def testInputArrays(self):
""" this is not supported, has to be list of ndarrays """
dtrajs = np.array([[0, 1, 2, 0, 0, 1, 2, 1, 0],
[0, 1, 2, 0, 0, 1, 2, 1, 1]])
with self.assertRaises(TypeError):
count_matrix(dtrajs, 1)
def test_count_matrix(self):
"""Small test cases"""
C = count_matrix([self.S1, self.S2], 1, sliding=True).toarray()
assert_allclose(C, self.B1_sliding)
C = count_matrix([self.S1, self.S2], 2, sliding=True).toarray()
assert_allclose(C, self.B2_sliding)
def test_count_matrix(self):
"""Small test cases"""
C = count_matrix([self.S1, self.S2], 1, sliding=True).toarray()
assert_allclose(C, self.B1_sliding)
C = count_matrix([self.S1, self.S2], 2, sliding=True).toarray()
assert_allclose(C, self.B2_sliding)
def test_count_matrix(self):
"""Small test cases"""
C = count_matrix(self.S_short, 1, sliding=False).toarray()
assert_allclose(C, self.B1_lag)
C = count_matrix(self.S_short, 2, sliding=False).toarray()
assert_allclose(C, self.B2_lag)
C = count_matrix(self.S_short, 3, sliding=False).toarray()
assert_allclose(C, self.B3_lag)
C = count_matrix(self.S_short, 1).toarray()
assert_allclose(C, self.B1_sliding)
C = count_matrix(self.S_short, 2).toarray()
assert_allclose(C, self.B2_sliding)
C = count_matrix(self.S_short, 3).toarray()
assert_allclose(C, self.B3_sliding)
"""Larger test cases"""
C = count_matrix(self.S_long, 1, sliding=False).toarray()
assert_allclose(C, self.C1_lag)
C = count_matrix(self.S_long, 7, sliding=False).toarray()
assert_allclose(C, self.C7_lag)
C = count_matrix(self.S_long, 13, sliding=False).toarray()
assert_allclose(C, self.C13_lag)
C = count_matrix(self.S_long, 1).toarray()
assert_allclose(C, self.C1_sliding)
C = count_matrix(self.S_long, 7).toarray()
assert_allclose(C, self.C7_sliding)
C = count_matrix(self.S_long, 13).toarray()
assert_allclose(C, self.C13_sliding)
"""Test raising of value error if lag greater than trajectory length"""
with self.assertRaises(ValueError):
C = count_matrix(self.S_short, 10)
def test_nstates_keyword(self):
C = count_matrix([self.S1, self.S2], 1, sliding=True, nstates=10)
self.assertTrue(C.shape == (10, 10))
with self.assertRaises(ValueError):
C = count_matrix([self.S1, self.S2], 1, sliding=True, nstates=1)
def test_nstates_keyword(self):
C = count_matrix(self.S_short, 1, nstates=10)
self.assertTrue(C.shape == (10, 10))
with self.assertRaises(ValueError):
C = count_matrix(self.S_short, 1, nstates=1)
def test_count_matrix(self):
"""Small test cases"""
C = count_matrix(self.S_short, 1, sliding=False).toarray()
assert_allclose(C, self.B1_lag)
C = count_matrix(self.S_short, 2, sliding=False).toarray()
assert_allclose(C, self.B2_lag)
C = count_matrix(self.S_short, 3, sliding=False).toarray()
assert_allclose(C, self.B3_lag)
C = count_matrix(self.S_short, 1).toarray()
assert_allclose(C, self.B1_sliding)
C = count_matrix(self.S_short, 2).toarray()
assert_allclose(C, self.B2_sliding)
C = count_matrix(self.S_short, 3).toarray()
assert_allclose(C, self.B3_sliding)
"""Larger test cases"""
C = count_matrix(self.S_long, 1, sliding=False).toarray()
assert_allclose(C, self.C1_lag)
C = count_matrix(self.S_long, 7, sliding=False).toarray()
assert_allclose(C, self.C7_lag)
C = count_matrix(self.S_long, 13, sliding=False).toarray()
assert_allclose(C, self.C13_lag)
C = count_matrix(self.S_long, 1).toarray()
assert_allclose(C, self.C1_sliding)
C = count_matrix(self.S_long, 7).toarray()
assert_allclose(C, self.C7_sliding)
C = count_matrix(self.S_long, 13).toarray()
assert_allclose(C, self.C13_sliding)
"""Test raising of value error if lag greater than trajectory length"""
with self.assertRaises(ValueError):
C = count_matrix(self.S_short, 10)
def test_nstates_keyword(self):
C = count_matrix([self.S1, self.S2], 1, sliding=True, nstates=10)
self.assertTrue(C.shape == (10, 10))
with self.assertRaises(ValueError):
C = count_matrix([self.S1, self.S2], 1, sliding=True, nstates=1)
def testInputFloat(self):
dtraj_with_floats = [0.0, 1, 0, 2, 3, 1, 0.0]
# dtraj_int = [0, 1, 0, 2, 3, 1, 0]
with self.assertRaises(TypeError):
C_f = count_matrix(dtraj_with_floats, 1)
def testInputArray(self):
dtrajs = np.array([0, 1, 2, 0, 0, 1, 2, 1, 0])
count_matrix(dtrajs, 1)
def testInputNestedListsDiffSize(self):
dtrajs = [[0, 1, 2, 0, 0, 1, 2, 1, 0],
[0, 1, 0, 1, 1, 1, 1, 0, 2, 1, 2, 1]]
count_matrix(dtrajs, 1)
def testInputList(self):
dtrajs = [0, 1, 2, 0, 0, 1, 2, 1, 0]
count_matrix(dtrajs, 1)
def test_nstates_keyword(self):
C = count_matrix(self.S_short, 1, nstates=10)
self.assertTrue(C.shape == (10, 10))
with self.assertRaises(ValueError):
C = count_matrix(self.S_short, 1, nstates=1)