# -*- coding: utf-8 -*-
#
# test_rate_neuron_communication.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/>.
# This test checks interactions between rate neurons, i.e.
# the delay, weight and nonlinearities of rate neurons.
import nest
import unittest
import math
import numpy as np
[docs]def H(x):
return 0.5 * (np.sign(x) + 1.)
[docs]@nest.check_stack
class RateNeuronCommunicationTestCase(unittest.TestCase):
"""Check rate_neuron"""
[docs] def setUp(self):
# test parameter
self.rtol = 0.05
# neuron parameters
self.neuron_params = {'tau': 5., 'std': 0.}
self.neuron_params2 = self.neuron_params.copy()
self.neuron_params2.update({'mult_coupling': True})
self.neuron_params3 = self.neuron_params.copy()
self.neuron_params3.update({'rectify_output': True, 'rate': 1.})
self.drive = 1.5
self.delay = 2.
self.weight = 0.5
# simulation parameters
self.simtime = 100.
self.dt = 0.1
nest.set_verbosity('M_WARNING')
nest.ResetKernel()
nest.SetKernelStatus(
{'resolution': self.dt, 'use_wfr': True, 'print_time': True})
# set up rate neuron network
self.rate_neuron_drive = nest.Create(
'lin_rate_ipn', params={'rate': self.drive,
'mean': self.drive, 'std': 0.})
self.rate_neuron_negative_drive = nest.Create(
'lin_rate_ipn', params={'rate': -self.drive,
'mean': -self.drive, 'std': 0.})
self.rate_neuron_1 = nest.Create(
'lin_rate_ipn', params=self.neuron_params)
self.rate_neuron_2 = nest.Create(
'tanh_rate_ipn', params=self.neuron_params)
self.rate_neuron_3 = nest.Create(
'threshold_lin_rate_ipn', params=self.neuron_params)
self.rate_neuron_4 = nest.Create(
'lin_rate_ipn', params=self.neuron_params2)
self.rate_neuron_5 = nest.Create(
'lin_rate_ipn', params=self.neuron_params3)
self.parrot_neuron = nest.Create(
'rate_transformer_sigmoid_gg_1998')
self.multimeter = nest.Create("multimeter",
params={'record_from': ['rate'],
'interval': self.dt})
# record rates and connect neurons
self.neurons = self.rate_neuron_1 + \
self.rate_neuron_2 + self.rate_neuron_3 + self.rate_neuron_4 + \
self.rate_neuron_5
nest.Connect(
self.multimeter, self.neurons, 'all_to_all', {'delay': 10.})
nest.Connect(
self.multimeter, self.parrot_neuron, 'all_to_all', {'delay': 10.})
nest.Connect(self.rate_neuron_drive, self.rate_neuron_1,
'all_to_all', {'model': 'rate_connection_delayed',
'delay': self.delay,
'weight': self.weight})
nest.Connect(self.rate_neuron_drive, self.rate_neuron_2,
'all_to_all', {'model': 'rate_connection_instantaneous',
'weight': self.weight})
nest.Connect(self.rate_neuron_drive, self.rate_neuron_3,
'all_to_all', {'model': 'rate_connection_instantaneous',
'weight': self.weight})
nest.Connect(self.rate_neuron_drive, self.rate_neuron_4,
'all_to_all', {'model': 'rate_connection_instantaneous',
'weight': self.weight})
nest.Connect(self.rate_neuron_negative_drive, self.rate_neuron_5,
'all_to_all', {'model': 'rate_connection_instantaneous',
'weight': self.weight})
nest.Connect(self.rate_neuron_drive, self.parrot_neuron,
'all_to_all', {'model': 'rate_connection_instantaneous',
'weight': self.weight})
[docs] def test_RateNeuronDelay(self):
"""Check the delay of the connection"""
# simulate
nest.Simulate(self.simtime)
# get noise from rate neuron
events = nest.GetStatus(self.multimeter)[0]["events"]
senders = events['senders']
times = events['times'][np.where(senders == self.rate_neuron_1)]
rate_1 = events['rate'][np.where(senders == self.rate_neuron_1)]
rate_2 = events['rate'][np.where(senders == self.rate_neuron_2)]
delay_rate_1 = times[np.where(rate_1 > 0)[0][0]]
test_delay_1 = self.delay + self.dt
self.assertTrue(np.isclose(delay_rate_1, test_delay_1))
self.assertTrue(rate_2[0] > 0.)
