def record_v(self):
sim.setup(timestep=1)
simtime = 100
input = sim.Population(1, sim.SpikeSourceArray(spike_times=[0, 30]),
label="input")
pop = sim.Population(32, sim.IF_curr_exp(), label="pop")
sim.Projection(input, pop, sim.AllToAllConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=1))
pop.record("v")
sim.run(simtime)
neo = pop.get_data("all")
pop.write_data(pickle_path, "all")
io = PickleIO(filename=pickle_path)
saved = io.read()[0]
neo_compare.compare_blocks(neo, saved)
assert len(neo.segments[0].spiketrains) == 0
assert len(neo.segments[0].filter(name="v")) > 0
assert len(neo.segments[0].filter(name="gsyn_exc")) == 0
v_neo = pop.get_data("v")
pop.write_data(pickle_path, "v")
io = PickleIO(filename=pickle_path)
v_saved = io.read()[0]
neo_compare.compare_blocks(v_neo, v_saved)
neo_compare.compare_blocks(v_neo, neo)
with self.assertRaises(ConfigurationException):
pop.get_data("spikes")
with self.assertRaises(ConfigurationException):
pop.get_data("gsyn_exc")
with self.assertRaises(ConfigurationException):
pop.write_data(pickle_path, "spikes")
with self.assertRaises(ConfigurationException):
pop.write_data(pickle_path, "gsyn_exc")
def test_script(self):
"""
test that tests the printing of v from a pre determined recording
:return:
"""
synfire_run.do_run(n_neurons, max_delay=14, time_step=1,
neurons_per_core=1, delay=1.7, run_times=[50],
spike_path=current_spike_file_path,
gsyn_path_exc=current_gsyn_file_path,
v_path=current_v_file_path, end_before_print=False)
spikes_read = synfire_run.get_output_pop_spikes_neo()
v_read = synfire_run.get_output_pop_voltage_neo()
gsyn_read = synfire_run.get_output_pop_gsyn_exc_neo()
io = PickleIO(filename=current_spike_file_path)
spikes_saved = io.read()[0]
io = PickleIO(filename=current_v_file_path)
v_saved = io.read()[0]
io = PickleIO(filename=current_gsyn_file_path)
gsyn_saved = io.read()[0]
neo_compare.compare_blocks(spikes_read, spikes_saved)
neo_compare.compare_blocks(v_read, v_saved)
neo_compare.compare_blocks(gsyn_read, gsyn_saved)
def test_print_voltage(self):
"""
test that tests the printing of v from a pre determined recording
:return:
"""
synfire_run.do_run(n_neurons, max_delay=max_delay, time_step=timestep,
neurons_per_core=neurons_per_core, delay=delay,
run_times=[runtime], v_path=current_v_file_path)
v_read = synfire_run.get_output_pop_voltage_neo()
io = PickleIO(filename=current_v_file_path)
v_saved = io.read()[0]
neo_compare.compare_blocks(v_read, v_saved)
os.remove(current_v_file_path)
def test_script(self):
"""
test that tests the printing of v from a pre determined recording
:return:
"""
try:
n_neurons = 20 # number of neurons in each population
current_file_path = os.path.dirname(os.path.abspath(__file__))
current_spike_file_path = os.path.join(current_file_path,
"spikes.pickle")
current_v_file_path = os.path.join(current_file_path, "v.pickle")
current_gsyn_file_path = os.path.join(current_file_path,
"gsyn.pickle")
synfire_run.do_run(n_neurons, max_delay=14, time_step=0.1,
neurons_per_core=1, delay=1.7, run_times=[50],
spike_path=current_spike_file_path,
gsyn_path_exc=current_gsyn_file_path,
v_path=current_v_file_path)
spikes_read = synfire_run.get_output_pop_spikes_neo()
v_read = synfire_run.get_output_pop_voltage_neo()
gsyn_read = synfire_run.get_output_pop_gsyn_exc_neo()
io = PickleIO(filename=current_spike_file_path)
spikes_saved = io.read()[0]
io = PickleIO(filename=current_v_file_path)
v_saved = io.read()[0]
io = PickleIO(filename=current_gsyn_file_path)
gsyn_saved = io.read()[0]
neo_compare.compare_blocks(spikes_read, spikes_saved)
neo_compare.compare_blocks(v_read, v_saved)
neo_compare.compare_blocks(gsyn_read, gsyn_saved)
except SpinnmanTimeoutException as ex:
