]
# for each column in column labels:
for i in range(1, reconstructed_markers.shape[1]):
# find index in original
j = original_markers.columns.get_loc(reconstructed_markers.columns[i])
# skip valid markers
if skip_valid_markers:
if (not reconstructed_markers.columns[i][:-2]
in missing_marker_labels):
continue
scale = 1000
position_unit = ' (mm)'
d_q = rmse_metric(scale * reconstructed_markers.iloc[:, i],
original_markers.iloc[:, j])
if not np.isnan(d_q): # NaN when siganl is zero
d_q_total.append(d_q)
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(5, 4))
ax.plot(original_markers.time,
original_markers.iloc[:, j],
label='Original')
ax.plot(reconstructed_markers.time,
scale * reconstructed_markers.iloc[:, i],
label='Reconstructed',
linestyle='--')
ax.axvspan(occlusion_start_perc,
occlusion_stop_perc,
label="Occlusion Period",
jr_rt = to_gait_cycle(jr_rt, t0, tf)
plot_sto_file(jr_rt_file, jr_rt_file + '.pdf', 3)
# %%
# compare
d_jr_total = []
with PdfPages(output_dir + 'joint_reaction_comparison_fm.pdf') as pdf:
for i in range(1, jr_rt.shape[1]):
# find index
key = jr_rt.columns[i]
j = jr_reference.columns.get_loc(key)
d_jr = rmse_metric(jr_reference.iloc[:, j], jr_rt.iloc[:, i])
if not np.isnan(d_jr): # NaN when siganl is zero
d_jr_total.append(d_jr)
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(5, 4))
ax.plot(jr_reference.time, jr_reference.iloc[:, j], label='OpenSim')
ax.plot(jr_rt.time,
jr_rt.iloc[:, i],
label='Real-time',
linestyle='--')
ax.set_title(jr_rt.columns[i])
if gait_cycle:
ax.set_xlabel('gait cycle (%)')
else:
tau_rt = to_gait_cycle(tau_rt, t0, tf)
plot_sto_file(tau_rt_file, tau_rt_file + '.pdf', 3)
# %%
# compare
d_tau_total = []
with PdfPages(output_dir + 'inverse_dynamics_comparison.pdf') as pdf:
for i in range(1, tau_reference.shape[1]):
# find index
key = tau_reference.columns[i].replace('_moment', '').replace('_force', '')
j = tau_rt.columns.get_loc(key)
d_tau = rmse_metric(tau_reference.iloc[:, i], tau_rt.iloc[:, j])
if not np.isnan(d_tau): # NaN when siganl is zero
d_tau_total.append(d_tau)
is_deg = True
if tau_rt.columns[i] in ['pelvis_tx', 'pelvis_ty', 'pelvis_tz']:
is_deg = False
units = ''
if is_deg:
units = ' (N m)'
else:
units = ' (N)'
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(5, 4))
fm_rt = to_gait_cycle(fm_rt, t0, tf)
plot_sto_file(fm_rt_file, fm_rt_file + '.pdf', 3)
# %%
# compare
d_fm_total = []
with PdfPages(output_dir + 'muscle_optimization_comparison.pdf') as pdf:
for i in range(1, fm_rt.shape[1]):
# find index
key = fm_rt.columns[i]
j = fm_reference.columns.get_loc(key)
d_tau = rmse_metric(fm_rt.iloc[:, i], fm_reference.iloc[:, j])
if not np.isnan(d_tau): # NaN when signal is zero
d_fm_total.append(d_tau)
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(5, 4))
ax.plot(fm_reference.time, fm_reference.iloc[:, j], label='OpenSim SO')
ax.plot(fm_rt.time,
fm_rt.iloc[:, i],
label='Real-time SO',
linestyle='--')
if gait_cycle:
ax.set_xlabel('gait cycle (%)')
else:
ax.set_xlabel('time (s)')
if q_reference.columns[i] in ['pelvis_tx', 'pelvis_ty', 'pelvis_tz']:
is_deg = False
position_unit = ''
velocity_unit = ''
acceleration_unit = ''
if is_deg:
position_unit = ' (deg)'
