class TestSingleTypeCompilation(unittest.TestCase):
"""
Check if the scaffold can create a single cell type.
"""
@classmethod
def setUpClass(self):
super(TestSingleTypeCompilation, self).setUpClass()
config = JSONConfig(file=single_neuron_config)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
def test_placement_statistics(self):
self.assertEqual(self.scaffold.statistics.cells_placed["test_cell"], 4)
self.assertEqual(self.scaffold.get_cell_total(), 4)
def test_network_cache(self):
pass
# TODO: Implement a check that the network cache contains the right amount of placed cells
def test_hdf5_cells(self):
pass
# TODO: Implement a check that the hdf5 file contains the right datasets under 'cells'
def test_from_hdf5(self):
scaffold_copy = from_hdf5(self.scaffold.output_formatter.file)
for key in self.scaffold.statistics.cells_placed:
self.assertEqual(
scaffold_copy.statistics.cells_placed[key],
self.scaffold.statistics.cells_placed[key],
)
self.assertEqual(scaffold_copy.get_cell_total(), 4)
self.assertRaises(OSError, from_hdf5, "doesntexist")
class TestEntities(unittest.TestCase):
@classmethod
def setUpClass(self):
import nest
nest.ResetKernel()
super(TestEntities, self).setUpClass()
config = JSONConfig(file=minimal_config_entities)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
hdf_config = _from_hdf5("minimal_entities.hdf5")
self.scaffold_fresh = Scaffold(hdf_config,
from_file="minimal_entities.hdf5")
def test_placement_statistics(self):
self.assertEqual(self.scaffold.statistics.cells_placed["entity_type"],
100)
@unittest.skipIf(
importlib.util.find_spec("nest") is None, "NEST is not importable.")
def test_creation_in_nest(self):
f = h5py.File("minimal_entities.hdf5", "r")
ids = list(f["entities"]["entity_type"])
self.assertEqual(ids, list(range(100)))
f.close()
# Try to load the network directly from the hdf5 file
nest_adapter = self.scaffold_fresh.get_simulation("test")
simulator = nest_adapter.prepare()
nest_adapter.simulate(simulator)
nest_ids = nest_adapter.entities["entity_type"].nest_identifiers
self.assertEqual(list(nest_ids), list(range(1, 101)))
class TestSingleNeuronTypeSetup(unittest.TestCase):
def setUp(self):
config = JSONConfig(file=single_neuron_config)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
self.nest_adapter = self.scaffold.configuration.simulations[
"test_single_neuron"]
self.nest_adapter.reset()
def tearDown(self):
self.nest_adapter.delete_lock()
def test_single_neuron(self):
self.scaffold.run_simulation("test_single_neuron")
test_cell_model = self.nest_adapter.cell_models["test_cell"]
self.assertEqual(test_cell_model.nest_identifiers, list(range(1, 5)))
test_neuron_status = self.nest_adapter.nest.GetStatus(
test_cell_model.nest_identifiers)
self.assertEqual(test_neuron_status[0]["t_ref"], 1.5)
self.assertEqual(test_neuron_status[0]["C_m"], 7.0)
self.assertEqual(test_neuron_status[0]["V_th"], -41.0)
self.assertEqual(test_neuron_status[0]["V_reset"], -70.0)
self.assertEqual(test_neuron_status[0]["E_L"], -62.0)
self.assertEqual(test_neuron_status[0]["I_e"], 0.0)
def setUp(self):
config = JSONConfig(file=single_neuron_config)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
self.nest_adapter = self.scaffold.configuration.simulations[
"test_single_neuron"]
self.nest_adapter.reset()
def setUpClass(self):
super(TestMultiInstance, self).setUpClass()
import nest
self.nest = nest
config = JSONConfig(file=single_neuron_config)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
self.hdf5 = self.scaffold.output_formatter.file
self.nest_adapter_0 = self.scaffold.get_simulation(
"test_single_neuron")
# When another test errors, the lock might remain, and all locking tests fail
self.nest_adapter_0.delete_lock()
self.nest_adapter_1 = self.scaffold.create_adapter(
"test_single_neuron")
self.nest_adapter_2 = self.scaffold.create_adapter(
"test_single_neuron")
self.nest_adapter_multi_1 = self.scaffold.create_adapter(
"test_single_neuron")
self.nest_adapter_multi_1.enable_multi("first")
self.nest_adapter_multi_1b = self.scaffold.create_adapter(
"test_single_neuron")
self.nest_adapter_multi_1b.enable_multi("first")
self.nest_adapter_multi_2 = self.scaffold.create_adapter(
"test_single_neuron")
self.nest_adapter_multi_2.enable_multi("second")
def setUpClass(self):
super(TestFiberIntersection, self).setUpClass()
# Make sure the MR exists
test_setup.prep_morphologies()
