def test_multiple_input_trajectories(self):
reader = FragmentedTrajectoryReader([[self.d, self.d], self.d, [self.d, self.d]])
reader.chunksize = 37
out = reader.get_output()
reader.chunksize = 0
out2 = reader.get_output()
expected0_2 = np.vstack((self.d, self.d))
for itraj in range(0, 3):
np.testing.assert_array_almost_equal(out[itraj], out2[itraj])
np.testing.assert_array_almost_equal(out[0], expected0_2)
np.testing.assert_array_almost_equal(out[1], self.d)
np.testing.assert_array_almost_equal(out[2], expected0_2)
def test_chunked_trajectory_with_lag(self):
data = np.vstack((self.d, self.d))
reader = FragmentedTrajectoryReader([self.d, self.d])
for lag in [0, 1, 3]:
for stride in [1, 3, 5]:
for chunksize in [1, 34, 53, 72]:
reader.chunksize = chunksize
if lag > 0:
collected = None
collected_lagged = None
for itraj, X, Y in reader.iterator(stride=stride,
lag=lag):
collected = X if collected is None else np.vstack(
(collected, X))
collected_lagged = Y if collected_lagged is None else np.vstack(
(collected_lagged, Y))
np.testing.assert_array_almost_equal(
data[::stride][0:len(collected_lagged)], collected)
np.testing.assert_array_almost_equal(
data[lag::stride], collected_lagged)
else:
collected = None
for itraj, X in reader.iterator(stride=stride):
collected = X if collected is None else np.vstack(
(collected, X))
np.testing.assert_array_almost_equal(
data[::stride], collected)
def test_full_trajectory_stridden(self):
for stride in [1, 3, 5, 7, 13, 20]:
reader = FragmentedTrajectoryReader([self.d, self.d])
reader.chunksize = 0
expected = np.vstack((self.d, self.d))[::stride]
out = reader.get_output(stride=stride)[0]
np.testing.assert_array_almost_equal(expected, out, err_msg="Failed for stride=%s" % stride)
def test_full_trajectory_stridden_with_lag(self):
reader = FragmentedTrajectoryReader([self.d, self.d])
data = np.vstack((self.d, self.d))
for lag in [1, 5, 7]:
for stride in [1, 3, 5, 7, 13, 20]:
reader.chunksize = 0
X, Y = None, None
# not chunked
for itraj, X, Y in reader.iterator(stride=stride, lag=lag):
pass
np.testing.assert_array_almost_equal(data[::stride][0:len(Y)], X)
np.testing.assert_array_almost_equal(data[lag::stride], Y)
def test_full_trajectory(self):
reader = FragmentedTrajectoryReader([self.d, self.d])
reader.chunksize = 0
expected = np.vstack((self.d, self.d))
np.testing.assert_array_almost_equal(expected,
reader.get_output(stride=1)[0])