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README.md

@@ -16,6 +16,23 @@ The files are intended for comparing policy inference outputs against OpenSim ID
 
 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
 
 ```text
@@ -47,18 +64,18 @@ Each file contains:
 | `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 aligned onto the kinematics timeline and divided by `subject_weight_kg`. Missing rows are `NaN`. |
+| `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 interpolated onto the kinematics timeline. Force-vector columns are divided by `subject_body_weight_n`; COP and torque columns remain in original units. |
+| `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 original units. |
+| `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

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