they illustrate how to use and interact with ITK classes and run ITK algorithms.

Getting Started

For general information about installing SimpleITK please see the SimpleITK wiki.

Setting Up a Python Environment

It is recommended to setup a separate Python virtual environment to run through these notebooks as a tutorial.

Under the best of circumstances (tested on OSX 10.9, 10.8, 10.7, RH6, Ubuntu 12) this environment can be setup with the following:

sudo pip install virtualenv
virtualenv ~/sitkpy --no-site-packages
~/sitkpy/bin/pip install ipython[all]
~/sitkpy/bin/pip install numpy
~/sitkpy/bin/pip install matplotlib

Note: On Linux platforms you may be able to obtain many of these packages as system packages which may suffice ( Ubuntu 12+). Note: On Window platforms some of these packages should be obtained as binary downloads and installed.

Install SimpleITK

For many common platforms, a built distribution is available as an Python egg. This can be downloading and installed with the following command:

source ~/sitkpy/bin/activate
~/sitkpy/bin/easy_install SimpleITK

Alternatively, you can manually download SimpleITK binaries and manually install them from Source Forge

Run the environment

To launch:

source ~/sitkpy/bin/activate
cd SimpleITK-Notebook-Answers
~/sitkpy/bin/ipython notebook

Maintainence

These notebooks are not maintained an are use just for illustrative purposes.