amathislab/Boo_LevelWalking

Policy Reference NPZ Data

This dataset contains per-subject, per-trial .npz files exported from processed OpenSim inverse dynamics results for level walking.

The files are intended for comparing policy inference outputs against OpenSim ID torques. Each exported trial uses the kinematics timeline as the master timeline, with time and timestep reset to start from zero.

ID torques are normalized by the subject's weight in kg from Subject_Demographics.xlsx. GRF force components are normalized by body weight in Newtons, computed as subject_weight_kg * 9.80665.

Processing Notes

The .npz files are exported from the processed OpenSim ID outputs in OpenSim_ID/batch_id_results.

Before inverse dynamics, the source pipeline applies the following trial-level processing:

• Step01 and Step02 kinematics and GRF files are combined into one Step01_Step02 window.
• Kinematics are low-pass filtered before ID.
• Subject-specific scaled OpenSim models are used when available, preferring OpenSim_ID/scaled_models/<subject>/<subject>_scaled.osim.
• Trials are processed only when both step GRF files pass the double-peak vertical GRF check used by the batch ID script.
• GRF point columns are converted from millimeters to meters when needed.
• GRF force channels are assigned to calcn_r or calcn_l using TRC heel/toe marker proximity during stance. If TRC marker matching is unavailable, the script falls back to the COP-based side heuristic.
• A per-trial, per-force-channel COP offset is estimated when the COP point is far from the assigned foot marker segment. This corrects force-plate point locations before ID, for example when one channel's COP is shifted by approximately a force-plate-length offset.
• Trials are skipped during batch ID if the corrected COP has too little early-to-late displacement along the assigned foot's heel-to-toe marker segment, too little early-to-late movement in the lab frame, or remains too far from the assigned foot after correction. These checks are normalized by the subject's heel-to-toe marker length, so the QC is not based on an absolute foot size.

The exported computed_grf therefore reflects the corrected GRF file used for inverse dynamics. Force-vector columns are normalized by body weight in Newtons in the .npz; COP and ground-torque columns remain in their corrected physical units.

Folder Structure

S011/
  S011_Trial01_Step01_Step02.npz
  S011_Trial02_Step01_Step02.npz
  ...
S012/
  S012_Trial01_Step01_Step02.npz
  ...

Each .npz file corresponds to one subject/trial/step window.

Arrays

Each file contains:

Key	Shape	Description
subject	scalar string	Subject ID, for example S011.
trial	scalar string	Trial name, for example Trial01.
step_label	scalar string	Step label, currently Step01_Step02.
timestep	(T,)	Zero-based integer timestep over the kinematics sequence.
time_sec	(T,)	Kinematics time in seconds, shifted so the first frame is 0.0.
source_time_sec	(T,)	Same zero-start kinematics time as time_sec.
original_kinematics_time_sec	(T,)	Original OpenSim kinematics timestamps before zero-shifting.
id_source_time_sec	(N_id,)	Original ID timestamps shifted relative to the first kinematics frame.
original_id_source_time_sec	(N_id,)	Original OpenSim ID timestamps before zero-shifting.
joint_angle	(T, N_angle)	Joint angle / coordinate values from kinematics, on the kinematics timeline.
joint_angle_columns	(N_angle,)	Column names for joint_angle.
joint_torque	(T, N_torque)	ID torques from the processed OpenSim ID run, aligned onto the kinematics timeline and divided by subject_weight_kg. Missing rows are NaN.
joint_torque_columns	(N_torque,)	Column names for joint_torque.
joint_torque_valid	(T,)	Boolean mask where joint_torque has valid ID values.
joint_torque_normalization	scalar string	Normalization applied to joint_torque, currently divided_by_subject_weight_kg.
joint_torque_units	scalar string	Normalized torque units, currently original_ID_units_per_kg.
subject_weight_kg	scalar float	Subject weight used for normalizing joint_torque.
subject_body_weight_n	scalar float	Subject body weight in Newtons, computed as subject_weight_kg * 9.80665.
computed_grf	(T, N_grf)	Corrected GRF values used by ID, interpolated onto the kinematics timeline. Force-vector columns are divided by subject_body_weight_n; COP and torque columns remain in corrected physical units.
computed_grf_columns	(N_grf,)	Column names for computed_grf.
computed_grf_valid	(T,)	Boolean mask where computed_grf has valid values.
computed_grf_normalization	scalar string	Normalization applied to computed_grf, currently force_columns_divided_by_subject_body_weight_n.
computed_grf_units	scalar string	Force columns are in body weight units; COP and torque columns remain in corrected physical units.
source_files	(3,)	Source kinematics, ID torque, and GRF file paths used for export.

Policy Comparison

Run policy inference using joint_angle. The policy output should have the same first dimension T.

Compare predicted normalized torque against OpenSim ID only where joint_torque_valid is true:

import numpy as np

data = np.load("S011/S011_Trial01_Step01_Step02.npz")

joint_angle = data["joint_angle"]
target_torque = data["joint_torque"]
valid = data["joint_torque_valid"]
subject_weight_kg = float(data["subject_weight_kg"])

predicted_torque = policy(joint_angle)
predicted_torque = predicted_torque / subject_weight_kg

error = predicted_torque[valid] - target_torque[valid]

Rows where joint_torque_valid is false correspond to kinematics frames without an ID result and should be skipped for torque comparison.