sarthak268/ripser.py

A Lean Persistent Homology Library for Python

Ripser.py

Ripser.py is a lean persistent homology package for Python. Building on the blazing fast C++ Ripser package as the core computational engine, Ripser.py provides an intuitive interface for

• computing persistence cohomology of sparse and dense data sets,
• visualizing persistence diagrams,
• computing lowerstar filtrations on images, and
• computing representative cochains.

Additionally, through extensive testing and continuous integration, Ripser.py is easy to install on Mac, Linux, and Windows platforms.

To aid your use of the package, we've put together a large set of notebooks that demonstrate many of the features available. Complete documentation about the package can be found at ripser.scikit-tda.org.

If you're looking for the original C++ library, you can find it at Ripser/ripser.

Setup

Installation requires Cython, but other than that, it is available on all platforms (if you are having trouble installing, please let us know!)

pip install Cython
pip install Ripser

Usage

The interface is as simple as can be:

import numpy as np
from ripser import ripser, plot_dgms

data = np.random.random((100,2))
diagrams = ripser(data)['dgms']
plot_dgms(diagrams)

We also supply a Scikit-learn transformer style object if you would prefer to use that:

import numpy as np
from ripser import Rips

rips = Rips()
data = np.random.random((100,2))
diagrams = rips.fit_transform(data)['dgms']
rips.plot(diagrams)

License

Ripser.py is available under an MIT license! The core C++ code is derived from Ripser, which is also available under an MIT license and copyright to Ulrich Baeur. The modifications, Python code, and documentation is copyright to Christopher Tralie and Nathaniel Saul.

Contributions

We welcome all kinds of contributions! There are lots of opportunities for potential projects, so please get in touch if you would like to help out. Everything from code to notebooks to examples and documentation are all equally valuable so please don't feel you can't contribute. To contribute please fork the project make your changes and submit a pull request. We will do our best to work through any issues with you and get your code merged into the main branch.