def _plot(self, trial, figure, invert_colors=False, line_width=1,
max_drawn=250, opacity=0.25, point_size=2):
features = trial.features.data
def as_frac(x=None, y=None):
f = figure
canvas_size_in_pixels = (f.get_figwidth()*f.get_dpi(),
f.get_figheight()*f.get_dpi())
return as_fraction(x=x, y=y,
canvas_size_in_pixels=canvas_size_in_pixels)
figure.set_facecolor(background[invert_colors])
figure.set_edgecolor(foreground[invert_colors])
figure.subplots_adjust(left=as_frac(x=80),
right=1.0-as_frac(x=35),
bottom=as_frac(y=40),
top=1.0-as_frac(y=25))
axes = figure.add_subplot(111)
for feature in sample_data(features, max_drawn):
if point_size > 0:
marker = 'o'
else:
marker = ''
axes.plot(feature, color=line_color[invert_colors],
alpha=opacity,
linewidth=line_width,
marker=marker,
markeredgecolor=line_color[invert_colors],
markerfacecolor=foreground[invert_colors],
markersize=point_size)
axes.text(0.98, 0.95, '%d drawn' % min(max_drawn, len(features)),
color=foreground[invert_colors],
horizontalalignment='right',
verticalalignment='center',
transform=axes.transAxes)
axes.set_ylabel('Feature Amplitude', color=foreground[invert_colors])
axes.set_xlabel('Feature Index (found features for %d events)' % len(features),
color=foreground[invert_colors])
# axes color fixing
frame = axes.patch
frame.set_facecolor(background[invert_colors])
frame.set_edgecolor(foreground[invert_colors])
for spine in axes.spines.values():
spine.set_color(foreground[invert_colors])
lines = axes.get_xticklines()
lines.extend(axes.get_yticklines())
for line in lines:
line.set_color(foreground[invert_colors])
labels = axes.get_xticklabels()
labels.extend(axes.get_yticklabels())
for label in labels:
label.set_color(foreground[invert_colors])
def _plot(self, trial, figure, invert_colors=False, line_width=1,
max_drawn=250, opacity=0.25, point_size=2, legend=False):
features = trial.features.data
def as_frac(x=None, y=None):
f = figure
canvas_size_in_pixels = (f.get_figwidth()*f.get_dpi(),
f.get_figheight()*f.get_dpi())
return as_fraction(x=x, y=y,
canvas_size_in_pixels=canvas_size_in_pixels)
figure.set_facecolor(background[invert_colors])
figure.set_edgecolor(foreground[invert_colors])
figure.subplots_adjust(left=as_frac(x=80),
right=1.0-as_frac(x=35),
bottom=as_frac(y=40),
top=1.0-as_frac(y=25))
axes = figure.add_subplot(111)
cfs = trial.clustered_features
for i, cluster_name in enumerate(sorted(cfs.keys())):
features = cfs[cluster_name]
num_drawn = min(max_drawn, len(features))
color=cluster_colors[invert_colors][
i%len(cluster_colors[invert_colors])]
if point_size > 0:
marker = 'o'
else:
marker = ''
label = None
alpha = opacity
for feature in sample_data(features, max_drawn):
axes.plot(feature,
color=color,
alpha=alpha,
linewidth=line_width,
marker=marker,
markeredgecolor=foreground[invert_colors],
markerfacecolor=color,
markersize=point_size,
label=label)
# plot the average spike window for this cluster.
average_feature = numpy.average(features, axis=0)
label = '%s: %d of %d drawn' % (cluster_name,
num_drawn, len(features))
alpha = 1.0
axes.plot(average_feature,
color=color,
alpha=alpha,
linewidth=line_width,
marker=marker,
markeredgecolor=foreground[invert_colors],
markerfacecolor=color,
markersize=point_size,
label=label)
axes.set_ylabel('Feature Amplitude', color=foreground[invert_colors])
axes.set_xlabel('Feature Index',
color=foreground[invert_colors])
# axes color fixing
frame = axes.patch
frame.set_facecolor(background[invert_colors])
frame.set_edgecolor(foreground[invert_colors])
for spine in axes.spines.values():
spine.set_color(foreground[invert_colors])
lines = axes.get_xticklines()
lines.extend(axes.get_yticklines())
for line in lines:
line.set_color(foreground[invert_colors])
labels = axes.get_xticklabels()
labels.extend(axes.get_yticklabels())
for label in labels:
label.set_color(foreground[invert_colors])
# setup legend
if legend:
l = axes.legend(loc='upper right')
frame = l.get_frame()
frame.set_facecolor(background[invert_colors])
frame.set_edgecolor(foreground[invert_colors])
for text in l.texts:
text.set_color(foreground[invert_colors])
def _plot(self, trial, figure, invert_colors=False, line_width=1,
max_drawn=250, opacity=0.25, point_size=0,
spikes='Detection Filtered', legend=False):
def as_frac(x=None, y=None):
f = figure
canvas_size_in_pixels = (f.get_figwidth()*f.get_dpi(),
f.get_figheight()*f.get_dpi())
return as_fraction(x=x, y=y,
canvas_size_in_pixels=canvas_size_in_pixels)
figure.set_facecolor(background[invert_colors])
figure.set_edgecolor(foreground[invert_colors])
figure.subplots_adjust(left=as_frac(x=80),
right=1.0-as_frac(x=35),
bottom=as_frac(y=40),
top=1.0-as_frac(y=25))
axes = figure.add_subplot(111)
if spikes == 'Detection Filtered':
csws = trial.clustered_df_spike_windows
sampling_freq = trial.df_sampling_freq.data
else:
csws = trial.clustered_ef_spike_windows
sampling_freq = trial.ef_sampling_freq.data
times = numpy.arange(0, csws.values()[0].shape[-1],
dtype=numpy.float64)/sampling_freq*1000.0
# plot the spike windows
for i, cluster_name in enumerate(sorted(csws.keys())):
spike_windows = csws[cluster_name]
num_drawn = min(max_drawn, len(spike_windows))
color=cluster_colors[invert_colors][
i%len(cluster_colors[invert_colors])]
if point_size > 0:
marker = 'o'
else:
marker = ''
label = None
alpha = opacity
for spike_window in sample_data(spike_windows, max_drawn):
axes.plot(times, spike_window,
color=color,
alpha=alpha,
linewidth=line_width,
marker=marker,
markeredgecolor=foreground[invert_colors],
markerfacecolor=color,
markersize=point_size,
label=label)
# plot the average spike window for this cluster.
average_spike_window = numpy.average(spike_windows, axis=0)
label = '%s: %d of %d drawn' % (cluster_name,
num_drawn, len(spike_windows))
alpha = 1.0
axes.plot(times, average_spike_window,
color=color,
alpha=alpha,
linewidth=line_width,
marker=marker,
markeredgecolor=foreground[invert_colors],
markerfacecolor=color,
markersize=point_size,
label=label)
axes.set_ylabel('Amplitude (mV)', color=foreground[invert_colors])
axes.set_xlabel('Time (ms)',
color=foreground[invert_colors])
# axes color fixing
frame = axes.patch
frame.set_facecolor(background[invert_colors])
frame.set_edgecolor(foreground[invert_colors])
for spine in axes.spines.values():
spine.set_color(foreground[invert_colors])
lines = axes.get_xticklines()
lines.extend(axes.get_yticklines())
for line in lines:
line.set_color(foreground[invert_colors])
labels = axes.get_xticklabels()
labels.extend(axes.get_yticklabels())
for label in labels:
label.set_color(foreground[invert_colors])
# setup legend
if legend:
l = axes.legend(loc='upper right')
frame = l.get_frame()
frame.set_facecolor(background[invert_colors])
frame.set_edgecolor(foreground[invert_colors])
for text in l.texts:
text.set_color(foreground[invert_colors])