def grp_plotter(activity_df, col_name, pdf_file_path, grp_c, plot_directives,
section):
with PdfPages(pdf_file_path) as grp_pdf:
for name, plot_dir in plot_directives.items():
fig = plt.figure()
ax = fig.subplots()
ind_lines = []
ind_leg_entries = []
avg_lines = []
avg_entries = []
quat_avg_lines = []
quat_avg_entries = []
for grp, grp_df in activity_df.groupby(col_name):
ind_plotter_fnc = partial(ind_plotter_color_spec,
c=grp_c[grp][0])
ind_traj_plot_lines, agg_lines, quat_mean_lines = summary_plotter(
grp_df['traj_interp'], plot_dir.traj, section[0],
section[1], section[2], section[3], plot_dir.decomp_method,
plot_dir.sub_rot, ax, ind_plotter_fnc, grp_c[grp][1],
grp_c[grp][2])
ind_lines.append(ind_traj_plot_lines.iloc[0][0])
ind_leg_entries.append(grp)
avg_lines.append(agg_lines[0])
avg_entries.append(grp + r' Mean$\pm$SE')
if quat_mean_lines is not None:
quat_avg_lines.append(quat_mean_lines[0])
quat_avg_entries.append(grp + ' Mean(Quat)')
ax.legend(ind_lines,
ind_leg_entries,
handlelength=0.75,
handletextpad=0.25,
columnspacing=0.5,
loc='lower right')
ax.xaxis.set_major_locator(plticker.MultipleLocator(base=10.0))
style_axes(ax, 'Humerothoracic Elevation (Deg)', plot_dir.y_label)
fig.tight_layout()
fig.suptitle(plot_dir.title)
if quat_avg_lines:
fig.legend(avg_lines + quat_avg_lines,
avg_entries + quat_avg_entries,
loc='lower left',
handlelength=0.75,
handletextpad=0.25,
ncol=2)
else:
fig.legend(avg_lines,
avg_entries,
loc='lower left',
handlelength=0.75,
handletextpad=0.25)
grp_pdf.savefig(fig)
fig.clf()
plt.close(fig)
db_elev = db.loc[db['Trial_Name'].str.contains('_CA_|_SA_|_FE_')].copy()
prepare_db(db_elev, params.torso_def, params.scap_lateral,
params.dtheta_fine, params.dtheta_coarse,
[params.min_elev, params.max_elev])
#%%
plt.rcParams['axes.prop_cycle'] = plt.cycler('color', plt.cm.tab20c.colors)
init_graphing(params.backend)
plt.close('all')
fig = plt.figure(figsize=(90 / 25.4, 190 / 25.4), dpi=params.dpi)
ax = fig.subplots(3, 1)
for i in range(3):
style_axes(ax[i], 'Humerothoracic Elevation (Deg)' if i == 2 else None,
'Axial Orientation (Deg)')
ax[i].xaxis.set_major_locator(ticker.MultipleLocator(base=20.0))
act_row = {'ca': 0, 'sa': 1, 'fe': 2}
for idx, (activity, activity_df) in enumerate(
db_elev.groupby('Activity', observed=True)):
cur_row = act_row[activity.lower()]
_, agg_lines, quat_mean_lines = \
summary_plotter(activity_df['traj_interp'], 'ht', 'ht_ea_up', 'up', 'common_ht_range_coarse',
'common_coarse_up', 'euler.ht_isb', 2, ax[cur_row], ind_plotter, 'black', 'red',
error_bars='std', alpha=0.5)
# remove the quaternion average line
quat_mean_lines[0].remove()
del quat_mean_lines[0]
make_interactive()
markers = ['^', 'o', 's', '*']
act_order = {'CA': -1, 'SA': 0, 'FE': 1}
x = db_elev.iloc[0]['traj_interp'].common_ht_range_fine
init_graphing(params.backend)
plt.close('all')
