# 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._fidelity.
Fidelity
"""
from ._token_distance import _TokenDistance
__all__ = ['Fidelity']
[docs]class Fidelity(_TokenDistance):
r"""Fidelity.
For two multisets X and Y drawn from an alphabet S, fidelity is
.. math::
sim_{Fidelity}(X, Y) =
\Bigg( \sum_{i \in S} \sqrt{|\frac{A_i}{|A|} \cdot
\frac{B_i}{|B|}|} \Bigg)^2
.. versionadded:: 0.4.0
"""
def __init__(self, tokenizer=None, **kwargs):
"""Initialize Fidelity instance.
Parameters
----------
tokenizer : _Tokenizer
A tokenizer instance from the :py:mod:`abydos.tokenizer` package
**kwargs
Arbitrary keyword arguments
Other Parameters
----------------
qval : int
The length of each q-gram. Using this parameter and tokenizer=None
will cause the instance to use the QGram tokenizer with this
q value.
.. versionadded:: 0.4.0
"""
super(Fidelity, self).__init__(tokenizer=tokenizer, **kwargs)
[docs] def sim(self, src, tar):
"""Return the fidelity of two strings.
Parameters
----------
src : str
Source string (or QGrams/Counter objects) for comparison
tar : str
Target string (or QGrams/Counter objects) for comparison
Returns
-------
float
fidelity
Examples
--------
>>> cmp = Fidelity()
>>> cmp.sim('cat', 'hat')
0.25
>>> cmp.sim('Niall', 'Neil')
0.1333333333333333
>>> cmp.sim('aluminum', 'Catalan')
0.013888888888888888
>>> cmp.sim('ATCG', 'TAGC')
0.0
.. versionadded:: 0.4.0
"""
self._tokenize(src, tar)
alphabet = self._total().keys()
src_mag = max(1, sum(self._src_tokens.values()))
tar_mag = max(1, sum(self._tar_tokens.values()))
return (
sum(
(
abs(
self._src_tokens[tok]
/ src_mag
* self._tar_tokens[tok]
/ tar_mag
)
)
** 0.5
for tok in alphabet
)
** 2
)
if __name__ == '__main__':
import doctest
doctest.testmod()