# The scaffold has only the Granular layer (100x100x150) with 20 GrCs
# and 1 GoC placed, as specified in the config file
self.config = JSONConfig(file=fiber_transform_config)
# Defining quivers field to include also voxels outside the scaffold
# volume
self.quivers_field = np.zeros(
shape=(3, 80, 80, 80)) # Each voxel in the volume has vol_res=25um
# Fake quiver, oriented as original fibers
basic_quiver = np.array([0, 1.0, 0.0])
self.quivers_field[0, :] = basic_quiver[0]
self.quivers_field[1, :] = basic_quiver[1]
self.quivers_field[2, :] = basic_quiver[2]
self.config.connection_types[
"parallel_fiber_to_golgi_bended"].transformation.quivers = self.quivers_field
self.config.connection_types[
"parallel_fiber_to_golgi_bended"].transformation.vol_start = [
-500.0, -500.0, -500.0
]
self.scaffold = Scaffold(self.config)
self.scaffold.morphology_repository = MorphologyRepository(morpho_file)
self.scaffold.compile_network()
class TestMorhologySetsRotations(unittest.TestCase):
"""
Test scaffold with cells associated to a certain rotated morphology
"""
@classmethod
def setUpClass(self):
import dbbs_models
test_setup.prep_morphologies()
test_setup.prep_rotations()
super().setUpClass()
config = JSONConfig(config_file)
self.scaffold = Scaffold(config)
self.scaffold.morphology_repository = MorphologyRepository(test_setup.mr_rot_path)
def test_morphology_map(self):
# Create and place a set of 10 Golgi cells and assign them to a morphology based on their rotation
cell_type = self.scaffold.get_cell_type("golgi_cell")
positions = np.random.rand(9, 3)
# Construct rotation matrix for cell_type
phi_values = np.linspace(0.0, 360.0, num=3)
theta_values = np.linspace(0.0, 360.0, num=3)
phi_values = np.repeat(
phi_values, 3
) # np.random.choice(len(phi_values), len(positions))
theta_values = np.repeat(
theta_values, 3
) # np.random.choice(len(theta_values), len(positions))
rotations = np.vstack((phi_values, theta_values)).T
# Place cells and generate hdf5 output
self.scaffold.place_cells(
cell_type, cell_type.placement.layer_instance, positions, rotations
)
self.scaffold.compile_output()
ps = PlacementSet(self.scaffold.output_formatter, cell_type)
ms = MorphologySet(self.scaffold, cell_type, ps)
self.assertEqual(
len(rotations),
len(ms._morphology_index),
"Not all cells assigned to a morphology!",
)
random_sel = np.random.choice(len(ms._morphology_index))
morpho_sel = ms._morphology_map[ms._morphology_index[random_sel]]
self.assertTrue(
morpho_sel.find(
"__"
+ str(int(rotations[random_sel, 0]))
+ "_"
+ str(int(rotations[random_sel, 1]))
)
!= -1,
"Wrong morphology map!",
)
def setUpClass(self):
import dbbs_models
test_setup.prep_morphologies()
test_setup.prep_rotations()
super().setUpClass()
config = JSONConfig(config_file)
self.scaffold = Scaffold(config)
self.scaffold.morphology_repository = MorphologyRepository(test_setup.mr_rot_path)
def setUpClass(self):
import nest
nest.ResetKernel()
super(TestEntities, self).setUpClass()
config = JSONConfig(file=minimal_config_entities)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
hdf_config = _from_hdf5("minimal_entities.hdf5")
self.scaffold_fresh = Scaffold(hdf_config,
from_file="minimal_entities.hdf5")
def setUpClass(self):
super().setUpClass()
import nest
self.nest = nest
config = JSONConfig(file=recorder_config)
self.scaffold = Scaffold(config)
def setUpClass(cls):
super().setUpClass()
config = JSONConfig(file=heterosyn_config)
cls.scaffold = Scaffold(config)
cls.scaffold.compile_network()
cls.nest_adapter = cls.scaffold.run_simulation(
"test_double_neuron_network_heterosyn")
def test_cortex_model_synapses(self):
cfg = JSONConfig(config)
_ = Scaffold(cfg)
for name, model in cfg.simulations["poc"].cell_models.items():
if model.relay:
continue
with self.subTest(model=name):
self._test_model(model.model_class)
def setUpClass(cls):
super().setUpClass()
config = JSONConfig(file=double_nn_config)
if not neuron_installed():
del config.simulations["neuron"]
cls.scaffold = Scaffold(config)
cls.scaffold.compile_network()
cls.nest_adapter = cls.scaffold.run_simulation(
"test_double_neuron_network_static")
def test_fiber_connections(self):
pre_type = "granule_cell"
pre_neu = self.scaffold.get_placement_set(pre_type)
conn_type = "parallel_fiber_to_golgi"
cs = self.scaffold.get_connectivity_set(conn_type)
num_conn = len(cs.connections)
