Examples#

This directory hosts the NRTK examples.

Implementation Guide#

Example notebooks should have an “Open in Colab” button. See other example notebooks for information on how to add a Colab cell.

Example notebooks that download or generate data should place that data in the data sub-directory.

Requirements#

Most of the examples require Jupyter Notebook and PyTorch.

Install these manually using pip or with the following command:

poetry install -E example_deps

Some notebooks may require additional dependencies. See the first cell of each notebook (“Set Up the Environment”) for instructions on how to install the relevant packages.

Additional Installs & Extras#

Many notebooks depend on optional extras from nrtk, which must be installed for the notebook to run correctly. These installs are included at the top of each notebook.

To support both local development and Colab execution (see next section), we use the following installation pattern:

!{sys.executable} -c "import nrtk" || !{sys.executable} -m pip install -q "nrtk[maite,albumentations]>=X.Y.Z"

Here, X.Y.Z is the minimum nrtk version required for the notebook.

This may look unusual, but it solves a practical issue:

  • On Colab, the package must be installed from PyPI rather than the local development environment.

  • During development, we want to use the local version of nrtk.

  • Without this approach, notebooks would fail prior to a release, since the required version wouldn’t yet be available on PyPI.

This check-and-install pattern ensures notebooks work in both contexts.

To help maintain a reproducible environment and simplify debugging (especially with nrtk’s extras), we also provide a utility function:

print_extras_status()

This prints out all extras, their dependencies, and whether they are installed.

Run the Notebooks from Colab#

Most of the notebooks have an “Open in Colab” button. Right-click on the button and select “Open Link in New Tab” to start a Colab page with the corresponding notebook content.

To use GPU resources through Colab, remember to change the runtime type to GPU:

  1. From the Runtime menu select Change runtime type.

  2. Choose GPU from the drop-down menu.

  3. Click SAVE.

This will reset the notebook and may ask you if you are a robot (these instructions assume you are not).

Running:

!nvidia-smi

in a cell will verify this has worked and show you what kind of hardware you have access to.

Note that after setting up the environment, you may need to “Restart Runtime” to resolve package version conflicts.

Data#

Some notebooks may require additional data. Most of this data will be downloaded when running the notebook. However, some notebooks rely on Git LFS being installed for data access.

Encountering Issues#

For issues relating to NRTK functionality or running an example, create an issue on the repository.

This README is adapted from MONAI Tutorials