def test_relabel_B_clusters_each_with_one_point(self):
# set-up
m = matching_matrix(10)
j_1, j_2 = m.relabel_B(0, 1, 0)
self.assertEqual(0, j_1)
self.assertEqual(1, j_2)
# there are 10 clusters 0-9 before the merge_cols
# after the merge we create cluster 10 which should map to 1
# in the row dictionary as we merge 0 into 1 arbitrarily taking the second
# cluster to be the largest
self.assertDictEqual({10: 1}, m.update_B)
def test_relabel_B_clusters_first_with_2_second_with_1(self):
# set-up
m = matching_matrix(10)
# merge 0 and 1 to create cluster 10 in step 0 and store it in column 1
m.merge_columns(0, 1, 0)
# merge 10 (stored in column 1) and 2 to create cluster 11 in step 1
j_1, j_2 = m.relabel_B(10, 2, 1)
self.assertEqual(2, j_1) # cluster 2 is the smallest
self.assertEqual(
1, j_2) # cluster 10 is the largest and is stored in column 1
self.assertDictEqual({11: 1}, m.update_B)
def test_relabel_A_clusters_first_with_1_second_with_2(self):
# set-up
m = matching_matrix(10)
# merge 0 and 1 to create cluster 10 in step 0 and store it in column 1
m.merge_rows(0, 1, 0)
# merge 2 and 10 (stored in column 1) to create cluster 11 in step 1
i_1, i_2 = m.relabel_A(10, 2, 1)
self.assertEqual(2, i_1) # cluster 2 is the smallest
self.assertEqual(
1, i_2) #c cluster 10 is the largest and is stored in column 1
self.assertDictEqual({11: 1}, m.update_A)
def test_init_correct_defaults(self):
# Arrange / Act
m = matching_matrix(4)
# Assert
expected_rows = {0: {0: 1}, 1: {1: 1}, 2: {2: 1}, 3: {3: 1}}
self.assertDictEqual(expected_rows, m.rows)
expected_columns = {0: {0: 1}, 1: {1: 1}, 2: {2: 1}, 3: {3: 1}}
self.assertDictEqual(expected_columns, m.columns)
self.assertDictEqual({0: 1, 1: 1, 2: 1, 3: 1}, m.rtot)
self.assertDictEqual({0: 1, 1: 1, 2: 1, 3: 1}, m.ctot)
self.assertEqual(4, m.n)
self.assertEqual(0, m.T)
self.assertEqual(0, m.P)
self.assertEqual(0, m.Q)
self.assertDictEqual({}, m.update_A)
self.assertDictEqual({}, m.update_B)
def TPQ_linkages(self, A, B):
"""
Calculates statistics on two hierarchical clusterings of the same set of objects
which can be used to calculate indices to compare two hierarchical clusterings
Parameters
----------
A : ndarray
A :math:`(n-1)` by 4 matrix encoding the linkage
(hierarchical clustering). See ``linkage`` documentation
for more information on its form.
B : A second :math:`(n-1)` by 4 matrix encoding the linkage
(hierarchical clustering).
Returns
-------
T : ndarray
A vector of size :math:'n-1' where the ``k``'th element
contains the number of pairs of objects placed into the
same cluster for both hierarchical clusterings after the
clusters in the ``k``'th row have been merged.
P : ndarray
A vector of size :math:'n-1' where the ``k``'th element
contains the number of pairs of objects placed into the
same cluster after the clusters in the ``k``th row
for the hierarchical clustering A only.
Q : ndarray
A vector of size :math:'n-1' where the ``k``'th element
contains the number of pairs of objects placed into the
same cluster after the clusters in the ``k``th row
for the hierarchical clustering B only.