# System sometimes times outs
raise SkipTest(ex)
def test_va_benchmark(self):
try:
exc_spikes = do_run()
# System intentional overload so may error
except SpinnmanTimeoutException as ex:
raise SkipTest(ex)
spike_count = neo_convertor.count_spikes(exc_spikes)
print(spike_count)
# CB Jan 14 2019 Result varie between runs
self.assertLessEqual(2558, spike_count)
self.assertGreaterEqual(2559, spike_count)
io = PickleIO(filename=neo_path)
recorded_spikes = io.read()[0]
neo_compare.compare_blocks(exc_spikes, recorded_spikes)
def test_get_gsyn(self):
synfire_run.do_run(n_neurons,
max_delay=max_delay,
time_step=timestep,
neurons_per_core=neurons_per_core,
delay=delay,
run_times=[runtime],
gsyn_path_exc=gsyn_path)
spikes = synfire_run.get_output_pop_spikes_numpy()
gsyn = synfire_run.get_output_pop_gsyn_exc_neo()
self.assertEqual(12, len(spikes))
spike_checker.synfire_spike_checker(spikes, n_neurons)
io = PickleIO(filename=gsyn_path)
gsyn_saved = io.read()[0]
neo_compare.compare_blocks(gsyn, gsyn_saved)
os.remove(gsyn_path)
def test_get_gsyn(self):
try:
synfire_run.do_run(n_neurons, max_delay=max_delay,
time_step=timestep,
neurons_per_core=neurons_per_core, delay=delay,
run_times=[runtime], gsyn_path_exc=gsyn_path)
spikes = synfire_run.get_output_pop_spikes_numpy()
g_syn = synfire_run.get_output_pop_gsyn_exc_numpy()
spike_checker.synfire_spike_checker(spikes, n_neurons)
io = PickleIO(filename=gsyn_path)
gsyn2_neo = io.read()[0]
gsyn2_numpy = neo_convertor.convert_data(
gsyn2_neo, run=0, name="gsyn_exc")
self.assertTrue(numpy.allclose(g_syn, gsyn2_numpy))
os.remove(gsyn_path)
except SpinnmanTimeoutException as ex:
# System intentional overload so may error
raise SkipTest(ex)
def test_print_voltage(self):
"""
test that tests the printing of v from a pre determined recording
:return:
"""
try:
synfire_run.do_run(n_neurons,
max_delay=max_delay,
time_step=timestep,
neurons_per_core=neurons_per_core,
delay=delay,
run_times=[runtime],
v_path=current_v_file_path)
v_read = synfire_run.get_output_pop_voltage_neo()
io = PickleIO(filename=current_v_file_path)
v_saved = io.read()[0]
neo_compare.compare_blocks(v_read, v_saved)
os.remove(current_v_file_path)
# System intentional overload so may error
except SpinnmanTimeoutException as ex:
raise SkipTest(ex)
def test_print_spikes(self):
try:
synfire_run.do_run(n_neurons,
time_step=timestep,
max_delay=max_delay,
delay=delay,
neurons_per_core=neurons_per_core,
run_times=[runtime],
spike_path=spike_path)
spikes = synfire_run.get_output_pop_spikes_neo()
try:
io = PickleIO(filename=spike_path)
read_in_spikes = io.read()[0]
neo_compare.compare_blocks(spikes, read_in_spikes)
except UnicodeDecodeError:
raise SkipTest(
"https://github.com/NeuralEnsemble/python-neo/issues/529")
except SpinnmanTimeoutException as ex:
# System intentional overload so may error
raise SkipTest(ex)
if __name__ == '__main__':
# Delayed imports so unit tests do not need them
from pyNN.utility.plotting import Figure
import matplotlib.pyplot as plt
synfire_run.do_run(n_neurons,
max_delay=max_delay,
time_step=timestep,
neurons_per_core=neurons_per_core,
delay=delay,
run_times=[runtime],
gsyn_path_exc=gsyn_path)
spikes = synfire_run.get_output_pop_spikes_numpy()
g_syn = synfire_run.get_output_pop_gsyn_exc_numpy()
spike_checker.synfire_spike_checker(spikes, n_neurons)
io = PickleIO(filename=gsyn_path)
gsyn2_neo = io.read()[0]
gsyn2_numpy = neo_convertor.convert_data(gsyn2_neo, run=0, name="gsyn_exc")
print(len(spikes))
Figure(SpynnakerPanel(spikes,
yticks=True,
xticks=True,
markersize=4,
xlim=(0, runtime)),
SpynnakerPanel(gsyn2_neo, yticks=True),
title="TestPrintGsyn".format(delay),
annotations="generated by {}".format(__file__))
plt.show()
os.remove(gsyn_path)