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Refractory tests and corrected hh_cond_exp_traub (fixes #473) #590

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merged 14 commits into from
Jan 11, 2017
Merged

Refractory tests and corrected hh_cond_exp_traub (fixes #473) #590

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146164e
corrected refractory implementation
Silmathoron Dec 3, 2016
70b46c2
Merge branch 'master' of git://github.com/nest/nest-simulator into tr…
Silmathoron Dec 12, 2016
1ec4881
added refractory test
Silmathoron Dec 12, 2016
c2e0238
support for multicompartment iaf
Silmathoron Dec 13, 2016
aa068bc
fixed formatting
Silmathoron Dec 13, 2016
299b2f4
Merge branch 'master' of git://github.com/nest/nest-simulator into tr…
Silmathoron Dec 14, 2016
3d5a563
changed test to check more models
Silmathoron Dec 14, 2016
b76cb4a
corrected tested_neurons list
Silmathoron Dec 14, 2016
f3b4b79
corrected tested_neurons list 2
Silmathoron Dec 14, 2016
412ba61
Merge branch 'master' of git://github.com/nest/nest-simulator into tr…
Silmathoron Dec 16, 2016
bcdced1
added ht_neuron
Silmathoron Dec 16, 2016
4a84dc1
corrections in response to @jschuecker's review
Silmathoron Jan 11, 2017
0b58324
correction 2
Silmathoron Jan 11, 2017
964b614
corrected pep8
Silmathoron Jan 11, 2017
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13 changes: 7 additions & 6 deletions pynest/nest/tests/test_refractory.py
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Original file line number Diff line number Diff line change
Expand Up @@ -134,14 +134,14 @@


# --------------------------------------------------------------------------- #
# Simulation and refractory time
# Simulation and refractory time limits
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@Silmathoron, Sorry, I meant to change this to "Simulation time and refractory time limits"

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easy ;)

# -------------------------
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you could change this to "refractory time limits" to avoid confusion as this are only the lower and upper bounds right?

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Done (and additional comments added)

#

simtime = 100
resolution = 0.1
min_steps = 1
max_steps = 200
min_steps = 1 # minimal number of refractory steps (t_ref = resolution in ms)
max_steps = 200 # maximal number of steps (t_ref = 200 * resolution in ms)


# --------------------------------------------------------------------------- #
Expand Down Expand Up @@ -201,12 +201,13 @@ def compute_reftime(self, model, sd, vm, neuron):
else:
Vr = nest.GetStatus(neuron, "V_reset")[0]
times = nest.GetStatus(vm, "events")[0]["times"]
idx_max = (np.argwhere(np.isclose(times, spike_times[1]))[0][0]
if len(spike_times) > 1 else -1)
# index of the 2nd spike
idx_max = np.argwhere(times == spike_times[1])[0][0]
name_Vm = "V_m.s" if model == "iaf_cond_alpha_mc" else "V_m"
Vs = nest.GetStatus(vm, "events")[0][name_Vm]
# get the index at which the spike occured
idx_spike = np.argwhere(times == spike_times[0])[0][0]
# find end of refractory period between 1st and 2nd spike
idx_end = np.where(
np.isclose(Vs[idx_spike:idx_max], Vr, 1e-6))[0][-1]
t_ref_sim = idx_end * resolution
Expand All @@ -226,7 +227,7 @@ def test_refractory_time(self, model):
vm_params = {"interval": resolution, "record_from": [name_Vm]}
vm = nest.Create("voltmeter", params=vm_params)
sd = nest.Create("spike_detector", params={'precise_times': True})
cg = nest.Create("dc_generator", params={"amplitude": 600.})
cg = nest.Create("dc_generator", params={"amplitude": 900.})
# for models that do not clamp V_m, use very large current to trigger
# almost immediate spiking => t_ref almost equals interspike
if model in neurons_interspike_ps:
Expand Down