rkwitt/simpleitk-notebooks

ipython notebooks for learning how to use SimpleITK

SimpleITK Notebooks

This is a collection of IPython Notebooks, designed for tutorials, presentations and demonstration of using SimpleITK in the "pylab" environment for interactive image process.

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

Getting Started

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

Additional Data Download

Additionally the SPL's "Multi-modality MRI-based Atlas of the Brain" should be downloaded and extracted into the SimpleITK-Notebooks/Data directory.

http://www.spl.harvard.edu/publications/item/view/2037

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 10.8 and 10.7.5, 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
~/sitkpy/bin/pip install ipython[zmq]
~/sitkpy/bin/pip install tornado
~/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:

~/sitkpy/bin/easy_install SimpleITK

As of this writing, SimpleITK version >=0.6r1 is required to run these notebooks. This version currently needs to be downloaded from Source Forge

Run the environment

To launch:

cd SimpleITK-Notebooks
~/sitkpy/bin/ipython notebook --pylab=inline