def plot(self, *args, **kwargs):
# Plot all the trials into separate pages.
data = self.trial_data
rl, rb, rr, rt = self.myc['raster_rect']
t_limits = self.myc['t_limits']
max_e_rate = self.myc.get('max_e_rate', True)
max_i_rate = self.myc.get('max_i_rate', True)
scale_bar = self.myc.get('scale_bar', 500)
scale_x = self.myc.get('scale_x', .85)
scale_y = self.myc.get('scale_y', -.05)
ann_ei = self.myc.get('ann_ei', True)
y_label_pos = self.myc.get('y_label_pos', -0.22)
reshape_senders = self.myc.get('reshape_senders', True)
saver = self.myc['fig_saver']
saver.set_file_name(self.get_fname('population_activity'))
saver.ext = "pdf"
saver.set_backend_params(dpi=300, transparent=True)
for trial_no in range(len(data)):
fig = self._get_final_fig(self.myc['fig_size'])
e_spikes = data[trial_no].get_e_spikes()
i_spikes = data[trial_no].get_i_spikes()
# Raster plot
ax_raster = fig.add_axes(Bbox.from_extents(rl, rb, rr, rt))
plotEIRaster(e_spikes,
i_spikes,
t_limits,
ax=ax_raster,
sigmaTitle=False,
markersize=2 * self.config['scale_factor'],
rasterized=True,
ann_EI=ann_ei,
scaleBar=scale_bar,
scaleX=scale_x,
scaleY=scale_y,
scaleTextYOffset=.02,
reshape_senders=reshape_senders,
ylabelPos=y_label_pos)
# E and I 2D population plots
win_dt = 125. # ms
winLen = 250. # ms
tStart = t_limits[0]
tEnd = t_limits[1] - win_dt
fr_e, frt_e = e_spikes.slidingFiringRate(tStart, tEnd, win_dt,
winLen)
e_max = examples.plotBumpSnapshots(
fr_e,
frt_e,
self.myc['snapshot_tstep'],
fig=fig,
axesCoords=self.myc['e_snapshots_rect'],
bumpQuality=False,
timeTitles=True,
maxRate=False,
fontsize='x-small',
rateYPos=-.2)
rateText = "%.0f Hz" % e_max
rect = self.myc['e_snapshots_rect']
fig.text(rect[2],
rect[3],
rateText,
ha='left',
va='top',
size='small',
weight='bold',
clip_on=False)
fr_i, frt_i = i_spikes.slidingFiringRate(tStart, tEnd, win_dt,
winLen)
i_max = examples.plotBumpSnapshots(
fr_i,
frt_i,
self.myc['snapshot_tstep'],
fig=fig,
axesCoords=self.myc['i_snapshots_rect'],
bumpQuality=False,
timeTitles=False,
maxRate=False,
fontsize='x-small')
rateText = "%.0f Hz" % i_max
rect = self.myc['i_snapshots_rect']
fig.text(rect[2],
rect[3],
rateText,
ha='left',
va='top',
size='small',
weight='bold',
clip_on=False)
saver.savefig(fig)
saver.close()
def plot(self, *args, **kwargs):