fig = plt.figure(figsize=(190 / 25.4, 230 / 25.4), dpi=params.dpi)
axs = fig.subplots(4, 2)
# style axes, add x and y labels
for i in range(4):
for j in range(2):
style_axes(
axs[i,
j], 'Humerothoracic Elevation (Deg)' if i == 3 else None,
'Axial Orientation (deg)'
if j == 0 else 'Axial Rotation (Deg)')
# set axes limits
for i in range(4):
axs[i, 1].set_ylim(-45, 55)
all_traj_isb_rm = np.stack(db_elev_equal['traj_interp'].apply(
extract_sub_rot_norm,
args=['gh', 'common_fine_up', 'euler.gh_isb', 2, 'up']),
axis=0)
all_traj_isb_poe_rm = np.stack(db_elev_equal['traj_interp'].apply(
extract_sub_rot_norm,
args=['gh', 'common_fine_up', 'euler.gh_isb', 0, 'up']),
axis=0)
alpha = 0.05
color_map = plt.get_cmap('Dark2')
markers = ['^', 'o', 's', '*']
plot_utils.init_graphing(params.backend)
plt.close('all')
fig = plt.figure(figsize=(190 / 25.4, 150 / 25.4), dpi=params.dpi)
axs = fig.subplots(2, 2)
ax_limits = [(-140, 15), (-110, 30)]
for row_idx, row in enumerate(axs):
for col_idx, ax in enumerate(row):
ax.xaxis.set_major_locator(plticker.MultipleLocator(base=10.0))
ax.yaxis.set_major_locator(plticker.MultipleLocator(base=25.0))
x_label = 'Percent Complete (%)' if row_idx == 1 else None
y_label = 'Axial Rotation (Deg)' if col_idx == 0 else None
style_axes(ax, x_label, y_label)
axs[row_idx, col_idx].set_ylim(ax_limits[row_idx][0],
ax_limits[row_idx][1])
spm_y = np.array([[13, 13], [27, 27]])
traj_name = 'gh'
mean_left_lns = []
mean_right_lns = []
for idx_act, (activity, activity_df) in enumerate(
db_er_endpts.groupby('Activity', observed=True)):
all_traj_true = np.stack(activity_df[traj_name + '_true'], axis=0)
all_traj_isb = np.stack(activity_df[traj_name + '_isb'], axis=0)
all_traj_isb_norm = np.stack(activity_df[traj_name + '_isb_norm'],
axis=0)
all_traj_phadke = np.stack(activity_df[traj_name + '_phadke'], axis=0)
infer_params = {'force_iterations': True}
alpha = 0.05
color_map = plt.get_cmap('Dark2')
markers = ['^', 'o', 's', '*']
act_row = {'ca': 0, 'sa': 1, 'fe': 2}
x = db_elev.iloc[0]['traj_interp'].common_ht_range_fine
init_graphing(params.backend)
plt.close('all')
fig_diff_hum = plt.figure(figsize=(100 / 25.4, 190 / 25.4))
axs_diff = fig_diff_hum.subplots(3, 1)
# style axes, add x and y labels
style_axes(axs_diff[0], None, 'Axial Rotation (Deg)')
style_axes(axs_diff[1], None, 'Axial Rotation (Deg)')
style_axes(axs_diff[2], 'Humerothoracic Elevation (Deg)', 'Axial Rotation (Deg)')
# plot
leg_patch_mean = []
for idx, (activity, activity_df) in enumerate(db_elev.groupby('Activity', observed=True)):
all_traj_isb = np.stack(activity_df['traj_interp'].apply(
extract_sub_rot_norm, args=['gh', 'common_fine_up', 'euler.gh_isb', 2, 'up']), axis=0)
all_traj_isb_poe = np.stack(activity_df['traj_interp'].apply(
extract_sub_rot_norm, args=['gh', 'common_fine_up', 'euler.gh_isb', 0, 'up']), axis=0)
all_traj_true = np.stack(activity_df['traj_interp'].apply(
