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.
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.
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
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.
pip install -r Python/requirements.txt
On Jupyter Notebooks version 5.2 or older activate the ipywidgets notebook extension:
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
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