def test_get_filepath_point():
with copy_config() as config_copy_path:
with edit_config(config_copy_path) as config:
config["components"][
"point_neuron_models_dir"] = "$COMPONENT_DIR/point_neuron_models"
circuit = Circuit(config_copy_path)
nodes = create_node_population(str(TEST_DATA_DIR / "nodes_points.h5"),
"default", circuit)
test_obj = test_module.NeuronModelsHelper(circuit.config["components"],
nodes)
node_id = 0
assert nodes.get(node_id,
properties=Node.MODEL_TEMPLATE) == "nml:empty_bio"
actual = test_obj.get_filepath(node_id)
expected = Path(
circuit.config["components"]["point_neuron_models_dir"],
"empty_bio.nml")
assert actual == expected
node_id = 1
assert nodes.get(
node_id,
properties=Node.MODEL_TEMPLATE) == "nml:/abs/path/empty_bio"
actual = test_obj.get_filepath(node_id)
expected = Path("/abs/path/empty_bio.nml")
assert actual == expected
def circuit(self):
"""Access to the circuit used for the simulation."""
from bluepysnap.circuit import Circuit
if "network" not in self._config:
raise BluepySnapError(
"No 'network' set in the simulation/global config file.")
return Circuit(self._config["network"])
def test_as_edge_source_target(self):
circuit = Circuit(str(TEST_DATA_DIR / 'circuit_config.json'))
assert circuit.nodes['default'].source_in_edges() == {
"default", 'default2'
}
assert circuit.nodes['default'].target_in_edges() == {
"default", 'default2'
}
def test_as_edge_source_target(self):
circuit = Circuit(str(TEST_DATA_DIR / "circuit_config.json"))
assert circuit.nodes["default"].source_in_edges() == {
"default", "default2"
}
assert circuit.nodes["default"].target_in_edges() == {
"default", "default2"
}
def test_property_dtypes_fail(self):
a = pd.Series(data=[dtype('int64'), dtype('float64')],
index=['syn_weight', 'efferent_surface_z']).sort_index()
b = pd.Series(data=[dtype('int32'), dtype('float64')],
index=['syn_weight', 'efferent_surface_z']).sort_index()
with patch("bluepysnap.edges.EdgePopulation.property_dtypes",
new_callable=PropertyMock) as mock:
mock.side_effect = [a, b]
circuit = Circuit(str(TEST_DATA_DIR / 'circuit_config.json'))
test_obj = test_module.Edges(circuit)
with pytest.raises(BluepySnapError):
test_obj.property_dtypes.sort_index()
def test_property_dtypes_fail(self):
a = pd.Series(data=[dtype('int64'), dtype('O')],
index=['layer', 'model_template']).sort_index()
b = pd.Series(data=[dtype('int32'), dtype('O')],
index=['layer', 'model_template']).sort_index()
with patch("bluepysnap.nodes.NodePopulation.property_dtypes",
new_callable=PropertyMock) as mock:
mock.side_effect = [a, b]
circuit = Circuit(str(TEST_DATA_DIR / 'circuit_config.json'))
test_obj = test_module.Nodes(circuit)
with pytest.raises(BluepySnapError):
test_obj.property_dtypes.sort_index()
def test_biophysical_in_library(self):
with copy_circuit() as (circuit_copy_path, config_copy_path):
with edit_config(config_copy_path) as config:
config["networks"]["nodes"][0]["nodes_file"] = "$NETWORK_DIR/nodes_quaternions.h5"
nodes_file = circuit_copy_path / 'nodes_quaternions.h5'
with h5py.File(nodes_file, 'r+') as h5f:
data = h5f['nodes/default/0/model_type'][:]
del h5f['nodes/default/0/model_type']
h5f.create_dataset('nodes/default/0/model_type',
data=np.zeros_like(data, dtype=int))
h5f.create_dataset('nodes/default/0/@library/model_type',
data=np.array(["biophysical", ], dtype=h5py.string_dtype()))
circuit = Circuit(str(config_copy_path))
assert isinstance(circuit.nodes['default'].morph, test_module.MorphHelper)
def test_not_biophysical_population(self):
with copy_circuit() as (circuit_copy_path, config_copy_path):
with edit_config(config_copy_path) as config:
config["networks"]["nodes"][0]["nodes_file"] = "$NETWORK_DIR/nodes_quaternions.h5"
nodes_file = circuit_copy_path / 'nodes_quaternions.h5'
with h5py.File(nodes_file, 'r+') as h5f:
data = h5f['nodes/default/0/model_type'][:]
del h5f['nodes/default/0/model_type']
h5f.create_dataset('nodes/default/0/model_type',
data=np.zeros_like(data, dtype=int))
h5f.create_dataset('nodes/default/0/@library/model_type',
data=np.array(["virtual", ], dtype=h5py.string_dtype()))
with pytest.raises(BluepySnapError):
circuit = Circuit(str(config_copy_path))
circuit.nodes['default'].morph
def setup(self):
circuit = Circuit(str(TEST_DATA_DIR / 'circuit_config.json'))
self.test_obj = test_module.Edges(circuit)
def setup(self):
circuit = Circuit(str(TEST_DATA_DIR / "circuit_config.json"))
self.test_obj = test_module.Nodes(circuit)