# Plot all the trials into separate pages.
data = self.trial_data
rl, rb, rr, rt = self.myc['raster_rect']
t_limits = self.myc['t_limits']
max_e_rate = self.myc.get('max_e_rate', True)
max_i_rate = self.myc.get('max_i_rate', True)
scale_bar = self.myc.get('scale_bar', 500)
scale_x = self.myc.get('scale_x', .85)
scale_y = self.myc.get('scale_y', -.05)
ann_ei = self.myc.get('ann_ei', True)
y_label_pos = self.myc.get('y_label_pos', -0.22)
reshape_senders = self.myc.get('reshape_senders', True)
saver = self.myc['fig_saver']
saver.set_file_name(self.get_fname('population_activity'))
saver.ext = "pdf"
saver.set_backend_params(dpi=300, transparent=True)
for trial_no in range(len(data)):
fig = self._get_final_fig(self.myc['fig_size'])
e_spikes = data[trial_no].get_e_spikes()
i_spikes = data[trial_no].get_i_spikes()
# Raster plot
ax_raster = fig.add_axes(Bbox.from_extents(rl, rb, rr, rt))
plotEIRaster(e_spikes,
i_spikes,
t_limits,
ax=ax_raster,
sigmaTitle=False,
markersize=2 * self.config['scale_factor'],
rasterized=True,
ann_EI=ann_ei,
scaleBar=scale_bar,
scaleX=scale_x,
scaleY=scale_y,
scaleTextYOffset=.02,
reshape_senders=reshape_senders,
ylabelPos=y_label_pos)
# E and I 2D population plots
win_dt = 125. # ms
winLen = 250. # ms
tStart = t_limits[0]
tEnd = t_limits[1] - win_dt
fr_e, frt_e = e_spikes.slidingFiringRate(tStart, tEnd, win_dt,
winLen)
e_max = examples.plotBumpSnapshots(fr_e, frt_e, self.myc['snapshot_tstep'],
fig=fig,
axesCoords=self.myc['e_snapshots_rect'],
bumpQuality=False,
timeTitles=True,
maxRate=False,
fontsize='x-small',
rateYPos=-.2)
rateText = "%.0f Hz" % e_max
rect = self.myc['e_snapshots_rect']
fig.text(rect[2], rect[3], rateText, ha='left',
va='top', size='small', weight='bold',
clip_on=False)
fr_i, frt_i = i_spikes.slidingFiringRate(tStart, tEnd, win_dt,
winLen)
i_max = examples.plotBumpSnapshots(fr_i, frt_i, self.myc['snapshot_tstep'],
fig=fig,
axesCoords=self.myc['i_snapshots_rect'],
bumpQuality=False,
timeTitles=False,
maxRate=False,
fontsize='x-small')
rateText = "%.0f Hz" % i_max
rect = self.myc['i_snapshots_rect']
fig.text(rect[2], rect[3], rateText, ha='left',
va='top', size='small', weight='bold',
clip_on=False)
saver.savefig(fig)
saver.close()
def plot(self, *args, **kwargs):
myc = self._get_class_config()
tLimits = [5.e3, 6e3]
fig = self._get_final_fig(self.myc['fig_size'])
gs = gridspec.GridSpec(3, 1, height_ratios=(2.5, 1, 1))
data = DataStorage.open(self.myc['data_file'], 'r')
trial_data = data['trials'][0]
events_e = trial_data['spikeMon_e']['events']
ESpikes = PopulationSpikes(trial_data['net_attr']['net_Ne'],
events_e['senders'], events_e['times'])
events_i = trial_data['spikeMon_i']['events']
ISpikes = PopulationSpikes(trial_data['net_attr']['net_Ni'],
events_i['senders'], events_i['times'])
# EI Raster
ax_raster = fig.add_subplot(gs[0, 0])
rasters.plotEIRaster(ESpikes,
ISpikes,
ylabelPos=self.myc['ylabelPos'],
tLimits=tLimits,
markersize=self.config['scale_factor'] *
self.myc['markersize'],
yticks=True,
sigmaTitle=False,
ann_EI=False,
scaleBar=125,
scaleX=.8,
scaleY=-.05,
scaleText='ms',
scaleTextYOffset=.03,
scaleHeight=.01,
rasterized=False,
reshape_senders=False)
# EI rates
ax_erates = fig.add_subplot(gs[1, 0])
ax_irates = fig.add_subplot(gs[2, 0])
rasters.plot_avg_firing_rate_spikes(ESpikes,
ylabelPos=self.myc['ylabelPos'],
color='red',
tLimits=tLimits,
ax=ax_erates,
dt=.5,
winLen=2.)
rasters.plot_avg_firing_rate_spikes(ISpikes,
ylabelPos=self.myc['ylabelPos'],
color='blue',
tLimits=tLimits,
ax=ax_irates,
dt=.5,
winLen=2.)
