def test_Cluster(self):
""" tests the Cluster class functionality """
root = Clusters.Cluster(index=1, position=1)
c1 = Clusters.Cluster(index=10, position=10)
c1.AddChild(Clusters.Cluster(index=30, position=30))
c1.AddChild(Clusters.Cluster(index=31, position=31))
t32 = Clusters.Cluster(index=32, position=32)
c1.AddChild(t32)
c2 = Clusters.Cluster(index=11)
# c2.AddChild(Clusters.Cluster(index=40))
# c2.AddChild(Clusters.Cluster(index=41))
c2.AddChildren(
[Clusters.Cluster(index=40),
Clusters.Cluster(index=41)])
root.AddChild(c1)
root.AddChild(c2)
nodes = ClusterUtils.GetNodeList(root)
indices = [x.GetIndex() for x in nodes]
assert indices == [30, 31, 32, 10, 40, 41, 11, 1], 'bad indices'
subtree = root.FindSubtree(11)
self.assertEqual(
[x.GetIndex() for x in ClusterUtils.GetNodeList(subtree)],
[40, 41, 11])
self.assertFalse(root.IsTerminal())
self.assertTrue(t32.IsTerminal())
self.assertEqual(root.GetData(), None)
root.SetData(3.14)
self.assertEqual(root.GetData(), 3.14)
self.assertEqual(root.GetMetric(), 0.0)
root.SetMetric(0.1)
self.assertEqual(root.GetMetric(), 0.1)
self.assertEqual(root.GetIndex(), 1)
root.SetIndex(100)
self.assertEqual(root.GetIndex(), 100)
self.assertEqual(root.GetPointsPositions(), [30, 31, 32, []])
root.RemoveChild(c1)
self.assertEqual(
[x.GetIndex() for x in ClusterUtils.GetNodeList(root)],
[40, 41, 11, 100])
self.assertEqual(root.GetName(), 'Cluster(100)')
root.SetName('abc')
self.assertEqual(root.GetName(), 'abc')
f = StringIO()
with redirect_stdout(f):
root.Print(showData=True)
self.assertIn('abc', f.getvalue())
self.assertIn('Cluster(41)', f.getvalue())
self.assertIn('Metric', f.getvalue())
def _ToClusters(data, nPts, ia, ib, crit, isDistData=0):
""" *Internal Use Only*
Converts the results of the Murtagh clustering code into
a cluster tree, which is returned in a single-entry list
"""
cs = [None] * nPts
for i in range(nPts):
cs[i] = Clusters.Cluster(metric=0.0, data=i, index=(i + 1))
nClus = len(ia) - 1
for i in range(nClus):
idx1 = ia[i] - 1
idx2 = ib[i] - 1
c1 = cs[idx1]
c2 = cs[idx2]
newClust = Clusters.Cluster(metric=crit[i],
children=[c1, c2],
index=nPts + i + 1)
cs[idx1] = newClust
return [newClust]
def testGetNodeList(self):
""" tests the GetNodeList functionality """
root = Clusters.Cluster(index=1)
c1 = Clusters.Cluster(index=10)
c1.AddChild(Clusters.Cluster(index=30))
c1.AddChild(Clusters.Cluster(index=31))
c1.AddChild(Clusters.Cluster(index=32))
c2 = Clusters.Cluster(index=11)
c2.AddChild(Clusters.Cluster(index=40))
c2.AddChild(Clusters.Cluster(index=41))
root.AddChild(c1)
root.AddChild(c2)
nodes = ClusterUtils.GetNodeList(root)
indices = [x.GetIndex() for x in nodes]
assert indices == [30, 31, 32, 10, 40, 41, 11, 1], 'bad indices'
def testDivide(self):
" tests the cluster division algorithms "
ca = Clusters.Cluster(index=1)
cb = Clusters.Cluster(index=2)
cc = Clusters.Cluster(index=3)
cd = Clusters.Cluster(index=4)
ce = Clusters.Cluster(index=5)
cf = Clusters.Cluster(index=6)
c1 = Clusters.Cluster(metric=10, children=[ca, cb], index=7)
c2 = Clusters.Cluster(metric=15, children=[cc, cd], index=8)
