def test_network_plot(self):
# Generate test signal
brunel_ai = ninemlcatalog.load('network/Brunel2000/AI.xml').as_network(
'Brunel2000AI')
scaled_brunel_ai_path = os.path.join(self.work_dir,
'brunel_scaled.xml')
brunel_ai.scale(0.01).write(scaled_brunel_ai_path)
argv = ("{} nest 100.0 0.1 "
"--record Exc.spike_output {}".format(
scaled_brunel_ai_path, self.network_signal_path))
simulate.run(argv.split())
# Run plotting command
for pop_name in self.recorded_pops:
out_path = '{}/{}.png'.format(self.work_dir, pop_name)
argv = ("{in_path} --save {out_path} --hide --dims 5 5 "
"--resolution 100.0".format(
in_path=self.network_signal_path,
out_path=out_path,
name='v'))
plot.run(argv.split())
image = img.imread(out_path)
self._ref_network_plot()
ref_image = img.imread(self.ref_network_path)
self.assertEqual(image.shape, ref_image.shape)
self.assertTrue(
(image == ref_image).all(),
"Plotted spike data using 'plot' command (saved to '{}') "
"did not match loaded image from '{}'".format(
out_path, self.ref_network_path))
def test_network_plot(self):
# Generate test signal
brunel_ai = ninemlcatalog.load(
'network/Brunel2000/AI.xml').as_network('Brunel2000AI')
scaled_brunel_ai_path = os.path.join(self.work_dir,
'brunel_scaled.xml')
brunel_ai.scale(0.01).write(scaled_brunel_ai_path)
argv = ("{} nest 100.0 0.1 "
"--record Exc.spike_output {}"
.format(scaled_brunel_ai_path, self.network_signal_path))
simulate.run(argv.split())
# Run plotting command
for pop_name in self.recorded_pops:
out_path = '{}/{}.png'.format(self.work_dir, pop_name)
argv = ("{in_path} --save {out_path} --hide --dims 5 5 "
"--resolution 100.0"
.format(in_path=self.network_signal_path,
out_path=out_path, name='v'))
plot.run(argv.split())
image = img.imread(out_path)
self._ref_network_plot()
ref_image = img.imread(self.ref_network_path)
self.assertEqual(
image.shape, ref_image.shape)
self.assertTrue(
(image == ref_image).all(),
"Plotted spike data using 'plot' command (saved to '{}') "
"did not match loaded image from '{}'"
.format(out_path, self.ref_network_path))
def test_single_cell_plot(self):
in_path = os.path.join(self.data_dir, 'v.neo.pkl')
out_path = '{}/single_cell.png'.format(self.tmpdir)
argv = ("{data_file} --name {name} --save {out_path} --hide"
.format(data_file=in_path, out_path=out_path, name='v'))
plot.run(argv.split())
image = img.imread(out_path)
ref_image = img.imread(self.ref_single_cell_path)
self.assertTrue(
all(image == ref_image),
"Ploted single cell data using 'plot' command did not match "
"loaded image from '{}'".format(self.ref_single_cell_path))
def test_single_cell_plot(self, show=False):
# First simulate input signal to have something to play into
# izhikevich cell
argv = ("catalog://input/StepCurrent#StepCurrent "
"nest {t_stop} {dt} "
"--record current_output {out_path} {rec_t_start} "
"--prop amplitude {amp} "
"--prop onset {onset} "
"--init_value current_output {init} "
"--build_mode force "
"--build_version Plot ".format(
out_path=self.cell_input_path,
rec_t_start='{} {}'.format(*self.rec_t_start),
t_stop=self.t_stop,
dt=self.dt,
amp='{} {}'.format(*self.isyn_amp),
onset='{} {}'.format(*self.isyn_onset),
init='{} {}'.format(*self.isyn_init)))
# Run input signal simulation
simulate.run(argv.split())
