forked from nest/nest-simulator
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request nest#118 from flinz/parrot-multiport
Extended parrot_neuron to allow connections onto port 0 and 1, not repeating spikes on port 1
- Loading branch information
Showing
4 changed files
with
200 additions
and
5 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,172 @@ | ||
| # -*- coding: utf-8 -*- | ||
| # | ||
| # test_parrot_neuron.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 script tests the parrot_neuron in NEST. | ||
|
|
||
| import nest | ||
| import unittest | ||
|
|
||
|
|
||
| @nest.check_stack | ||
| class ParrotNeuronTestCase(unittest.TestCase): | ||
| """Check parrot_neuron spike repetition properties""" | ||
|
|
||
| def setUp(self): | ||
| nest.set_verbosity('M_WARNING') | ||
| nest.ResetKernel() | ||
|
|
||
| # set up source spike generator, as well as parrot neurons | ||
| self.spike_time = 1. | ||
| self.delay = .2 | ||
| self.source = nest.Create("spike_generator", 1, {"spike_times": [self.spike_time]}) | ||
| self.parrot = nest.Create('parrot_neuron') | ||
| self.spikes = nest.Create("spike_detector") | ||
|
|
||
| # record source and parrot spikes | ||
| nest.Connect(self.source, self.spikes) | ||
| nest.Connect(self.parrot, self.spikes) | ||
|
|
||
| def test_ParrotNeuronRepeatSpike(self): | ||
| """Check parrot_neuron repeats spikes on port 0""" | ||
|
|
||
| # connect with arbitrary delay | ||
| nest.Connect(self.source, self.parrot, syn_spec={"delay": self.delay}) | ||
| nest.Simulate(self.spike_time + 2 * self.delay) | ||
|
|
||
| # get spike from parrot neuron | ||
| events = nest.GetStatus(self.spikes)[0]["events"] | ||
| post_time = events['times'][events['senders'] == self.parrot[0]] | ||
|
|
||
| # assert spike was repeated at correct time | ||
| assert post_time, "Parrot neuron failed to repeat spike." | ||
| assert self.spike_time + self.delay == post_time, "Parrot neuron repeated spike at wrong delay" | ||
|
|
||
| def test_ParrotNeuronIgnoreSpike(self): | ||
| """Check parrot_neuron ignores spikes on port 1""" | ||
|
|
||
| # connect with arbitrary delay to port 1 | ||
| nest.Connect(self.source, self.parrot, syn_spec={"receptor_type": 1, "delay": self.delay}) | ||
| nest.Simulate(self.spike_time + 2. * self.delay) | ||
|
|
||
| # get spike from parrot neuron, assert it was ignored | ||
| events = nest.GetStatus(self.spikes)[0]["events"] | ||
| post_time = events['times'][events['senders'] == self.parrot[0]] | ||
| assert len(post_time) == 0, "Parrot neuron failed to ignore spike arriving on port 1" | ||
|
|
||
|
|
||
| @nest.check_stack | ||
| class ParrotNeuronSTDPTestCase(unittest.TestCase): | ||
| """ | ||
| Check STDP protocol between two parrot_neurons connected by a stdp_synapse. | ||
| Exact pre- and post-synaptic spike times are set by spike_generators | ||
| connected to each parrot neuron. Additional spikes sent through the | ||
| stdp_synapse are explicitly ignored in the postsynaptic parrot_neuron | ||
| by setting the stdp_synapse to connect to port 1. | ||
| """ | ||
|
|
||
| def run_protocol(self, dt): | ||
|
|
||
| """Set up a network with pre-post spike pairings with t_post - t_pre = dt""" | ||
|
|
||
| nest.set_verbosity("M_WARNING") | ||
| nest.ResetKernel() | ||
|
|
||
| # set pre and postsynaptic spike times | ||
| delay = 1. # delay for connections | ||
| dspike = 100. # ISI | ||
|
|
||
| # set the correct real spike times for generators (correcting for delays) | ||
| pre_times = [100., 100. + dspike] | ||
| post_times = [k+dt for k in pre_times] | ||
|
|
||
| # create spike_generators with these times | ||
| pre_spikes = nest.Create("spike_generator", 1, {"spike_times": pre_times}) | ||
| post_spikes = nest.Create("spike_generator", 1, {"spike_times": post_times}) | ||
|
|
||
| # create parrot neurons and connect spike_generators | ||
| pre_parrot = nest.Create("parrot_neuron", 1) | ||
| post_parrot = nest.Create("parrot_neuron", 1) | ||
|
|
||
| nest.Connect(pre_spikes, pre_parrot, syn_spec={"delay": delay}) | ||
| nest.Connect(post_spikes, post_parrot, syn_spec={"delay": delay}) | ||
|
|
||
| # create spike detector | ||
| spikes = nest.Create("spike_detector") | ||
| nest.Connect(pre_parrot, spikes) | ||
| nest.Connect(post_parrot, spikes) | ||
|
|
||
| # connect both parrot neurons with a stdp synapse onto port 1 | ||
| # thereby spikes transmitted through the stdp connection are | ||
| # not repeated postsynaptically. | ||
| syn_spec = { | ||
| "model": "stdp_synapse", | ||
| "receptor_type": 1, # set receptor 1 postsynaptically, to not generate extra spikes | ||
| } | ||
| conn_spec = { | ||
| "rule": "one_to_one", | ||
| } | ||
| nest.Connect(pre_parrot, post_parrot, syn_spec=syn_spec, conn_spec=conn_spec) | ||
|
|
||
| # get STDP synapse and weight before protocol | ||
| syn = nest.GetConnections(source=pre_parrot, synapse_model="stdp_synapse") | ||
| syn_status = nest.GetStatus(syn)[0] | ||
| w_pre = syn_status['weight'] | ||
|
|
||
| last_time = max(pre_times[-1], post_times[-1]) | ||
| nest.Simulate(last_time + 2 * delay) | ||
|
|
||
| # get weight post protocol | ||
| syn_status = nest.GetStatus(syn)[0] | ||
| w_post = syn_status['weight'] | ||
|
|
||
| return w_pre, w_post | ||
|
|
||
| def test_ParrotNeuronSTDPProtocolPotentiation(self): | ||
| """Check pre-post spike pairings between parrot_neurons increments weights.""" | ||
|
|
||
| dt = 10. | ||
| w_pre, w_post = self.run_protocol(dt) | ||
| assert w_pre < w_post, "Parrot neuron STDP potentiation protocol failed to elicit positive weight changes." | ||
|
|
||
| def test_ParrotNeuronSTDPProtocolDepression(self): | ||
| """Check post-pre spike pairings between parrot_neurons decrement weights.""" | ||
|
|
||
| dt = -10. | ||
| w_pre, w_post = self.run_protocol(dt) | ||
| assert w_pre > w_post, "Parrot neuron STDP potentiation protocol failed to elicit negative weight changes." | ||
|
|
||
|
|
||
| def suite(): | ||
|
|
||
| # makeSuite is sort of obsolete http://bugs.python.org/issue2721 | ||
| # using loadTestsFromTestCase instead. | ||
| suite1 = unittest.TestLoader().loadTestsFromTestCase(ParrotNeuronTestCase) | ||
| suite2 = unittest.TestLoader().loadTestsFromTestCase(ParrotNeuronSTDPTestCase) | ||
| return unittest.TestSuite([suite1, suite2]) | ||
|
|
||
|
|
||
| def run(): | ||
| runner = unittest.TextTestRunner(verbosity=2) | ||
| runner.run(suite()) | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| run() |