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dowker_persistence

Code for computing Dowker persistence diagrams

https://github.com/irishryoon/dowker_persistence

Science Score: 54.0%

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Keywords

dowker-complexes persistent-homology topological-data-analysis
Last synced: 11 months ago · JSON representation ·

Repository

Code for computing Dowker persistence diagrams

Basic Info
  • Host: GitHub
  • Owner: irishryoon
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 2.47 MB
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  • Watchers: 1
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  • Releases: 1
Topics
dowker-complexes persistent-homology topological-data-analysis
Created almost 4 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

Dowker persistence

This repository contains code for computing the Dowker persistence diagrams of two point clouds in dimensions 0 or 1. Please note that we use the term "Dowker" and "Witness" interchangeably.

DOI

Install

Download Julia. You may run into dependency issues for more recent versions of Julia. I recommend using Julia version 1.7.2.

Quick start

``` import Pkg Pkg.activate(".") Pkg.instantiate() include("dowkerpersistence.jl") include("Eirenevar.jl) using .Dowker using .Eirene_var using DelimitedFiles

load points

P1 = readdlm("toyexample/R1coordinates.csv", ',', Float64) P2 = readdlm("toyexample/R2coordinates.csv", ',', Float64)

compute cross-system distance

D1, D2, DP1P2, DP2P1 = compute_distance(P1, P2)

compute Dowker persistence

WP1P2 = computeWitnesspersistence(DP1P2, maxdim = 1) Wbarcode = Eirenevar.barcode(WP1P2["eirene_output"], dim = 1)

plot Dowker persistence diagram

plotPD(Wbarcode, title = "Dowker persistence diagram") ```

Examples

  • See 1_compute_dowker_persistence.ipynb for example computation of Dowker persistence diagram, cycle representatives, and persistence images.
  • See 2_more_examples.ipynb for Dowker persistence diagrams on a few toy examples.

Owner

  • Name: Iris Yoon
  • Login: irishryoon
  • Kind: user

Mathematician & Data Scientist

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Yoon
    given-names: Hee Rhang
    orcid: https://orcid.org/0000-0003-0638-9195
title: "Dowker persistence"
version: 1.0.0
doi: 10.5281/zenodo.7492624
date-released: 2022-10-02

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