argv = ("catalog://neuron/Izhikevich#SampleIzhikevichFastSpiking "
"nest {} {} "
"--record V {} "
"--init_value U 1.625 pA "
"--init_value V -65.0 mV "
"--play iSyn {in_path} "
"--init_regime subVb "
"--build_version Plot "
"--device_delay 0.5 ms "
"--min_delay 0.5 ms ".format(self.t_stop,
self.dt,
self.cell_signal_path,
in_path=self.cell_input_path))
simulate.run(argv.split())
# Run plotting command
out_path = '{}/single_cell.png'.format(self.work_dir)
argv = ("{in_path} --save {out_path} --dims 5 5 "
"--resolution 100.0 {hide}".format(
in_path=self.cell_signal_path,
out_path=out_path,
name='v',
hide=('' if show else '--hide')))
plot.run(argv.split())
image = img.imread(out_path)
self._ref_single_cell_plot()
ref_image = img.imread(self.ref_single_cell_path)
self.assertEqual(image.shape, ref_image.shape)
self.assertTrue(
(image == ref_image).all(),
"Ploted single cell data using 'plot' command (saved to '{}') did "
"not match loaded image from '{}'".format(
out_path, self.ref_single_cell_path))
def test_network_plot(self):
in_path = os.path.join(self.data_dir, 'brunel.neo.pkl')
for pop_name in self.recorded_pops:
out_path = '{}/{}.png'.format(self.tmpdir)
argv = ("{data_file} --name {name} --save {out_path} --hide"
.format(in_path=in_path, out_path=out_path, name='v'))
plot.run(argv.split())
image = img.imread(out_path)
ref_image = img.imread(self.ref_single_cell_path)
self.assertTrue(
all(image == ref_image),
"Ploted spike data from '{name}' using 'plot' command did not "
"match loaded image from '{ref_dir}/{name}'"
.format(name=pop_name, ref_dir=self.data_dir))
def test_single_cell_plot(self, show=False):
# First simulate input signal to have something to play into
# izhikevich cell
argv = ("catalog://input/StepCurrent#StepCurrent "
"nest {t_stop} {dt} "
"--record current_output {out_path} {rec_t_start} "
"--prop amplitude {amp} "
"--prop onset {onset} "
"--init_value current_output {init} "
"--build_mode force "
"--build_version Plot "
.format(out_path=self.cell_input_path,
rec_t_start='{} {}'.format(*self.rec_t_start),
t_stop=self.t_stop, dt=self.dt,
amp='{} {}'.format(*self.isyn_amp),
onset='{} {}'.format(*self.isyn_onset),
init='{} {}'.format(*self.isyn_init)))
# Run input signal simulation
simulate.run(argv.split())
argv = (
"catalog://neuron/Izhikevich#SampleIzhikevichFastSpiking "
"nest {} {} "
"--record V {} "
"--init_value U 1.625 pA "
"--init_value V -65.0 mV "
"--play iSyn {in_path} "
"--init_regime subVb "
"--build_version Plot "
"--device_delay 0.5 ms "
"--min_delay 0.5 ms "
.format(self.t_stop, self.dt, self.cell_signal_path,
in_path=self.cell_input_path))
simulate.run(argv.split())
# Run plotting command
out_path = '{}/single_cell.png'.format(self.work_dir)
argv = ("{in_path} --save {out_path} --dims 5 5 "
"--resolution 100.0 {hide}"
.format(in_path=self.cell_signal_path, out_path=out_path,
name='v', hide=('' if show else '--hide')))
plot.run(argv.split())
image = img.imread(out_path)
self._ref_single_cell_plot()
ref_image = img.imread(self.ref_single_cell_path)
self.assertEqual(image.shape, ref_image.shape)
self.assertTrue(
(image == ref_image).all(),
"Ploted single cell data using 'plot' command (saved to '{}') did "
"not match loaded image from '{}'"
.format(out_path, self.ref_single_cell_path))