# Check that no more connections are formed than the number of
# presynaptic neurons - how could happen otherwise?
self.assertTrue(num_conn <= len(pre_neu.identifiers))
# Check that increasing resolution in FiberIntersection does not change
# connection number if there are no transformations (and thus the fibers
# are parallel to main axes)
conn_type_HR = "parallel_fiber_to_golgi_HR"
cs_HR = self.scaffold.get_connectivity_set(conn_type_HR)
self.assertEqual(num_conn, len(cs_HR.connections))
# Check that half (+- 5) connections are obtained with half the affinity
conn_type_affinity = "parallel_fiber_to_golgi_affinity"
cs_affinity = self.scaffold.get_connectivity_set(conn_type_affinity)
self.assertAlmostEqual(num_conn / 2,
len(cs_affinity.connections),
delta=5)
# Check that same number of connections are obtained when a fake quiver
# transformation is applied
conn_type_transform = "parallel_fiber_to_golgi_bended"
cs_fake_transform = self.scaffold.get_connectivity_set(
conn_type_transform)
self.assertEqual(len(cs_fake_transform.connections), num_conn)
# Check that less connections are obtained when the PC surface is
# oriented according to orientation vector of 45° rotation in yz plane,
# for how the Golgi cell is placed and the parallel fibers are rotated
basic_quiver = np.array([0, 0.7, 0.7])
self.quivers_field[0, :] = basic_quiver[0]
self.quivers_field[1, :] = basic_quiver[1]
self.quivers_field[2, :] = basic_quiver[2]
self.config.connection_types[
"parallel_fiber_to_golgi_bended"].transformation.quivers = self.quivers_field
self.scaffold = Scaffold(self.config)
self.scaffold.compile_network()
cs_transform = self.scaffold.get_connectivity_set(conn_type_transform)
self.assertTrue(len(cs_transform.connections) <= num_conn)
def test_teaching_connection_missing(self):
from bsb.exceptions import ConfigurationError
with open(heterosyn_config, "r") as f:
stream = f.read()
stream = stream.replace('"teaching": "teaching_cell_to_cell",', "")
with self.assertRaises(ConfigurationError) as ce:
config = JSONConfig(stream=stream)
self.scaffold = Scaffold(config)
def test_representatives(self):
"""
Test that 1 cell per non-relay cell model is chosen.
"""
from patch import p
config = JSONConfig(double_nn_config)
scaffold = Scaffold(config)
scaffold.compile_network()
adapter = scaffold.create_adapter("neuron")
adapter.h = p
adapter.load_balance()
device = adapter.devices["test_representatives"]
device.initialise_targets()
targets = adapter.devices["test_representatives"].get_targets()
self.assertEqual(
1,
len(targets),
"Targetting type `representatives` did not return the correct amount of representatives.",
)
def test_spoofing(self):
"""
Assert that fake detailed connections can be made
"""
config = JSONConfig(file=_config)
scaffold = Scaffold(config)
scaffold.compile_network()
original_connections = len(
scaffold.cell_connections_by_tag["connection"])
sd = SpoofDetails()
sd.presynaptic = "from_cell"
sd.postsynaptic = "to_cell"
