def test_external_link():
data_original = np.zeros(10)
f = nwb.create_blank_file(force=True)
scale = nwb.Scale(np.zeros(10), 'time', 'second')
nwb.TimeSeries(data_original,
scale=scale,
dimension='voltage',
unit='volt',
metadata={
'foo': 1
}).add_to_acquisition(f)
temp_file_name = f.filename
f.close()
f = h5py.File(temp_file_name, 'r')
f2 = nwb.create_blank_file(force=True)
data = nwb.TimeSeries.get_acquisition(f, 0)
data.add_to_acquisition(f2)
f.close()
temp_file_name_2 = f2.filename
f2.close()
f = h5py.File(temp_file_name_2)
data = nwb.TimeSeries.get_acquisition(f, 0)
np.testing.assert_almost_equal(data.data, data_original)
assert data.data.file.filename == temp_file_name
f.close()
os.remove(temp_file_name)
os.remove(temp_file_name_2)
def test_create_blank_file():
nwb.create_blank_file()
f = nwb.create_blank_file(close=False)
file_name = f.filename
f.close()
nwb.create_blank_file(file_name, force=True)
os.remove(file_name)
def test_create_blank_file_force():
temp_file_name = nwb.get_temp_file_name()
nwb.create_blank_file(temp_file_name, force=True)
try:
nwb.create_blank_file(temp_file_name)
except IOError:
exception_caught = True
assert exception_caught
os.remove(temp_file_name)
def test_grayscale_movie():
t_values = np.arange(20) * .1
row_values = np.arange(5)
col_values = np.arange(10)
data_values = np.empty((20, 5, 10))
f = nwb.create_blank_file(close=False, force=True)
t_scale = nwb.Scale(t_values, 'time', 'second')
row_scale = nwb.Scale(row_values, 'distance', 'pixel')
col_scale = nwb.Scale(col_values, 'distance', 'pixel')
data = nwb.GrayScaleMovie(data_values,
scale=(t_scale, row_scale, col_scale),
metadata={'foo': 5})
data.add_to_stimulus(f)
data.add_to_acquisition(f)
data.add_to_processing(f, 'step_0')
data.add_to_analysis(f, 'step_0')
round_trip = nwb.GrayScaleMovie.get_stimulus(f, 0)
np.testing.assert_almost_equal(round_trip.data[:], data.data[:], 12)
round_trip = nwb.GrayScaleMovie.get_acquisition(f, 0)
np.testing.assert_almost_equal(round_trip.data[:], data.data[:], 12)
round_trip = nwb.GrayScaleMovie.get_processing(f, 'step_0', 0)
np.testing.assert_almost_equal(round_trip.data[:], data.data[:], 12)
round_trip = nwb.GrayScaleMovie.get_analysis(f, 'step_0', 0)
np.testing.assert_almost_equal(round_trip.data[:], data.data[:], 12)
f.close()
def test_writable():
y_values = 10 * np.ones(10)
scale = nwb.DtScale(.1, 'time', 'second')
data = nwb.FiringRate(y_values, scale=scale)
f = nwb.create_blank_file(close=True)
try:
data.add_to_stimulus(f)
except TypeError as e:
assert str(e).replace(
'\'', '') == "NoneType object has no attribute __getitem__"
f = nwb.create_blank_file(close=False)
f.close()
try:
data.add_to_stimulus(f)
except Exception as e:
assert str(e) == 'File not valid: <Closed HDF5 file>'
def test_different_scales():
y_values = 10 * np.ones(10)
f = nwb.create_blank_file(close=False)
scale = nwb.DtScale(.1, 'time', 'second')
data = nwb.FiringRate(y_values, scale=scale)
data.add_to_stimulus(f)
spike_train = nwb.FiringRate.get_stimulus(f, 0)
y_values_new = spike_train.data[:]
np.testing.assert_almost_equal(y_values_new, y_values)
f.close()
def test_nullscale():
y_values = np.array([.1, .5, .51])
f = nwb.create_blank_file(force=True)
data = nwb.SpikeTrain(y_values, unit='second')
data.add_to_stimulus(f)
spike_train = nwb.SpikeTrain.get_stimulus(f)
y_values_new = spike_train.data[:]
np.testing.assert_almost_equal(y_values, y_values_new)
assert isinstance(spike_train.scales[0], nwb.NullScale)
f.close()
def test_set_data_file_handle():
f = nwb.create_blank_file(close=False)
s0 = nwb._set_scale(f, '0', np.arange(3), 'time', 'second', "Scale")
s1 = nwb._set_scale(f, '1', np.arange(4), 'time', 'second', "Scale")
s2 = nwb._set_scale(f, '2', np.arange(5), 'time', 'second', "Scale")
nwb._set_data(f, '1D', np.zeros(3), s0, 'firing_rate', 'hertz')
nwb._set_data(f, '2D', np.zeros((3, 4)), (s0, s1), 'firing_rate', 'hertz')
nwb._set_data(f, '3D', np.zeros((3, 4, 5)), (s0, s1, s2), 'firing_rate',
'hertz')
file_name = f.filename
f.close()
os.remove(file_name)
def test_metadata():
f = nwb.create_blank_file(close=False)
