def plot_marker_data(self, title: str, y_label: str, kine_var: str, fig_num: int, add_sd: bool = True,
clip_graph: bool = False, marker: str = '') -> matplotlib.figure.Figure:
"""Plot raw, filtered, and smoothed kinematic (position, velocity, acceleration) marker data, allowing the
addition of confidence bounds."""
fig = plt.figure(num=fig_num)
ax = fig.subplots(3, 1, sharex=True)
lines_raw = marker_graph_init(ax, getattr(self.raw.means, kine_var), y_label, x_data=self.frames,
color='indigo', marker=marker)
lines_filtered = marker_graph_add(ax, getattr(self.filtered.means, kine_var), self.filtered_frames, color='red')
lines_smoothed = marker_graph_add(ax, getattr(self.smoothed.means, kine_var), self.filtered_frames,
color='limegreen')
if add_sd:
marker_graph_add_cov(ax, getattr(self.filtered.means, kine_var), getattr(self.filtered.covars, kine_var),
self.filtered_frames, 'red')
marker_graph_add_cov(ax, getattr(self.smoothed.means, kine_var), getattr(self.smoothed.covars, kine_var),
self.filtered_frames, 'limegreen')
if clip_graph:
for c_ax in ax:
c_ax.set_xlim(self.vicon_frame_endpts[0], self.vicon_frame_endpts[1])
else:
add_vicon_start_stop(ax, self.vicon_frame_endpts[0], self.vicon_frame_endpts[1])
fig.legend((lines_raw[0], lines_filtered[0], lines_smoothed[0]), ('Raw', 'Filtered', 'Smoothed'), 'upper right',
labelspacing=0.1)
marker_graph_title(fig, title)
make_interactive()
return fig
def plot_marker_data_diff_hist(self, title: str, x_label: str, fig_num: int, clip_graph: bool = True) \
-> matplotlib.figure.Figure:
"""Plot histogram of smoothed marker positions - raw marker positions."""
if clip_graph:
endpts = np.zeros((2,), dtype=np.int)
if self.vicon_endpts[0] > self.filtered.endpts[0]:
endpts[0] = self.vicon_endpts[0] - self.filtered.endpts[0]
if self.vicon_endpts[1] < self.filtered.endpts[1]:
endpts[1] = self.vicon_endpts[1] - self.filtered.endpts[0]
else:
endpts[1] = self.filtered.endpts[1] - self.filtered.endpts[0]
smoothed_diff = self.smoothed_pos_diff[endpts[0]:endpts[1]]
else:
smoothed_diff = self.smoothed_pos_diff
fig = plt.figure(num=fig_num)
ax = fig.subplots(1, 3, sharey=True)
lines_smoothed = marker_diff_his_init(ax, smoothed_diff, x_label, 'limegreen')
fig.legend([lines_smoothed[0]], ['Smoothed'], 'upper right', labelspacing=0.1)
marker_graph_title(fig, title)
make_interactive()
return fig
def plot_biplane_vicon(self, title: str, fig_num: int, vicon_field: str, vicon_type: str) \
-> matplotlib.figure.Figure:
"""Plot overlayed marker position data as measured via Vicon and biplane fluoroscopy."""
fig = plt.figure(num=fig_num)
ax = fig.subplots(3, 1, sharex=True)
lines_vicon = marker_graph_init(ax,
getattr(self, vicon_field),
'Distance (mm)',
self.vicon_frames,
color='limegreen',
marker='.',
lw=1,
ms=2)
lines_biplane = marker_graph_add(ax,
self.biplane_data,
self.vicon_frames,
color='indigo',
marker='.')
fig.legend((lines_biplane[0], lines_vicon[0]),
('Biplane', vicon_type + ' Vicon'),
'upper right',
ncol=3,
columnspacing=0.3,
handlelength=1.0)
marker_graph_title(fig, title)
make_interactive()
return fig
def plot(self) -> List[matplotlib.figure.Figure]:
"""Plot marker_data onto 3 row subplots on Figure 0."""
fig = plt.figure(num=0)
ax = fig.subplots(3, 1, sharex=True)
marker_graph_init(ax, self.marker_pos_labeled, 'Pos (mm)', x_data=self.frame_nums, color='blue')
add_vicon_start_stop(ax, self.vicon_endpts[0] + 1, self.vicon_endpts[1])
marker_graph_title(fig, self.trial_name + ' ' + self.marker_name)
make_interactive()
return [fig]
def plot_marker_data_diff(self, title: str, y_label: str, fig_num: int) -> matplotlib.figure.Figure:
"""Plot smoothed marker positions - raw marker positions."""
fig = plt.figure(num=fig_num)
ax = fig.subplots(3, 1, sharex=True)
lines_smoothed = marker_graph_init(ax, self.smoothed_pos_diff, y_label, x_data=self.filtered_frames,
color='limegreen')
fig.legend([lines_smoothed[0]], ['Smoothed'], 'upper right', labelspacing=0.1)
add_vicon_start_stop(ax, self.vicon_frame_endpts[0], self.vicon_frame_endpts[1])
marker_graph_title(fig, title)
make_interactive()
return fig
def plot_marker_data_smooth(self, title: str, y_label: str, kine_var: str, fig_num: int) \
-> matplotlib.figure.Figure:
"""Plot smoothed kinematic (position, velocity, acceleration) marker data."""
fig = plt.figure(num=fig_num)
ax = fig.subplots(3, 1, sharex=True)
lines_smoothed = marker_graph_init(ax, getattr(self.smoothed.means, kine_var), y_label,
x_data=self.filtered_frames, color='limegreen')
fig.legend([lines_smoothed[0]], ['Smoothed'], 'upper right', labelspacing=0.1)
add_vicon_start_stop(ax, self.vicon_frame_endpts[0], self.vicon_frame_endpts[1])
marker_graph_title(fig, title)
make_interactive()
return fig
def plot_cov(self, title: str, y_labels: Sequence[str], fig_num: int) -> matplotlib.figure.Figure:
"""Plot overlayed variance of filtered and smoothed kinematic variables (position, velocity, acceleration) in
separate rows with 3 columns for each spatial dimension (3x3). """
fig = plt.figure(num=fig_num)
ax = fig.subplots(3, 3, sharex='all', sharey='row')
lines_filtered = cov_trend_graph_init(ax, self.filtered.covars, self.filtered_frames, y_labels, np.sqrt,
color='red')
lines_smooth = cov_trend_graph_add(ax, self.smoothed.covars, self.filtered_frames, np.sqrt, color='limegreen')
fig.legend((lines_filtered[0][0], lines_smooth[0][0]), ('Filtered', 'Smoothed'), 'upper right',
labelspacing=0.1, ncol=2)
add_vicon_start_stop(ax, self.vicon_frame_endpts[0], self.vicon_frame_endpts[1])
marker_graph_title(fig, title)
make_interactive()
return fig
