Improve memory use in ripser_interface - Githubissues

giotto-ai / giotto-tda

A high-performance topological machine learning toolbox in Python

https://giotto-ai.github.io/gtda-docs

Other

845 stars 173 forks source link

Improve memory use in ripser_interface #507

Closed ulupo closed 4 years ago

ulupo commented 4 years ago

Reference issues/PRs Small continuation of #501.

Types of changes

[ ] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)

Description

Implements suggestions in https://github.com/giotto-ai/giotto-tda/pull/501#issuecomment-695283066
Uses scipy's squareform function for fast and easy-to-read extraction of the upper diagonal part of dm

Checklist

[x] I have read the guidelines for contributing.
[x] My code follows the code style of this project. I used flake8 to check my Python changes.
[x] My change requires a change to the documentation.
[x] I have updated the documentation accordingly.
[x] I have added tests to cover my changes.
[x] All new and existing tests passed. I used pytest to check this on Python tests.

MonkeyBreaker commented 4 years ago

I tested on the torus dataset (50e3 points), worked like a charm :smiley: ! I got the same memory consumption as with the ugly method I used previously

Nice found with the squareform method :+1: