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Refactor NEST integration test #1224

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93b4a3c
refactor NEST integration test
Jun 11, 2025
88f2f42
Merge remote-tracking branch 'upstream/master' into nest_integration_…
Jun 16, 2025
6e8c029
Merge remote-tracking branch 'upstream/master' into nest_integration_…
Jul 15, 2025
0e38d25
refactor NEST integration test
Jul 15, 2025
fbe2645
refactor NEST integration test
Jul 15, 2025
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91 changes: 50 additions & 41 deletions tests/nest_tests/nest_integration_test.py → ...sts/test_nest_neuron_model_equivalence.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# -*- coding: utf-8 -*-
#
# nest_integration_test.py
# test_nest_neuron_model_equivalence.py
#
# This file is part of NEST.
#
Expand Down Expand Up @@ -45,7 +45,7 @@ def get_model_doc_title(model_fname: str):

@pytest.mark.skipif(NESTTools.detect_nest_version().startswith("v2"),
reason="This test does not support NEST 2")
class TestNestIntegration:
class TestNESTNeuronModelEquivalence:

def generate_all_models(self):
codegen_opts = {}
Expand Down Expand Up @@ -89,7 +89,7 @@ def generate_all_models(self):
suffix="_alt_int_nestml",
codegen_opts=alt_codegen_opts)

def test_nest_integration(self):
def test_nest_neuron_model_equivalence(self):
self.generate_all_models()
nest.Install("nestml_allmodels_module")
nest.Install("nestml_alt_allmodels_module")
Expand Down Expand Up @@ -179,19 +179,19 @@ def _test_model_equivalence_curr_inj(self, nest_model_name, nestml_model_name, g
# ResetKernel() does not unload modules for NEST Simulator < v3.7; ignore exception if module is already loaded on earlier versions
pass

neuron1 = nest.Create(nest_model_name, params=nest_model_parameters)
neuron2 = nest.Create(nestml_model_name, params=nestml_model_parameters)
nest_neuron = nest.Create(nest_model_name, params=nest_model_parameters)
nestml_neuron = nest.Create(nestml_model_name, params=nestml_model_parameters)
if model_initial_state is not None:
nest.SetStatus(neuron1, model_initial_state)
nest.SetStatus(neuron2, model_initial_state)
nest.SetStatus(nest_neuron, model_initial_state)
nest.SetStatus(nestml_neuron, model_initial_state)

# if gsl_error_tol is not None:
# nest.SetStatus(neuron2, {"gsl_error_tol": gsl_error_tol})
# nest.SetStatus(nestml_neuron, {"gsl_error_tol": gsl_error_tol})

dc = nest.Create("dc_generator", params={"amplitude": 0.})

nest.Connect(dc, neuron1)
nest.Connect(dc, neuron2)
nest.Connect(dc, nest_neuron)
nest.Connect(dc, nestml_neuron)

multimeter1 = nest.Create("multimeter")
multimeter2 = nest.Create("multimeter")
Expand All @@ -200,8 +200,8 @@ def _test_model_equivalence_curr_inj(self, nest_model_name, nestml_model_name, g
nest.SetStatus(multimeter1, {"record_from": [V_m_specifier]})
nest.SetStatus(multimeter2, {"record_from": [V_m_specifier]})

nest.Connect(multimeter1, neuron1)
nest.Connect(multimeter2, neuron2)
nest.Connect(multimeter1, nest_neuron)
nest.Connect(multimeter2, nestml_neuron)

if NESTTools.detect_nest_version().startswith("v2"):
sd_reference = nest.Create("spike_detector")
Expand All @@ -210,8 +210,8 @@ def _test_model_equivalence_curr_inj(self, nest_model_name, nestml_model_name, g
sd_reference = nest.Create("spike_recorder")
sd_testant = nest.Create("spike_recorder")

nest.Connect(neuron1, sd_reference)
nest.Connect(neuron2, sd_testant)
nest.Connect(nest_neuron, sd_reference)
nest.Connect(nestml_neuron, sd_testant)

