Merge pull request #2985 from janskaar/sli2py_iaf_psc_exp

Port test_iaf_psc_exp to py

testsuite/pytests/sli2py_neurons/test_iaf_psc_exp.py

@@ -0,0 +1,101 @@
+# -*- coding: utf-8 -*-
+#
+# test_iaf_psc_exp.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/>.
+
+"""
+Name: testsuite::test_iaf_psc_exp
+
+Synopsis: (test_iaf_psc_exp) run -> compares response to current step with analytical solution
+
+Description:
+A DC current is injected into the neuron using a current generator
+device. The membrane potential as well as the spiking activity are
+recorded by corresponding devices.
+
+It can be observed how the current charges the membrane, a spike
+is emitted, the neuron becomes absolute refractory, and finally
+starts to recover.
+
+The timing of the various events on the simulation grid is of
+particular interest and crucial for the consistency of the
+simulation scheme.
+
+Although 0.1 cannot be represented in the IEEE double data type, it
+is safe to simulate with a resolution (computation step size) of 0.1
+ms because by default nest is built with a timebase enabling exact
+representation of 0.1 ms.
+
+Author:  July 2004, Diesmann
+     March 2006, Moritz Helias
+"""
+
+import nest
+import numpy as np
+import numpy.testing as nptest
+import pytest
+
+
+def test_iaf_psc_exp_dc_input():
+    dt = 0.1
+    dc_amp = 1000.0
+
+    nest.ResetKernel()
+    nest.set(resolution=dt, local_num_threads=1)
+
+    dc_gen = nest.Create("dc_generator", {"amplitude": dc_amp})
+    nrn = nest.Create("iaf_psc_exp", 1)
+    vm = nest.Create("voltmeter", {"interval": 0.1})
+
+    syn_spec = {"synapse_model": "static_synapse", "weight": 1.0, "delay": dt}
+    nest.Connect(dc_gen, nrn, syn_spec=syn_spec)
+    nest.Connect(vm, nrn, syn_spec=syn_spec)
+
+    nest.Simulate(8.0)
+
+    times = vm.get("events", "times")
+    times -= dt  # account for delay to multimeter
+
+    tau_m = nrn.get("tau_m")
+    R = tau_m / nrn.get("C_m")
+
+    # array for analytical solution
+    V_m_analytical = np.empty_like(times)
+    V_m_analytical[:] = nrn.get("E_L")
+
+    # first index for which the DC current is received by neuron.
+    # DC current will be integrated from this time step
+    start_index = 1
+
+    # analytical solution without delay and threshold
+    vm_soln = nrn.get("E_L") + (1 - np.exp(-times / tau_m)) * R * dc_amp
+
+    # rise until threshold
+    V_m_analytical[start_index:] = vm_soln[:-start_index]
+
+    # set refractory potential
+    crossing_ind = (V_m_analytical > nrn.get("V_th")).argmax()
+    num_ref = int(nrn.get("t_ref") / dt)
+    V_m_analytical[crossing_ind : crossing_ind + num_ref] = nrn.get("V_reset")
+
+    # rise after refractory period
+    num_inds = len(times) - crossing_ind - num_ref
+    V_m_analytical[crossing_ind + num_ref :] = vm_soln[:num_inds]
+
+    nptest.assert_array_almost_equal(V_m_analytical, vm.get("events", "V_m"))