gs = GridSpec(nrows=nrows, ncols=ncols)
fig.suptitle('RANK {}'.format(RANK))
counter = 0
# somatic traces
tvec = np.arange(PSET.tstop / PSET.dt + 1) * PSET.dt
tinds = tvec >= PSET.TRANSIENT
for i, name in enumerate(PSET.populationParameters['me_type']):
population = network.populations[name]
for j, cell in enumerate(population.cells):
ax = fig.add_subplot(gs[counter, 0])
if counter == 0:
ax.set_title('somatic voltages')
ax.plot(tvec[tinds][::PSET.decimate_q],
decimate(cell.somav[tinds], q=PSET.decimate_q),
color=colors[i],
lw=1.5,
label=name)
ax.set_ylabel('gid {}'.format(population.gids[j]),
rotation='horizontal',
labelpad=30)
ax.axis(ax.axis('tight'))
ax.set_ylim(-90, -20)
ax.legend(loc='best')
ax.yaxis.set_major_locator(MaxNLocator(nbins=3))
counter += 1
if counter == nrows:
ax.set_xlabel('time (ms)')
else:
ax.set_xticklabels([])
gs = GridSpec(nrows=nrows, ncols=ncols)
fig.suptitle('RANK {}'.format(RANK))
counter = 0
# somatic traces
tvec = np.arange(PSET.tstop / PSET.dt + 1)*PSET.dt
tinds = tvec >= PSET.TRANSIENT
for i, name in enumerate(PSET.populationParameters['me_type']):
population = network.populations[name]
for j, cell in enumerate(population.cells):
ax = fig.add_subplot(gs[counter, 0])
if counter == 0:
ax.set_title('somatic voltages')
ax.plot(tvec[tinds][::PSET.decimate_q],
decimate(cell.somav[tinds],
q=PSET.decimate_q),
color=colors[i], lw=1.5, label=name)
ax.set_ylabel('gid {}'.format(population.gids[j]),
rotation='horizontal', labelpad=30)
ax.axis(ax.axis('tight'))
ax.set_ylim(-90, -20)
ax.legend(loc='best')
ax.yaxis.set_major_locator(MaxNLocator(nbins=3))
counter += 1
if counter == nrows:
ax.set_xlabel('time (ms)')
else:
ax.set_xticklabels([])
# save figure output
fig.savefig(os.path.join(PSET.OUTPUTPATH,
fontsize=16, fontweight='demibold',
transform=axes[0].transAxes)
# PANEL C Extracellular potential
gs0 = GridSpecFromSubplotSpec(12, 1, subplot_spec=gs[:2, 2])
ax = fig.add_subplot(gs0[:-2])
f = h5py.File(os.path.join(PSET.OUTPUTPATH, 'example_parallel_network_output.h5'), 'r')
for data, title, color in zip(
[f['SUMMED_OUTPUT'].value['imem']],
['extracellular potentials, summed'],
['k']):
ax.set_title(title)
vlimround = plotting.draw_lineplot(ax=ax, data=plotting.decimate(data, q=PSET.decimate_q),
dt=PSET.dt*PSET.decimate_q,
T=T, color=color, scalebarbasis='log10')
f.close()
ax.set_xticklabels([])
ax.set_xlabel('')
ax.set_ylabel('')
ax.text(-0.1, 1.055, alphabet[2],
horizontalalignment='center',
verticalalignment='center',
fontsize=16, fontweight='demibold',
transform=ax.transAxes)
verticalalignment='center',
fontsize=16,
fontweight='demibold',
transform=axes[0].transAxes)
# PANEL C Extracellular potential
gs0 = GridSpecFromSubplotSpec(12, 1, subplot_spec=gs[:2, 2])
ax = fig.add_subplot(gs0[:-2])
f = h5py.File(
os.path.join(PSET.OUTPUTPATH, 'example_parallel_network_output.h5'),
'r')
for data, title, color in zip([f['SUMMED_OUTPUT'][()]['imem']],
['extracellular potentials, summed'], ['k']):
ax.set_title(title)
vlimround = plotting.draw_lineplot(ax=ax,
data=plotting.decimate(
data, q=PSET.decimate_q),
dt=PSET.dt * PSET.decimate_q,
T=T,
color=color,
scalebarbasis='log10')
f.close()
ax.set_xticklabels([])
ax.set_xlabel('')
ax.set_ylabel('')
ax.text(-0.1,
1.055,
alphabet[2],
horizontalalignment='center',
verticalalignment='center',
fontsize=16,
# Set up figure and subplots
fig = plt.figure(figsize=(16, 12))
gs = GridSpec(15, 5, left=0.075, right=0.975,
top=0.95, bottom=0.05, wspace=0.3, hspace=0.2)
alphabet = 'ABCDEFGHIJKLMNOPQ'
for j, (m_type, me_type) in enumerate(zip(PSET.populationParameters['m_type'], PSET.populationParameters['me_type'])):
ax = fig.add_subplot(gs[:8, j])
f = h5py.File(os.path.join(PSET.OUTPUTPATH, 'example_parallel_network_output.h5'), 'r')
for data, title, color in zip(
[f['SUMMED_OUTPUT'].value[me_type]],
[m_type],
['k']):
ax.set_title(title)
vlimround = plotting.draw_lineplot(ax=ax, data=plotting.decimate(data, q=PSET.decimate_q),
dt=PSET.dt*PSET.decimate_q,
T=T, color=color,
scalebarbasis='log10')
if j > 0:
ax.set_yticklabels([])
ax.set_ylabel('')
ax.text(-0.1, 1.05, alphabet[j],
horizontalalignment='center',
verticalalignment='center',
fontsize=16, fontweight='demibold',
transform=ax.transAxes)
gs0 = GridSpecFromSubplotSpec(12, 1, subplot_spec=gs[:2, 2])
ax = fig.add_subplot(gs0[:-2])
f = h5py.File(
os.path.join(
PSET.OUTPUTPATH,
'example_parallel_network_output.h5'),
'r')
for data, title, color in zip(
[f['SUMMED_OUTPUT'][()]['imem']],
['extracellular potentials, summed'],
['k']):
ax.set_title(title)
vlimround = plotting.draw_lineplot(
ax=ax,
data=plotting.decimate(
data,
q=PSET.decimate_q),
dt=PSET.dt *
PSET.decimate_q,
T=T,
color=color,
scalebarbasis='log10')
f.close()
ax.set_xticklabels([])
ax.set_xlabel('')
ax.set_ylabel('')
ax.text(-0.1, 1.055, alphabet[2],
horizontalalignment='center',
verticalalignment='center',
fontsize=16, fontweight='demibold',
wspace=0.3,
hspace=0.2)
alphabet = 'ABCDEFGHIJKLMNOPQ'
for j, (m_type, me_type) in enumerate(
zip(PSET.populationParameters['m_type'],
PSET.populationParameters['me_type'])):
ax = fig.add_subplot(gs[:8, j])
f = h5py.File(
os.path.join(PSET.OUTPUTPATH,
'example_parallel_network_output.h5'), 'r')
for data, title, color in zip([f['SUMMED_OUTPUT'][()][me_type]],
[m_type], ['k']):
ax.set_title(title)
vlimround = plotting.draw_lineplot(ax=ax,
data=plotting.decimate(
data, q=PSET.decimate_q),
dt=PSET.dt * PSET.decimate_q,
T=T,
color=color,
scalebarbasis='log10')
if j > 0:
ax.set_yticklabels([])
ax.set_ylabel('')
ax.text(-0.1,
1.05,
alphabet[j],
horizontalalignment='center',
verticalalignment='center',
fontsize=16,
