def test_elementPow_valid(self):
""" elementPow correctly scales all elements and updates self.Power"""
for m in self.matrices:
# Test square all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=list(n.keys()),ColOrder=list(n.keys()),\
Pad=False)
dm.elementPow(2)
self.assertEqual(dm.Power, 2)
self.assertEqual(dm['A']['A'], m['A']['A']**2)
self.assertEqual(dm['B']['A'], m['B']['A']**2)
self.assertEqual(dm['B']['C'], m['B']['C']**2)
# Test cube square root of all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=list(n.keys()),ColOrder=list(n.keys()),\
Pad=False)
dm.elementPow(3)
dm.elementPow(1. / 2.)
self.assertEqual(dm.Power, 3. / 2.)
self.assertEqual(dm['A']['A'], m['A']['A']**(3. / 2.))
self.assertEqual(dm['B']['A'], m['B']['A']**(3. / 2.))
self.assertEqual(dm['B']['C'], m['B']['C']**(3. / 2.))
def test_attribute_init(self):
""" Proper initialization of all attributes """
# proper setting to defaults
d = DistanceMatrix(data={'a': {'a': 1}})
self.assertEqual(d.RowOrder, self.default_keys)
self.assertEqual(d.ColOrder, self.default_keys)
self.assertEqual(d.Pad, True)
self.assertEqual(d.Default, None)
self.assertEqual(d.RowConstructor, dict)
# differ from defaults
d = DistanceMatrix(data={'a':{'b':1}},RowOrder=['a'],\
ColOrder=['b'],Pad=False,Default=42,RowConstructor=Freqs)
self.assertEqual(d.RowOrder, ['a'])
self.assertEqual(d.ColOrder, ['b'])
self.assertEqual(d.Pad, False)
self.assertEqual(d.Default, 42)
self.assertEqual(d.RowConstructor, Freqs)
# differ from defaults and no data
d = DistanceMatrix(RowOrder=['a'],\
ColOrder=['b'],Pad=False,Default=42,RowConstructor=Freqs)
self.assertEqual(d.RowOrder, ['a'])
self.assertEqual(d.ColOrder, ['b'])
self.assertEqual(d.Pad, False)
self.assertEqual(d.Default, 42)
self.assertEqual(d.RowConstructor, Freqs)
def test_colKeys(self):
""" colKeys functions properly """
dm = DistanceMatrix(data={'a':{'b':1}})
goal = self.default_keys + ['b']
goal.sort()
actual = dm.colKeys()
actual.sort()
self.assertEqual(actual,goal)
def test_colKeys(self):
""" colKeys functions properly """
dm = DistanceMatrix(data={'a': {'b': 1}})
goal = self.default_keys + ['b']
goal.sort()
actual = dm.colKeys()
actual.sort()
self.assertEqual(actual, goal)
def test_scale(self):
""" Scale correctly applies function to all elements """
for m in self.matrices:
# Test square all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=m.keys(), Pad=False)
dm.scale(lambda x: x**2)
self.assertEqual(dm['A']['A'],m['A']['A']**2)
self.assertEqual(dm['B']['A'],m['B']['A']**2)
self.assertEqual(dm['B']['C'],m['B']['C']**2)
# Test cube all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=m.keys(), Pad=False)
dm.scale(lambda x: x**3)
self.assertEqual(dm['A']['A'],m['A']['A']**3)
self.assertEqual(dm['B']['A'],m['B']['A']**3)
self.assertEqual(dm['B']['C'],m['B']['C']**3)
# Test linearize all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=m.keys(), Pad=False)
dm.scale(lambda x: 10**-(x/10.0))
self.assertFloatEqual(dm['A']['A'],10**-(m['A']['A']/10.))
self.assertFloatEqual(dm['B']['A'],10**-(m['B']['A']/10.))
self.assertFloatEqual(dm['B']['C'],10**-(m['B']['C']/10.))