extract_sub_rot_norm, args=['gh', 'common_fine_up', 'true_axial_rot', None, 'up']), axis=0)
all_traj_isb_norm = all_traj_isb + all_traj_isb_poe
all_traj_isb_max = np.stack(activity_df['traj_interp'].apply(
infer_params = {'force_iterations': True}
alpha = 0.05
color_map = plt.get_cmap('Dark2')
markers = ['^', 'o', 's', 'd']
act_row = {'ca': 0, 'sa': 1, 'fe': 2}
x = db_elev.iloc[0]['traj_interp'].common_ht_range_fine
init_graphing(params.backend)
plt.close('all')
fig_diff = plt.figure(figsize=(190 / 25.4, 190 / 25.4), dpi=params.dpi)
axs_diff = fig_diff.subplots(3, 2)
# style axes, add x and y labels
style_axes(axs_diff[0, 0], None, 'Axial Rotation (Deg)')
style_axes(axs_diff[1, 0], None, 'Axial Rotation (Deg)')
style_axes(axs_diff[2, 0], 'Humerothoracic Elevation (Deg)',
'Axial Rotation (Deg)')
style_axes(axs_diff[0, 1], None, None)
style_axes(axs_diff[1, 1], None, None)
style_axes(axs_diff[2, 1], 'Humerothoracic Elevation (Deg)', None)
# set axes limits
# ax_limits = [(-27, 50), (-30, 42), (-52, 25)]
for i in range(3):
# axs_diff[i, 0].set_ylim(ax_limits[i][0], ax_limits[i][1])
# axs_diff[i, 1].set_ylim(ax_limits[i][0], ax_limits[i][1])
axs_diff[i, 0].yaxis.set_major_locator(ticker.MultipleLocator(10))
axs_diff[i, 1].yaxis.set_major_locator(ticker.MultipleLocator(10))
axs_diff[0, 1].yaxis.set_major_locator(ticker.MultipleLocator(20))
#%%
# plot
color_map = plt.get_cmap('Dark2')
markers = ['^', 'o', 's', '*']
act_row = {'ca': 0, 'sa': 1, 'fe': 2}
ours_ht = db_elev.iloc[0]['traj_interp'].common_ht_range_coarse
init_graphing(params.backend)
plt.close('all')
# ############ EULER ANGLE COMPARISONS FOR GH ##################################
fig_std_hum = plt.figure(figsize=(190 / 25.4, 190 / 25.4))
axs_std_hum = fig_std_hum.subplots(3, 2)
# style axes, add x and y labels
style_axes(axs_std_hum[0, 0], None, 'Elevation/PoE (Deg)')
style_axes(axs_std_hum[1, 0], None, 'Elevation/PoE (Deg)')
style_axes(axs_std_hum[2, 0], 'Humerothoracic Elevation (Deg)',
'Elevation/PoE (Deg)')
style_axes(axs_std_hum[0, 1], None, 'Axial Orientation (Deg)')
style_axes(axs_std_hum[1, 1], None, 'Axial Orientation (Deg)')
style_axes(axs_std_hum[2, 1], 'Humerothoracic Elevation (Deg)',
'Axial Rotation (Deg)')
# add arrows indicating direction
axs_std_hum[0, 0].arrow(20,
-40,
0,
-40,
length_includes_head=True,
head_width=2,
plot_dir.decomp_method, plot_dir.sub_rot, ax,
ind_plotter, 'black', 'red')
if quat_mean_lines:
ax.legend([agg_lines.lines[0], quat_mean_lines[0]],
[r'Mean$\pm$SE', 'Mean(Quat)'],
loc='lower right',
handlelength=0.75,
handletextpad=0.25)
else:
ax.legend([agg_lines.lines[0]], [r'Mean$\pm$SE'],
loc='lower right',
handlelength=0.75,
handletextpad=0.25)
ax.xaxis.set_major_locator(
plticker.MultipleLocator(base=10.0))
style_axes(ax, 'Humerothoracic Elevation (Deg)',
plot_dir.y_label)
fig.tight_layout()
fig.subplots_adjust(bottom=0.2)
fig.suptitle(plot_dir.title)