[docs] def test_RateNeuronWeight(self):
"""Check the weight of the connection"""
# simulate
nest.Simulate(self.simtime)
# get noise from rate neuron
events = nest.GetStatus(self.multimeter)[0]["events"]
senders = events['senders']
rate_1 = events['rate'][np.where(senders == self.rate_neuron_1)]
value = rate_1[-1]
value_test = self.drive * self.weight
self.assertTrue(np.isclose(value, value_test))
[docs] def test_RateNeuronNL(self):
"""Check the non-linearity of the neuron"""
gs = [1., 2.]
lin_sums = [True, False]
for g, ls in zip(gs, lin_sums):
nest.SetStatus(self.neurons, {'g': g, 'linear_summation': ls})
# simulate
nest.Simulate(self.simtime)
# get noise from rate neuron
events = nest.GetStatus(self.multimeter)[0]["events"]
senders = events['senders']
rate_1 = events['rate'][
np.where(senders == self.rate_neuron_1)][-1]
rate_2 = events['rate'][
np.where(senders == self.rate_neuron_2)][-1]
rate_3 = events['rate'][
np.where(senders == self.rate_neuron_3)][-1]
rate_4 = events['rate'][
np.where(senders == self.rate_neuron_4)][-1]
rates = np.array([rate_1, rate_2, rate_3, rate_4])
# for multiplicative coupling
a = g * self.drive * self.weight * \
nest.GetStatus(self.rate_neuron_4)[0]['g_ex']
theta = nest.GetStatus(self.rate_neuron_4)[0]['theta_ex']
if ls:
rates_test = np.array(
[g * self.drive * self.weight,
np.tanh(g * self.drive * self.weight),
g * self.drive * self.weight * H(self.drive *
self.weight),
a * theta / (1 + a)])
else:
rates_test = np.array(
[g * self.drive * self.weight,
self.weight * np.tanh(g * self.drive),
self.weight * self.drive * g * H(self.drive),
a * theta / (1 + a)])
self.assertTrue(np.allclose(rates, rates_test))
[docs] def test_RectifyOutput(self):
"""Check the rectification of the output"""
# simulate
nest.Simulate(self.simtime)
# get activity from rate neuron
events = nest.GetStatus(self.multimeter)[0]["events"]
senders = events['senders']
rate_5 = events['rate'][np.where(senders == self.rate_neuron_5)]
value = rate_5[-1]
value_test = 0.
self.assertTrue(np.isclose(value, value_test))
[docs] def test_ParrotRateNeuron(self):
"""Check the parrot rate neuron with sigm non-linearity"""
nest.SetStatus(self.parrot_neuron, {'g': 0.1})
# simulate
nest.Simulate(self.simtime)
# get activity from rate neuron
events = nest.GetStatus(self.multimeter)[0]["events"]
senders = events['senders']
parrot_rate = events['rate'][np.where(senders == self.parrot_neuron)]
value = parrot_rate[-1]
g = nest.GetStatus(self.parrot_neuron)[0]['g']
value_test = (g * self.weight * self.drive)**4 / \
(0.1**4 + (g * self.weight * self.drive)**4)
self.assertTrue(np.isclose(value, value_test))
[docs]def suite():
# makeSuite is sort of obsolete http://bugs.python.org/issue2721
# using loadTestsFromTestCase instead.
suite1 = unittest.TestLoader().loadTestsFromTestCase(
RateNeuronCommunicationTestCase)
return unittest.TestSuite([suite1])
[docs]def run():
runner = unittest.TextTestRunner(verbosity=2)
runner.run(suite())
if __name__ == "__main__":
run()
