def test():
"""Test"""
# -- Create QApplication
import guidata
_app = guidata.qapplication()
# --
from numpy import linspace, sin
x = linspace(-10, 10, 200)
dy = x / 100.0
y = sin(sin(sin(x)))
x2 = linspace(-10, 10, 20)
y2 = sin(sin(sin(x2)))
curve2 = make.curve(x2, y2, color="g", curvestyle="Sticks")
curve2.setTitle("toto")
plot(
make.curve(x, y, color="b"),
curve2,
make.curve(x, sin(2 * y), color="r"),
make.merror(x, y / 2, dy),
make.label("Relative position <b>outside</b>", (x[0], y[0]),
(-10, -10), "BR"),
make.label("Relative position <i>inside</i>", (x[0], y[0]), (10, 10),
"TL"),
make.label("Absolute position", "R", (0, 0), "R"),
make.legend("TR"),
make.marker(
position=(5.0, 0.8),
label_cb=lambda x, y: "A = %.2f" % x,
markerstyle="|",
movable=False,
),
)
def test():
"""Test"""
# -- Create QApplication
import guidata
_app = guidata.qapplication()
# --
from numpy import linspace, sin
x = linspace(-10, 10, 200)
dy = x / 100.0
y = sin(sin(sin(x)))
x2 = linspace(-10, 10, 20)
y2 = sin(sin(sin(x2)))
curve2 = make.curve(x2, y2, color="g", curvestyle="Sticks")
curve2.setTitle("toto")
plot(
make.curve(x, y, color="b"),
curve2,
make.curve(x, sin(2 * y), color="r"),
make.merror(x, y / 2, dy),
make.label("Relative position <b>outside</b>", (x[0], y[0]), (-10, -10), "BR"),
make.label("Relative position <i>inside</i>", (x[0], y[0]), (10, 10), "TL"),
make.label("Absolute position", "R", (0, 0), "R"),
make.legend("TR"),
make.marker(position=(5.0, 0.8), label_cb=lambda x, y: "A = %.2f" % x, markerstyle="|", movable=False),
)
def add_epochs(plot, epochs, units=None):
""" Add Epoch markers to a guiqwt plot.
:param plot: The plot object.
:type plot: :class:`guiqwt.baseplot.BasePlot`
:param sequence epochs: The epochs (neo :class:`neo.Epoch` objects).
:param units: The x-scale of the plot. If this is ``None``,
the time unit of the events will be use.
"""
for e in epochs:
if units:
start = e.time.rescale(units)
end = (e.time + e.duration).rescale(units)
else:
start = e.time
end = e.time + e.duration
time = (start + end) / 2.0
o = make.range(start, end)
o.setTitle(e.label)
o.set_readonly(True)
o.set_movable(False)
o.set_resizable(False)
o.set_selectable(False)
o.set_rotatable(False)
plot.add_item(o)
nameObject = _MarkerName(e.label)
plot.add_item(make.marker(
(time, 0), nameObject.get_name,
movable=False, markerstyle='|', color='k', linestyle='NoPen',
linewidth=1))
def create_rt_ms2_marker():
marker = make.marker(position=(0, 0),
markerstyle="|",
label_cb=lambda x, y: "<div style='color:red'>rt_ms2</div>",
constraint_cb=lambda x, y: (x, y),
movable=False,
readonly=False,
color="#ff7777",
linewidth=1)
# else the get_unique_item methods in modified_guiqwt fail:
class DummyMarkerAsOnlyOneTrueMarkerIsAllowed(Marker):
pass
marker.__class__ = DummyMarkerAsOnlyOneTrueMarkerIsAllowed
return marker
def _split_plot_hor(channels, spikes, ref_units, time_unit, progress, plot):
""" Fill a plot with spikeshorizontally split by channel. Returns legend.
