def test_get_timeseries_tt_negativeistop():
data = list(range(100, 200, 10))
ts = TimeSeries(name='test_timeseries',
data=data,
unit='m',
starting_time=0.,
rate=1.0)
tt = get_timeseries_tt(ts, istop=-1)
np.testing.assert_array_equal(tt, [0., 1., 2., 3., 4., 5., 6., 7.])
def test_get_timeseries_tt_negativeistop():
data = list(range(100, 200, 10))
ts = TimeSeries(name="test_timeseries",
data=data,
unit="m",
starting_time=0.0,
rate=1.0)
tt = get_timeseries_tt(ts, istop=-1)
np.testing.assert_array_equal(tt, [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0])
def test_get_timeseries_tt_infstarting_time():
data = list(range(100, 200, 10))
ts = TimeSeries(name='test_timeseries',
data=data,
unit='m',
starting_time=np.inf,
rate=1.0)
tt = get_timeseries_tt(ts)
np.testing.assert_array_equal(tt, [0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])
def test_get_timeseries_tt_infstarting_time():
data = list(range(100, 200, 10))
ts = TimeSeries(name="test_timeseries",
data=data,
unit="m",
starting_time=np.inf,
rate=1.0)
tt = get_timeseries_tt(ts)
np.testing.assert_array_equal(
tt, [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0])
def trials_psth(self,
before=1.5,
after=1.5,
figsize=(6, 6)): # time_window
"""
Trial data by event times and plot
Parameters
----------
before: float
Time before that event (should be positive)
after: float
Time after that event
figsize: tuple, optional
Returns
-------
matplotlib.Figure
"""
# mask = (self.events > time_window[0]) \
# & (self.events < time_window[1])
# active_events = self.events[mask]
starts = self.events - before
stops = self.events + after
trials = align_by_times_with_rate(self.spatial_series, starts, stops)
if trials.size == 0:
return print("No trials present")
tt = get_timeseries_tt(self.spatial_series,
istart=self.spatial_series.starting_time)
zero_ind = before * (1 / (tt[1] - tt[0]))
if len(np.shape(trials)) == 3:
diff_x = trials[:, :, 0].T - trials[:, int(zero_ind), 0]
diff_y = trials[:, :, 1].T - trials[:, int(zero_ind), 1]
diffs = np.dstack([diff_x, diff_y])
distance = np.linalg.norm(diffs, axis=2)
elif len(np.shape(trials)) == 2:
diff_x = trials[:, :].T - trials[:, int(zero_ind)]
elif len(np.shape(trials)) == 1:
diff_x = trials
fig, axs = plt.subplots(1, 1, figsize=figsize)
axs.set_title("Event-triggered Wrist Displacement")
self.show_psth(distance, axs, before, after)
return fig
def on_change(change):
time_window = self.controls["time_window"].value
istart = timeseries_time_to_ind(timeseries, time_window[0])
istop = timeseries_time_to_ind(timeseries, time_window[1])
tt = get_timeseries_tt(timeseries, istart, istop)
yy, units = get_timeseries_in_units(timeseries, istart, istop)
with self.out_fig.batch_update():
if len(yy.shape) == 1:
self.out_fig.data[0].x = tt
self.out_fig.data[0].y = yy
else:
for k, key in enumerate(POSITION_KEYS):
data = positions[key]
yy, units = get_timeseries_in_units(
data, istart, istop)
for i, dd in enumerate(yy.T):
self.out_fig.data[(k * data_dim) + i].x = tt
self.out_fig.data[(k * data_dim) + i].y = dd
def test_get_timeseries_tt_timestamp(self):
tt = get_timeseries_tt(self.ts)
np.testing.assert_array_equal(tt,
[0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])
def test_get_timeseries_tt_timestamp(self):
tt = get_timeseries_tt(self.ts_rate)
np.testing.assert_array_equal(
tt, [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0])
def tab1(self, nwb_file):
position_keys = list(nwb_file.processing["behavior"].
data_interfaces["Position"].spatial_series.keys())
spatial_series = nwb_file.processing["behavior"].data_interfaces[
"Position"][position_keys[0]]
tt = get_timeseries_tt(spatial_series,
istart=spatial_series.starting_time)
time_trace_window_controller = StartAndDurationController(tmax=tt[-1],
tmin=tt[0],
start=0,
duration=5)
reach_arm = (nwb_file.processing["behavior"].
