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Python implementation persistent images representation of persistence diagrams.

Project description

Build Status codecov License: MIT

Persim

Persim is a Python implementation of Persistence Images as first introduced in https://arxiv.org/abs/1507.06217.

It is designed to interface with Ripser, though any persistence diagram should work fine.

Setup

Currently, the only option is to install the library from source:

pip install persim

Usage

First, construct a diagram. In this example, we will use Ripser.

import numpy as np
from ripser import Rips

data = np.random.random((100,2))
rips = Rips()
dgm = rips.fit_transform(data)
diagram = dgm[1] # Just diagram for H1

Then from this diagram, we construct the persistence image

from persim import PersImage

pim = PersImage(diagram)
img = pim.transform()
pim.show(img)

TODO

  • The API needs a little work, not quite sklearn compliant. Please do offer any suggestions.
  • Implement more varieties of weighting and kernel functions.
  • Build tests.

Project details


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