sd.scaffold = scaffold
# Raise error because here's no morphologies registered for the cell types.
with self.assertRaises(
MorphologyDataError,
msg="Missing morphologies during spoofing not caught."):
sd.after_connectivity()
# Add some morphologies
setattr(
config.cell_types["from_cell"].morphology,
"detailed_morphologies",
{"names": ["GranuleCell"]},
)
setattr(
config.cell_types["to_cell"].morphology,
"detailed_morphologies",
{"names": ["GranuleCell"]},
)
# Run the spoofing again
sd.after_connectivity()
cs = scaffold.get_connectivity_set("connection")
scaffold.compile_output()
# Use the intersection property. It throws an error should the detailed
# information be missing
try:
i = cs.intersections
for inter in i:
fl = inter.from_compartment.labels
tl = inter.to_compartment.labels
self.assertIn("axon", fl,
"From compartment type is not an axon")
self.assertIn("dendrites", tl,
"From compartment type is not a dendrite")
self.assertNotEqual(len(i), 0, "Empty intersection data")
self.assertEqual(len(i), original_connections,
"Different amount of spoofed connections")
except MissingMorphologyError:
self.fail("Could not find the intersection data on spoofed set")
# Set both types to relays and try spoofing again
config.cell_types["from_cell"].relay = True
config.cell_types["to_cell"].relay = True
with self.assertRaises(MorphologyError,
msg="Did not catch double relay spoofing!"):
sd.after_connectivity()
def setUpClass(self):
import dbbs_models
test_setup.prep_morphologies()
test_setup.prep_rotations()
super().setUpClass()
config = JSONConfig(config_file)
self.scaffold = Scaffold(config)
mr = MorphologyRepository(test_setup.mr_rot_path)
self.scaffold.morphology_repository = mr
self.morphology_cache = MorphologyCache(mr)
self.morphologies_start = ["GranuleCell", "GolgiCell", "GolgiCell_A"]
self.morphologies_rotated = mr.list_morphologies(include_rotations=True)
def test_sc_pc(self):
# 9) GrC - SC
# 3 random synapses on the dendrites. AMPA/NMDA, 10 spikes at 100Hz.
# It should do a burst of 5 spikes.
config = JSONConfig(sc_pc_config)
scaffold = Scaffold(config)
scaffold.place_cell_types()
scaffold.compile_output()
scaffold = from_hdf5(scaffold.output_formatter.file)
scaffold.run_simulation("test")
from glob import glob
from plotly import graph_objs as go
results = glob("results_test_*")[-1]
with h5py.File(results, "r") as f:
go.Figure([
go.Scatter(
x=f["recorders/soma_voltages/0"][:, 0],
y=f["recorders/soma_voltages/0"][:, 1],
),
]).show()
def test_mf_granule(self):
config = JSONConfig(mf_grc_config)
scaffold = Scaffold(config)
scaffold.place_cell_types()
scaffold.compile_output()
mf_to_glom = scaffold.configuration.connection_types[
"mossy_to_glomerulus"]
glom_to_grc = scaffold.configuration.connection_types[
"glomerulus_to_granule"]
mfs = scaffold.get_placement_set("mossy_fibers").identifiers
gloms = scaffold.get_placement_set("glomerulus").identifiers
grcs = scaffold.get_placement_set("granule_cell").identifiers
scaffold.connect_cells(
mf_to_glom, np.array([[mfs[0], gloms[0]], [mfs[1], gloms[1]]]))
scaffold.connect_cells(
mf_to_glom, np.array([[mfs[0], gloms[0]], [mfs[1], gloms[1]]]))
conns = np.array([[gloms[0], grcs[0]], [gloms[1], grcs[0]]])
morpho_map = ["GranuleCell"]
morphologies = np.array([[0, 0], [0, 0]])
compartments = np.array([[0, 9], [0, 18]])
scaffold.connect_cells(
glom_to_grc,
conns,
morphologies=morphologies,
compartments=compartments,
morpho_map=morpho_map,
)
scaffold.compile_output()
scaffold = from_hdf5(scaffold.output_formatter.file)
scaffold.run_simulation("test")
from glob import glob
from plotly import graph_objs as go
results = glob("results_test_*")[-1]
with h5py.File(results, "r") as f:
go.Figure(
go.Scatter(
x=f["recorders/soma_voltages/0"][:, 0],
y=f["recorders/soma_voltages/0"][:, 1],
)).show()
def test_grc_sc(self):
