def testIteratorAccess2(self):
reader = FeatureReader([self.trajfile, self.trajfile], self.topfile)
reader.chunksize = 100
frames = 0
data = []
for i, X in reader:
frames += X.shape[0]
data.append(X)
self.assertEqual(frames, reader.trajectory_lengths()[0] * 2)
# restore shape of input
data = np.array(
data[0:reader.trajectory_lengths()[0] / reader.chunksize]).reshape(self.xyz.shape)
self.assertTrue(np.allclose(data, self.xyz))
def testIteratorAccess2(self):
reader = FeatureReader([self.trajfile, self.trajfile], self.topfile)
reader.chunksize = 100
frames = 0
data = []
for i, X in reader:
frames += X.shape[0]
data.append(X)
self.assertEqual(frames, reader.trajectory_lengths()[0] * 2)
# restore shape of input
data = np.array(data[0:reader.trajectory_lengths()[0] /
reader.chunksize]).reshape(self.xyz.shape)
self.assertTrue(np.allclose(data, self.xyz))
def testTimeLaggedIterator(self):
lag = 10
reader = FeatureReader(self.trajfile, self.topfile)
frames = 0
data = []
lagged = []
for _, X, Y in reader.iterator(lag=lag):
frames += X.shape[0]
data.append(X)
lagged.append(Y)
assert len(data) == len(lagged)
# .reshape(self.xyz.shape)
merged_lagged = np.concatenate(lagged, axis=0)
# reproduce outcome
xyz_s = self.xyz.shape
fake_lagged = self.xyz.reshape((xyz_s[0], -1))[lag:]
self.assertTrue(np.allclose(merged_lagged, fake_lagged))
# restore shape of input
data = np.vstack(data).reshape(self.xyz[lag:].shape)
self.assertEqual(frames, reader.trajectory_lengths()[0] - lag)
self.assertTrue(np.allclose(data, self.xyz[:len(self.xyz) - lag]))
def testTimeLaggedIterator(self):
lag = 10
reader = FeatureReader(self.trajfile, self.topfile)
frames = 0
data = []
lagged = []
for _, X, Y in reader.iterator(lag=lag):
frames += X.shape[0]
data.append(X)
lagged.append(Y)
assert len(data) == len(lagged)
merged_lagged = np.concatenate(lagged, axis=0) # .reshape(self.xyz.shape)
# reproduce outcome
xyz_s = self.xyz.shape
fake_lagged = np.empty((xyz_s[0]-lag, xyz_s[1]*xyz_s[2]))
fake_lagged = self.xyz.reshape((xyz_s[0], -1))[lag:]
self.assertTrue(np.allclose(merged_lagged, fake_lagged))
# restore shape of input
data = np.array(data).reshape(self.xyz.shape)
self.assertEqual(frames, reader.trajectory_lengths()[0])
self.assertTrue(np.allclose(data, self.xyz))