def setUp(self):
"""
|| 0| 1| 2| 3|
=========================
0 || 11| 12| 13| 14|
1 || 21| 22| 23| 24|
2 || 31| 32| 33| 34|
"""
self.a = Matrix(
3, 4,
list(range(11, 15)) + list(range(21, 25)) + list(range(31, 35)))
self.singlecol = Matrix(3, 1, [1, 2, 3])
self.singlerow = Matrix(1, 3, [1, 2, 3])
def test_simsilarity_arg_forwarding(self):
with patch.object(HPOSet, '_sim_score',
return_value=Matrix(1, 1, [1])) as mock_simscore:
set1 = HPOSet([self.terms[0]])
set2 = HPOSet([self.terms[1]])
_ = set1.similarity(set2)
mock_simscore.assert_called_once_with(set1, set2, '', '')
mock_simscore.reset_mock()
_ = set1.similarity(set2, 'foo')
mock_simscore.assert_called_once_with(set1, set2, 'foo', '')
mock_simscore.reset_mock()
_ = set1.similarity(set2, kind='foo')
mock_simscore.assert_called_once_with(set1, set2, 'foo', '')
mock_simscore.reset_mock()
_ = set1.similarity(set2, 'foo', 'bar')
mock_simscore.assert_called_once_with(set1, set2, 'foo', 'bar')
mock_simscore.reset_mock()
_ = set1.similarity(set2, kind='foo', method='bar')
mock_simscore.assert_called_once_with(set1, set2, 'foo', 'bar')
mock_simscore.reset_mock()
_ = set1.similarity(set2, method='bar')
mock_simscore.assert_called_once_with(set1, set2, '', 'bar')
mock_simscore.reset_mock()
_ = set1.similarity(set2, None, 'bar')
mock_simscore.assert_called_once_with(set1, set2, None, 'bar')
mock_simscore.reset_mock()
def setUp(self):
"""
|| 0| 1| 2| 3|
=========================
0 || 11| 12| 13| 14|
1 || 21| 22| 23| 24|
2 || 31| 32| 33| 34|
"""
# a will be edited
self.a = Matrix(
3, 4,
list(range(11, 15)) + list(range(21, 25)) + list(range(31, 35)))
# b will be used as reference
self.b = Matrix(
3, 4,
list(range(11, 15)) + list(range(21, 25)) + list(range(31, 35)))
def _sim_score(set1: 'HPOSet',
set2: 'HPOSet',
kind: str = '',
method: str = '') -> Matrix:
"""
Calculates similarity matrix between HPOSets
.. warning::
This method should not be used by itself.
Use :func:`pyhpo.set.HPOSet.similarity` instead.
Parameters
----------
set1: HPOSet
One HPOSet to measure the similarity from
set2: HPOSet
Another HPOSet to measure the similarity to
kind: str
Which kind of information content should be calculated.
See :function:`pyhpo.HPOTerm.similarity_score` for options
method: string
The method to use to calculate the similarity.
See :function:`pyhpo.HPOTerm.similarity_score` for options
Returns
-------
float
The one-way similarity from one to the other HPOSet
"""
if not len(set1) or not len(set2):
return Matrix(0, 0)
scores = []
for set1_term in set1:
for set2_term in set2:
scores.append(
set1_term.similarity_score(set2_term, kind, method))
return Matrix(len(set1), len(set2), scores)
def test_invalid_combine_method(self):
with patch.object(HPOSet,
'_sim_score',
return_value=Matrix(
2, 4,
[1, 0.5, 2, 4, 2, 3, 1, 1])) as mock_simscore:
with self.assertRaises(RuntimeError) as context:
set1 = HPOSet([self.terms[0]])
set2 = HPOSet([self.terms[1]])
_ = set1.similarity(set2, combine='invalid')
mock_simscore.assert_called_once_with(set1, set2, '', '')
self.assertEqual(str(context.exception),
'Invalid combine method specified')
def test_empty_sets(self):
with patch.object(HPOSet, '_sim_score',
return_value=Matrix(0, 0, [])) as mock_simscore:
"""
Row maxes: 4, 3 ==> 7 ==> 7
Col maxes: 2, 3, 2, 4 ==> 11 ==> 11
==> 18 / 6
"""
set1 = HPOSet([self.terms[0]])
set2 = HPOSet([self.terms[1]])
res = set1.similarity(set2, combine='BMA')
mock_simscore.assert_called_once_with(set1, set2, '', '')
self.assertEqual(res, 0)
def test_funSimMax(self):
with patch.object(HPOSet,
'_sim_score',
return_value=Matrix(
2, 4,
[1, 0.5, 2, 4, 2, 3, 1, 1])) as mock_simscore:
"""
Row maxes: 4, 3 ==> 7 ==> 7/2 = 3.5
Col maxes: 2, 3, 2, 4 ==> 11 ==> 11/4 = 2.75
"""
set1 = HPOSet([self.terms[0]])
set2 = HPOSet([self.terms[1]])
res = set1.similarity(set2, combine='funSimMax')
mock_simscore.assert_called_once_with(set1, set2, '', '')
self.assertEqual(res, 3.5)
def test_init(self):
x = Matrix(2, 3)
self.assertEqual(x._data, [None] * 6)
self.assertEqual(x.n_rows, 2)
self.assertEqual(x.n_cols, 3)
def test_string(self):
a = Matrix(2, 3, range(6))
self.assertEqual(
str(a),
' || 0| 1| 2|\n=================\n0 || 0| 1| 2|\n1 || 3| 4| 5|' # noqa: E501
)
def test_init_error_checking(self):
with self.assertRaises(RuntimeError) as context:
a = Matrix(2, 4, [1, 2, 3]) # noqa: F841
self.assertEqual('Wrong number of data items in `data`',
str(context.exception))