# 9) GrC - SC
# 3 random synapses on the dendrites. AMPA/NMDA, 10 spikes at 100Hz.
# It should do a burst of 5 spikes.
config = JSONConfig(grc_sc_config)
scaffold = Scaffold(config)
scaffold.place_cell_types()
scaffold.compile_output()
grc_to_golgi = scaffold.configuration.connection_types[
"granule_to_stellate"]
grcs = scaffold.get_placement_set("granule_cell").identifiers
golgis = scaffold.get_placement_set("stellate_cell").identifiers
m_grc = scaffold.morphology_repository.get_morphology("GranuleCell")
m_gol = scaffold.morphology_repository.get_morphology("StellateCell")
comps = m_gol.get_compartments(["dendrites"])
conns = np.array([[grcs[0], golgis[0]]] * 3)
morpho_map = ["GranuleCell", "StellateCell"]
morphologies = np.array([[0, 1]] * 3)
compartments = np.ones(
(3, 2)) * m_grc.get_compartments(["ascending_axon"])[0].id
compartments[:, 1] = np.random.choice([c.id for c in comps], size=3)
scaffold.connect_cells(
grc_to_golgi,
conns,
morphologies=morphologies,
compartments=compartments,
morpho_map=morpho_map,
)
scaffold.compile_output()
scaffold = from_hdf5(scaffold.output_formatter.file)
scaffold.run_simulation("test")
from glob import glob
from plotly import graph_objs as go
results = glob("results_test_*")[-1]
with h5py.File(results, "r") as f:
go.Figure([
go.Scatter(
x=f["recorders/soma_voltages/0"][:, 0],
y=f["recorders/soma_voltages/0"][:, 1],
),
go.Scatter(
x=f["recorders/soma_voltages/1"][:, 0],
y=f["recorders/soma_voltages/1"][:, 1],
),
]).show()
def test_pf_goc(self):
# 7) GrC (pf) - GoC
# The same as 5) except on 80 apical dendrites.
config = JSONConfig(aa_goc_config)
scaffold = Scaffold(config)
scaffold.place_cell_types()
scaffold.compile_output()
grc_to_golgi = scaffold.configuration.connection_types[
"granule_to_golgi"]
grcs = scaffold.get_placement_set("granule_cell").identifiers
golgis = scaffold.get_placement_set("golgi_cell").identifiers
m_gol = scaffold.morphology_repository.get_morphology("GolgiCell")
m_grc = scaffold.morphology_repository.get_morphology("GranuleCell")
comps = m_gol.get_compartments(["apical_dendrites"])
conns = np.array([[grcs[0], golgis[0]]] * 80)
morpho_map = ["GranuleCell", "GolgiCell"]
morphologies = np.array([[0, 1]] * 80)
compartments = np.ones(
(80, 2)) * m_grc.get_compartments(["ascending_axon"])[0].id
compartments[:, 1] = np.random.choice([c.id for c in comps], size=80)
scaffold.connect_cells(
grc_to_golgi,
conns,
morphologies=morphologies,
compartments=compartments,
morpho_map=morpho_map,
)
scaffold.compile_output()
scaffold = from_hdf5(scaffold.output_formatter.file)
scaffold.run_simulation("test")
from glob import glob
from plotly import graph_objs as go
results = glob("results_test_*")[-1]
with h5py.File(results, "r") as f:
go.Figure([
go.Scatter(
x=f["recorders/soma_voltages/0"][:, 0],
y=f["recorders/soma_voltages/0"][:, 1],
),
go.Scatter(
x=f["recorders/soma_voltages/1"][:, 0],
y=f["recorders/soma_voltages/1"][:, 1],
),
]).show()
class TestPlacementSets(unittest.TestCase):
"""
Check if the scaffold can create a single cell type.
"""
@classmethod
def setUpClass(self):
super(TestPlacementSets, self).setUpClass()
test_setup.prep_morphologies()
config = JSONConfig(file=double_neuron_config)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
def test_hdf5_structure(self):
with h5py.File(self.scaffold.output_formatter.file, "r") as h:
for key in ["from", "to"]:
group = h["cells/placement/" + key + "_cell"]
self.assertTrue(
"identifiers" in group,
"Identifiers dataset missing for the " + key + "_cell",
)
self.assertTrue(
"positions" in group,
"Positions dataset missing for the " + key + "_cell",
)
self.assertEqual(
group["positions"].shape,
(4, 3),
"Incorrect position dataset size for the " + key + "_cell",
)
self.assertTrue(
group["positions"].dtype == np.float64,
"Incorrect position dataset dtype ({}) for the ".format(
group["positions"].dtype) + key + "_cell",
)
self.assertEqual(
group["identifiers"].shape,
(2, ),
"Incorrect or noncontinuous identifiers dataset size for the "
+ key + "_cell",
)
self.assertTrue(
group["identifiers"].dtype == np.int32,
"Incorrect identifiers dataset dtype ({}) for the ".format(
group["identifiers"].dtype) + key + "_cell",
)
def test_placement_set_properties(self):
for key in ["from", "to"]:
cell_type = self.scaffold.get_cell_type(key + "_cell")
ps = PlacementSet(self.scaffold.output_formatter, cell_type)
self.assertEqual(
ps.identifiers.shape,
(4, ),
"Incorrect identifiers shape for " + key + "_cell",
)
self.assertEqual(
ps.positions.shape,
(4, 3),
"Incorrect positions shape for " + key + "_cell",
)
self.assertRaises(DatasetNotFoundError, lambda: ps.rotations)
self.assertEqual(type(ps.cells[0]), Cell,
"PlacementSet.cells did not return Cells")
self.assertEqual(
ps.cells[1].id,
1 if key == "from" else 5,
"PlacementSet.cells identifiers incorrect",
)
self.assertEqual(
ps.cells[1].position.shape,
(3, ),
"PlacementSet.cells positions wrong shape",
)
def test_pf_pc(self):
