├── .gitignore ├── LICENSE ├── MAIN_StaticOptimization.m ├── README.md ├── TestData ├── EMG_allMuscles.sto ├── Geometry │ ├── capitate_lvs.vtp │ ├── capitate_rvs.vtp │ ├── hamate_lvs.vtp │ ├── hamate_rvs.vtp │ ├── hat_jaw.vtp │ ├── hat_ribs_scap.vtp │ ├── hat_skull.vtp │ ├── hat_spine.vtp │ ├── humerus_lv.vtp │ ├── humerus_rv.vtp │ ├── index_distal_lvs.vtp │ ├── index_distal_rvs.vtp │ ├── index_medial_lvs.vtp │ ├── index_medial_rvs.vtp │ ├── index_proximal_lvs.vtp │ ├── index_proximal_rvs.vtp │ ├── l_bofoot.vtp │ ├── l_femur.vtp │ ├── l_fibula.vtp │ ├── l_foot.vtp │ ├── l_patella.vtp │ ├── l_pelvis.vtp │ ├── l_talus.vtp │ ├── l_tibia.vtp │ ├── l_tibia_SOMEINVERTEDFACES.vtp │ ├── little_distal_lvs.vtp │ ├── little_distal_rvs.vtp │ ├── little_medial_lvs.vtp │ ├── little_medial_rvs.vtp │ ├── little_proximal_lvs.vtp │ ├── little_proximal_rvs.vtp │ ├── lunate_lvs.vtp │ ├── lunate_rvs.vtp │ ├── metacarpal1_lvs.vtp │ ├── metacarpal1_rvs.vtp │ ├── metacarpal2_lvs.vtp │ ├── metacarpal2_rvs.vtp │ ├── metacarpal3_lvs.vtp │ ├── metacarpal3_rvs.vtp │ ├── metacarpal4_lvs.vtp │ ├── metacarpal4_rvs.vtp │ ├── metacarpal5_lvs.vtp │ ├── metacarpal5_rvs.vtp │ ├── middle_distal_lvs.vtp │ ├── middle_distal_rvs.vtp │ ├── middle_medial_lvs.vtp │ ├── middle_medial_rvs.vtp │ ├── middle_proximal_lvs.vtp │ ├── middle_proximal_rvs.vtp │ ├── pisiform_lvs.vtp │ ├── pisiform_rvs.vtp │ ├── r_bofoot.vtp │ ├── r_femur.vtp │ ├── r_fibula.vtp │ ├── r_foot.vtp │ ├── r_patella.vtp │ ├── r_pelvis.vtp │ ├── r_talus.vtp │ ├── r_tibia.vtp │ ├── r_tibia_SOMEINVERTEDFACES.vtp │ ├── radius_lv.vtp │ ├── radius_rv.vtp │ ├── ring_distal_lvs.vtp │ ├── ring_distal_rvs.vtp │ ├── ring_medial_lvs.vtp │ ├── ring_medial_rvs.vtp │ ├── ring_proximal_lvs.vtp │ ├── ring_proximal_rvs.vtp │ ├── sacrum.vtp │ ├── scaphoid_lvs.vtp │ ├── scaphoid_rvs.vtp │ ├── thumb_distal_lvs.vtp │ ├── thumb_distal_rvs.vtp │ ├── thumb_proximal_lvs.vtp │ ├── thumb_proximal_rvs.vtp │ ├── trapezium_lvs.vtp │ ├── trapezium_rvs.vtp │ ├── trapezoid_lvs.vtp │ ├── trapezoid_rvs.vtp │ ├── triquetrum_lvs.vtp │ ├── triquetrum_rvs.vtp │ ├── ulna_lv.vtp │ └── ulna_rv.vtp ├── Rajagopal_scaled_Sub1_gasAvoid.osim ├── activationExampleOutput.jpg ├── results_SO │ ├── API_staticOpt_settings.m │ ├── JrxnSetup.xml │ ├── results_JointReaction_JointRxn_ReactionLoads.sto │ ├── results_forces.sto │ ├── results_states.sto │ └── staticOptAPI_log.txt ├── results_id.sto ├── results_ik.sto └── walking_baseline1_forces.mot └── Utilities ├── CostFunction.m ├── DynamicsConstraint_accelerationMatching.m ├── DynamicsConstraint_momentMatching.m ├── StaticOptimizationAPIVectorized.asv ├── StaticOptimizationAPIVectorized.m └── getMuscleParams.m /.gitignore: -------------------------------------------------------------------------------- 1 | *.asv -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Apache License 2 | Version 2.0, January 2004 3 | http://www.apache.org/licenses/ 4 | 5 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 6 | 7 | 1. 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Author: Scott Uhlrich, Stanford 2 | % University, 2020. Please cite: 3 | % Uhlrich, S.D., Jackson, R.W., Seth, A., Kolesar, J.A., Delp S.L. 4 | % Muscle coordination retraining inspired by musculoskeletal simulations 5 | % reduces knee contact force. Sci Rep 12, 9842 (2022). 