c3 = Clusters.Cluster(metric=20, children=[ce, cf], index=9)
c4 = Clusters.Cluster(metric=25, children=[c2, c3], index=10)
c5 = Clusters.Cluster(metric=30, children=[c4, c1], index=11)
cs = ClusterUtils.SplitIntoNClusters(c5, 4, breadthFirst=1)
assert len(cs) == 4, 'bad split length'
indices = [x.GetIndex() for x in cs]
for index in [9, 8, 1, 2]:
assert index in indices, 'index %d not found in %s' % (
index, str(indices))
# we may not want to preserve order, but test it for now
assert indices == [9, 8, 1, 2], 'bad index order'
cs2 = ClusterUtils.SplitIntoNClusters(c5, 4, breadthFirst=0)
indices = [x.GetIndex() for x in cs2]
for index in [8, 7, 5, 6]:
assert index in indices, 'index %d not found in %s' % (
index, str(indices))
# we may not want to preserve order, but test it for now
assert indices == [8, 7, 5, 6], 'bad index order'
def testDivide(self):
" tests the cluster division algorithms "
ca = Clusters.Cluster(index=1)
cb = Clusters.Cluster(index=2)
cc = Clusters.Cluster(index=3)
cd = Clusters.Cluster(index=4)
ce = Clusters.Cluster(index=5)
cf = Clusters.Cluster(index=6)
c1 = Clusters.Cluster(metric=10, children=[ca, cb], index=7)
c2 = Clusters.Cluster(metric=15, children=[cc, cd], index=8)
c3 = Clusters.Cluster(metric=20, children=[ce, cf], index=9)
c4 = Clusters.Cluster(metric=25, children=[c2, c3], index=10)
c5 = Clusters.Cluster(metric=30, children=[c4, c1], index=11)
cs = ClusterUtils.SplitIntoNClusters(c5, 4, breadthFirst=True)
assert len(cs) == 4, 'bad split length'
indices = [x.GetIndex() for x in cs]
for index in [9, 8, 1, 2]:
assert index in indices, 'index %d not found in %s' % (
index, str(indices))
# we may not want to preserve order, but test it for now
assert indices == [9, 8, 1, 2], 'bad index order'
cs2 = ClusterUtils.SplitIntoNClusters(c5, 4, breadthFirst=False)
indices = [x.GetIndex() for x in cs2]
for index in [8, 7, 5, 6]:
assert index in indices, 'index %d not found in %s' % (
index, str(indices))
# we may not want to preserve order, but test it for now
assert indices == [8, 7, 5, 6], 'bad index order'
# Exceptions and edge cases
self.assertRaises(ValueError, ClusterUtils.SplitIntoNClusters, c5,
len(c5) + 1)
self.assertEqual(ClusterUtils.SplitIntoNClusters(c5, len(c5)),
c5.GetPoints())
self.assertEqual(ClusterUtils.SplitIntoNClusters(c5, 0), [c5])
for n in range(len(c5)):
if n >= 7: # Code fails for n = 7 and above
self.assertRaises(AssertionError,
ClusterUtils.SplitIntoNClusters,
c5,
n,
breadthFirst=True)
else:
ClusterUtils.SplitIntoNClusters(c5, n, breadthFirst=True)
self.assertRaises(ValueError,
ClusterUtils.SplitIntoNClusters,
c5,
len(c5) + 1,
breadthFirst=False)
self.assertEqual(
ClusterUtils.SplitIntoNClusters(c5, len(c5), breadthFirst=False),
c5.GetPoints())
self.assertEqual(
ClusterUtils.SplitIntoNClusters(c5, 0, breadthFirst=False), [c5])
for n in range(len(c5)):
if n >= 7: # Code fails for n = 7 and above
self.assertRaises(AssertionError,
ClusterUtils.SplitIntoNClusters,
c5,
n,
breadthFirst=False)
else:
ClusterUtils.SplitIntoNClusters(c5, n, breadthFirst=False)