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