def test_attribute_forwarder_integrity_after_copy(self):
""" Integrity of attribute forwarding following a copy()"""
dm = DistanceMatrix(data=self.m2, RowOrder=self.m2.keys(), info=self.aar)
c = dm.copy()
# dm.ID == '5'
self.assertEqual(c.ID, dm.ID)
self.assertEqual(c.Correlating, dm.Correlating)
self.assertEqual(c.Data['R'], dm.Data['R'])
c.ID = '0'
self.assertNotEqual(c.ID,dm.ID)
def test_transpose(self):
""" transpose functions as expected """
for m in self.matrices:
d = DistanceMatrix(data=m)
t = d.copy()
t.transpose()
# Note, this line will fail on a matrix where transpose = original
self.assertNotEqual(t,d)
for r in t:
for c in t[r]:
self.assertEqual(t[r][c],d[c][r])
t.transpose()
self.assertEqual(t,d)
def test_transpose(self):
""" transpose functions as expected """
for m in self.matrices:
d = DistanceMatrix(data=m)
t = d.copy()
t.transpose()
# Note, this line will fail on a matrix where transpose = original
self.assertNotEqual(t, d)
for r in t:
for c in t[r]:
self.assertEqual(t[r][c], d[c][r])
t.transpose()
self.assertEqual(t, d)
def test_copy(self):
""" Copy functions as expected"""
dm = DistanceMatrix(data=self.m2, RowOrder=self.m2.keys(), info=self.aar)
c = dm.copy()
self.assertEqual(c['A']['A'],dm['A']['A'])
self.assertEqual(c.RowOrder,dm.RowOrder)
self.assertEqual(c.ColOrder,dm.ColOrder)
self.assertEqual(c.Pad,dm.Pad)
self.assertEqual(c.Power,dm.Power)
# Make sure it's a separate object
c['A']['A'] = 999
self.assertNotEqual(c['A']['A'],dm['A']['A'])
def test_elementPow_valid(self):
""" elementPow correctly scales all elements and updates self.Power"""
for m in self.matrices:
# Test square all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=n.keys(),ColOrder=n.keys(),\
Pad=False)
dm.elementPow(2)
self.assertEqual(dm.Power, 2)
self.assertEqual(dm['A']['A'],m['A']['A']**2)
self.assertEqual(dm['B']['A'],m['B']['A']**2)
self.assertEqual(dm['B']['C'],m['B']['C']**2)
# Test cube square root of all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=n.keys(),ColOrder=n.keys(),\
Pad=False)
dm.elementPow(3)
dm.elementPow(1./2.)
self.assertEqual(dm.Power, 3./2.)
self.assertEqual(dm['A']['A'],m['A']['A']**(3./2.))
self.assertEqual(dm['B']['A'],m['B']['A']**(3./2.))
self.assertEqual(dm['B']['C'],m['B']['C']**(3./2.))
def test_reflect(self):
""" reflect functions as expected """
for m in self.matrices:
d = DistanceMatrix(data=m)
n = d.copy()
# Only testing one method, all other are tested in superclass, so
# redundant testing is probably not necessary
n.reflect(method=largest)
for r in d.RowOrder:
for c in d.ColOrder:
if d[r][c] > d[c][r]:
goal = d[r][c]
else:
goal = d[c][r]
self.assertEqual(n[r][c],goal)
self.assertEqual(n[c][r],goal)
def test_default_padding(self):
""" Default padding functions as expected """
for m in self.matrices:
dm = DistanceMatrix(data=m)
for r in self.default_keys:
for c in self.default_keys:
dm[r][c]
def test_reflect(self):
""" reflect functions as expected """
for m in self.matrices:
d = DistanceMatrix(data=m)
n = d.copy()
# Only testing one method, all other are tested in superclass, so
# redundant testing is probably not necessary
n.reflect(method=largest)
for r in d.RowOrder:
for c in d.ColOrder:
if d[r][c] > d[c][r]:
goal = d[r][c]
else:
goal = d[c][r]
self.assertEqual(n[r][c], goal)
self.assertEqual(n[c][r], goal)
def test_Order_parameters(self):
""" RowOrder and ColOrder are set to paramters as expected """
row_order = ['a']
col_order = ['b']
for m in self.matrices:
dm = DistanceMatrix(data=m, RowOrder=row_order, ColOrder=col_order)
self.assertEqual(dm.RowOrder, row_order)
self.assertEqual(dm.ColOrder, col_order)
def test_elementPow_invalid_pow(self):
""" elementPow correctly raises error on invalid power """
for m in self.matrices:
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=n.keys(),ColOrder=n.keys(),\
Pad=False)
self.assertRaises(TypeError,dm.elementPow,None,ignore_invalid=False)
self.assertRaises(TypeError,dm.elementPow,'a',ignore_invalid=False)
def test_setDiag(self):
""" setDiag works as expected """
for m in self.matrices:
# create a deep copy so we can test against original
# matrix without it being effected by altering the object
# based on it
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=list(m.keys()))
# set diag to 42
dm.setDiag(42)
# test that diag is 42
for k in dm:
self.assertEqual(dm[k][k], 42)
# test that no diag is unchanged
self.assertEqual(dm['B']['A'], m['B']['A'])
self.assertEqual(dm['B']['C'], m['B']['C'])
def test_toDelimited(self):
"""DistanceMatrix toDelimited functions as expected"""
d = DistanceMatrix(self.square,Pad=False)
d.RowOrder = d.ColOrder = 'abc'
self.assertEqual(d.toDelimited(), \
'-\ta\tb\tc\na\t1\t2\t3\nb\t2\t4\t6\nc\t3\t6\t9')
self.assertEqual(d.toDelimited(headers=False), \
'1\t2\t3\n2\t4\t6\n3\t6\t9')
#set up a custom formatter...
