As of this writing, SimpleITK version >=2.0.0 or newer is required to run these notebooks. This version is available from PyPi and Anaconda Cloud.
We recommend setting up a separate Python virtual environment to run through these notebooks as a tutorial.
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
To launch:
conda activate sitkpy
jupyter notebook
To deactivate the conda environment:
conda deactivate
Install virtualenv and create the environment called sitkpy.
sudo pip install virtualenv
virtualenv ~/sitkpy --no-site-packages
Install all of the required packages and SimpleITK, and activate the ipywidgets notebook extension.
~/sitkpy/bin/pip install -r Python/requirements.txt
jupyter nbextension enable --py --sys-prefix widgetsnbextension
The requirements.txt file just lists the required packages (see).
The data is automatically downloaded to the "Data" directory when you execute the notebooks.
Alternatively, to download all the data before hand:
cd SimpleITK-Notebooks
Utilities/downloaddata.py Data/ Data/manifest.json
To launch:
cd SimpleITK-Notebooks/Python
~/sitkpy/bin/jupyter notebook
In some situations, such as a tutorial session, you may not have internet access. This requires that you:
- Download the data in advance - see above.
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