6 | % https://doi.org/10.1038/s41598-022-13386-9 7 | 8 | function [] = MAIN_StaticOptimizationAPI() 9 | % This main loop allows you to run StaticOptimizationAPI.m 10 | 11 | clear all; close all; format compact; clc; fclose all; 12 | 13 | % % Path to the data and utility functions. No need to change this, unless 14 | % you rearrange the folder structure, differently from github. 15 | baseDir = [pwd '\TestData\'] ; % Base Directory to base results directory. 16 | addpath(genpath('Utilities')) 17 | 18 | % % % Fill Path names 19 | INPUTS.trialname = 'walking_baseline1' ; 20 | INPUTS.forceFilePath = [baseDir '\walking_baseline1_forces.mot'] ; % Full path of forces file 21 | INPUTS.ikFilePath = [baseDir '\results_ik.sto'] ; % Full path of IK file 22 | INPUTS.idFilePath = [baseDir '\results_id.sto'] ; % Full path of ID file 23 | INPUTS.emgFilePath = [baseDir '\EMG_allMuscles.sto'] ; % location of *.mot file with normalized EMG (if using EMG) 24 | INPUTS.outputFilePath = [baseDir '\results_SO\'] ; % full path for SO & JRA outputs 25 | INPUTS.modelDir = [baseDir] ; % full path to folder where model is 26 | INPUTS.modelName = 'Rajagopal_scaled_Sub1_gasAvoid.osim' ; % model file name 27 | geometryPath = [baseDir '\Geometry'] ; % full path to geometry folder for Model. If pointing to Geometry folder in OpenSim install, leave this field blank: [] 28 | 29 | % % % Set time for simulation % % % 30 | INPUTS.startTime = 10.9 ; 31 | INPUTS.endTime = 11.7 ; 32 | 33 | INPUTS.leg = 'l' ; % If deleteContralateralMuscles flag is true, actuates this leg 34 | % with muscles and contralateral leg with coordinate actuators 35 | % only. If deleteContralateralMuscles flag is false, 36 | % this input doesn't matter. 37 | 38 | % Flags 39 | 40 | % % Load up the INPUTS structure for static optimization parameters that are constant across all 41 | % trials and subjects 42 | INPUTS.filtFreq = 6 ; % Lowpass filter frequency for IK coordinates. -1 if no filtering 43 | 44 | % Flags 45 | INPUTS.appendActuators = true ; % Append reserve actuators at all coordinates? 46 | INPUTS.appendForces = true ; % True if you want to append grfs? 47 | INPUTS.deleteContralateralMuscles = false ; % replace muscles on contralateral leg with powerful reserve actuators (makes SO faster) 48 | INPUTS.useEmgRatios = false ; % true if you want to track EMG ratios defined in INPUTS.emgRatioPairs 49 | INPUTS.useEqualMuscles = false ; % true if you want to constrain INPUTS.equalMuscles muscle pairs to be equivalent 50 | INPUTS.useEmgConstraints = false ; % true if you want to constrain muscle activations to follow EMG input INPUTS.emgConstrainedMuscles 51 | INPUTS.changePassiveForce = false ; % true if want to turn passive forces off 52 | INPUTS.ignoreTendonCompliance = false ; % true if making all tendons rigid 53 | 54 | 55 | % Degrees of Freedom to ignore (patellar coupler constraints, etc.) during moment matching constraint 56 | INPUTS.fixedDOFs = {'knee_angle_r_beta','knee_angle_l_beta'} ; 57 | 58 | % EMG file 59 | INPUTS.emgRatioPairs = {} ; % nPairs x 2 cell for muscle names whos ratios you want to constrain with EMG. Can leave off '_[leg]' if you want it to apply to both 60 | INPUTS.equalMuscles = {} ; % nPairs x 2 cell of muscles for whom you want equal activations 61 | INPUTS.emgConstrainedMuscles = {} ; % nMuscles x 1 cell of muscles for which you want activation to track EMG. Can leave off '_[leg]' if you want it to apply to both 62 | 63 | INPUTS.emgSumThreshold = 0 ; % If sum of emg pairs is less than this it won't show up in the constraint or cost (wherever you put it) 64 | 65 | % Weights for reserves, muscles. The weight is in 66 | % the cost function as sum(w*(whatever^2)), so the weight is not squared. 