gsl = .12
gsb = .02
gsr = .95
gst = .95
#fig.text(0.01, gst, 'B', size=16, weight='bold',
# va='bottom', ha='left')
gs.update(left=gsl, bottom=gsb, right=gsr, top=gst, hspace=.2)
ax_theta = fig.add_axes(
Bbox.from_extents(gsl, gst - .015, gsr, gst + .01))
t = np.arange(tLimits[0], tLimits[1] + self.dt, self.dt)
theta = self.const + .5 * (1. + np.cos(2 * np.pi * self.freq * 1e-3 *
t - np.pi)) * (1 - self.const)
ax_theta.fill_between(t,
theta,
edgecolor='None',
color=self.myc['theta_color'])
ax_theta.set_xlim([tLimits[0], tLimits[1]])
ax_theta.set_ylim(-.02, 1.02)
ax_theta.axis('off')
plt.savefig(self.get_fname('pastoll_et_al_rasters.pdf'),
dpi=300,
transparent=True)
plt.close(fig)
def plot(self, *args, **kwargs):
myc= self._get_class_config()
tLimits = [5.e3, 6e3]
fig = self._get_final_fig(self.myc['fig_size'])
gs = gridspec.GridSpec(3, 1, height_ratios=(2.5, 1, 1))
data = DataStorage.open(self.myc['data_file'], 'r')
trial_data = data['trials'][0]
events_e = trial_data['spikeMon_e']['events']
ESpikes = PopulationSpikes(trial_data['net_attr']['net_Ne'],
events_e['senders'],
events_e['times'])
events_i = trial_data['spikeMon_i']['events']
ISpikes = PopulationSpikes(trial_data['net_attr']['net_Ni'],
events_i['senders'],
events_i['times'])
# EI Raster
ax_raster = fig.add_subplot(gs[0, 0])
rasters.plotEIRaster(
ESpikes, ISpikes,
ylabelPos=self.myc['ylabelPos'],
tLimits=tLimits,
markersize=self.config['scale_factor']*self.myc['markersize'],
yticks=True,
sigmaTitle=False,
ann_EI=False,
scaleBar=125, scaleX=.8, scaleY=-.05, scaleText='ms',
scaleTextYOffset=.03, scaleHeight=.01,
rasterized=False,
reshape_senders=False)
# EI rates
ax_erates = fig.add_subplot(gs[1, 0])
ax_irates = fig.add_subplot(gs[2, 0])
rasters.plot_avg_firing_rate_spikes(ESpikes,
ylabelPos=self.myc['ylabelPos'],
color='red',
tLimits=tLimits,
ax=ax_erates,
dt=.5,
winLen=2.)
rasters.plot_avg_firing_rate_spikes(ISpikes,
ylabelPos=self.myc['ylabelPos'],
color='blue',
tLimits=tLimits,
ax=ax_irates,
dt=.5,
winLen=2.)
gsl = .12
gsb = .02
gsr = .95
gst = .95
#fig.text(0.01, gst, 'B', size=16, weight='bold',
# va='bottom', ha='left')
gs.update(left=gsl, bottom=gsb, right=gsr, top=gst, hspace=.2)
ax_theta = fig.add_axes(Bbox.from_extents(gsl, gst - .015,
gsr, gst + .01))
t = np.arange(tLimits[0], tLimits[1]+self.dt, self.dt)
theta = self.const + .5 * (1. +
np.cos(2*np.pi*self.freq*1e-3*t - np.pi)) * (1 - self.const)
ax_theta.fill_between(t, theta, edgecolor='None',
color=self.myc['theta_color'])
ax_theta.set_xlim([tLimits[0], tLimits[1]])
ax_theta.set_ylim(-.02, 1.02)
ax_theta.axis('off')
plt.savefig(self.get_fname('pastoll_et_al_rasters.pdf'), dpi=300,
transparent=True)
plt.close(fig)