# 6) GrC (aa) - PC
# 100 random syn, on the apical dendrites. AMPA only, 10 spikes
# 500Hz. The response should be a burst composed by 3 spikes.
config = JSONConfig(aa_pc_config)
scaffold = Scaffold(config)
scaffold.place_cell_types()
scaffold.compile_output()
grc_to_golgi = scaffold.configuration.connection_types[
"granule_to_purkinje"]
grcs = scaffold.get_placement_set("granule_cell").identifiers
golgis = scaffold.get_placement_set("purkinje_cell").identifiers
m_gol = scaffold.morphology_repository.get_morphology("PurkinjeCell")
m_grc = scaffold.morphology_repository.get_morphology("GranuleCell")
comps = [c.id for c in m_gol.compartments if c.type == 3]
conns = np.array([[grcs[0], golgis[0]]] * 80)
morpho_map = ["GranuleCell", "PurkinjeCell"]
morphologies = np.array([[0, 1]] * 80)
compartments = np.ones(
(80, 2)) * m_grc.get_compartments(["parallel_fiber"])[0].id
compartments[:, 1] = np.random.choice(comps, size=80)
scaffold.connect_cells(
grc_to_golgi,
conns,
morphologies=morphologies,
compartments=compartments,
morpho_map=morpho_map,
)
scaffold.compile_output()
scaffold = from_hdf5(scaffold.output_formatter.file)
scaffold.run_simulation("test")
from glob import glob
from plotly import graph_objs as go
results = glob("results_test_*")[-1]
with h5py.File(results, "r") as f:
go.Figure([
go.Scatter(
x=f["recorders/soma_voltages/0"][:, 0],
y=f["recorders/soma_voltages/0"][:, 1],
),
go.Scatter(
x=f["recorders/soma_voltages/1"][:, 0],
y=f["recorders/soma_voltages/1"][:, 1],
),
]).show()
def test_aa_goc(self):
# 5) GrC (aa) - GoC
# To check it, 20syn on basal dendrites, not near the soma.
# AMPA/NMDA syn with a burst of 5 spike at 100Hz. The response should be a burst
# composed by 3 spikes
config = JSONConfig(aa_goc_config)
scaffold = Scaffold(config)
scaffold.place_cell_types()
scaffold.compile_output()
grc_to_golgi = scaffold.configuration.connection_types[
"granule_to_golgi"]
grcs = scaffold.get_placement_set("granule_cell").identifiers
golgis = scaffold.get_placement_set("golgi_cell").identifiers
m_gol = scaffold.morphology_repository.get_morphology("GolgiCell")
m_grc = scaffold.morphology_repository.get_morphology("GranuleCell")
comps = m_gol.get_compartments(["basal_dendrites"])
conns = np.array([[grcs[0], golgis[0]]] * 20)
morpho_map = ["GranuleCell", "GolgiCell"]
morphologies = np.array([[0, 1]] * 20)
compartments = np.ones(
(20, 2)) * m_grc.get_compartments(["ascending_axon"])[0].id
compartments[:, 1] = np.random.choice([c.id for c in comps], size=20)
scaffold.connect_cells(
grc_to_golgi,
conns,
morphologies=morphologies,
compartments=compartments,
morpho_map=morpho_map,
)
scaffold.compile_output()
scaffold = from_hdf5(scaffold.output_formatter.file)
scaffold.run_simulation("test")
from glob import glob
from plotly import graph_objs as go
results = glob("results_test_*")[-1]
with h5py.File(results, "r") as f:
go.Figure([
go.Scatter(
x=f["recorders/soma_voltages/0"][:, 0],
y=f["recorders/soma_voltages/0"][:, 1],
),
go.Scatter(
x=f["recorders/soma_voltages/1"][:, 0],
y=f["recorders/soma_voltages/1"][:, 1],
),
]).show()
def test_glom_golgi_granule(self):
config = JSONConfig(mf_gol_config)
scaffold = Scaffold(config)
scaffold.place_cell_types()
scaffold.compile_output()