67 | INPUTS.reserveActuatorWeights = 1 ; 68 | INPUTS.muscleWeights = 1 ; 69 | INPUTS.ipsilateralActuatorStrength = 1 ; 70 | INPUTS.contralateralActuatorStrength = 100 ; 71 | INPUTS.weightsToOverride = {} ; % Overrides the general actuator weight for muscles or reserves. 72 | % Can be a partial name. Eg. 'hip_rotation' will change hip_rotation_r and hip_rotation_l 73 | % or 'gastroc' to override the weight for the right and left gastroc muscles 74 | INPUTS.overrideWeights = [] ; % A column vector the same size as weights 75 | INPUTS.prescribedActuationCoords = {} ; % A column cell with coordinates (exact name) that will be prescribed from ID moments eg. 'knee_adduction_r' 76 | % The muscles will not aim to balance the moment at this DOF, 77 | % but their contribution to the moment will be computed at the 78 | % end of the optimization step, and the remaining moment generated by 79 | % the reserve actuator 80 | 81 | 82 | % External Forces Definitions 83 | INPUTS.externalForceName = {'GRF_r','GRF_l'} ; % nForces x 1 cell 84 | INPUTS.applied_to_body = {'calcn_r','calcn_l'} ; 85 | INPUTS.force_expressed_in_body = {'ground','ground'} ; 86 | INPUTS.force_identifier = {'ground_force_v','1_ground_force_v'} ; 87 | INPUTS.point_expressed_in_body = {'ground','ground'} ; 88 | INPUTS.point_identifier = {'ground_force_p','1_ground_force_p'} ; 89 | 90 | % Joint Reaction Fields 91 | INPUTS.jRxn.inFrame = 'child' ; 92 | INPUTS.jRxn.onBody = 'child' ; 93 | INPUTS.jRxn.jointNames = ['all'] ; 94 | 95 | INPUTS.passiveForceStrains = [3 4] ; % Default = [0,.7] this is strain at zero force and strain at 1 norm force in Millard model 96 | % This only matters if ignorePassiveForces = true 97 | 98 | % % % % % END OF USER INPUTS % % % % %% % % % %% % % % %% % % % %% % % % % 99 | 100 | 101 | if ~isempty(INPUTS.overrideWeights) 102 | disp('YOU ARE OVERRIDING SOME ACTUATOR WEIGHTS'); 103 | end 104 | 105 | if ~isempty(geometryPath) 106 | org.opensim.modeling.ModelVisualizer.addDirToGeometrySearchPaths(geometryPath) 107 | end 108 | 109 | % Run it! 110 | StaticOptimizationAPIVectorized(INPUTS) ; % Run StaticOptimizationAPI 111 | 112 | % Save this script in the folder to reference settings 113 | FileNameAndLocation=[mfilename('fullpath')]; 114 | newbackup=[INPUTS.outputFilePath 'API_staticOpt_settings.m']; 115 | currentfile=strcat(FileNameAndLocation, '.m'); 116 | copyfile(currentfile,newbackup); 117 | 118 | end % Main 119 | 120 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Static Optimization in Matlab 2 | This code solves the muscle redundancy problem using static optimization in Matlab. Cost and constraint functions can be defined in Matlab using the OpenSim API. For example, you can track muscle activations from electromyography. Details about the implementation can be found in Uhlrich et al., 2021. 3 | 4 | ## Publications 5 | Please cite this paper if you use this code in your work: 6 |
