# 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._sift4_extended.
Sift4 Extended approximate string distance
"""
from ._distance import _Distance
from ._sift4 import Sift4
from ..tokenizer import CharacterTokenizer
__all__ = ['Sift4Extended']
[docs]class Sift4Extended(_Distance):
r"""Sift4 Extended version.
This is an approximation of edit distance, described in
:cite:`Zackwehdex:2014`.
.. versionadded:: 0.4.0
"""
_sift4 = Sift4()
def __init__(
self,
max_offset=5,
max_distance=0,
tokenizer=None,
token_matcher=None,
matching_evaluator=None,
local_length_evaluator=None,
transposition_cost_evaluator=None,
transpositions_evaluator=None,
**kwargs
):
"""Initialize Sift4Extended instance.
Parameters
----------
max_offset : int
The number of characters to search for matching letters
max_distance : int
The distance at which to stop and exit
tokenizer : _Tokenizer
A tokenizer instance (character tokenization by default)
token_matcher : function
A token matcher function of two parameters (equality by default).
:math:`Sift4Extended.sift4_token_matcher` is also supplied.
matching_evaluator : function
A token match quality function of two parameters (1 by default).
:math:`Sift4Extended.sift4_matching_evaluator` is also supplied.
local_length_evaluator : function
A local length evaluator function (its single parameter by
default). :math:`Sift4Extended.reward_length_evaluator` and
:math:`Sift4Extended.reward_length_evaluator_exp` are also
supplied.
transposition_cost_evaluator : function
A transposition cost evaluator function of two parameters (1 by
default).
:math:`Sift4Extended.longer_transpositions_are_more_costly` is also
supplied.
transpositions_evaluator : function
A transpositions evaluator function of two parameters (the second
parameter subtracted from the first, by default).
**kwargs
Arbitrary keyword arguments
.. versionadded:: 0.4.0
"""
super(_Distance, self).__init__(**kwargs)
self._max_offset = max_offset
self._max_distance = max_distance
self._tokenizer = tokenizer
self._token_matcher = token_matcher
self._matching_evaluator = matching_evaluator
self._local_length_evaluator = local_length_evaluator
self._transposition_cost_evaluator = transposition_cost_evaluator
self._transpositions_evaluator = transpositions_evaluator
if self._tokenizer is None:
self._tokenizer = CharacterTokenizer()
if self._token_matcher is None:
self._token_matcher = lambda t1, t2: t1 == t2
if self._matching_evaluator is None:
self._matching_evaluator = lambda t1, t2: 1
if self._local_length_evaluator is None:
self._local_length_evaluator = lambda local_cs: local_cs
if self._transposition_cost_evaluator is None:
self._transposition_cost_evaluator = lambda c1, c2: 1
if self._transpositions_evaluator is None:
self._transpositions_evaluator = lambda lcss, trans: lcss - trans
[docs] def dist_abs(self, src, tar):
"""Return the Sift4 Extended distance between two strings.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
int
The Sift4 distance according to the extended formula
Examples
--------
>>> cmp = Sift4Extended()
>>> cmp.dist_abs('cat', 'hat')
1
>>> cmp.dist_abs('Niall', 'Neil')
2
>>> cmp.dist_abs('aluminum', 'Catalan')
5
>>> cmp.dist_abs('ATCG', 'TAGC')
2
.. versionadded:: 0.4.0
"""
src = self._tokenizer.tokenize(src).get_list()
tar = self._tokenizer.tokenize(tar).get_list()
if not src:
return len(tar)
if not tar:
return len(src)
src_len = len(src)
tar_len = len(tar)
src_cur = 0
tar_cur = 0
lcss = 0
