def testConnectivity(self):
self.setUpNetwork(self.conn_dict)
# make sure all connections do exist
M = connect_test_base.get_connectivity_matrix(self.pop1, self.pop2)
connect_test_base.mpi_assert(M, np.identity(self.N), self)
# make sure no connections were drawn from the target to the source
# population
M = connect_test_base.get_connectivity_matrix(self.pop2, self.pop1)
connect_test_base.mpi_assert(M, np.zeros((self.N, self.N)), self)
def testConnectivity(self):
self.setUpNetwork(self.conn_dict)
# make sure all connections do exist
M = connect_test_base.get_connectivity_matrix(self.pop1, self.pop2)
M_all = np.ones((len(self.pop2), len(self.pop1)))
connect_test_base.mpi_assert(M, M_all, self)
# make sure no connections were drawn from the target to the source
# population
M = connect_test_base.get_connectivity_matrix(self.pop2, self.pop1)
M_none = np.zeros((len(self.pop1), len(self.pop2)))
connect_test_base.mpi_assert(M, M_none, self)
def testSymmetricFlag(self):
conn_dict_symmetric = self.conn_dict.copy()
conn_dict_symmetric['make_symmetric'] = True
self.setUpNetwork(conn_dict_symmetric)
M1 = connect_test_base.get_connectivity_matrix(self.pop1, self.pop2)
M2 = connect_test_base.get_connectivity_matrix(self.pop2, self.pop1)
# test that connections were created in both directions
connect_test_base.mpi_assert(
M1, np.transpose(connect_test_base.gather_data(M2)), self)
# test that no other connections were created
connect_test_base.mpi_assert(M1,
np.zeros_like(M1) + np.identity(self.N),
self)
def testInDegree(self):
conn_params = self.conn_dict.copy()
conn_params['allow_autapses'] = False
conn_params['allow_multapses'] = False
self.setUpNetwork(conn_params)
# make sure the indegree is right
M = connect_test_base.get_connectivity_matrix(self.pop1, self.pop2)
inds = np.sum(M, axis=1)
connect_test_base.mpi_assert(inds, self.Nin * np.ones(self.N2), self)
# make sure no connections were drawn from the target to the source
# population
M = connect_test_base.get_connectivity_matrix(self.pop2, self.pop1)
M_none = np.zeros((len(self.pop1), len(self.pop2)))
connect_test_base.mpi_assert(M, M_none, self)
def testTotalNumberOfConnections(self):
conn_params = self.conn_dict.copy()
self.setUpNetwork(conn_params)
total_conn = len(nest.GetConnections(self.pop1, self.pop2))
connect_test_base.mpi_assert(total_conn, self.Nconn, self)
# make sure no connections were drawn from the target to the source
# population
M = connect_test_base.get_connectivity_matrix(self.pop2, self.pop1)
M_none = np.zeros((len(self.pop1), len(self.pop2)))
connect_test_base.mpi_assert(M, M_none, self)
def testAutapsesFalse(self):
conn_params = self.conn_dict.copy()
N = 10
# test that autapses were excluded
conn_params['p'] = 1. - 1. / N
conn_params['allow_autapses'] = False
pop = nest.Create('iaf_psc_alpha', N)
nest.Connect(pop, pop, conn_params)
M = connect_test_base.get_connectivity_matrix(pop, pop)
connect_test_base.mpi_assert(np.diag(M), np.zeros(N), self)
def testAutapsesFalse(self):
conn_params = self.conn_dict.copy()
N = 3
# test that autapses were excluded
conn_params['N'] = N * (N - 1)
conn_params['allow_autapses'] = False
pop = nest.Create('iaf_psc_alpha', N)
nest.Connect(pop, pop, conn_params)
# make sure all connections do exist
M = connect_test_base.get_connectivity_matrix(pop, pop)
connect_test_base.mpi_assert(np.diag(M), np.zeros(N), self)
def testAutapsesTrue(self):
conn_params = self.conn_dict.copy()
N = 10
conn_params['allow_multapses'] = False
# test that autapses exist
conn_params['p'] = 1.
conn_params['allow_autapses'] = True
pop = nest.Create('iaf_psc_alpha', N)
nest.Connect(pop, pop, conn_params)
# make sure all connections do exist
M = connect_test_base.get_connectivity_matrix(pop, pop)
connect_test_base.mpi_assert(np.diag(M), np.ones(N), self)
def testMultapsesFalse(self):
conn_params = self.conn_dict.copy()
N = 3
conn_params['allow_autapses'] = True
# test that no multapses exist
conn_params['indegree'] = N
conn_params['allow_multapses'] = False
pop = nest.Create('iaf_psc_alpha', N)
nest.Connect(pop, pop, conn_params)
M = connect_test_base.get_connectivity_matrix(pop, pop)
M = connect_test_base.gather_data(M)
if M is not None:
self.assertTrue(M.flatten, np.ones(N * N))
def testAutapsesTrue(self):
conn_params = self.conn_dict.copy()
N = 3
# test that autapses exist
conn_params['N'] = N * N * N
conn_params['allow_autapses'] = True
pop = nest.Create('iaf_psc_alpha', N)
nest.Connect(pop, pop, conn_params)
# make sure all connections do exist
M = connect_test_base.get_connectivity_matrix(pop, pop)
M = connect_test_base.gather_data(M)
if M is not None:
self.assertTrue(np.sum(np.diag(M)) > N)
def testMakeSymmetric(self):
conn_params = self.conn_dict.copy()
N = 100
# test that all connections are symmetric
conn_params['make_symmetric'] = True
nest.ResetKernel()
pop = nest.Create('iaf_psc_alpha', N)
nest.Connect(pop, pop, conn_params)
M = connect_test_base.get_connectivity_matrix(pop, pop)
print(M)
M_all = connect_test_base.gather_data(M)
print(M_all)
if M_all is not None:
self.assertTrue(np.array_equal(M_all, M_all.T))