# 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_zlib.
NCD using zlib
"""
import zlib
from deprecation import deprecated
from ._distance import _Distance
from .. import __version__
__all__ = ['NCDzlib', 'dist_ncd_zlib', 'sim_ncd_zlib']
[docs]class NCDzlib(_Distance):
"""Normalized Compression Distance using zlib compression.
Cf. https://zlib.net/
Normalized compression distance (NCD) :cite:`Cilibrasi:2005`.
.. versionadded:: 0.3.6
"""
def __init__(self, level=zlib.Z_DEFAULT_COMPRESSION, **kwargs):
"""Initialize zlib compressor.
Parameters
----------
level : int
The compression level (0 to 9)
.. versionadded:: 0.3.6
"""
super().__init__(**kwargs)
self._level = level
[docs] def dist(self, src, tar):
"""Return the NCD between two strings using zlib compression.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float
Compression distance
Examples
--------
>>> cmp = NCDzlib()
>>> cmp.dist('cat', 'hat')
0.3333333333333333
>>> cmp.dist('Niall', 'Neil')
0.45454545454545453
>>> cmp.dist('aluminum', 'Catalan')
0.5714285714285714
>>> cmp.dist('ATCG', 'TAGC')
0.4
.. versionadded:: 0.3.5
.. versionchanged:: 0.3.6
Encapsulated in class
"""
if src == tar:
return 0.0
src = src.encode('utf-8')
tar = tar.encode('utf-8')
src_comp = zlib.compress(src, self._level)
tar_comp = zlib.compress(tar, self._level)
concat_comp = zlib.compress(src + tar, self._level)
concat_comp2 = zlib.compress(tar + src, self._level)
return (
min(len(concat_comp), len(concat_comp2))
- (min(len(src_comp), len(tar_comp)))
) / (max(len(src_comp), len(tar_comp)) - 2)
[docs]@deprecated(
deprecated_in='0.4.0',
removed_in='0.6.0',
current_version=__version__,
details='Use the NCDzlib.dist method instead.',
)
def dist_ncd_zlib(src, tar):
"""Return the NCD between two strings using zlib compression.
This is a wrapper for :py:meth:`NCDzlib.dist`.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float
Compression distance
Examples
--------
>>> dist_ncd_zlib('cat', 'hat')
0.3333333333333333
>>> dist_ncd_zlib('Niall', 'Neil')
0.45454545454545453
>>> dist_ncd_zlib('aluminum', 'Catalan')
0.5714285714285714
>>> dist_ncd_zlib('ATCG', 'TAGC')
0.4
.. versionadded:: 0.3.5
"""
return NCDzlib().dist(src, tar)
[docs]@deprecated(
deprecated_in='0.4.0',
removed_in='0.6.0',
current_version=__version__,
details='Use the NCDzlib.sim method instead.',
)
def sim_ncd_zlib(src, tar):
"""Return the NCD similarity between two strings using zlib compression.
This is a wrapper for :py:meth:`NCDzlib.sim`.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float: Compression similarity
Examples
--------
>>> sim_ncd_zlib('cat', 'hat')
0.6666666666666667
>>> sim_ncd_zlib('Niall', 'Neil')
0.5454545454545454
>>> sim_ncd_zlib('aluminum', 'Catalan')
0.4285714285714286
>>> sim_ncd_zlib('ATCG', 'TAGC')
0.6
.. versionadded:: 0.3.5
"""
return NCDzlib().sim(src, tar)
if __name__ == '__main__':
import doctest
doctest.testmod()