def test_dims(self):
assembly = brainio.get_assembly('dicarlo.Rust2012.array')
# (neuroid: 296, presentation: 53700, time_bin: 6)
assert assembly.dims == ("neuroid", "presentation", "time_bin")
assert len(assembly['neuroid']) == 296
assert len(assembly['presentation']) == 53700
assert len(assembly['time_bin']) == 6
def test_dims(self):
assembly = brainio.get_assembly('dicarlo.Rust2012.single')
# (neuroid: 285, presentation: 1500, time_bin: 1)
assert assembly.dims == ("neuroid", "presentation", "time_bin")
assert len(assembly['neuroid']) == 285
assert len(assembly['presentation']) == 1500
assert len(assembly['time_bin']) == 1
def test_coords(self):
assembly = brainio.get_assembly('dicarlo.Seibert2019')
assert len(set(assembly['image_id'].values)) == 5760
assert len(set(assembly['neuroid_id'].values)) == 258
assert len(set(assembly['animal'].values)) == 3
assert len(set(assembly['region'].values)) == 2
assert len(set(assembly['variation'].values)) == 3
def test_dims(self):
assembly = brainio.get_assembly('dicarlo.Seibert2019')
# neuroid: 258 presentation: 286080 time_bin: 1
assert assembly.dims == ("neuroid", "presentation", "time_bin")
assert len(assembly['neuroid']) == 258
assert len(assembly['presentation']) == 286080
assert len(assembly['time_bin']) == 1
def test_assembly(self, identifier, num_neuroids, properties,
stimulus_set_identifier):
assembly = brainio.get_assembly(identifier)
assert set(assembly.dims) == {'neuroid', 'neuronal_property'}
assert len(assembly['neuroid']) == num_neuroids
assert set(assembly['neuronal_property'].values) == set(properties)
assert assembly.stimulus_set is not None
assert assembly.stimulus_set.identifier == stimulus_set_identifier
def test_klab_Zhang2018search():
assembly = brainio.get_assembly('klab.Zhang2018search_obj_array')
assert set(assembly.dims) == {'presentation', 'fixation', 'position'}
assert len(assembly['presentation']) == 4500
assert len(set(assembly['image_id'].values)) == 300
assert len(set(assembly['subjects'].values)) == 15
assert len(assembly['fixation']) == 8
assert len(assembly['position']) == 2
assert assembly.stimulus_set is not None
def test_v1_v2_alignment(self, identifier):
assembly = brainio.get_assembly(identifier)
v1 = assembly[{
'neuroid':
[region == 'V1' for region in assembly['region'].values]
}]
v2 = assembly[{
'neuroid':
[region == 'V2' for region in assembly['region'].values]
}]
assert len(v1['presentation']) == len(v2['presentation'])
assert set(v1['image_id'].values) == set(v2['image_id'].values)
def test_num_neurons(self, identifier):
assembly = brainio.get_assembly(identifier)
assert len(assembly['neuroid']) == 205
v1 = assembly[{
'neuroid':
[region == 'V1' for region in assembly['region'].values]
}]
assert len(v1['neuroid']) == 102
v2 = assembly[{
'neuroid':
[region == 'V2' for region in assembly['region'].values]
}]
assert len(v2['neuroid']) == 103
def test_aperture(self, identifier, image_id, expected_amount_gray,
ratio_gray):
""" test a random image for the correct amount of gray pixels """
assembly = brainio.get_assembly(identifier)
stimulus_set = assembly.stimulus_set
image_path = Path(stimulus_set.get_image(image_id))
assert image_path.is_file()
# count number of gray pixels in image
image = Image.open(image_path)
image = np.array(image)
amount_gray = 0
for index in np.ndindex(image.shape[:2]):
color = image[index]
gray = [128, 128, 128]
if (color == gray).all():
amount_gray += 1
assert amount_gray / image.size == approx(ratio_gray, abs=.0001)
assert amount_gray == expected_amount_gray
def test_BashivanKar2019(assembly, shape, nans):
assy = brainio.get_assembly(assembly)
assert assy.shape == shape
assert np.count_nonzero(np.isnan(assy)) == nans
def test_coords(self):
assembly = brainio.get_assembly('dicarlo.Rust2012.array')
assert len(set(assembly['image_id'].values)) == 300
assert len(set(assembly['neuroid_id'].values)) == 296
assert len(set(assembly['animal'].values)) == 2
assert len(set(assembly['region'].values)) == 2
def test_coords(self):
assembly = brainio.get_assembly('dicarlo.Rust2012.single')
assert len(set(assembly['image_id'].values)) == 300
assert len(set(assembly['neuroid_id'].values)) == 285
assert len(set(assembly['region'].values)) == 2
def test_content(self):
assembly = brainio.get_assembly('dicarlo.Seibert2019')
assert np.count_nonzero(np.isnan(assembly)) == 19118720
assert assembly.stimulus_set_identifier == "dicarlo.hvm"
hvm = assembly.stimulus_set
assert hvm.shape == (5760, 18)
def test_nonzero(self, identifier):
assembly = brainio.get_assembly(identifier)
nonzero = np.count_nonzero(assembly)
assert nonzero > 0
def test_existence(assembly_identifier):
assert brainio.get_assembly(assembly_identifier) is not None