migrate to ghactions for ci/cd
sauln
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#!/usr/bin/python
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# -*- coding: utf-8 -*-
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"""
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The persistent entropy has been defined in [1]. A precursor of this definition was given in [2]
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to measure how different bars of the barcode are in length.
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[1] M. Rucco, F. Castiglione, E. Merelli, M. Pettini, Characterisation of the
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idiotypic immune network through persistent entropy, in: Proc. Complex, 2015.
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[2] H. Chintakunta, T. Gentimis, R. Gonzalez-Diaz, M.-J. Jimenez,
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H. Krim, An entropy-based persistence barcode, Pattern Recognition
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48 (2) (2015) 391–401.
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Implementation of persistent entropy
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Author: Eduardo Paluzo Hidalgo (cimagroup, University of Seville)
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contact: epaluzo@us.es
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"""
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from __future__ import division |
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import numpy as np |
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__all__ = ["persistent_entropy"] |
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def persistent_entropy( |
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dgms, keep_inf=False, val_inf=None, normalize=False |
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):
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"""
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Perform the persistent entropy values of a family of persistence barcodes (or persistence diagrams).
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Assumes that the input diagrams are from a determined dimension. If the infinity bars have any meaning
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in your experiment and you want to keep them, remember to give the value you desire to val_Inf.
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Parameters
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-----------
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dgms: ndarray (n_pairs, 2) or list of diagrams
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array or list of arrays of birth/death pairs of a persistence barcode of a determined dimension.
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keep_inf: bool, default False
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if False, the infinity bars are removed.
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if True, the infinity bars remain.
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val_inf: float, default None
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substitution value to infinity.
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normalize: bool, default False
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if False, the persistent entropy values are not normalized.
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if True, the persistent entropy values are normalized.
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Returns
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--------
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ps: ndarray (n_pairs,)
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array of persistent entropy values corresponding to each persistence barcode.
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"""
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if isinstance(dgms, list) == False: |
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dgms = [dgms] |
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# Step 1: Remove infinity bars if keep_inf = False. If keep_inf = True, infinity value is substituted by val_inf.
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if keep_inf == False: |
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dgms = [(dgm[dgm[:, 1] != np.inf]) for dgm in dgms] |
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if keep_inf == True: |
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if val_inf != None: |
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dgms = [ |
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np.where(dgm == np.inf, val_inf, dgm) |
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for dgm in dgms |
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]
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else: |
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raise Exception( |
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"Remember: You need to provide a value to infinity bars if you want to keep them."
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)
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# Step 2: Persistent entropy computation.
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ps = [] |
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for dgm in dgms: |
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l = dgm[:, 1] - dgm[:, 0] |
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if all(l > 0): |
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L = np.sum(l) |
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p = l / L |
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E = -np.sum(p * np.log(p)) |
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if normalize == True: |
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E = E / np.log(len(l)) |
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ps.append(E) |
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else: |
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raise Exception("A bar is born after dying") |
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return np.array(ps) |
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