Source code for abydos.distance._ncd_arith

# Copyright 2014-2020 by Christopher C. Little.
# This file is part of Abydos.
#
# Abydos is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Abydos is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Abydos. If not, see <http://www.gnu.org/licenses/>.

"""abydos.distance._ncd_arith.

NCD using Arithmetic Coding
"""

from fractions import Fraction
from typing import Any, Dict, Optional, Tuple

from ._distance import _Distance
from ..compression import Arithmetic

__all__ = ['NCDarith']


[docs] class NCDarith(_Distance): """Normalized Compression Distance using arithmetic coding. Cf. https://en.wikipedia.org/wiki/Arithmetic_coding Normalized compression distance (NCD) :cite:`Cilibrasi:2005`. .. versionadded:: 0.3.6 """ def __init__( self, probs: Optional[Dict[str, Tuple[Fraction, Fraction]]] = None, **kwargs: Any ) -> None: """Initialize the arithmetic coder object. Parameters ---------- probs : dict A dictionary trained with :py:meth:`Arithmetic.train` .. versionadded:: 0.3.6 .. versionchanged:: 0.3.6 Encapsulated in class """ super(NCDarith, self).__init__(**kwargs) self._coder = Arithmetic() self._probs = probs
[docs] def dist(self, src: str, tar: str) -> float: """Return the NCD between two strings using arithmetic coding. Parameters ---------- src : str Source string for comparison tar : str Target string for comparison Returns ------- float Compression distance Examples -------- >>> cmp = NCDarith() >>> cmp.dist('cat', 'hat') 0.5454545454545454 >>> cmp.dist('Niall', 'Neil') 0.6875 >>> cmp.dist('aluminum', 'Catalan') 0.8275862068965517 >>> cmp.dist('ATCG', 'TAGC') 0.6923076923076923 .. versionadded:: 0.3.5 .. versionchanged:: 0.3.6 Encapsulated in class """ if src == tar: return 0.0 if self._probs is None: # lacking a reasonable dictionary, train on the strings themselves self._coder.train(src + tar) else: self._coder.set_probs(self._probs) src_comp = self._coder.encode(src)[1] tar_comp = self._coder.encode(tar)[1] concat_comp = self._coder.encode(src + tar)[1] concat_comp2 = self._coder.encode(tar + src)[1] return ( min(concat_comp, concat_comp2) - min(src_comp, tar_comp) ) / max(src_comp, tar_comp)
if __name__ == '__main__': import doctest doctest.testmod()