def my_formatter(x):
try:
return '%1.1f' % x
except:
return str(x)
#...and use it
self.assertEqual(d.toDelimited(headers=True, item_delimiter='x', \
row_delimiter='y', formatter=my_formatter), \
'-xaxbxcyax1.0x2.0x3.0ybx2.0x4.0x6.0ycx3.0x6.0x9.0')
def test_setDiag(self):
""" setDiag works as expected """
for m in self.matrices:
# create a deep copy so we can test against original
# matrix without it being effected by altering the object
# based on it
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=m.keys())
# set diag to 42
dm.setDiag(42)
# test that diag is 42
for k in dm:
self.assertEqual(dm[k][k],42)
# test that no diag is unchanged
self.assertEqual(dm['B']['A'], m['B']['A'])
self.assertEqual(dm['B']['C'], m['B']['C'])
def test_sparse_init(self):
""" Init correctly from a sparse dict """
d = DistanceMatrix(data={'A': {'C': 0.}})
for r in self.default_keys:
for c in self.default_keys:
if (r == 'A') and (c == 'C'):
self.assertEqual(d[r][c], 0.)
else:
self.assertEqual(d[r][c], None)
def test_init_data_types(self):
""" Correct init from varying data types """
# No data
goal = {}.fromkeys(self.default_keys)
for r in goal:
goal[r] = {}.fromkeys(self.default_keys)
dm = DistanceMatrix()
self.assertEqual(dm,goal)
# data is dict of dicts
dm = DistanceMatrix(data={'a':{'b':1}}, Pad=False)
self.assertEqual(dm,{'a':{'b':1}})
# data is list of lists
dm = DistanceMatrix(data=[[1]],RowOrder=['a'],ColOrder=['b'], Pad=False)
self.assertEqual(dm,{'a':{'b':1}})
# data is in Indices form
dm = DistanceMatrix(data=[('a','b',1)], Pad=False)
self.assertEqual(dm,{'a':{'b':1}})
def toDistanceMatrix(self, include_stops=False):
""" Builds a DistanceMatrix object based on self """
data = self._toSquareDistanceMatrix(include_stops=include_stops)
# If there is missing or invalid data, data will be None
# if that's the case return None for easy detection, otherwise
# return a new DistanceMatrix object
if data:
return DistanceMatrix(data=data, info=self)
return None
def test_all_init_parameters(self):
""" All parameters to init are handled correctly """
# will fail if any paramters are not recognized
d = DistanceMatrix()
d = DistanceMatrix(data={})
d = DistanceMatrix(RowOrder=[])
d = DistanceMatrix(ColOrder=[])
d = DistanceMatrix(Pad=True)
d = DistanceMatrix(Default=42)
d = DistanceMatrix(data={},RowOrder=[],ColOrder=[],Pad=True,Default=42)
def test_elementPow_error_on_invalid(self):
""" elementPow correctly raises error on invalid data"""
for m in self.matrices:
# Test square all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=n.keys(),ColOrder=n.keys(),\
Pad=False)
dm['A']['A'] = 'p'
self.assertRaises(TypeError,dm.elementPow,2,ignore_invalid=False)
dm['A']['A'] = None
self.assertRaises(TypeError,dm.elementPow,2,ignore_invalid=False)
def test_sharedColKeys(self):
""" sharedColKeys functions properly """
# no shared keys b/c a is not in RowOrder and therefore not padded
dm = DistanceMatrix(data={'a': {'b': 1}})
self.assertEqual(dm.sharedColKeys(), [])
# shared should be only self.default_keys b/c 'b' not in ColOrder
dm = DistanceMatrix(data={'a':{'b':1}},\
RowOrder=self.default_keys + ['a'])
actual = dm.sharedColKeys()
actual.sort()
self.assertEqual(actual, self.default_keys)
# shared should be self.default_keys + 'b'
dm = DistanceMatrix(data={'a':{'b':1}},\
RowOrder=self.default_keys + ['a'],\
ColOrder=self.default_keys + ['b'])
actual = dm.sharedColKeys()
actual.sort()
self.assertEqual(actual, self.default_keys + ['b'])
def test_elementPow_ignore_invalid(self):
""" elementPow correctly detects and ignores invalid data"""
for m in self.matrices:
# Test square all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=list(n.keys()),ColOrder=list(n.keys()),\
Pad=False)
dm['A']['A'] = 'p'
dm.elementPow(2)
self.assertEqual(dm.Power, 2.)