velocity_unit = ' (deg / s)'
acceleration_unit = ' (deg / $s^2$)'
else:
position_unit = ' (m)'
velocity_unit = ' (m / s)'
acceleration_unit = ' (m / $s^2$)'
d_q = rmse_metric(q_reference.iloc[:, i],
scale * q_filtered.iloc[:, j])
d_u = rmse_metric(q_dot_reference.iloc[:, i],
scale * q_dot_filtered.iloc[:, j])
d_a = rmse_metric(q_ddot_reference.iloc[:, i],
scale * q_ddot_filtered.iloc[:, j])
d_q_sp = rmse_metric(q_reference.iloc[:, i],
scale * q_filtered_sp.iloc[:, j])
d_u_sp = rmse_metric(q_dot_reference.iloc[:, i],
scale * q_dot_filtered_sp.iloc[:, j])
d_a_sp = rmse_metric(q_ddot_reference.iloc[:, i],
scale * q_ddot_filtered_sp.iloc[:, j])
if not np.isnan(d_q): # NaN when siganl is zero
d_q_total.append(d_q)
d_u_total.append(d_u)
d_a_total.append(d_a)
# find index
j = q_pipeline.columns.get_loc(q_reference.columns[i])
is_deg = True
if q_reference.columns[i] in ['pelvis_tx', 'pelvis_ty', 'pelvis_tz']:
is_deg = False
position_unit = ''
if is_deg:
position_unit = ' (deg)'
else:
position_unit = ' (m)'
dim = min(q_pipeline.shape[0], q_reference.shape[0])
d_q = rmse_metric(q_reference.iloc[:dim, i], q_pipeline.iloc[:dim, j])
if not np.isnan(d_q): # NaN when siganl is zero
d_q_total.append(d_q)
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(5, 4))
ax.plot(q_reference.time, q_reference.iloc[:, i], label='Test IK')
ax.plot(q_pipeline.time,
q_pipeline.iloc[:, j],
label='Pipeline IK',
linestyle='--')
if gait_cycle:
ax.set_xlabel('gait cycle (%)')
else:
ax.set_xlabel('time (s)')
'_tz' in q_reference.columns[i]:
scale = 1
else:
scale = 57.295779513
is_deg = True
if q_reference.columns[i] in ['pelvis_tx', 'pelvis_ty', 'pelvis_tz']:
is_deg = False
position_unit = ''
if is_deg:
position_unit = ' (deg)'
else:
position_unit = ' (m)'
d_q = rmse_metric(q_reference.iloc[:, i], scale * q_rt.iloc[:, j])
if not np.isnan(d_q): # NaN when siganl is zero
d_q_total.append(d_q)
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(5, 4))
ax.plot(q_reference.time, q_reference.iloc[:, i], label='OpenSim IK')
ax.plot(q_rt.time, scale * q_rt.iloc[:, j], label='Real-time IK',
linestyle='--')
if gait_cycle:
ax.set_xlabel('gait cycle (%)')
else:
ax.set_xlabel('time (s)')
ax.set_ylabel('generalized coordinates' + position_unit)
ax.set_title(q_rt.columns[j])
# %%
# compare
d_q_total = []
d_u_total = []
d_a_total = []
with PdfPages(output_dir + 'filter_comparison.pdf') as pdf:
for i in range(1, q_reference.shape[1]):
# if 'mtp' in q_reference.columns[i] or \
# 'subtalar' in q_reference.columns[i] or \
# 'ankle_angle_l' in q_reference.columns[i]:
# # ankle added because it was too noisy
# continue
d_q = rmse_metric(q_reference.iloc[:, i], q_filtered.iloc[:, i])
d_u = rmse_metric(q_dot_reference.iloc[:, i], q_dot_filtered.iloc[:,
i])
d_a = rmse_metric(q_ddot_reference.iloc[:, i], q_ddot_filtered.iloc[:,
i])
if not np.isnan(d_q): # NaN when siganl is zero
d_q_total.append(d_q)
d_u_total.append(d_u)
d_a_total.append(d_a)
fig, ax = plt.subplots(nrows=1, ncols=3, figsize=(12, 4))
ax[0].plot(q_reference.time, q_reference.iloc[:, i], label='OpenSim')
ax[0].plot(q_filtered.time, q_filtered.iloc[:, i], label='filtered')
ax[0].set_xlabel('time (s)')
ax[0].set_ylabel('coordinate (deg | m)')