fig.legend(ncol=10,
handlelength=0.75,
handletextpad=0.25,
columnspacing=0.5,
loc='lower left',
fontsize=8)
activity_pdf.savefig(fig)
fig.clf()
plt.close(fig)
# plot by gender
pdf_file_path = output_path / (activity + '_' + params.torso_def +
spm_test = spm1d.stats.nonparam.ttest
infer_params = {"force_iterations": True}
alpha = 0.05
color_map = plt.get_cmap('Dark2')
markers = ['^', 'o', 's', '*']
act_row = {'ca': 0, 'sa': 1, 'fe': 2}
x = db_elev.iloc[0]['traj_interp'].common_ht_range_fine
init_graphing(params.backend)
plt.close('all')
fig_diff0_hum = plt.figure(figsize=(190 / 25.4, 190 / 25.4))
axs_diff0 = fig_diff0_hum.subplots(3, 2)
# style axes, add x and y labels
style_axes(axs_diff0[0, 0], None, 'Axial Rotation (Deg)')
style_axes(axs_diff0[1, 0], None, 'Axial Rotation (Deg)')
style_axes(axs_diff0[2, 0], 'Humerothoracic Elevation (Deg)',
'Axial Rotation (Deg)')
style_axes(axs_diff0[0, 1], None, 'SPM{t}')
style_axes(axs_diff0[1, 1], None, 'SPM{t}')
style_axes(axs_diff0[2, 1], 'Humerothoracic Elevation (Deg)', 'SPM{t}')
fig_diff0_dist = plt.figure(figsize=(110 / 25.4, 190 / 25.4))
axs_diff0_dist = fig_diff0_dist.subplots(3, 1)
style_axes(axs_diff0_dist[0], None, 'p-value')
style_axes(axs_diff0_dist[1], None, 'p-value')
style_axes(axs_diff0_dist[2], 'Humerothoracic Elevation (Deg)', 'p-value')
# plot
leg_patch_mean = []
params.scap_lateral,
params.dtheta_fine,
params.dtheta_coarse, [params.min_elev, params.max_elev],
should_clean=False)
(db['up_min_ht'], db['up_max_ht'], db['down_min_ht'],
db['down_max_ht']) = zip(
*(db['up_down_analysis'].apply(extract_up_down_min_max)))
plot_utils.init_graphing(params.backend)
plot_dirs = [['ht', 'ht_isb', 'HT'], ['gh', 'gh_isb', 'GH'],
['st', 'st_isb', 'ST']]
for plot_dir in plot_dirs:
traj = db.loc['U35_002_SA_t01', plot_dir[0]]
traj_euler = getattr(traj, 'euler')
fig = plt.figure(figsize=(14, 7), tight_layout=True)
ax = fig.subplots(2, 3)
for i in range(3):
ax[0, i].plot(np.rad2deg(getattr(traj_euler, plot_dir[1])[:, i]))
ax[1, i].plot(traj.pos[:, i])
if i == 0:
plot_utils.style_axes(ax[0, i], None, 'Orientation (deg)')
plot_utils.style_axes(ax[1, i], 'Frame Index (Zero-Based)',
'Position (mm)')
else:
plot_utils.style_axes(ax[0, i], None, None)
plot_utils.style_axes(ax[1, i], 'Frame Index (Zero-Based)',
None)
fig.suptitle(plot_dir[2])
plot_utils.make_interactive()
plt.show()
plot_dir = {
'GH': (get_trajs_gh, get_trajs_gh_start),
'HT': (get_trajs_ht, get_trajs_ht_start),
'ST': (get_trajs_st, get_trajs_st_start)
}
x = db_elev.iloc[0]['traj_interp'].common_ht_range_fine
init_graphing(params.backend)
plt.close('all')
for traj, traj_fnc in plot_dir.items():
fig_plane = plt.figure(figsize=(190 / 25.4, 190 / 25.4))
axs_plane = fig_plane.subplots(3, 2)
# style axes, add x and y labels
style_axes(axs_plane[0, 0], None, 'Axial Rotation (Deg)')
style_axes(axs_plane[1, 0], None, 'Axial Rotation (Deg)')