mf_to_glom = scaffold.configuration.connection_types[
"mossy_to_glomerulus"]
glom_to_gc = scaffold.configuration.connection_types[
"glomerulus_to_golgi"]
gc_to_grc = scaffold.configuration.connection_types["golgi_to_granule"]
mfs = scaffold.get_placement_set("mossy_fibers").identifiers
gloms = scaffold.get_placement_set("glomerulus").identifiers
golgis = scaffold.get_placement_set("golgi_cell").identifiers
granules = scaffold.get_placement_set("granule_cell").identifiers
scaffold.connect_cells(mf_to_glom, np.array([[mfs[0], gloms[0]]]))
conns = np.array([[gloms[0], golgis[0]]] * 20)
m = scaffold.morphology_repository.get_morphology("GolgiCell")
morpho_map = ["GolgiCell"]
morphologies = np.zeros((20, 2))
compartments = np.zeros((20, 2))
compartments[:, 1] = np.random.choice(
[c.id for c in m.compartments if c.type == 302], size=20)
scaffold.connect_cells(
glom_to_gc,
conns,
morphologies=morphologies,
compartments=compartments,
morpho_map=morpho_map,
)
conns_grc = np.array([[golgis[0], granules[0]]] * 4)
morpho_map_grc = ["GranuleCell", "GolgiCell"]
morphologies_grc = np.zeros((4, 2))
morphologies_grc[:, 0] = [1] * 4
compartments_grc = np.zeros((4, 2))
compartments_grc[:, 0] = [c.id for c in m.compartments
if c.type == 2][0:4]
compartments_grc[:, 1] = [9 * (i + 1) for i in range(4)]
scaffold.connect_cells(
gc_to_grc,
conns_grc,
morphologies=morphologies_grc,
compartments=compartments_grc,
morpho_map=morpho_map_grc,
)
scaffold.compile_output()
scaffold = from_hdf5(scaffold.output_formatter.file)
scaffold.run_simulation("test")
from glob import glob
from plotly import graph_objs as go
results = glob("results_test_*")[-1]
with h5py.File(results, "r") as f:
g = f["recorders/soma_voltages"]
a = f["recorders/axons"]
def L(g, s):
h = g[s]
return {"x": h[:, 0], "y": h[:, 1], "name": h.attrs["label"]}
go.Figure([
*(go.Scatter(**L(g, i)) for i in g),
*(go.Scatter(**L(a, i)) for i in a),
]).show()
def setUpClass(self):
super(TestPlacementSets, self).setUpClass()
test_setup.prep_morphologies()
config = JSONConfig(file=double_neuron_config)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
def test_minimal(self):
config = JSONConfig(file=minimal_config)
self.scaffold = Scaffold(config)
class TestMultiInstance(unittest.TestCase):
@classmethod
def setUpClass(self):
super(TestMultiInstance, self).setUpClass()
import nest
self.nest = nest
config = JSONConfig(file=single_neuron_config)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
self.hdf5 = self.scaffold.output_formatter.file
self.nest_adapter_0 = self.scaffold.get_simulation(
"test_single_neuron")
# When another test errors, the lock might remain, and all locking tests fail
self.nest_adapter_0.delete_lock()
self.nest_adapter_1 = self.scaffold.create_adapter(
"test_single_neuron")
self.nest_adapter_2 = self.scaffold.create_adapter(
"test_single_neuron")
self.nest_adapter_multi_1 = self.scaffold.create_adapter(
"test_single_neuron")
self.nest_adapter_multi_1.enable_multi("first")
self.nest_adapter_multi_1b = self.scaffold.create_adapter(
"test_single_neuron")
self.nest_adapter_multi_1b.enable_multi("first")
self.nest_adapter_multi_2 = self.scaffold.create_adapter(
"test_single_neuron")
self.nest_adapter_multi_2.enable_multi("second")
def tearDown(self):
