Source code for nest.tests.test_connect_fixed_total_number
# -*- coding: utf-8 -*-
#
# test_connect_fixed_total_number.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# NEST is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with NEST. If not, see <http://www.gnu.org/licenses/>.
import numpy as np
import unittest
import scipy.stats
from . import test_connect_helpers as hf
from .test_connect_parameters import TestParams
[docs]class TestFixedTotalNumber(TestParams):
# specify connection pattern and specific params
rule = 'fixed_total_number'
conn_dict = {'rule': rule}
# sizes of source-, target-population and outdegree for connection test
N1 = 50
N2 = 70
Nconn = 100
conn_dict['N'] = Nconn
# sizes of source-, target-population and total number of connections for
# statistical test
N_s = 20
N_t = 20
N = 100
# Critical values and number of iterations of two level test
stat_dict = {'alpha2': 0.05, 'n_runs': 150}
# tested on each mpi process separately
[docs] def testErrorMessages(self):
got_error = False
conn_params = self.conn_dict.copy()
conn_params['autapses'] = True
conn_params['multapses'] = False
conn_params['N'] = self.N1 * self.N2 + 1
try:
self.setUpNetwork(conn_params)
except hf.nest.NESTError:
got_error = True
self.assertTrue(got_error)
[docs] def testTotalNumberOfConnections(self):
conn_params = self.conn_dict.copy()
self.setUpNetwork(conn_params)
total_conn = len(hf.nest.GetConnections(self.pop1, self.pop2))
hf.mpi_assert(total_conn, self.Nconn, self)
# make sure no connections were drawn from the target to the source
# population
M = hf.get_connectivity_matrix(self.pop2, self.pop1)
M_none = np.zeros((len(self.pop1), len(self.pop2)))
hf.mpi_assert(M, M_none, self)
[docs] def testStatistics(self):
conn_params = self.conn_dict.copy()
conn_params['autapses'] = True
conn_params['multapses'] = True
conn_params['N'] = self.N
for fan in ['in', 'out']:
expected = hf.get_expected_degrees_totalNumber(
self.N, fan, self.N_s, self.N_t)
pvalues = []
for i in range(self.stat_dict['n_runs']):
hf.reset_seed(123456 * i % 511, self.nr_threads)
self.setUpNetwork(conn_dict=conn_params,
N1=self.N_s, N2=self.N_t)
degrees = hf.get_degrees(fan, self.pop1, self.pop2)
degrees = hf.gather_data(degrees)
if degrees is not None:
chi, p = hf.chi_squared_check(degrees, expected)
pvalues.append(p)
hf.mpi_barrier()
if degrees is not None:
ks, p = scipy.stats.kstest(pvalues, 'uniform')
self.assertTrue(p > self.stat_dict['alpha2'])
[docs] def testAutapsesTrue(self):
conn_params = self.conn_dict.copy()
N = 3
# test that autapses exist
conn_params['N'] = N * N * N
conn_params['autapses'] = True
pop = hf.nest.Create('iaf_psc_alpha', N)
hf.nest.Connect(pop, pop, conn_params)
# make sure all connections do exist
M = hf.get_connectivity_matrix(pop, pop)
M = hf.gather_data(M)
if M is not None:
self.assertTrue(np.sum(np.diag(M)) > N)
[docs] def testAutapsesFalse(self):
conn_params = self.conn_dict.copy()
N = 3
# test that autapses were excluded
conn_params['N'] = N * (N - 1)
conn_params['autapses'] = False
pop = hf.nest.Create('iaf_psc_alpha', N)
hf.nest.Connect(pop, pop, conn_params)
# make sure all connections do exist
M = hf.get_connectivity_matrix(pop, pop)
hf.mpi_assert(np.diag(M), np.zeros(N), self)
[docs]def suite():
suite = unittest.TestLoader().loadTestsFromTestCase(TestFixedTotalNumber)
return suite
[docs]def run():
runner = unittest.TextTestRunner(verbosity=2)
runner.run(suite())
if __name__ == '__main__':
run()