data_interfaces["ReachEvents"].description)
reach_arm = map(lambda x: x.capitalize(), reach_arm.split("_"))
reach_arm = list(reach_arm)
reach_arm = "_".join(reach_arm)
jointpos_widget = AllPositionTracesPlotlyWidget(
nwb_file.processing["behavior"].data_interfaces["Position"]
[reach_arm],
foreign_time_window_controller=time_trace_window_controller,
)
text = "(b) Movement segments"
jointpos_label = widgets.HTML(value=f"<b><font size=4>{text}</b>")
jointpos = widgets.VBox([jointpos_label, jointpos_widget],
layout=self.box_layout)
skeleton_widget = SkeletonPlot(
nwb_file.processing["behavior"].data_interfaces["Position"],
foreign_time_window_controller=time_trace_window_controller,
)
text = "(a) Tracked joints"
skeleton_label = widgets.HTML(value=f"<b><font size=4>{text}</b>")
skeleton = widgets.VBox([skeleton_label, skeleton_widget],
layout=self.box_layout)
ecog_widget = ElectricalSeriesWidget(
nwb_file.acquisition["ElectricalSeries"],
foreign_time_window_controller=time_trace_window_controller,
)
text = "(d) Raw ECoG"
ecog_label = widgets.HTML(value=f"<b><font size=4>{text}</b>")
ecog = widgets.VBox([ecog_label, ecog_widget], layout=self.box_layout)
brain_widget = HumanElectrodesPlotlyWidget(nwb_file.electrodes)
text = "(c) Subject electrode locations"
brain_label = widgets.HTML(value=f"<b><font size=4>{text}</b>")
brain = widgets.VBox([brain_label, brain_widget],
layout=self.box_layout)
tab1_hbox_header = widgets.HBox([time_trace_window_controller])
tab1_row1_widgets = widgets.HBox(
[skeleton, jointpos],
layout=self.row_layout,
)
tab1_row2_widgets = widgets.HBox(
[brain, ecog],
layout=self.row_layout,
)
tab1 = widgets.VBox(
[tab1_hbox_header, tab1_row1_widgets, tab1_row2_widgets],
layout=self.box_layout,
)
return tab1
def __init__(
self,
events: Events,
position: Position,
acquisition: ElectricalSeries = None,
foreign_time_window_controller: StartAndDurationController = None,
):
super().__init__()
before_ft = widgets.FloatText(1.5,
min=0,
description="before (s)",
layout=Layout(width="200px"))
after_ft = widgets.FloatText(1.5,
min=0,
description="after (s)",
layout=Layout(width="200px"))
# Extract reach arm label from events, format to match key in Position
# spatial series
reach_arm = events.description
reach_arm = map(lambda x: x.capitalize(), reach_arm.split("_"))
reach_arm = list(reach_arm)
reach_arm = "_".join(reach_arm)
self.spatial_series = position.spatial_series[reach_arm]
# if foreign_time_window_controller is None:
self.tt = get_timeseries_tt(self.spatial_series,
istart=self.spatial_series.starting_time)
# self.time_window_controller = StartAndDurationController(
# tmax=self.tt[-1],
# tmin=self.tt[0],
# start=0,
# duration=5
# )
# show_time_controller = True
# else:
# self.time_window_controller = foreign_time_window_controller
# show_time_controller = False
# Store events in object
self.events = events.timestamps[:]
self.controls = dict(after=after_ft, before=before_ft)
out_fig = interactive_output(self.trials_psth, self.controls)
# self.time_window_controller.observe(self.updated_time_range)
# self.fig = go.FigureWidget()
# self.ecog_psth(acquisition)
# if show_time_controller:
# header_row = widgets.HBox([before_ft,
# after_ft,
# self.time_window_controller
# ]
# )
# else:
header_row = widgets.HBox([
before_ft,
after_ft,
])
self.children = [header_row, out_fig]
def set_out_fig(self):
timeseries = self.controls["timeseries"].value
time_window = self.controls["time_window"].value
istart = timeseries_time_to_ind(timeseries, time_window[0])
istop = timeseries_time_to_ind(timeseries, time_window[1])
data, units = get_timeseries_in_units(timeseries, istart, istop)
tt = get_timeseries_tt(timeseries, istart, istop)
positions = self.timeseries.get_ancestor("Position")
position_colors = {
key: color