s0 = nwb._set_scale(f, '0', np.arange(3), 'time', 'second', "Scale")
nwb._set_data(f,
'test_metadata',
np.zeros(3),
s0,
'firing_rate',
'hertz',
metadata={'name': 'foo'})
_, _, _, _, metadata = nwb._get_data(f['test_metadata'])
assert metadata['name'] == 'foo'
file_name = f.filename
f.close()
os.remove(file_name)
def test_set_data_force():
f = nwb.create_blank_file(close=False)
s0 = nwb._set_scale(f, '0', np.arange(3), 'time', 'second', "Scale")
nwb._set_data(f, 'test_force', np.zeros(3), s0, 'firing_rate', 'hertz')
nwb._set_data(f,
'test_force',
np.zeros(3),
s0,
'firing_rate',
'hertz',
force=True)
file_name = f.filename
f.close()
os.remove(file_name)
def test_timeseries():
y_values = np.array([.1, .2, .1])
f = nwb.create_blank_file()
scale = nwb.DtScale(.1, 'time', 'second')
nwb.TimeSeries(y_values, scale=scale, dimension='voltage',
unit='volt').add_to_acquisition(f)
data = nwb.TimeSeries.get_acquisition(f)
assert data.scales[0].dt == .1
assert data.scales[0].unit == 'second'
np.testing.assert_almost_equal(data.data[:], y_values)
assert data.unit == 'volt'
file_name = f.filename
f.close()
os.remove(file_name)
def test_spike_train():
t_values = np.arange(5) * .1
y_values = np.array([0, 1, 2, 2, 1])
f = nwb.create_blank_file(close=False, force=True)
scale = nwb.Scale(t_values, 'time', 'second')
data = nwb.SpikeTrain(y_values, scale=scale)
data.add_to_stimulus(f)
data.add_to_acquisition(f)
data.add_to_processing(f, 'step_0')
data.add_to_analysis(f, 'step_0')
round_trip = nwb.SpikeTrain.get_stimulus(f, 0)
assert round_trip == data
file_name = f.filename
f.close()
os.remove(file_name)
def test_firing_rate():
t_values = np.arange(10)
y_values = 10 * np.ones(10)
f = nwb.create_blank_file(close=False, force=True)
scale = nwb.Scale(t_values, 'time', 'second')
data = nwb.FiringRate(y_values, scale=scale)
data.add_to_stimulus(f)
data.add_to_acquisition(f)
data.add_to_processing(f, 'step_0')
data.add_to_analysis(f, 'step_0')
round_trip = nwb.FiringRate.get_stimulus(f, 0)
assert round_trip == data
file_name = f.filename
f.close()
os.remove(file_name)
def test_analysis():
t_values = np.arange(10)
y_values = 10 * np.ones(10)
f = nwb.create_blank_file(close=False)
scale = nwb.Scale(t_values, 'time', 'second')
data = nwb.FiringRate(y_values, scale=scale)
data.add_to_analysis(f, 'step_0')
scale = nwb.Scale(t_values, 'time', 'second')
data = nwb.FiringRate(y_values, scale=scale)
data.add_to_analysis(f, 'step_0')
scale = nwb.Scale(t_values, 'time', 'second')
data = nwb.FiringRate(y_values, scale=scale)
data.add_to_analysis(f, 'step_1')
file_name = f.filename
f.close()
os.remove(file_name)
def test_add_shared_scale():
f = nwb.create_blank_file(close=False, force=True)
t_values = np.arange(10)
shared_scale = nwb.Scale(t_values, 'time', 'second')
data_0 = nwb.FiringRate(10 * np.ones(10), scale=shared_scale)
data_0.add_to_stimulus(f)
data_1 = nwb.FiringRate(20 * np.ones(10), scale=shared_scale)
data_1.add_to_stimulus(f)
round_trip_0 = nwb.FiringRate.get_stimulus(f, 0)
assert data_0 == round_trip_0
round_trip_1 = nwb.FiringRate.get_stimulus(f, 1)
assert data_1 == round_trip_1
rt0, rt1 = nwb.FiringRate.get_stimulus(f)
assert data_0 == rt0
assert data_1 == rt1
file_name = f.filename
f.close()
os.remove(file_name)
def test_get_data():
s0_tuple = '0', np.arange(3), 'distance', 'pixel', "Scale"
s1_tuple = '1', np.arange(4), 'distance', 'pixel', "Scale"
data, dimension, unit = np.ones((3, 4)), 'brightness', 'intensity'
f = nwb.create_blank_file(close=False)
s0 = nwb._set_scale(f, *s0_tuple)
s1 = nwb._set_scale(f, *s1_tuple)
scales = (s0, s1)
nwb._set_data(f, 'test', data, scales, dimension, unit)
data_new, scales_new, dimension_new, unit_new, metadata = nwb._get_data(
f['test'])
np.testing.assert_almost_equal(data, data_new)
assert len(metadata) == 0
assert dimension == dimension_new
assert unit == unit_new
for scale_tuple, scale_new in zip((s0_tuple, s1_tuple), scales_new):
np.testing.assert_almost_equal(scale_tuple[1], scale_new[:])
assert scale_tuple[2] == scale_new.attrs['dimension']
assert scale_tuple[3] == scale_new.attrs['unit']
file_name = f.filename
f.close()
os.remove(file_name)