7 | Uhlrich SD, Jackson RW, Seth A, Kolesar JA, Delp SL, 2022. Muscle coordination retraining inspired by musculoskeletal simulations reduces knee contact force. *Scientific Reports* __12__, 9842. https://doi.org/10.1038/s41598-022-13386-9. 8 | 9 | ## Running demo 10 | Install the latest version of OpenSim (this code has been tested with OpenSim 4.2 and Matlab R2020b), and follow the instructions to set up OpenSim scripting in Matlab. 11 | 12 | Running the demo requires MATLAB's Optimization Toolbox and the DPS System or Signal Processing Toolbox. Information about acquiring MATLAB toolboxes can be found on the [MathWorks website](https://www.mathworks.com/products/alphabetical.html). 13 | 14 | Clone the repository and use the MAIN_StaticOptimization.m script to run the code to solve for muscle activations for the provided example stance phase of walking. This should take around 50s on a normal desktop computer and produce an interactive plot of muscle activations and reserve actuator controls, shown in Figure 1. 15 | 16 | ![alt text](https://github.com/stanfordnmbl/MatlabStaticOptimization/blob/main/TestData/activationExampleOutput.jpg) 17 | Figure 1: Example interactive Matlab figure showing the resulting muscle activations and actuator controls from a stance phase of walking. 18 | 19 | ## Example data 20 | Data for a 26-year-old healthy male walking on a treadmill are included in the TestData folder. Inverse Kinematics and Inverse Dynamics have already been run. For more data and examples, view the Coordination Retraining Project on SimTK. 21 | 22 | ## Running static optimization with your own data 23 | To run this code using your own data, you must scale a model and run Inverse Kinematics and Inverse Dynamics. Then change the paths in MAIN_StaticOptimization.m and settings to match your data and desired simulation settings. 24 | 25 | ## Functionality 26 | Like the OpenSim static optimization algorithm, this approach solves for muscle activations at each timestep, however there are several differences. 27 | 1. This code has the option to estimate muscle lengths with a compliant tendon (see Uhlrich et al. 2020 for details). When tendon compliance is used, the force-velocity multiplier is set to 1. 28 | 2. This code has the option to include passive muscle forces. 29 | 3. This code allows for the cost and constraint functions to be defined in Matlab. Without changing settings, it minimizes the sum of squared muscle activations, but adding EMG or EMG ratio tracking to the cost or constraint function is also implemented. Changing the weight on individual actuators (muscles or coordinate actuators) is also implemented. Adding quantities that can be computed with a model and state using the OpenSim API (e.g. joint reaction forces) could also be easily added to the cost or constraint functions. For quantities that require changing the state of the model in the cost/constraint function, the 'DynamicsConstraint_momentMatching.m' constraint function must be replaced by the 'DynamicsConstraint_accelerationMatching.m' function in the 'StaticOptimizationAPI_Vectorized.m' function. The "momentMatching" implementation pre-computes all model parameters before the optimization, so does not need to call the OpenSim API when evaluating the cost or constraint functions, increasing computational efficiency. If the model state must be updated to compute the cost or constraint, then the "acceleration matching" technique must be used where the model's joint accelerations are constrained to match the accelerations computed by differentiating the inverse kinematics results. 