# Copyright 2019-2020 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_paq9a.
NCD using PAQ9A
"""
from ._distance import _Distance
try:
import paq
except ImportError: # pragma: no cover
# If the system lacks the paq9a library, that's fine, but PAQ9A compression
# similarity won't be supported.
paq = None
__all__ = ['NCDpaq9a']
[docs]class NCDpaq9a(_Distance):
"""Normalized Compression Distance using PAQ9A compression.
Cf. http://mattmahoney.net/dc/#paq9a
Normalized compression distance (NCD) :cite:`Cilibrasi:2005`.
.. versionadded:: 0.4.0
"""
[docs] def dist(self, src, tar):
"""Return the NCD between two strings using PAQ9A compression.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float
Compression distance
Raises
------
ValueError
Install the paq module in order to use PAQ9A
Examples
--------
>>> cmp = NCDpaq9a()
>>> cmp.dist('cat', 'hat')
0.42857142857142855
>>> cmp.dist('Niall', 'Neil')
0.5555555555555556
>>> cmp.dist('aluminum', 'Catalan')
0.5833333333333334
>>> cmp.dist('ATCG', 'TAGC')
0.5
.. versionadded:: 0.4.0
"""
if src == tar:
return 0.0
src = src.encode('utf-8')
tar = tar.encode('utf-8')
if paq is not None:
src_comp = paq.compress(src)
tar_comp = paq.compress(tar)
concat_comp = paq.compress(src + tar)
concat_comp2 = paq.compress(tar + src)
else: # pragma: no cover
raise ValueError('Install the paq module in order to use PAQ9A')
# Each string returned by PAQ9A's compressor has 4 header bytes
# followed by a byte of information then 3 null bytes. And it is
# concluded with 3 bytes of \xff. So 4+3+3 invariant bytes are
# subtracted here.
return (
(min(len(concat_comp), len(concat_comp2)) - 10)
- (min(len(src_comp), len(tar_comp)) - 10)
) / (max(len(src_comp), len(tar_comp)) - 10)
if __name__ == '__main__':
import doctest
doctest.testmod()