calculate_muscle_activations = True
calculate_joint_reactions = True
##
# scale
os.chdir('scale/')
call(['opensim-cmd', 'run-tool', 'setup_scale.xml'])
os.chdir(subject_dir)
##
# inverse kinematics
os.chdir('inverse_kinematics/')
call(['opensim-cmd', 'run-tool', 'setup_ik.xml'])
plot_sto_file('task_InverseKinematics.mot', 'task_InverseKinematics.pdf', 3)
plot_sto_file('task_ik_marker_errors.sto', 'task_ik_marker_errors.pdf', 3)
plot_sto_file('task_ik_model_marker_locations.sto',
'task_ik_model_marker_locations.pdf', 3)
os.chdir(subject_dir)
##
# residual reduction algorithm and model adjustment
os.chdir('residual_reduction_algorithm/')
rra_output = run(['opensim-cmd', 'run-tool', 'setup_rra.xml'],
stdout=PIPE, stderr=PIPE, universal_newlines=True)
print(rra_output.stdout)
# find mass change from RRA output (perform only when RRA does not suggest much
# mass change)
from subprocess import PIPE, run, call
from utils import adjust_model_mass, subject_specific_isometric_force
from utils import plot_sto_file
# %%
# subject data
# 1.8m, 72 kg
subject_height = 1.803
subject_dir = os.path.abspath('../')
os.chdir(subject_dir)
# %%
# experimental data
plot_sto_file('experimental_data/task.trc', 'experimental_data/task.pdf', 3)
plot_sto_file('experimental_data/task_grf.mot',
'experimental_data/task_grf.pdf', 3)
# %%
# scale
os.chdir('scale/')
call(['opensim-cmd', 'run-tool', 'setup_scale.xml'])
os.chdir(subject_dir)
# %%
# inverse kinematics
os.chdir('inverse_kinematics/')
call(['opensim-cmd', 'run-tool', 'setup_ik.xml'])
'inverse_dynamics/task_InverseDynamics.sto')
tau_rt_file = os.path.join(output_dir, 'tau.sto')
# %%
# read data
tau_reference = read_from_storage(tau_reference_file)
tau_rt = read_from_storage(tau_rt_file)
if gait_cycle:
t0 = 0.6 # right heel strike
tf = 1.83 # next right heel strike
tau_reference = to_gait_cycle(tau_reference, t0, tf)
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)
# %%
# data
gait_cycle = True
subject_dir = os.path.abspath('../')
output_dir = os.path.join(subject_dir, 'real_time/muscle_optimization/')
fm_reference_file = os.path.join(
subject_dir, 'static_optimization/task_StaticOptimization_force.sto')
fm_rt_file = os.path.join(output_dir, 'fm.sto')
am_rt_file = os.path.join(output_dir, 'am.sto')
tauRes_rt_file = os.path.join(output_dir, 'tauRes.sto')
plot_sto_file(am_rt_file, am_rt_file + '.pdf', 3)
plot_sto_file(tauRes_rt_file, tauRes_rt_file + '.pdf', 3)
# %%
# read data
fm_reference = read_from_storage(fm_reference_file)
fm_rt = read_from_storage(fm_rt_file)
if gait_cycle:
t0 = 0.6 # right heel strike
tf = 1.83 # next right heel strike
fm_reference = to_gait_cycle(fm_reference, t0, tf)
fm_rt = to_gait_cycle(fm_rt, t0, tf)
plot_sto_file(fm_rt_file, fm_rt_file + '.pdf', 3)
# %%
# read data
jr_reference = read_from_storage(jr_reference_file)
jr_rt = read_from_storage(jr_rt_file)
# make very small number zero before plotting
jr_reference[jr_reference.abs() < 1e-9] = 0
jr_rt[jr_reference.abs() < 1e-9] = 0
if gait_cycle:
t0 = 0.6 # right heel strike
tf = 1.83 # next right heel strike
jr_reference = to_gait_cycle(jr_reference, t0, tf)
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
rotate_data_table(forces_task, [1, 0, 0], -90)
# conversion of unit (f -> N, p -> mm, tau -> Nmm)
mm_to_m(forces_task, 'p1')
mm_to_m(forces_task, 'p2')
mm_to_m(forces_task, 'm1')
mm_to_m(forces_task, 'm2')
# refine ground reaction forces
refine_ground_reaction_wrench(forces_task, ['f1', 'p1', 'm1'],
stance_threshold=50,
tau=0.001)
refine_ground_reaction_wrench(forces_task, ['f2', 'p2', 'm2'],
stance_threshold=50,
tau=0.001)
# export forces (assume two force plates)
time = forces_task.getIndependentColumn()
forces_task = forces_task.flatten(['x', 'y', 'z'])