"""
legend_items = []
offset = 0 * time_unit
for c in channels:
for u in spikes.keys():
first_wave = True
color = helper.get_object_color(u)
for s in spikes[u]:
if s.waveform is None or s.sampling_rate is None:
raise SpykeException(
'Cannot create waveform plot: '
'At least one spike has no '
'waveform or sampling rate!')
x = (sp.arange(s.waveform.shape[0]) /
s.sampling_rate).rescale(time_unit)
curve = make.curve(
x + offset,
s.waveform[:, c].rescale(ref_units), u.name,
color=color)
if c == channels[0] and first_wave:
legend_curve = make.curve(
sp.array([0]), sp.array([0]), u.name,
color=color, linewidth=2)
legend_items.append(legend_curve)
plot.add_item(legend_curve)
first_wave = False
plot.add_item(curve)
progress.step()
offset += x[-1]
if c != channels[-1]:
plot.add_item(
make.marker((offset, 0), lambda x, y: '',
movable=False, markerstyle='|',
color='k', linestyle='-', linewidth=1))
l = make.legend(restrict_items=legend_items)
plot.add_item(l)
plot.set_axis_title(BasePlot.Y_LEFT, 'Voltage')
plot.set_axis_unit(
BasePlot.Y_LEFT, ref_units.dimensionality.string)
return l
def add_events(plot, events, units=None):
""" Add Event markers to a guiqwt plot.
:param plot: The plot object.
:type plot: :class:`guiqwt.baseplot.BasePlot`
:param sequence events: The events (neo :class:`neo.Event` objects).
:param Quantity units: The x-scale of the plot. If this is ``None``,
the time unit of the events will be use.
"""
for m in events:
nameObject = _MarkerName(m.label)
if units:
time = m.time.rescale(units)
else:
time = m.time
plot.add_item(
make.marker(
(time, 0), nameObject.get_name,
movable=False, markerstyle='|', color='k', linestyle=':',
linewidth=1))
def add_events(plot, events, units=None):
""" Add Event markers to a guiqwt plot.
:param plot: The plot object.
:type plot: :class:`guiqwt.baseplot.BasePlot`
:param sequence events: The events (neo :class:`neo.Event` objects).
:param Quantity units: The x-scale of the plot. If this is ``None``,
the time unit of the events will be use.
"""
for m in events:
nameObject = _MarkerName(m.label)
if units:
time = m.time.rescale(units)
else:
time = m.time
plot.add_item(
make.marker((time, 0),
nameObject.get_name,
movable=False,
markerstyle='|',
color='k',
linestyle=':',
linewidth=1))
def add_epochs(plot, epochs, units=None):
""" Add Epoch markers to a guiqwt plot.
:param plot: The plot object.
:type plot: :class:`guiqwt.baseplot.BasePlot`
:param sequence epochs: The epochs (neo :class:`neo.Epoch` objects).
:param units: The x-scale of the plot. If this is ``None``,
the time unit of the events will be use.
"""
for e in epochs:
if units:
start = e.time.rescale(units)
end = (e.time + e.duration).rescale(units)
else:
start = e.time
end = e.time + e.duration
time = (start + end) / 2.0
o = make.range(start, end)
o.setTitle(e.label)
o.set_readonly(True)
o.set_movable(False)
o.set_resizable(False)
o.set_selectable(False)
o.set_rotatable(False)
plot.add_item(o)
nameObject = _MarkerName(e.label)
plot.add_item(
make.marker((time, 0),
nameObject.get_name,
movable=False,
markerstyle='|',
color='k',
linestyle='NoPen',
linewidth=1))
def _split_plot_hor(channels, spikes, strong, fade, ref_units, time_unit,
progress, plot):
""" Fill a plot with spikeshorizontally split by channel. Returns legend.
"""
offset = 0 * time_unit
for c in channels:
x_off = 0 * time_unit
for u in spikes:
color = helper.get_object_color(u)
qcol = Qt.QColor(color)
alpha = fade if fade > 0.0 else 1.0
alpha_step = 1.0 - fade if fade > 0.0 else -1.0 - fade
alpha_step /= len(spikes[u])
if len(spikes[u]) == 1:
alpha = 1.0
for s in spikes[u]:
if s.waveform is None or s.sampling_rate is None:
raise SpykeException('Cannot create waveform plot: '
'At least one spike has no '
'waveform or sampling rate!')
x = (sp.arange(s.waveform.shape[0]) /
s.sampling_rate).rescale(time_unit)
x_off = max(x_off, x[-1])
curve = make.curve(x + offset,
s.waveform[:, c].rescale(ref_units),
u.name,
color=color)
qcol.setAlphaF(alpha)
curve.setPen(Qt.QPen(qcol))
alpha += alpha_step
plot.add_item(curve)
progress.step()
for u in strong:
color = helper.get_object_color(u)
for s in strong[u]:
x = (sp.arange(s.waveform.shape[0]) /
s.sampling_rate).rescale(time_unit)
x_off = max(x_off, x[-1])
outline = make.curve(x + offset,
s.waveform[:, c].rescale(ref_units),
color='#000000',
linewidth=4)
curve = make.curve(x + offset,
s.waveform[:, c].rescale(ref_units),
color=color,
linewidth=2)
plot.add_item(outline)
plot.add_item(curve)
progress.step()
offset += x_off
if c != channels[-1]:
plot.add_item(
make.marker((offset, 0),
lambda x, y: '',
movable=False,
markerstyle='|',
color='k',
linestyle='-',
linewidth=1))
l = _add_legend(plot, spikes, strong)
return l
def _split_plot_hor(channels, spikes, strong, fade, ref_units, time_unit,
progress, plot):
""" Fill a plot with spikeshorizontally split by channel. Returns legend.
"""
offset = 0 * time_unit
for c in channels:
x_off = 0 * time_unit
for u in spikes:
color = helper.get_object_color(u)
qcol = Qt.QColor(color)
alpha = fade if fade > 0.0 else 1.0
alpha_step = 1.0 - fade if fade > 0.0 else -1.0 - fade
alpha_step /= len(spikes[u])
if len(spikes[u]) == 1:
alpha = 1.0
for s in spikes[u]:
if s.waveform is None or s.sampling_rate is None:
raise SpykeException(
'Cannot create waveform plot: '
'At least one spike has no '
'waveform or sampling rate!')
x = (sp.arange(s.waveform.shape[0]) /
s.sampling_rate).rescale(time_unit)
x_off = max(x_off, x[-1])
curve = make.curve(
x + offset,
s.waveform[:, c].rescale(ref_units), u.name,
color=color)
qcol.setAlphaF(alpha)
curve.setPen(Qt.QPen(qcol))
alpha += alpha_step
plot.add_item(curve)
progress.step()
for u in strong:
color = helper.get_object_color(u)
for s in strong[u]:
x = (sp.arange(s.waveform.shape[0]) /
s.sampling_rate).rescale(time_unit)
x_off = max(x_off, x[-1])
outline = make.curve(
x + offset, s.waveform[:, c].rescale(ref_units),
color='#000000', linewidth=4)
curve = make.curve(
x + offset, s.waveform[:, c].rescale(ref_units),
color=color, linewidth=2)
plot.add_item(outline)
plot.add_item(curve)
progress.step()
offset += x_off
if c != channels[-1]:
plot.add_item(
make.marker((offset, 0), lambda x, y: '',
movable=False, markerstyle='|',
color='k', linestyle='-', linewidth=1))
l = _add_legend(plot, spikes, strong)
return l
def spikes(spikes, axes_style, anti_alias=False, time_unit=pq.ms,
progress=None):
""" Create a plot dialog with spike waveforms.
:param dict spikes: A dictionary of spike lists.
:param int axes_style: Plotting mode. The following values are possible:
1 Show each channel in a seperate plot.
2 Show all channels in the same plot vertically.
3 Show all channels in the same plot horizontally.
:param bool anti_alias: Determines whether an antialiased plot is created.
:param Quantity time_unit: The (time) unit for the x axis
:param progress: Set this parameter to report progress.