nest.Simulate(t_pulse_start)
dc.amplitude = I_stim * 1E12 # 1E12: convert A to pA
Expand All @@ -236,7 +236,7 @@ def _test_model_equivalence_curr_inj(self, nest_model_name, nestml_model_name, g
for _ax in ax:
_ax.legend(loc="upper right")
_ax.grid()
plt.savefig("/tmp/nestml_nest_integration_test_pulse_[" + nest_model_name + "]_[" + nestml_model_name + "]_[I_stim=" + str(I_stim) + "].png")
plt.savefig("/tmp/test_nest_neuron_model_equivalence_pulse_[" + nest_model_name + "]_[" + nestml_model_name + "]_[I_stim=" + str(I_stim) + "].png")
plt.close(fig)

np.testing.assert_allclose(Vms1, Vms2)
Expand All @@ -262,19 +262,19 @@ def _test_model_equivalence_fI_curve(self, nest_model_name, nestml_model_name, g
# ResetKernel() does not unload modules for NEST Simulator < v3.7; ignore exception if module is already loaded on earlier versions
pass

neuron1 = nest.Create(nest_model_name, params=nest_model_parameters)
neuron2 = nest.Create(nestml_model_name, params=nestml_model_parameters)
nest_neuron = nest.Create(nest_model_name, params=nest_model_parameters)
nestml_neuron = nest.Create(nestml_model_name, params=nestml_model_parameters)
if model_initial_state is not None:
nest.SetStatus(neuron1, model_initial_state)
nest.SetStatus(neuron2, model_initial_state)
nest.SetStatus(nest_neuron, model_initial_state)
nest.SetStatus(nestml_neuron, model_initial_state)

# if gsl_error_tol is not None:
# nest.SetStatus(neuron2, {"gsl_error_tol": gsl_error_tol})
# nest.SetStatus(nestml_neuron, {"gsl_error_tol": gsl_error_tol})

dc = nest.Create("dc_generator", params={"amplitude": 1E12 * I_stim}) # 1E12: convert A to pA

nest.Connect(dc, neuron1)
nest.Connect(dc, neuron2)
nest.Connect(dc, nest_neuron)
nest.Connect(dc, nestml_neuron)

multimeter1 = nest.Create("multimeter")
multimeter2 = nest.Create("multimeter")
Expand All @@ -283,8 +283,8 @@ def _test_model_equivalence_fI_curve(self, nest_model_name, nestml_model_name, g
nest.SetStatus(multimeter1, {"record_from": [V_m_specifier]})
nest.SetStatus(multimeter2, {"record_from": [V_m_specifier]})

nest.Connect(multimeter1, neuron1)
nest.Connect(multimeter2, neuron2)
nest.Connect(multimeter1, nest_neuron)
nest.Connect(multimeter2, nestml_neuron)

if NESTTools.detect_nest_version().startswith("v2"):
sd_reference = nest.Create("spike_detector")
Expand All @@ -293,8 +293,8 @@ def _test_model_equivalence_fI_curve(self, nest_model_name, nestml_model_name, g
sd_reference = nest.Create("spike_recorder")
sd_testant = nest.Create("spike_recorder")

nest.Connect(neuron1, sd_reference)
nest.Connect(neuron2, sd_testant)
nest.Connect(nest_neuron, sd_reference)
nest.Connect(nestml_neuron, sd_testant)

nest.Simulate(t_stop)

Expand All @@ -317,7 +317,7 @@ def _test_model_equivalence_fI_curve(self, nest_model_name, nestml_model_name, g
_ax.legend(loc="upper right")
_ax.grid()
fig.suptitle("Rate: " + str(rate_testant[i]) + " Hz")
plt.savefig("/tmp/nestml_nest_integration_test_subthreshold_[" + nest_model_name + "]_[" + nestml_model_name + "]_[I_stim=" + str(I_stim) + "].png")
plt.savefig("/tmp/test_nest_neuron_model_fI_curve_[" + nest_model_name + "]_[" + nestml_model_name + "]_[I_stim=" + str(I_stim) + "].png")
plt.close(fig)

if TEST_PLOTS:
Expand All @@ -333,7 +333,7 @@ def _test_model_equivalence_fI_curve(self, nest_model_name, nestml_model_name, g
_ax.grid()
_ax.set_ylabel("Firing rate [Hz]")
ax[1].set_xlabel("$I_{inj}$ [pA]")
plt.savefig("/tmp/nestml_nest_integration_test_subthreshold_[" + nest_model_name + "]_[" + nestml_model_name + "].png")
plt.savefig("/tmp/test_nest_neuron_model_equivalence_subthreshold_[" + nest_model_name + "]_[" + nestml_model_name + "].png")
plt.close(fig)