"""
# Convert to array if not already.
A = np.array(A, 'double')
B = np.array(B, 'double')
# Performs checks
is_valid_linkage(A, throw=True)
is_valid_linkage(B, throw=True)
n = len(A) + 1
n2 = len(B) + 1
if n != n2:
raise ValueError(
"The hierarchical clusterings must be of the same size")
self.T = np.zeros(n - 2)
self.P = np.zeros(n - 2)
self.Q = np.zeros(n - 2)
self.n = n
# Creates a new matching matrix (identity of size n)
m = matching_matrix(n)
# Merges the required clusters as specified by the input files
for k, (rows_A, rows_B) in enumerate(zip(A, B)):
if k != n - 2:
self.T[k], self.P[k], self.Q[k] = m.merge(
rows_A[0], rows_A[1], rows_B[0], rows_B[1], k)
def test_worked_example(self):
#================
#-------A--------
#================
# i1, i2
#[ 3, 4 ]
#[ 1, 5 ]
#[ 0, 2 ]
#[ 6, 7 ]
#================
#-------B--------
#================
# j1, j2, j_size
#[ 3, 4, 2]
#[ 0, 2, 2]
#[ 1, 5, 3]
#[ 6, 7, 5]
# Arrange
m = matching_matrix(5)
''' Merge 0 in A
0, 1, 2, 3, 4
0 [ 1, 0, 0, 0, 0] 1
1 [ 0, 1, 0, 0, 0] 1
2 [ 0, 0, 1, 0, 0] 1
5 [ 0, 0, 0, 1, 1] 2
1 1 1 1 1
'''
m.merge_rows(i_1=3, i_2=4, k=0)
self.assertEqual(0, m.T)
self.assertEqual(1, m.P)
self.assertEqual(0, m.Q)
''' Merge 0 in B
0, 1, 2, 5
0 [ 1, 0, 0, 0 ] 1
1 [ 0, 1, 0, 0 ] 1
2 [ 0, 0, 1, 0 ] 1
5 [ 0, 0, 0, 2 ] 2
1, 1, 1, 2
'''
m.merge_columns(j_1=3, j_2=4, k=0)
self.assertEqual(1, m.T)
self.assertEqual(1, m.P)
self.assertEqual(1, m.Q)
''' Merge 1 in A
0, 1, 2, 5
0 [ 1, 0, 0, 0 ] 1
2 [ 0, 0, 1, 0 ] 1
6 [ 0, 1, 0, 2 ] 3
1, 1, 1, 2
'''
m.merge_rows(i_1=1, i_2=5, k=1)
self.assertEqual(1, m.T)
self.assertEqual(3, m.P)
self.assertEqual(1, m.Q)
''' Merge 1 in B
6 1 5
0 [ 1, 0, 0 ] 1
2 [ 1, 0, 0 ] 1
6 [ 0, 1, 2 ] 3
2, 1, 2
'''
m.merge_columns(j_1=0, j_2=2, k=1)
self.assertEqual(1, m.T)
self.assertEqual(3, m.P)
self.assertEqual(2, m.Q)
''' Merge 2 in A
6 1 5
7 [ 2, 0, 0 ] 2
6 [ 0, 1, 2 ] 3
2, 1, 2
'''
m.merge_rows(i_1=0, i_2=2, k=2)
self.assertEqual(2, m.T)
self.assertEqual(4, m.P)
self.assertEqual(2, m.Q)
''' Merge 2 in B
6 7
7 [ 2, 0 ] 2
6 [ 0, 3 ] 3
2, 3
'''
m.merge_columns(j_1=1, j_2=5, k=2)
self.assertEqual(4, m.T)
self.assertEqual(4, m.P)
self.assertEqual(4, m.Q)
''' Merge 3 in A
6 7
8 [ 2, 3 ] 5
2, 3
'''
m.merge_rows(i_1=6, i_2=7, k=3)
self.assertEqual(4, m.T)
self.assertEqual(10, m.P)
self.assertEqual(4, m.Q)
''' Merge 3 in B
8
8 [ 5 ] 5
5
'''
m.merge_columns(j_1=6, j_2=7, k=3)
self.assertEqual(10, m.T)
self.assertEqual(10, m.P)
self.assertEqual(10, m.Q)