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_pos_data(self, title: str, y_label: str, kine_var: str, fig_num: int, add_sd: bool = True,
clip_graph: bool = False) -> matplotlib.figure.Figure:
"""Plot overlayed raw, filled, and smoothed marker position data."""
fig = plt.figure(num=fig_num)
ax = fig.subplots(3, 1, sharex=True)
lines_filled = marker_graph_init(ax, self.filled.means.pos, y_label, x_data=self.frames, color='red')
lines_raw = marker_graph_add(ax, self.raw.means.pos, self.frames, color='indigo', marker='.')
lines_smoothed = marker_graph_add(ax, getattr(self.smoothed.means, kine_var), self.filtered_frames,
color='limegreen', lw=1)
if add_sd:
marker_graph_add_cov(ax, self.smoothed.means.pos, self.smoothed.covars.pos, 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])
plt.tight_layout(pad=1.0, w_pad=1.0, h_pad=0)
fig.suptitle(title, x=0.25, fontsize=11, fontweight='bold')
plt.subplots_adjust(top=0.94)
fig.legend((lines_raw[0], lines_filled[0], lines_smoothed[0]), ('Raw', 'Filled', 'Smoothed'), 'upper right',
labelspacing=0.1, ncol=3, columnspacing=0.3)
make_interactive()
return fig
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_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_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
