def test_only_npy(self):
reader = NumPyFileReader(self.npy_files)
from_files = [np.load(f) for f in self.npy_files]
concatenated = np.vstack(from_files)
output = reader.get_output()
self.assertEqual(reader.number_of_trajectories(), len(self.npy_files))
self.assertEqual(reader.n_frames_total(), concatenated.shape[0])
for x, y in zip(output, from_files):
np.testing.assert_array_almost_equal(x, y)
def test_npz(self):
reader = NumPyFileReader(self.npz)
all_data = reader.get_output()
fh = np.load(self.npz)
data = [x[1] for x in fh.items()]
fh.close()
self.assertEqual(reader.number_of_trajectories(), len(data))
for outp, inp in zip(all_data, data):
np.testing.assert_equal(outp, inp)
def test_npz(self):
reader = NumPyFileReader(self.npz)
all_data = reader.get_output()
fh = np.load(self.npz)
data = [x[1] for x in list(fh.items())]
fh.close()
self.assertEqual(reader.number_of_trajectories(), len(data))
for outp, inp in zip(all_data, data):
np.testing.assert_equal(outp, inp)
def test_only_npy(self):
reader = NumPyFileReader(self.npy_files)
from_files = [np.load(f) for f in self.npy_files]
concatenated = np.vstack(from_files)
output = reader.get_output()
self.assertEqual(reader.number_of_trajectories(), len(self.npy_files))
self.assertEqual(reader.n_frames_total(), concatenated.shape[0])
for x, y in zip(output, from_files):
np.testing.assert_array_almost_equal(x, y)
def test_lagged_stridden_access_multiple_files(self):
reader = NumPyFileReader(self.files2d)
strides = [2, 3, 5, 7, 15]
lags = [1, 3, 7, 10, 30]
for stride in strides:
for lag in lags:
chunks = {
i: []
for i in range(reader.number_of_trajectories())
}
for itraj, _, Y in reader.iterator(stride, lag):
chunks[itraj].append(Y)
for i, k in enumerate(chunks.values()):
stack = np.vstack(k)
d = np.load(self.files2d[i])
np.testing.assert_equal(
stack, d[lag::stride], "not equal for stride=%i"
" and lag=%i" % (stride, lag))