:type progress: :class:`spykeutils.progress_indicator.ProgressIndicator`
"""
if not spikes or sum((len(l) for l in spikes.itervalues())) < 1:
raise SpykeException('No spikes for spike waveform plot!')
if not progress:
progress = ProgressIndicator()
progress.begin('Creating waveform plot')
progress.set_ticks(sum((len(l) for l in spikes.itervalues())))
win_title = 'Spike waveforms'
win = PlotDialog(toolbar=True, wintitle=win_title)
indices = spikes.keys()
ref_spike = spikes[spikes.keys()[0]][0]
if ref_spike.waveform is None:
raise SpykeException('Cannot create waveform plot: At least one spike '
'has no waveform or sampling rate!')
ref_units = ref_spike.waveform.units
channels = range(ref_spike.waveform.shape[1])
plot = None
if axes_style == 1: # Separate channel plots
for c in channels:
pW = BaseCurveWidget(win)
plot = pW.plot
plot.set_antialiasing(anti_alias)
for u in indices:
color = helper.get_object_color(u)
for s in spikes[u]:
if s.waveform is None or s.sampling_rate is None:
raise SpykeException('Cannot create waveform plot: '
'At least one spike has no '
'waveform or sampling rate!')
x = (sp.arange(s.waveform.shape[0]) /
s.sampling_rate).rescale(time_unit)
curve = make.curve(x, s.waveform[:, c].rescale(ref_units),
title=u.name, color=color)
plot.add_item(curve)
progress.step()
win.add_plot_widget(pW, c)
helper.make_window_legend(win, indices, True)
else: # Only one plot needed
pW = BaseCurveWidget(win)
plot = pW.plot
plot.set_antialiasing(anti_alias)
legend_items = []
if axes_style == 3: # Horizontal split
offset = 0 * time_unit
for c in channels:
for u in indices:
first_wave = True
color = helper.get_object_color(u)
for s in spikes[u]:
if s.waveform is None or s.sampling_rate is None:
raise SpykeException('Cannot create waveform plot: '
'At least one spike has no '
'waveform or sampling rate!')
x = (sp.arange(s.waveform.shape[0]) /
s.sampling_rate).rescale(time_unit)
curve = make.curve(x + offset,
s.waveform[:, c].rescale(ref_units), u.name,
color=color)
if c == channels[0] and first_wave == True:
legend_items.append(curve)
first_wave = False
plot.add_item(curve)
progress.step()
offset += x[-1]
if c != channels[-1]:
plot.add_item(make.marker((offset, 0), lambda x,y: '',
movable=False, markerstyle='|', color='k',
linestyle='-', linewidth=1))
else: # Vertical split
channels.reverse()
# Find plot y offset
maxY = []
minY = []
for i, c in enumerate(channels):
maxY.append(max(max(s.waveform[:, c].max() for s in d)
for d in spikes.itervalues()))
minY.append(min(min(s.waveform[:, c].min() for s in d)
for d in spikes.itervalues()))
maxOffset = 0 * ref_units
for i in range(1, len(channels)):
offset = maxY[i - 1] - minY[i]
if offset > maxOffset:
maxOffset = offset
offset = 0 * ref_units
for c in channels:
for u in indices:
first_wave = True
color = helper.get_object_color(u)
for s in spikes[u]:
if s.waveform is None or s.sampling_rate is None:
raise SpykeException('Cannot create waveform plot: '
'At least one spike has no '
'waveform or sampling rate!')
x = (sp.arange(s.waveform.shape[0]) /
s.sampling_rate).rescale(time_unit)
curve = make.curve(x,
s.waveform[:, c].rescale(ref_units) + offset,
u.name, color=color)
if c == channels[0] and first_wave == True:
legend_items.append(curve)
first_wave = False
plot.add_item(curve)
progress.step()
offset += maxOffset
l = make.legend(restrict_items=legend_items)
plot.add_item(l)
win.add_plot_widget(pW, 0)
win.add_legend_option([l], True)
win.add_custom_curve_tools()
progress.done()
win.show()
plot.set_axis_title(BasePlot.X_BOTTOM, 'Time')
plot.set_axis_unit(BasePlot.X_BOTTOM, x.dimensionality.string)
if axes_style == 1:
win.add_x_synchronization_option(True, channels)
win.add_y_synchronization_option(True, channels)
if len(channels) == 1 or axes_style > 1:
plot.set_axis_title(BasePlot.Y_LEFT, 'Voltage')
plot.set_axis_unit(BasePlot.Y_LEFT, ref_units.dimensionality.string)
return win
