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Surrogate 1.3
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‎Step-6-Surrogate-Model/README.md

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# Step 6 Surrogate Model Preview
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# Step 6 Surrogate Model Sampling
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During Synergy-Driven Treatment Optimization, muscle-tendon length is calculated using polynomial fits of OpenSim length calculations so that the Muscle Analysis tool is not needed at every iteration. Muscle-tendon velocity and moment arms are calculated as analytical derivatives of these polynomials. The script in this folder shows a preview of how well a surrogate model created during Treatment Optimization with the given settings will match Muscle Analysis results.
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During Synergy-Driven Treatment Optimization, muscle-tendon length is calculated using polynomial fits of OpenSim length calculations so that the Muscle Analysis tool is not needed at every iteration. Muscle-tendon velocity and moment arms are calculated as analytical derivatives of these polynomials. The script in this folder uses Latin Hypercube Sampling to generate kinematic configurations within a range of the reference kinematics to use in fitting surrogate muscle models.
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## Running a Surrogate Model Preview
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## Running the Surrogate Model Sampling
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To run this step:
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- Make sure the nmsm-core project is loaded (double-click `Project.prj` in the root of nmsm-core if it is not loaded).
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- Navigate to the nmsm-tutorial/Step-6-Surrogate-Model directory.
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- Open and run the MATLAB script `surrogate.m`.
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- Open and run the MATLAB script `surrogateKinematicsScript.m`.
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The results will be plotted after surrogate models are created.
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This will generate a new set of kinematics within a data directory structure for surrogate model sampling. To complete the surrogate model data directory, a MuscleAnalysis must be run in the OpenSim GUI, using the motion file in IKData as the motion (with no filtering), and with output going to the MAData directory.

‎Step-6-Surrogate-Model/RightLegAndPelvis.osim

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‎Step-6-Surrogate-Model/UF_Subject_3_reduced_muscles.osim

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‎Step-6-Surrogate-Model/preprocessed/EMGData/gait_1.sto

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‎Step-6-Surrogate-Model/preprocessed/GRFData/gait_1.sto

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‎Step-6-Surrogate-Model/preprocessed/IDData/gait_1.sto

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‎Step-6-Surrogate-Model/preprocessed/IDData/kick_1.sto

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Inverse Dynamics Generalized Forces
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version=1
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nRows=55
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nColumns=15
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inDegrees=no
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endheader
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time pelvis_tilt_moment pelvis_list_moment pelvis_rotation_moment pelvis_tx_force pelvis_ty_force pelvis_tz_force hip_flexion_r_moment hip_adduction_r_moment hip_rotation_r_moment knee_angle_r_moment knee_angle_r_beta_force ankle_angle_r_moment subtalar_angle_r_moment mtp_angle_r_moment
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