def perform(chunksize, stride):
try:
transformed_output = tica.get_output(chunk=chunksize, stride=stride)
tica.write_to_hdf5(out, group=group, chunksize=chunksize, stride=stride)
import h5py
with h5py.File(out) as f:
assert len(f[group]) == len(data)
for (itraj, actual), desired in zip(f[group].items(), transformed_output):
np.testing.assert_equal(actual, desired, err_msg='failed for cs=%s, stride=%s'
%(chunksize, stride))
finally:
os.remove(out)
def test_write_h5(self):
from pyemma.coordinates import tica
dim = 10
data = [
np.random.random((np.random.randint(50, 150), dim))
for _ in range(4)
]
tica = tica(data, lag=1)
import tempfile
out = tempfile.mktemp()
group = '/test'
def perform(chunksize, stride):
try:
transformed_output = tica.get_output(chunk=chunksize,
stride=stride)
tica.write_to_hdf5(out,
group=group,
chunksize=chunksize,
stride=stride)
assert os.path.exists(out), "File did not get created"
import h5py
with h5py.File(out, mode='r') as f:
assert len(f[group]) == len(data)
for (itraj,
actual), desired in zip(f[group].items(),
transformed_output):
np.testing.assert_equal(
actual,
desired,
err_msg='failed for cs=%s, stride=%s' %
(chunksize, stride))
finally:
if os.path.exists(out):
os.remove(out)
for cs in [0, 1, 3, 10, 42, 50]:
for s in [1, 2, 3, 10]:
perform(cs, s)
# test overwrite
try:
tica.write_to_hdf5(out, group=group)
with self.assertRaises(ValueError):
tica.write_to_hdf5(out, group=group)
os.remove(out)
tica.write_to_hdf5(out)
with self.assertRaises(ValueError) as ctx:
tica.write_to_hdf5(out)
assert 'Refusing to overwrite data' in ctx.exception.args[0]
os.remove(out)
tica.write_to_hdf5(out, group=group)
tica.write_to_hdf5(out, group=group, overwrite=True)
os.remove(out)
import h5py
with h5py.File(out, mode='a') as f:
f.create_group('empty').create_dataset('0000', shape=(1, 1))
with self.assertRaises(ValueError):
tica.write_to_hdf5(out, group='empty')
tica.write_to_hdf5(out, group='empty', overwrite=True)
finally:
os.remove(out)