for key, color in zip(POSITION_KEYS, DEFAULT_PLOTLY_COLORS)
}
data_dim = data.shape[1]
subplot_titles = np.repeat(POSITION_KEYS, data_dim)
if (len(data.shape) > 1) | len(POSITION_KEYS) > 1:
self.out_fig = go.FigureWidget(
make_subplots(rows=len(POSITION_KEYS),
cols=2,
subplot_titles=subplot_titles))
self.out_fig["layout"].update(width=800, height=700)
for k, key in enumerate(POSITION_KEYS):
data = positions[key].data[:]
color = position_colors[key]
for i, (yy, xyz) in enumerate(zip(data.T, ("x", "y", "z"))):
self.out_fig.add_trace(
go.Scattergl(x=tt,
y=yy,
marker_color=color,
showlegend=False),
row=k + 1,
col=i + 1,
)
if units:
yaxes_label = f"{xyz} ({units})"
else:
yaxes_label = xyz
self.out_fig.update_yaxes(title_text=yaxes_label,
row=k + 1,
col=i + 1)
self.out_fig.update_xaxes(showticklabels=False,
row=k + 1,
col=i + 1)
self.out_fig["layout"]["annotations"][(k * data_dim) +
i]["text"] = f"{key}"
self.out_fig.update_xaxes(showticklabels=True, row=k + 1, col=i)
self.out_fig.update_xaxes(showticklabels=True,
row=k + 1,
col=i + 1)
self.out_fig.update_xaxes(title_text="time (s)", row=k + 1, col=i)
self.out_fig.update_xaxes(title_text="time (s)",
row=k + 1,
col=i + 1)
else:
self.out_fig = go.FigureWidget()
self.out_fig.add_trace(go.Scatter(x=tt, y=data))
self.out_fig.update_xaxes(title_text="time (s)")
def on_change(change):
time_window = self.controls["time_window"].value
istart = timeseries_time_to_ind(timeseries, time_window[0])
istop = timeseries_time_to_ind(timeseries, time_window[1])
tt = get_timeseries_tt(timeseries, istart, istop)
yy, units = get_timeseries_in_units(timeseries, istart, istop)
with self.out_fig.batch_update():
if len(yy.shape) == 1:
self.out_fig.data[0].x = tt
self.out_fig.data[0].y = yy
else:
for k, key in enumerate(POSITION_KEYS):
data = positions[key]
yy, units = get_timeseries_in_units(
data, istart, istop)
for i, dd in enumerate(yy.T):
self.out_fig.data[(k * data_dim) + i].x = tt
self.out_fig.data[(k * data_dim) + i].y = dd
self.controls["time_window"].observe(on_change)
def update_traces(select_start_time, select_duration):
ctx = dash.callback_context
trigger_source = ctx.triggered[0]['prop_id'].split('.')[1]
if not trigger_source:
raise dash.exceptions.PreventUpdate
time_window = [
select_start_time, select_start_time + select_duration
]
# Update electrophys trace
timeseries = self.ecephys_trace
istart = timeseries_time_to_ind(timeseries, time_window[0])
istop = timeseries_time_to_ind(timeseries, time_window[1])
yy, units = get_timeseries_in_units(timeseries, istart, istop)
xx = get_timeseries_tt(timeseries, istart, istop)
xrange0, xrange1 = min(xx), max(xx)
self.traces.data[0].x = xx
self.traces.data[0].y = list(yy)
self.traces.update_layout(yaxis={
"range": [min(yy), max(yy)],
"autorange": False
},
xaxis={
"range": [xrange0, xrange1],
"autorange": False
})
# Update ophys trace
timeseries = self.ophys_trace
istart = timeseries_time_to_ind(timeseries, time_window[0])
istop = timeseries_time_to_ind(timeseries, time_window[1])
yy, units = get_timeseries_in_units(timeseries, istart, istop)
xx = get_timeseries_tt(timeseries, istart, istop)
self.traces.data[1].x = xx
self.traces.data[1].y = list(yy)
self.traces.update_layout(yaxis3={
"range": [min(yy), max(yy)],
"autorange": False
},
xaxis3={
"range": [xrange0, xrange1],
"autorange": False
})
# Update spikes traces
self.update_spike_traces(time_window=time_window)
self.traces.update_layout(xaxis2={
"range": [xrange0, xrange1],
"autorange": False
})
# Update frame trace
self.start_frame_x = (xrange1 + xrange0) / 2
self.traces.update_layout(shapes=[{
'type': 'line',
'x0': (xrange1 + xrange0) / 2,
'x1': (xrange1 + xrange0) / 2,
'xref': 'x',
'y0': -1000,
'y1': 1000,
'yref': 'paper',
'line': {
'width': 4,
'color': 'rgb(30, 30, 30)'
}
}])
return {'display': "inline-block"}, self.traces