for figsize, fname_snip in zip([(8, 5), (4, 3)], ["", "_small"]):
Expand Down Expand Up @@ -365,26 +365,35 @@ def _test_model_equivalence_psc(self, nest_model_name, nestml_model_name, gsl_er
# ResetKernel() does not unload modules for NEST Simulator < v3.7; ignore exception if module is already loaded on earlier versions
pass

neuron1 = nest.Create(nest_model_name, params=nest_model_parameters)
neuron2 = nest.Create(nestml_model_name, params=nestml_model_parameters)
nest_neuron = nest.Create(nest_model_name, params=nest_model_parameters)
nestml_neuron = nest.Create(nestml_model_name, params=nestml_model_parameters)

if model_initial_state is not None:
nest.SetStatus(neuron1, model_initial_state)
nest.SetStatus(neuron2, model_initial_state)
nest.SetStatus(nest_neuron, model_initial_state)
nest.SetStatus(nestml_neuron, model_initial_state)

# if gsl_error_tol is not None:
# nest.SetStatus(neuron2, {"gsl_error_tol": gsl_error_tol})
# nest.SetStatus(nestml_neuron, {"gsl_error_tol": gsl_error_tol})

spikegenerator = nest.Create("spike_generator",
params={"spike_times": spike_times, "spike_weights": spike_weights})

nest.Connect(spikegenerator, neuron1, syn_spec=syn_spec)
nest.Connect(spikegenerator, neuron2, syn_spec=syn_spec)
nest.Connect(spikegenerator, nest_neuron, syn_spec=syn_spec)

if "receptor_types" in nestml_neuron.get().keys() and len(nestml_neuron.get("receptor_types")) > 1:
# this NESTML neuron is written as having separate input ports for excitatory and inhibitory spikes
syn_spec_nestml = syn_spec
if syn_spec_nestml is None:
syn_spec_nestml = {}
syn_spec_nestml.update({"receptor_type": nestml_neuron.get("receptor_types")["EXC_SPIKES"]})
nest.Connect(spikegenerator, nestml_neuron, syn_spec=syn_spec_nestml)
else:
# this NESTML neuron is written as having one input port for excitatory and inhibitory spikes (with sign of the weight telling the difference)
nest.Connect(spikegenerator, nestml_neuron, syn_spec=syn_spec)

spike_recorder1 = nest.Create("spike_recorder")
spike_recorder2 = nest.Create("spike_recorder")
nest.Connect(neuron1, spike_recorder1)
nest.Connect(neuron2, spike_recorder2)
nest.Connect(nest_neuron, spike_recorder1)
nest.Connect(nestml_neuron, spike_recorder2)

multimeter1 = nest.Create("multimeter")
multimeter2 = nest.Create("multimeter")
Expand All @@ -393,8 +402,8 @@ def _test_model_equivalence_psc(self, nest_model_name, nestml_model_name, gsl_er
nest.SetStatus(multimeter1, {"record_from": [V_m_specifier]})
nest.SetStatus(multimeter2, {"record_from": [V_m_specifier]})

nest.Connect(multimeter1, neuron1)
nest.Connect(multimeter2, neuron2)
nest.Connect(multimeter1, nest_neuron)
nest.Connect(multimeter2, nestml_neuron)

nest.Simulate(400.)

Expand All @@ -416,7 +425,7 @@ def _test_model_equivalence_psc(self, nest_model_name, nestml_model_name, gsl_er
for _ax in ax:
_ax.legend(loc="upper right")
_ax.grid()
plt.savefig("/tmp/nestml_nest_integration_test_psc_[" + nest_model_name + "]_[" + nestml_model_name + "].png")
plt.savefig("/tmp/test_nest_neuron_model_equivalence_psc_[" + nest_model_name + "]_[" + nestml_model_name + "].png")
plt.close(fig)

np.testing.assert_allclose(ts1, ts2)
Expand Down
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