ds4m.github.io

Topological Data Analysis

This subfolder contains persistent homology examples

This repository contains scripts for using Ripser (https://github.com/Ripser/ripser) and Hera (https://bitbucket.org/grey_narn/hera) with a Python interface.

1. To run Ripser on a collection of distance matrices use getBarCodes.py
2. To separate Ripser output by dimension to a input that is compatible with Hera, use separateRipser.py IMPORTANT: Code assumes there are just dimension 0 and dimension 1 barcodes. Code can be adapted easily.
3. To plot PDs, use plotPDs.py (Must use output of separateRipser, not output of getBarCodes.py)
4. To compute distances between two barcodes, use computePDDists.py.

For usage help, run python [filename] –h

Author: Melissa McGuirl Contact: melissa_mcguirl@brown.edu

HENRY NOTE: Our plan is to update this to instead use scikit-tda?