# Clean up any remaining locks to keep the test functions independent.
# Otherwise a chain reaction of failures is evoked.
self.nest_adapter_0.delete_lock()
def test_single_instance_unwanted_usage(self):
# Test AdapterError when trying to unlock unlocked adapter
self.assertRaises(AdapterError, self.nest_adapter_0.release_lock)
# Test whether the scaffold throws an AdapterError when the same
# adapter is prepared twice.
self.nest_adapter_0.prepare()
self.assertRaises(AdapterError, self.nest_adapter_0.prepare)
self.nest_adapter_0.release_lock()
self.nest_adapter_0.reset()
def test_single_instance_single_lock(self):
self.nest_adapter_1.reset()
# Lock kernel. Prepare adapter and thereby lock NEST kernel
self.nest_adapter_1.prepare()
lock_data = self.nest_adapter_1.read_lock()
self.assertEqual(lock_data["multi"], False)
self.assertEqual(self.nest_adapter_1.multi, False)
self.assertEqual(self.nest_adapter_1.has_lock, True)
# Release lock.
self.nest_adapter_1.release_lock()
self.assertEqual(self.nest_adapter_1.read_lock(), None)
self.assertEqual(self.nest_adapter_1.has_lock, False)
self.nest_adapter_1.reset()
def test_multi_instance_single_lock(self):
# Test that a 2nd single-instance adapter can't manage a locked kernel.
self.nest_adapter_1.prepare()
self.assertRaises(KernelLockedError, self.nest_adapter_2.prepare)
self.assertEqual(self.nest_adapter_2.is_prepared, False)
self.nest_adapter_1.release_lock()
self.nest_adapter_1.reset()
self.nest_adapter_2.reset()
def test_single_instance_multi_lock(self):
self.nest_adapter_multi_1.reset()
# Test functionality of the multi lock.
self.nest_adapter_multi_1.prepare()
lock_data = self.nest_adapter_multi_1.read_lock()
self.assertEqual(self.nest_adapter_multi_1.suffix, "first")
self.assertEqual(lock_data["multi"], True)
self.assertEqual(lock_data["suffixes"][0],
self.nest_adapter_multi_1.suffix)
self.assertEqual(self.nest_adapter_multi_1.multi, True)
self.assertEqual(self.nest_adapter_multi_1.is_prepared, True)
self.assertEqual(self.nest_adapter_multi_1.has_lock, True)
self.nest_adapter_multi_1.release_lock()
self.assertEqual(self.nest_adapter_multi_1.multi, True)
self.assertEqual(self.nest_adapter_multi_1.has_lock, False)
self.nest_adapter_multi_1.reset()
self.assertEqual(self.nest_adapter_multi_1.is_prepared, False)
def test_multi_instance_multi_lock(self):
# Test functionality of the multi lock.
self.nest_adapter_multi_1.prepare()
# Test that we have 1 lock.
lock_data = self.nest_adapter_multi_1.read_lock()
# Check multi instance multi lock
self.nest_adapter_multi_2.cell_models["test_cell"].parameters[
"t_ref"] = 3.0
self.nest_adapter_multi_2.prepare()
# Check that we have 2 locks
lock_data = self.nest_adapter_multi_1.read_lock()
self.assertEqual(len(lock_data["suffixes"]), 2)
# Test that we set the right parameters on the right classes.
try:
params = self.nest.GetDefaults("test_cell_first")
except Exception as e:
self.fail("First suffixed NEST models not found")
try:
params = self.nest.GetDefaults("test_cell_second")
except Exception as e:
self.fail("Second suffixed NEST models not found")
# Test that the adapters have the correct nest_identifiers
id1 = self.nest_adapter_multi_1.cell_models[
"test_cell"].nest_identifiers
id2 = self.nest_adapter_multi_2.cell_models[
"test_cell"].nest_identifiers
self.assertEqual(id1, [1, 2, 3, 4])
self.assertEqual(id2, [5, 6, 7, 8])
# Test that the adapter nodes have the right model
self.assertTrue(
all(
map(
lambda x: str(x["model"]) == "test_cell_first",
self.nest.GetStatus(id1),
)))
self.assertTrue(
all(
map(
lambda x: str(x["model"]) == "test_cell_second",
self.nest.GetStatus(id2),
)))
# Test that the adapter nodes have the right differential parameter t_ref
self.assertTrue(
all(map(lambda x: x["t_ref"] == 1.5, self.nest.GetStatus(id1))))
self.assertTrue(
all(map(lambda x: x["t_ref"] == 3.0, self.nest.GetStatus(id2))))
# Check duplicate suffixes
self.assertRaises(SuffixTakenError, self.nest_adapter_multi_1b.prepare)
self.nest_adapter_multi_1.release_lock()
self.nest_adapter_multi_1.reset()
# Test that we have 1 lock again after release.
lock_data = self.nest_adapter_multi_1.read_lock()
self.assertEqual(lock_data["suffixes"][0], "second")
self.nest_adapter_multi_2.release_lock()
self.nest_adapter_multi_2.reset()
def setUpClass(self):
super(TestSingleTypeCompilation, self).setUpClass()
config = JSONConfig(file=single_neuron_config)
self.scaffold = Scaffold(config)
self.scaffold.compile_network()
