def test_alternate_morphology(self):
alternate_morphs = {"h5v1": str(self.morph_path)}
test_obj = test_module.MorphHelper(
None, self.nodes, alternate_morphologies=alternate_morphs
)
node_id = CircuitNodeId("default", 1)
assert self.nodes.get(node_id, properties="morphology") == "morph-B"
expected = self.morph_path / "morph-B.h5"
actual = test_obj.get_filepath(node_id, extension="h5")
assert actual == expected
alternate_morphs = {"neurolucida-asc": str(self.morph_path)}
test_obj = test_module.MorphHelper(
None, self.nodes, alternate_morphologies=alternate_morphs
)
node_id = CircuitNodeId("default", 1)
assert self.nodes.get(node_id, properties="morphology") == "morph-B"
expected = self.morph_path / "morph-B.asc"
actual = test_obj.get_filepath(node_id, extension="asc")
assert actual == expected
with pytest.raises(BluepySnapError, match="'morphologies_dir' is not defined in config"):
node_id = CircuitNodeId("default", 0)
test_obj.get_filepath(node_id)
def test_get_morphology_standard_rotation(self):
nodes = create_node_population(str(TEST_DATA_DIR / 'nodes.h5'),
"default")
test_obj = test_module.MorphHelper(str(self.morph_path), nodes)
node_id = 0
actual = test_obj.get(node_id, transform=True).points
# check if the input node positions / orientation values are still the same
pdt.assert_series_equal(
self.nodes.positions(node_id),
pd.Series([101., 102., 103.],
index=[Node.X, Node.Y, Node.Z],
name=0))
npt.assert_almost_equal(nodes.orientations(node_id), [
[0.738219, 0., 0.674560],
[0., 1., 0.],
[-0.674560, 0., 0.738219],
],
decimal=6)
assert len(actual) == 32
expected = [[100.7637696, 103, 103.2158592, 0.725],
[100.7637696, 102.9, 103.2158592, 0.820]]
npt.assert_almost_equal(expected, actual[:2])
def test_get_morphology_standard_rotation(self):
nodes = create_node_population(str(TEST_DATA_DIR / "nodes.h5"), "default")
test_obj = test_module.MorphHelper(str(self.morph_path), nodes)
node_id = 0
actual = test_obj.get(node_id, transform=True).points
# check if the input node positions / orientation values are still the same
pdt.assert_series_equal(
self.nodes.positions(node_id),
pd.Series([101.0, 102.0, 103.0], index=[Node.X, Node.Y, Node.Z], name=0),
)
npt.assert_almost_equal(
nodes.orientations(node_id),
[
[0.738219, 0.0, 0.674560],
[0.0, 1.0, 0.0],
[-0.674560, 0.0, 0.738219],
],
decimal=6,
)
assert len(actual) == 13
expected = [[101.0, 107.0, 103.0], [102.47644, 111.0, 101.65088]]
npt.assert_almost_equal(actual[:2], expected, decimal=6)
def test_MorphHelper_cache_2(nm_load):
nodes = Mock()
nodes.get.side_effect = ['morph-A', 'morph-A']
with patch.object(test_module.MorphHelper,
'_is_biophysical',
return_value=True):
test_obj = test_module.MorphHelper('morph-dir', nodes)
nm_load.side_effect = Mock
morph1 = test_obj.get(0)
# same morphology, but no caching
assert test_obj.get(1) is not morph1
def test_get_alternate_morphology(self):
alternate_morphs = {"h5v1": str(self.morph_path)}
test_obj = test_module.MorphHelper(
None, self.nodes, alternate_morphologies=alternate_morphs
)
actual = test_obj.get(0, extension="h5")
assert len(actual.points) == 13
expected = [
[0.0, 5.0, 0.0],
[2.0, 9.0, 0.0],
]
npt.assert_almost_equal(expected, actual.points[:2])
npt.assert_almost_equal([2.0, 2.0], actual.diameters[:2])
def test_MorphHelper_cache_1(nm_load):
nodes = Mock()
nodes.get.side_effect = ['morph-A', 'morph-A', 'morph-B', 'morph-A']
with patch.object(test_module.MorphHelper,
'_is_biophysical',
return_value=True):
test_obj = test_module.MorphHelper('morph-dir', nodes)
nm_load.side_effect = Mock
morph0 = test_obj.get(0)
# should get cached object for 'morph-A'
assert test_obj.get(1) is morph0
# should get new object ('morph-B')
assert test_obj.get(2) is not morph0
# 'morph-A' was evicted from cache
assert test_obj.get(3) is not morph0
def setup(self):
self.nodes = create_node_population(
str(TEST_DATA_DIR / 'nodes_quaternions.h5'), "default")
self.morph_path = TEST_DATA_DIR / 'morphologies'
self.test_obj = test_module.MorphHelper(str(self.morph_path),
self.nodes)