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Merge pull request #646 from apdavison/issue645
Fix for #645
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""" | ||
A demonstration of the use of callbacks to update the spike times in a SpikeSourceArray. | ||
Usage: update_spike_source_array.py [-h] [--plot-figure] simulator | ||
positional arguments: | ||
simulator neuron, nest, brian or another backend simulator | ||
optional arguments: | ||
-h, --help show this help message and exit | ||
--plot-figure Plot the simulation results to a file. | ||
""" | ||
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import numpy as np | ||
from pyNN.utility import get_simulator, normalized_filename, ProgressBar | ||
from pyNN.utility.plotting import Figure, Panel | ||
from pyNN.parameters import Sequence | ||
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sim, options = get_simulator(("--plot-figure", "Plot the simulation results to a file.", | ||
{"action": "store_true"})) | ||
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rate_increment = 20 | ||
interval = 200 | ||
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class SetRate(object): | ||
""" | ||
A callback which changes the firing rate of a population of spike | ||
sources at a fixed interval. | ||
""" | ||
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def __init__(self, population, rate_generator, update_interval=20.0): | ||
assert isinstance(population.celltype, sim.SpikeSourceArray) | ||
self.population = population | ||
self.update_interval = update_interval | ||
self.rate_generator = rate_generator | ||
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def __call__(self, t): | ||
try: | ||
rate = next(rate_generator) | ||
if rate > 0: | ||
isi = 1000.0/rate | ||
times = t + np.arange(0, self.update_interval, isi) | ||
# here each neuron fires with the same isi, | ||
# but there is a phase offset between neurons | ||
spike_times = [ | ||
Sequence(times + phase * isi) | ||
for phase in self.population.annotations["phase"] | ||
] | ||
else: | ||
spike_times = [] | ||
self.population.set(spike_times=spike_times) | ||
except StopIteration: | ||
pass | ||
return t + self.update_interval | ||
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class MyProgressBar(object): | ||
""" | ||
A callback which draws a progress bar in the terminal. | ||
""" | ||
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def __init__(self, interval, t_stop): | ||
self.interval = interval | ||
self.t_stop = t_stop | ||
self.pb = ProgressBar(width=int(t_stop / interval), char=".") | ||
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def __call__(self, t): | ||
self.pb(t / self.t_stop) | ||
return t + self.interval | ||
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sim.setup() | ||
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# === Create a population of poisson processes =============================== | ||
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p = sim.Population(50, sim.SpikeSourceArray()) | ||
p.annotate(phase=np.random.uniform(0, 1, size=p.size)) | ||
p.record('spikes') | ||
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# === Run the simulation, with two callback functions ======================== | ||
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rate_generator = iter(range(0, 100, rate_increment)) | ||
sim.run(1000, callbacks=[MyProgressBar(10.0, 1000.0), | ||
SetRate(p, rate_generator, interval)]) | ||
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# === Retrieve recorded data, and count the spikes in each interval ========== | ||
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data = p.get_data().segments[0] | ||
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all_spikes = np.hstack([st.magnitude for st in data.spiketrains]) | ||
spike_counts = [((all_spikes >= x) & (all_spikes < x + interval)).sum() | ||
for x in range(0, 1000, interval)] | ||
expected_spike_counts = [p.size * rate * interval / 1000.0 | ||
for rate in range(0, 100, rate_increment)] | ||
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print("\nActual spike counts: {}".format(spike_counts)) | ||
print("Expected mean spike counts: {}".format(expected_spike_counts)) | ||
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if options.plot_figure: | ||
Figure( | ||
Panel(data.spiketrains, xlabel="Time (ms)", xticks=True, markersize=0.5), | ||
title="Incrementally updated SpikeSourceArrays", | ||
annotations="Simulated with %s" % options.simulator.upper() | ||
).save(normalized_filename("Results", "update_spike_source_array", "png", options.simulator)) | ||
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sim.end() |
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