style_axes(axs_plane[2, 0], 'Humerothoracic Elevation (Deg)',
'Axial Rotation (Deg)')
style_axes(axs_plane[0, 1], None, 'SPM{t}')
style_axes(axs_plane[1, 1], None, 'SPM{t}')
style_axes(axs_plane[2, 1], 'Humerothoracic Elevation (Deg)', 'SPM{t}')
all_traj_isb, all_traj_phadke, all_traj_true = traj_fnc[0](db_elev)
all_traj_isb = all_traj_isb - all_traj_isb[:, 0][..., np.newaxis]
all_traj_phadke = all_traj_phadke - all_traj_phadke[:, 0][...,
np.newaxis]
all_traj_true = all_traj_true - all_traj_true[:, 0][..., np.newaxis]
group = (db_elev['Activity'].map({
'CA': 1,
'SA': 2,
color_map = plt.get_cmap('Dark2')
markers = ['^', 'o', 's', '*']
act_row = {'ca': 0, 'sa': 1, 'fe': 2}
x = db_elev.iloc[0]['traj_interp'].common_ht_range_fine
init_graphing(params.backend)
plt.close('all')
# plot
for idx, (activity, activity_df) in enumerate(
db_elev.groupby('Activity', observed=True)):
fig_gender = plt.figure(figsize=(190 / 25.4, 190 / 25.4))
axs_gender = fig_gender.subplots(3, 2)
# style axes, add x and y labels
style_axes(axs_gender[0, 0], None, 'Axial Rotation (Deg)')
style_axes(axs_gender[1, 0], None, 'Axial Rotation (Deg)')
style_axes(axs_gender[2, 0], 'Humerothoracic Elevation (Deg)',
'Axial Rotation (Deg)')
style_axes(axs_gender[0, 1], None, 'SPM{t}')
style_axes(axs_gender[1, 1], None, 'SPM{t}')
style_axes(axs_gender[2, 1], 'Humerothoracic Elevation (Deg)',
'SPM{t}')
activity_df_m = activity_df.loc[activity_df['Gender'] == 'M']
activity_df_f = activity_df.loc[activity_df['Gender'] == 'F']
all_traj_isb_m = np.stack(activity_df_m['traj_interp'].apply(
extract_sub_rot, args=['gh', 'common_fine_up', 'euler.gh_isb', 2]),
axis=0)
all_traj_phadke_m = np.stack(activity_df_m['traj_interp'].apply(
#%%
x = np.arange(0, 100 + params.dtheta_fine, params.dtheta_fine)
# we need more colors to encompass all subjects than the default color scale offers
plt.rcParams['axes.prop_cycle'] = plt.cycler('color', plt.cm.tab20c.colors)
plot_utils.init_graphing(params.backend)
plt.close('all')
for activity, activity_df in db_er.groupby('Activity', observed=True):
# overall
pdf_file_path = output_path / (activity + '_' + params.torso_def +
('_' + params.scap_lateral) + '.pdf')
with PdfPages(pdf_file_path) as activity_pdf:
for dir_name, plot_directive in plot_directives.items():
fig = plt.figure()
ax = fig.subplots()
ax.xaxis.set_major_locator(plticker.MultipleLocator(base=10.0))
plot_utils.style_axes(ax, 'Percent Completion (%)',
plot_directive.y_label)
for trial_name, interp_data in zip(activity_df['Trial_Name'],
activity_df[dir_name]):
ax.plot(x,
np.rad2deg(interp_data),
label='_'.join(trial_name.split('_')[0:2]))
fig.tight_layout()
fig.subplots_adjust(bottom=0.2)
fig.suptitle(activity + ' ' + plot_directive.title)
fig.legend(ncol=10,
handlelength=0.75,
handletextpad=0.25,
columnspacing=0.5,
loc='lower left',
fontsize=8)
activity_pdf.savefig(fig)