local_cs = 0
trans = 0
offset_arr = []
while (src_cur < src_len) and (tar_cur < tar_len):
if self._token_matcher(src[src_cur], tar[tar_cur]):
local_cs += self._matching_evaluator(
src[src_cur], tar[tar_cur]
)
is_trans = False
i = 0
while i < len(offset_arr):
ofs = offset_arr[i]
if src_cur <= ofs['src_cur'] or tar_cur <= ofs['tar_cur']:
is_trans = abs(tar_cur - src_cur) >= abs(
ofs['tar_cur'] - ofs['src_cur']
)
if is_trans:
trans += self._transposition_cost_evaluator(
src_cur, tar_cur
)
elif not ofs['trans']:
ofs['trans'] = True
trans += self._transposition_cost_evaluator(
ofs['tar_cur'], ofs['src_cur']
)
break
elif src_cur > ofs['tar_cur'] and tar_cur > ofs['src_cur']:
del offset_arr[i]
else:
i += 1
offset_arr.append(
{'src_cur': src_cur, 'tar_cur': tar_cur, 'trans': is_trans}
)
else:
lcss += self._local_length_evaluator(local_cs)
local_cs = 0
if src_cur != tar_cur:
src_cur = tar_cur = min(src_cur, tar_cur)
for i in range(self._max_offset):
if not (
(src_cur + i < src_len) or (tar_cur + i < tar_len)
):
break
if (src_cur + i < src_len) and (
self._token_matcher(src[src_cur + i], tar[tar_cur])
):
src_cur += i - 1
tar_cur -= 1
break
if (tar_cur + i < tar_len) and (
self._token_matcher(src[src_cur], tar[tar_cur + i])
):
src_cur -= 1
tar_cur += i - 1
break
src_cur += 1
tar_cur += 1
if self._max_distance:
temporary_distance = self._local_length_evaluator(
max(src_cur, tar_cur)
) - self._transpositions_evaluator(lcss, trans)
if temporary_distance >= self._max_distance:
return round(temporary_distance)
if (src_cur >= src_len) or (tar_cur >= tar_len):
lcss += self._local_length_evaluator(local_cs)
local_cs = 0
src_cur = tar_cur = min(src_cur, tar_cur)
lcss += self._local_length_evaluator(local_cs)
return round(
self._local_length_evaluator(max(src_len, tar_len))
- self._transpositions_evaluator(lcss, trans)
)
[docs] @staticmethod
def sift4_token_matcher(src, tar):
"""Sift4 Token Matcher.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
bool
Whether the Sift4 similarity of the two tokens is over 0.7
.. versionadded:: 0.4.0
"""
return Sift4Extended.sift4_matching_evaluator(src, tar) > 0.7
[docs] @staticmethod
def sift4_matching_evaluator(src, tar):
"""Sift4 Matching Evaluator.
Parameters
----------
src : str
Source string for comparison
tar : str
Target string for comparison
Returns
-------
float
The Sift4 similarity of the two tokens
.. versionadded:: 0.4.0
"""
return Sift4Extended._sift4.sim(src, tar)
[docs] @staticmethod
def reward_length_evaluator(length):
"""Reward Length Evaluator.
Parameters
----------
length : int
The length of a local match
Returns
-------
float
A reward value that grows sub-linearly
.. versionadded:: 0.4.0
"""
if length < 1:
return 1
return length - 1 / (length + 1)
[docs] @staticmethod
def reward_length_evaluator_exp(length):
"""Reward Length Evaluator.
Parameters
----------
length : int
The length of a local match
Returns
-------
float
A reward value that grows exponentially
.. versionadded:: 0.4.0
"""
return length ** 1.5
[docs] @staticmethod
def longer_transpositions_are_more_costly(pos1, pos2):
"""Longer Transpositions Are More Costly.
Parameters
----------
pos1 : int
The position of the first transposition
pos2 : int
The position of the second transposition
Returns
-------
float
A cost that grows as difference in the positions increases
.. versionadded:: 0.4.0
"""
return abs(pos2 - pos1) / 9 + 1
if __name__ == '__main__':
import doctest
doctest.testmod()