First steps - how to run tutorialsΒΆ

The OpenCMISS-Iron tutorials have been created as Jupyter notebooks. Follow the steps below to obtain a local copy of these tutorials that you can run on your own machine.

  1. Navigate to https://github.com/OpenCMISS-Examples/OpenCMISS-Iron-tutorials
  2. Download the repository as a zip as shown in the screenshot below:
Download tutorials
  1. Extract the zip file.
  • If you will be running the tutorial using an OpenCMISS-Iron Docker container, move the extracted folder into a directory that can be accessed from an OpenCMISS-Iron Docker container (ie, a directory that is mounted within the container), such as your main working folder (opt). By default, this is located in:
  • ~/oc/opt on Linux and Mac; or
  • C:/Users/${env:UserName}/Documents/oc/opt on Windows.

See the Installation Section of the Getting Started Section for more information regarding the directories that are mounted with the Docker Containers.

  1. If you are not using OpenCMISS-Iron Dockers:
  1. Download the threejs_visualiser.py python script that will be used for embedding visualisations.
  2. Specify the folder containing this script directly in the Jupyter notebook of a given tutorial by adding the following lines at the top of the notebook:
import sys
# Specify path to the threejs_visualiser.py.
sys.path.insert(1, 'path/to/threejs_visualiser.py')
  1. Open a given tutorial (located in the tutorials folder of the downloaded repository) in your software of choice.

Note

If you are new to OpenCMISS, we recommend using the OpenCMISS-Iron Dockers, and following the instructions for running JupyterLab (See the Installation and Running Sections of the Getting Started Section for more information).