self.assertEqual(dm['A']['A'], 'p')
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=list(n.keys()),ColOrder=list(n.keys()),\
Pad=False)
dm['A']['A'] = None
dm.elementPow(2)
self.assertEqual(dm.Power, 2.)
self.assertEqual(dm['A']['A'], None)
def test_sharedColKeys(self):
""" sharedColKeys functions properly """
# no shared keys b/c a is not in RowOrder and therefore not padded
dm = DistanceMatrix(data={'a':{'b':1}})
self.assertEqual(dm.sharedColKeys(),[])
# shared should be only self.default_keys b/c 'b' not in ColOrder
dm = DistanceMatrix(data={'a':{'b':1}},\
RowOrder=self.default_keys + ['a'])
actual = dm.sharedColKeys()
actual.sort()
self.assertEqual(actual, self.default_keys)
# shared should be self.default_keys + 'b'
dm = DistanceMatrix(data={'a':{'b':1}},\
RowOrder=self.default_keys + ['a'],\
ColOrder=self.default_keys + ['b'])
actual = dm.sharedColKeys()
actual.sort()
self.assertEqual(actual, self.default_keys + ['b'])
def test_elementPow_ignore_invalid(self):
""" elementPow correctly detects and ignores invalid data"""
for m in self.matrices:
# Test square all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=n.keys(),ColOrder=n.keys(),\
Pad=False)
dm['A']['A'] = 'p'
dm.elementPow(2)
self.assertEqual(dm.Power, 2.)
self.assertEqual(dm['A']['A'],'p')
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=n.keys(),ColOrder=n.keys(),\
Pad=False)
dm['A']['A'] = None
dm.elementPow(2)
self.assertEqual(dm.Power, 2.)
self.assertEqual(dm['A']['A'],None)
def test_dict_integrity(self):
""" Integrity of key -> value pairs """
for m in self.matrices:
dm = DistanceMatrix(data=m)
self.assertEqual(dm['A']['A'], m['A']['A'])
self.assertEqual(dm['B']['C'], m['B']['C'])
def test_Order_defaults(self):
""" RowOrder and ColOrder are set to default as expected """
for m in self.matrices:
dm = DistanceMatrix(data=m)
self.assertEqual(dm.RowOrder, self.default_keys)
self.assertEqual(dm.ColOrder, self.default_keys)
def test_scale(self):
""" Scale correctly applies function to all elements """
for m in self.matrices:
# Test square all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=list(m.keys()), Pad=False)
dm.scale(lambda x: x**2)
self.assertEqual(dm['A']['A'], m['A']['A']**2)
self.assertEqual(dm['B']['A'], m['B']['A']**2)
self.assertEqual(dm['B']['C'], m['B']['C']**2)
# Test cube all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=list(m.keys()), Pad=False)
dm.scale(lambda x: x**3)
self.assertEqual(dm['A']['A'], m['A']['A']**3)
self.assertEqual(dm['B']['A'], m['B']['A']**3)
self.assertEqual(dm['B']['C'], m['B']['C']**3)
# Test linearize all elements
# explicit tests
n = deepcopy(m)
dm = DistanceMatrix(data=n, RowOrder=list(m.keys()), Pad=False)
dm.scale(lambda x: 10**-(x / 10.0))
self.assertFloatEqual(dm['A']['A'], 10**-(m['A']['A'] / 10.))
self.assertFloatEqual(dm['B']['A'], 10**-(m['B']['A'] / 10.))
self.assertFloatEqual(dm['B']['C'], 10**-(m['B']['C'] / 10.))
def test_attribute_forwarder_integrity(self):
""" Integrity of attribute forwarding """
dm = DistanceMatrix(data=self.m2, info=self.aar)
self.assertEqual(dm.ID, '5')
self.assertEqual(dm.Correlating, [0.987, 0.783, 1., 0])
self.assertEqual(dm.Data['C'], 0.15)