force_sto = create_opensim_storage(time, forces_task.getMatrix(), labels_force)
force_sto.setName('GRF')
force_sto.printResult(force_sto, 'task_grf', output_dir, 0.01, '.mot')
# plot
plot_sto_file(os.path.join(output_dir, 'task.trc'),
os.path.join(output_dir, 'task.pdf'), 3)
plot_sto_file(os.path.join(output_dir, 'task_grf.mot'),
os.path.join(output_dir, 'task_grf.pdf'), 3)
##
for muscle in muscles:
# right leg
labels.append('R_' + muscle)
right = acq.GetAnalog('R_' + muscle).GetData().GetValues().reshape(-1)
emg_raw.append(right)
emg_env.append(calculate_emg_linear_envelope(right, f_s))
# left leg
labels.append('L_' + muscle)
left = acq.GetAnalog('L_' + muscle).GetData().GetValues().reshape(-1)
emg_raw.append(left)
emg_env.append(calculate_emg_linear_envelope(left, f_s))
##
# save data
emg_raw_sto = create_opensim_storage(
time, np_array_to_simtk_matrix(np.array(emg_raw).transpose()), labels)
emg_raw_sto.setName('emg_raw')
emg_raw_sto.printResult(emg_raw_sto, 'emg_raw', output_dir, 1.0 / f_s, '.sto')
plot_sto_file(os.path.join(output_dir, 'emg_raw.sto'),
os.path.join(output_dir, 'emg_raw.pdf'), 2)
emg_env_sto = create_opensim_storage(
time, np_array_to_simtk_matrix(np.array(emg_env).transpose()), labels)
emg_env_sto.setName('emg_env')
emg_env_sto.printResult(emg_env_sto, 'emg_env', output_dir, 1.0 / f_s, '.sto')
plot_sto_file(os.path.join(output_dir, 'emg_env.sto'),
os.path.join(output_dir, 'emg_env.pdf'), 2)
##
q_ddot_filtered_sp = read_from_storage(q_ddot_filtered_sp_file)
if gait_cycle:
t0 = 0.6 # right heel strike
tf = 1.83 # next right heel strike
q_reference = to_gait_cycle(q_reference, t0, tf)
q_dot_reference = to_gait_cycle(q_dot_reference, t0, tf)
q_ddot_reference = to_gait_cycle(q_ddot_reference, t0, tf)
q_filtered = to_gait_cycle(q_filtered, t0, tf)
q_dot_filtered = to_gait_cycle(q_dot_filtered, t0, tf)
q_ddot_filtered = to_gait_cycle(q_ddot_filtered, t0, tf)
q_filtered_sp = to_gait_cycle(q_filtered_sp, t0, tf)
q_dot_filtered_sp = to_gait_cycle(q_dot_filtered_sp, t0, tf)
q_ddot_filtered_sp = to_gait_cycle(q_ddot_filtered_sp, t0, tf)
plot_sto_file(q_reference_file, q_reference_file + '.pdf', 2)
plot_sto_file(q_filtered_file, q_filtered_file + '.pdf', 2)
# %%
# 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
# weight regression model
if adapt_muscle_strength:
subject_specific_isometric_force('../model/model_generic.osim',
'model_scaled.osim', generic_height,
subject_height)
os.chdir(subject_dir)
##
# inverse kinematics
os.chdir('inverse_kinematics/')
call(['opensim-cmd', 'run-tool', 'setup_ik.xml'])
plot_sto_file('task_InverseKinematics.mot', 'task_InverseKinematics.pdf', 3)
plot_sto_file('task_ik_marker_errors.sto', 'task_ik_marker_errors.pdf', 3)
plot_sto_file('task_ik_model_marker_locations.sto',
'task_ik_model_marker_locations.pdf', 3)
os.chdir(subject_dir)
##
# inverse dynamics
os.chdir('inverse_dynamics/')
call(['opensim-cmd', 'run-tool', 'setup_id.xml'])
plot_sto_file('task_InverseDynamics.sto', 'task_InverseDynamics.pdf', 3)
'inverse_kinematics/task_InverseKinematics.mot')
q_rt_file = os.path.join(output_dir, 'q.sto')
# %%
# read data
q_reference = read_from_storage(q_reference_file)
q_rt = read_from_storage(q_rt_file)
if gait_cycle:
t0 = 0.6 # right heel strike
tf = 1.83 # next right heel strike
q_reference = to_gait_cycle(q_reference, t0, tf)
q_rt = to_gait_cycle(q_rt, t0, tf)
plot_sto_file(q_rt_file, q_rt_file + '.pdf', 3)
# %%
# compare
d_q_total = []
with PdfPages(output_dir + 'inverse_kinematics_comparison.pdf') as pdf:
for i in range(1, q_reference.shape[1]):
# find index
j = q_rt.columns.get_loc(q_reference.columns[i])
# deg to rad for rotational degrees of freedom
if '_tx' in q_reference.columns[i] or \
'_ty' in q_reference.columns[i] or \
'_tz' in q_reference.columns[i]: