def _ISI_plot(win, trains, bin_size, cut_off, bar_plot, unit):
""" Fill a plot window with a interspike interval histogram of units
"""
bin_size.rescale(unit)
cut_off.rescale(unit)
bins = sp.arange(0*unit, cut_off, bin_size) * unit
pW = BaseCurveWidget(win)
plot = pW.plot
legend_items = []
if bar_plot:
u = trains.keys()[0]
if 'unique_id' in u.annotations:
color = helper.get_color(u.annotations['unique_id'])
else:
color = helper.get_color(hash(u))
win.add_unit_color(color)
for u, train_list in trains.iteritems():
intervals = []
for t in train_list:
t = t.rescale(unit)
sTrain = sp.asarray(t)
sTrain.sort()
intervals.extend(sp.diff(sTrain))
(isi, bins) = sp.histogram(intervals, bins)
if isinstance(u, neo.Unit):
color = helper.get_object_color(u)
name = u.name
else:
name = 'No unit'
color = 'k'
if not bar_plot:
curve = make.curve(bins, isi, name,
color=color)
legend_items.append(curve)
plot.add_item(curve)
else:
show_isi = list(isi)
show_isi.insert(0, show_isi[0])
curve = make.curve(bins, show_isi, name, color='k',
curvestyle="Steps", shade=1.0)
plot.add_item(curve)
break
win.add_plot_widget(pW, 0)
if not bar_plot:
legend = make.legend(restrict_items=legend_items)
plot.add_item(legend)
win.add_legend_option([legend], True)
plot.set_axis_title(BasePlot.Y_LEFT, 'Number of intervals')
plot.set_axis_title(BasePlot.X_BOTTOM, 'Interval length')
plot.set_axis_unit(BasePlot.X_BOTTOM, unit.dimensionality.string)
win.add_custom_curve_tools()
win.show()
if bar_plot: # Rescale Bar ISI
scale = plot.axisScaleDiv(BasePlot.Y_LEFT)
plot.setAxisScale(BasePlot.Y_LEFT, 0, scale.upperBound())
plot.set_antialiasing(False)
else:
plot.set_antialiasing(True)
return True
def ISI(trains, bin_size, cut_off, bar_plot=False, unit=pq.ms):
""" Create a plot dialog with an interspike interval histogram.
:param dict trains: Dictionary with lists of spike trains indexed by
units for which to display ISI histograms
:param bin_size: Bin size (time)
:type bin_size: Quantity scalar
:param cut_off: End of histogram (time)
:type bin_size: Quantity scalar
:param bool bar_plot: If ``True``, create a bar ISI histogram
(automatically limits plot to just the first of the given units).
Else, create a line ISI histogram.
:param Quantity unit: Unit of X-Axis. If None, milliseconds are used.
"""
if not trains:
raise SpykeException('No spike trains for ISI histogram')
win_title = 'ISI Histogram | Bin size: ' + str(bin_size)
win = PlotDialog(toolbar=True, wintitle=win_title)
bin_size.rescale(unit)
cut_off.rescale(unit)
bins = sp.arange(0*unit, cut_off, bin_size) * unit
pW = BaseCurveWidget(win)
plot = pW.plot
legend_items = []
if bar_plot:
u = trains.keys()[0]
if 'unique_id' in u.annotations:
color = helper.get_color(u.annotations['unique_id'])
else:
color = helper.get_color(hash(u))
win.add_unit_color(color)
for u, train_list in trains.iteritems():
intervals = []
for t in train_list:
t = t.rescale(unit)
sTrain = sp.asarray(t)
sTrain.sort()
intervals.extend(sp.diff(sTrain))
(isi, bins) = sp.histogram(intervals, bins)
if isinstance(u, neo.Unit):
color = helper.get_object_color(u)
name = u.name
else:
name = 'No unit'
color = 'k'
if not bar_plot:
curve = make.curve(bins, isi, name,
color=color)
legend_items.append(curve)
plot.add_item(curve)
else:
show_isi = list(isi)
show_isi.insert(0, show_isi[0])
curve = make.curve(bins, show_isi, name, color='k',
curvestyle="Steps", shade=1.0)
plot.add_item(curve)
break
win.add_plot_widget(pW, 0)
if not bar_plot:
legend = make.legend(restrict_items=legend_items)
plot.add_item(legend)
win.add_legend_option([legend], True)
plot.set_axis_title(BasePlot.Y_LEFT, 'Number of intervals')
plot.set_axis_title(BasePlot.X_BOTTOM, 'Interval length')
plot.set_axis_unit(BasePlot.X_BOTTOM, unit.dimensionality.string)
win.add_custom_curve_tools()
win.show()
if bar_plot: # Rescale Bar ISI
scale = plot.axisScaleDiv(BasePlot.Y_LEFT)
plot.setAxisScale(BasePlot.Y_LEFT, 0, scale.upperBound())
plot.set_antialiasing(False)
else:
plot.set_antialiasing(True)
return win
