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[MRG+1] Pass affinity to fix connectivity in linkage tree #9357

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Merged
merged 1 commit into from
Jul 18, 2017
Merged

[MRG+1] Pass affinity to fix connectivity in linkage tree #9357

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9 changes: 5 additions & 4 deletions sklearn/cluster/hierarchical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,7 @@
# For non fully-connected graphs


def _fix_connectivity(X, connectivity, n_components=None,
affinity="euclidean"):
def _fix_connectivity(X, connectivity, affinity):
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Much clearer.

"""
Fixes the connectivity matrix

Expand Down Expand Up @@ -190,7 +189,8 @@ def ward_tree(X, connectivity=None, n_clusters=None, return_distance=False):
else:
return children_, 1, n_samples, None

connectivity, n_components = _fix_connectivity(X, connectivity)
connectivity, n_components = _fix_connectivity(X, connectivity,
affinity='euclidean')
if n_clusters is None:
n_nodes = 2 * n_samples - 1
else:
Expand Down Expand Up @@ -415,7 +415,8 @@ def linkage_tree(X, connectivity=None, n_components=None,
return children_, 1, n_samples, None, distances
return children_, 1, n_samples, None

connectivity, n_components = _fix_connectivity(X, connectivity)
connectivity, n_components = _fix_connectivity(X, connectivity,
affinity=affinity)

connectivity = connectivity.tocoo()
# Put the diagonal to zero
Expand Down
27 changes: 27 additions & 0 deletions sklearn/cluster/tests/test_hierarchical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -518,3 +518,30 @@ def test_agg_n_clusters():
msg = ("n_clusters should be an integer greater than 0."
" %s was provided." % str(agc.n_clusters))
assert_raise_message(ValueError, msg, agc.fit, X)


def test_affinity_passed_to_fix_connectivity():
# Test that the affinity parameter is actually passed to the pairwise
# function

size = 2
rng = np.random.RandomState(0)
X = rng.randn(size, size)
mask = np.array([True, False, False, True])

connectivity = grid_to_graph(n_x=size, n_y=size,
mask=mask, return_as=np.ndarray)

class FakeAffinity:
def __init__(self):
self.counter = 0

def increment(self, *args, **kwargs):
self.counter += 1
return self.counter

fa = FakeAffinity()

linkage_tree(X, connectivity=connectivity, affinity=fa.increment)

assert_equal(fa.counter, 3)