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# -*- coding: utf-8 -*- |
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# Copyright 2014-2018 by Christopher C. Little. |
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# This file is part of Abydos. |
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# |
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# Abydos is free software: you can redistribute it and/or modify |
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# it under the terms of the GNU General Public License as published by |
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# the Free Software Foundation, either version 3 of the License, or |
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# (at your option) any later version. |
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# |
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# Abydos is distributed in the hope that it will be useful, |
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# but WITHOUT ANY WARRANTY; without even the implied warranty of |
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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# GNU General Public License for more details. |
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# |
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# You should have received a copy of the GNU General Public License |
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# along with Abydos. If not, see <http://www.gnu.org/licenses/>. |
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"""abydos.distance._ncd_arith. |
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NCD using Arithmetic Coding |
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""" |
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from __future__ import ( |
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absolute_import, |
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division, |
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print_function, |
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unicode_literals, |
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) |
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from ._distance import _Distance |
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from ..compression import Arithmetic |
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__all__ = ['NCDarith', 'dist_ncd_arith', 'sim_ncd_arith'] |
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class NCDarith(_Distance): |
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"""Normalized Compression Distance using Arithmetic Coding. |
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Normalized compression distance (NCD) :cite:`Cilibrasi:2005`. |
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""" |
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_coder = None |
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def __init__(self): |
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"""Initialize the arithmetic coder object.""" |
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self._coder = Arithmetic() |
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def dist(self, src, tar, probs=None): |
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"""Return the NCD between two strings using arithmetic coding. |
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Parameters |
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---------- |
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src : str |
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Source string for comparison |
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tar : str |
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Target string for comparison |
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probs : dict |
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A dictionary trained with :py:meth:`Arithmetic.train` |
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Returns |
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------- |
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float |
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Compression distance |
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Examples |
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-------- |
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>>> cmp = NCDarith() |
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>>> cmp.dist('cat', 'hat') |
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0.5454545454545454 |
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>>> cmp.dist('Niall', 'Neil') |
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0.6875 |
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>>> cmp.dist('aluminum', 'Catalan') |
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0.8275862068965517 |
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>>> cmp.dist('ATCG', 'TAGC') |
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0.6923076923076923 |
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""" |
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if src == tar: |
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return 0.0 |
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if probs is None: |
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# lacking a reasonable dictionary, train on the strings themselves |
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self._coder.train(src + tar) |
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else: |
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self._coder.set_probs(probs) |
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src_comp = self._coder.encode(src)[1] |
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tar_comp = self._coder.encode(tar)[1] |
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concat_comp = self._coder.encode(src + tar)[1] |
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concat_comp2 = self._coder.encode(tar + src)[1] |
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return ( |
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min(concat_comp, concat_comp2) - min(src_comp, tar_comp) |
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) / max(src_comp, tar_comp) |
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def dist_ncd_arith(src, tar, probs=None): |
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"""Return the NCD between two strings using arithmetic coding. |
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This is a wrapper for :py:meth:`NCDarith.dist`. |
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Parameters |
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---------- |
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src : str |
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Source string for comparison |
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tar : str |
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Target string for comparison |
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probs : dict |
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A dictionary trained with :py:meth:`Arithmetic.train` |
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Returns |
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------- |
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float |
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Compression distance |
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Examples |
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-------- |
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>>> dist_ncd_arith('cat', 'hat') |
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0.5454545454545454 |
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>>> dist_ncd_arith('Niall', 'Neil') |
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0.6875 |
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>>> dist_ncd_arith('aluminum', 'Catalan') |
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0.8275862068965517 |
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>>> dist_ncd_arith('ATCG', 'TAGC') |
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0.6923076923076923 |
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""" |
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return NCDarith().dist(src, tar, probs) |
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def sim_ncd_arith(src, tar, probs=None): |
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"""Return the NCD similarity between two strings using arithmetic coding. |
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This is a wrapper for :py:meth:`NCDarith.sim`. |
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Parameters |
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---------- |
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src : str |
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Source string for comparison |
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tar : str |
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Target string for comparison |
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probs : dict |
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A dictionary trained with :py:meth:`Arithmetic.train` |
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Returns |
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------- |
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float |
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Compression similarity |
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Examples |
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-------- |
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>>> sim_ncd_arith('cat', 'hat') |
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0.4545454545454546 |
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>>> sim_ncd_arith('Niall', 'Neil') |
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0.3125 |
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>>> sim_ncd_arith('aluminum', 'Catalan') |
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0.1724137931034483 |
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>>> sim_ncd_arith('ATCG', 'TAGC') |
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0.3076923076923077 |
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""" |
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return NCDarith().sim(src, tar, probs) |
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if __name__ == '__main__': |
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import doctest |
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doctest.testmod() |
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chrislit /
abydos
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