def setUp(self):
sim.setup(num_processes=2, rank=1, min_delay=0.123)
self.p1 = sim.Population(4, sim.IF_cond_exp(), structure=space.Line())
self.p2 = sim.Population(5, sim.HH_cond_exp(), structure=space.Line())
assert_array_equal(self.p2._mask_local,
numpy.array([0, 1, 0, 1, 0], dtype=bool))
connection_list = [
(0, 0, 0.0, 1.0),
(3, 0, 0.0, 1.0),
(2, 3, 0.0, 1.0), # local
(2, 2, 0.0, 1.0),
(0, 1, 0.0, 1.0), # local
]
list_connector = connectors.FromListConnector(connection_list)
syn = sim.StaticSynapse()
self.ref_prj = sim.Projection(self.p1, self.p2, list_connector, syn)
self.orig_gather_dict = recording.gather_dict # create reference to original function
# The gather_dict function in recording needs to be temporarily replaced so it can work with
# a mock version of the function to avoid it throwing an mpi4py import error when setting
# the rank in pyNN.mock by hand to > 1
def mock_gather_dict(D, all=False):
return D
recording.gather_dict = mock_gather_dict
def test_connect_with_empty_list(self, sim=sim):
connection_list = []
C = connectors.FromListConnector(connection_list)
syn = sim.StaticSynapse()
prj = sim.Projection(self.p1, self.p2, C, syn)
self.assertEqual(prj.get(["weight", "delay"], format='list'),
[])
def test_connect_unique_connection_neuron_0_to_neuron_0(self, sim=sim):
connection_list = [
(0, 0, 0.1, 0.18)
]
C = connectors.FromListConnector(connection_list)
syn = sim.StaticSynapse()
prj = sim.Projection(self.p1, self.p2, C, syn)
self.assertEqual(prj.get(["weight", "delay"], format='list'),
[(0, 0, 0.1, 0.18)])
def test_connect_with_out_of_range_index(self):
connection_list = [
(0, 0, 0.1, 0.1), # 17 -> 79
(3, 0, 0.2, 0.11), # 20 -> 79
(2, 3, 0.3, 0.12), # 19 -> 82 local
(5, 2, 0.4, 0.13), # NON-EXISTENT -> 81
(0, 1, 0.5, 0.14), # 17 -> 80 local
]
C = connectors.FromListConnector(connection_list)
assert_raises(errors.ConnectionError, C.connect, self.prj)
def test_connect_with_out_of_range_index(self):
connection_list = [
(0, 0, 0.1, 0.1),
(3, 0, 0.2, 0.11),
(2, 3, 0.3, 0.12), # local
(5, 1, 0.4, 0.13), # NON-EXISTENT
(0, 1, 0.5, 0.14), # local
]
C = connectors.FromListConnector(connection_list)
syn = sim.StaticSynapse()
self.assertRaises(errors.ConnectionError, sim.Projection, self.p1, self.p2, C, syn)
def test_connect_with_valid_list(self):
connection_list = [
(0, 0, 0.1, 0.1),
(3, 0, 0.2, 0.11),
(2, 3, 0.3, 0.12), # local
(2, 2, 0.4, 0.13),
(0, 1, 0.5, 0.14), # local
]
C = connectors.FromListConnector(connection_list)
syn = sim.StaticSynapse()
prj = sim.Projection(self.p1, self.p2, C, syn)
self.assertEqual(prj.get(["weight", "delay"], format='list', gather=False), # use gather False because we are faking the MPI
[(0, 1, 0.5, 0.14),
(2, 3, 0.3, 0.12)])
def test_with_plastic_synapse(self):
connection_list = [
(0, 0, 0.1, 0.1, 100, 400),
(3, 0, 0.2, 0.11, 101, 500),
(2, 3, 0.3, 0.12, 102, 600), # local
(2, 2, 0.4, 0.13, 103, 700),
(0, 1, 0.5, 0.14, 104, 800), # local
]
C = connectors.FromListConnector(connection_list, column_names=["weight", "delay", "U", "tau_rec"])
syn = sim.TsodyksMarkramSynapse(U=99, tau_facil=88.8)
prj = sim.Projection(self.p1, self.p2, C, syn)
self.assertEqual(prj.get(["weight", "delay", "tau_facil", "tau_rec", "U"], format='list', gather=False), # use gather False because we are faking the MPI
[(0, 1, 0.5, 0.14, 88.8, 800.0, 104.0),
(2, 3, 0.3, 0.12, 88.8, 600.0, 102.0)])
def test_connect_with_valid_list(self, sim=sim):
connection_list = [
(0, 0, 0.1, 0.18),
(3, 0, 0.2, 0.17),
(2, 3, 0.3, 0.16), # local
(2, 2, 0.4, 0.15),
(0, 1, 0.5, 0.14), # local
]
C = connectors.FromListConnector(connection_list)
syn = sim.StaticSynapse()
prj = sim.Projection(self.p1, self.p2, C, syn)
self.assertEqual(prj.get(["weight", "delay"], format='list'),
[(0, 0, 0.1, 0.18),
(3, 0, 0.2, 0.17),
(0, 1, 0.5, 0.14),
(2, 2, 0.4, 0.15),
(2, 3, 0.3, 0.16)])
def test_with_stdp_synapse(self, sim=sim):
connection_list = [
(0, 0, 0.1, 0.1, 10.0, 0.4),
(3, 0, 0.2, 0.11, 10.1, 0.5),
(2, 3, 0.3, 0.12, 10.2, 0.6), # local
(2, 2, 0.4, 0.13, 10.3, 0.7),
(0, 1, 0.5, 0.14, 10.4, 0.8), # local
]
C = connectors.FromListConnector(connection_list, column_names=[
"weight", "delay", "tau_plus", "w_max"])
syn = sim.STDPMechanism(timing_dependence=sim.SpikePairRule(tau_plus=12.3, tau_minus=33.3),
weight_dependence=sim.MultiplicativeWeightDependence(w_max=1.11),
weight=0.321, delay=0.2)
prj = sim.Projection(self.p1, self.p2, C, syn)
self.assertEqual(prj.get(["weight", "delay", "tau_plus", "tau_minus", "w_max"], format='list', gather=False), # use gather False because we are faking the MPI
[(0, 1, 0.5, 0.14, 10.4, 33.3, 0.8),
(2, 3, 0.3, 0.12, 10.2, 33.3, 0.6)])
def test_connect_with_valid_list(self):
connection_list = [
(0, 0, 0.1, 0.1), # 17 -> 79
(3, 0, 0.2, 0.11), # 20 -> 79
(2, 3, 0.3, 0.12), # 19 -> 82 local
(2, 2, 0.4, 0.13), # 19 -> 81
(0, 1, 0.5, 0.14), # 17 -> 80 local
]
C = connectors.FromListConnector(connection_list)
C.progressbar = Mock()
C.progression = Mock()
C.connect(self.prj)
# note that ListConnector does not filter out non-local connections
assert_equal(self.prj.connections, [(17, 79, 0.1, 0.1),
(17, 80, 0.5, 0.14),
(19, 82, 0.3, 0.12),
(19, 81, 0.4, 0.13),
(20, 79, 0.2, 0.11)])
