A series of Jupyter Notebooks are provided that demonstrate how to use the TopoStats package in a more interactive manner, calling individual steps. This is useful as it allows the user to explore interactively and with rapid feedback the parameters that may need adjusting in order to process a batch of scans. The notebooks can be found in the notebook/ directory after cloning the GitHub repository.

Notebook Description
00-Walkthrough-minicircle.ipynb Step-by-step walkthrough of processing minicircle.spm from the tests/resources/ directory.
01-Walthrhgouh-interactive.ipynb Work in Progress As above but uploading a single scan. Will be deployed in Google Colab/Binder for interactive use.
02-Summary-statistics-and-plots.ipynb Plotting statistics interactively.
03-Plotting-scans.ipynb Plotting NumPy arrays of scans from different stages of processing.


To be able to run the Notebooks you need some additional Python packages installed. You will have to clone the repository from GitHub (see installation) and then install the Notebook dependencies with the following commands under your Virtual Environment (e.g. Conda)…

cd TopoStats
pip install ".[notebooks]"

Running Notebooks#

Start a Jupyter server under the Virtual Environment you have installed the dependencies from and a web-browser page will open from which you can choose which notebook to launch.

cd TopoStats/notebooks
jupyter notebook

For more on Jupyter Notebooks please refer to the official documentation.