30 | -------------------------------------------------------------------------------- /TestData/Geometry/capitate_lvs.vtp: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -0.850679 -0.525458 -0.015466 8 | -0.795084 0.254980 0.550296 9 | -0.925442 0.270628 0.265173 10 | -0.957385 -0.195340 -0.212735 11 | -0.786748 -0.539937 0.299158 12 | -0.103721 -0.993953 0.036035 13 | -0.204106 -0.927770 -0.312385 14 | -0.374321 -0.766884 -0.521319 15 | -0.821271 0.539541 0.185499 16 | -0.254865 -0.469416 0.845395 17 | -0.615790 0.441827 0.652374 18 | 0.135474 0.086726 0.986978 19 | -0.939578 0.334432 -0.073133 20 | -0.872961 -0.112735 -0.474583 21 | 0.367093 -0.573977 0.731979 22 | -0.019325 -0.955343 -0.294867 23 | 0.308760 -0.893900 0.324976 24 | -0.495147 -0.758038 -0.424509 25 | -0.676226 -0.286344 -0.678768 26 | -0.364806 -0.517208 -0.774217 27 | -0.708473 0.685778 -0.166655 28 | -0.658253 0.483144 0.577300 29 | -0.951291 0.262146 -0.162253 30 | -0.755394 0.650652 0.077664 31 | -0.131130 0.272086 0.953296 32 | 0.488331 -0.306142 0.817196 33 | 0.247957 -0.193108 0.949329 34 | -0.774129 0.401012 -0.489810 35 | -0.039770 -0.921917 0.385339 36 | -0.222336 -0.734528 -0.641120 37 | -0.339310 -0.920901 -0.191862 38 | -0.626070 0.215179 -0.749489 39 | -0.310900 -0.254044 -0.915862 40 | -0.420070 -0.086330 -0.903376 41 | -0.017282 -0.190023 -0.981628 42 | -0.843011 0.483333 -0.236055 43 | -0.730245 0.426863 -0.533413 44 | -0.789158 0.482735 -0.379731 45 | -0.976620 0.172534 0.128238 46 | -0.440370 0.552290 0.707849 47 | -0.932443 -0.246849 -0.263848 48 | -0.385800 0.502020 0.774037 49 | 0.025627 -0.069445 0.997256 50 | 0.491809 -0.395722 0.775583 51 | 0.397779 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420 423 426 429 432 435 438 441 444 318 | 319 | 320 | 321 | 322 | 323 | -------------------------------------------------------------------------------- /TestData/Geometry/hamate_rvs.vtp: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 0.782337 -0.130674 -0.608993 8 | 0.773586 0.621459 -0.123912 9 | 0.993452 -0.076257 -0.085079 10 | 0.665987 -0.293810 -0.685665 11 | 0.441926 -0.290312 -0.848776 12 | 0.638121 0.190355 -0.746034 13 | 0.467242 0.800123 -0.376149 14 | 0.433803 0.489824 0.756232 15 | -0.153155 0.455794 0.876810 16 | 0.121669 0.800685 0.586601 17 | 0.831468 -0.538250 0.137649 18 | 0.323808 -0.065828 0.943830 19 | 0.555348 -0.642069 -0.528523 20 | 0.176828 -0.697916 -0.694007 21 | 0.325339 0.173217 -0.929597 22 | 0.187992 -0.624477 -0.758081 23 | -0.299437 -0.693563 -0.655216 24 | -0.022898 -0.526725 -0.849727 25 | 0.305052 0.910520 -0.279099 26 | -0.190351 -0.049779 0.980453 27 | 0.135623 0.347888 0.927674 28 | 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363 366 369 372 375 378 381 384 387 390 393 396 399 402 405 408 411 414 417 420 423 426 306 | 307 | 308 | 309 | 310 | 311 | -------------------------------------------------------------------------------- /TestData/Geometry/scaphoid_rvs.vtp: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -0.756283 -0.628058 -0.183248 8 | -0.987479 -0.049826 0.149676 9 | -0.718028 -0.373592 -0.587252 10 | -0.500405 -0.527912 -0.686225 11 | -0.294811 -0.889068 -0.350208 12 | -0.780185 -0.424034 0.459899 13 | -0.540409 -0.838664 -0.067830 14 | -0.622767 -0.764515 0.166367 15 | -0.402198 -0.900425 -0.165744 16 | -0.501666 0.578789 0.642911 17 | -0.908651 0.417036 0.020858 18 | -0.928360 -0.158736 -0.336082 19 | -0.636446 0.164726 0.753526 20 | 0.151268 -0.161676 -0.975182 21 | 0.005035 -0.480153 -0.877170 22 | -0.580456 -0.560503 -0.590684 23 | 0.127418 -0.231226 -0.964520 24 | 0.049079 -0.520769 -0.852286 25 | 0.260803 -0.948818 -0.178116 26 | 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333 336 339 342 345 348 351 354 357 360 363 366 369 372 375 378 274 | 275 | 276 | 277 | 278 | 279 | -------------------------------------------------------------------------------- /TestData/Geometry/trapezoid_rvs.vtp: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 0.125313 0.970835 0.204391 8 | -0.415886 0.854322 -0.311724 9 | -0.384101 0.799662 0.461526 10 | 0.300854 0.953602 0.011419 11 | 0.348987 0.762317 0.545051 12 | 0.106861 0.415729 0.903189 13 | 0.066189 0.971918 -0.225820 14 | -0.798862 0.601322 -0.015224 15 | -0.027330 0.680764 -0.731992 16 | -0.059100 0.897654 -0.436721 17 | -0.439386 0.639542 -0.630813 18 | -0.746213 0.509261 -0.428741 19 | -0.234561 0.382135 0.893842 20 | 0.201064 0.977815 -0.058743 21 | 0.058700 0.355338 0.932893 22 | 0.376811 0.919803 0.109435 23 | 0.257761 0.752496 0.606060 24 | -0.649812 -0.090349 0.754706 25 | -0.970131 0.193340 -0.146512 26 | -0.241732 0.346438 -0.906392 27 | 0.201221 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315 318 321 324 327 330 333 336 339 342 345 348 351 354 357 360 363 366 369 372 375 378 274 | 275 | 276 | 277 | 278 | 279 | -------------------------------------------------------------------------------- /TestData/Geometry/triquetrum_lvs.vtp: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 0.121126 -0.174726 -0.977138 8 | -0.324815 0.084002 -0.942040 9 | -0.258180 0.781421 -0.568088 10 | 0.257943 0.806183 -0.532479 11 | 0.272477 -0.766924 -0.581019 12 | 0.302514 -0.788904 -0.534898 13 | 0.289927 -0.025192 -0.956717 14 | 0.187781 -0.695542 -0.693513 15 | -0.853329 0.479610 -0.204459 16 | -0.740014 -0.398208 -0.542043 17 | -0.628527 0.773796 0.078695 18 | -0.039496 0.919321 -0.391521 19 | 0.816589 0.469746 -0.335442 20 | 0.542471 0.495205 -0.678600 21 | 0.758921 0.651023 -0.014417 22 | 0.275945 0.902133 -0.331678 23 | -0.704388 -0.683895 -0.190065 24 | -0.325644 -0.892909 -0.310919 25 | 0.608309 0.103392 -0.786937 26 | 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450 453 456 459 462 465 468 471 474 477 480 483 486 346 | 347 | 348 | 349 | 350 | 351 | -------------------------------------------------------------------------------- /TestData/Geometry/triquetrum_rvs.vtp: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -0.258180 0.781421 0.568088 8 | -0.324815 0.084002 0.942040 9 | 0.121126 -0.174726 0.977138 10 | 0.257943 0.806183 0.532479 11 | -0.853329 0.479610 0.204459 12 | -0.628527 0.773796 -0.078695 13 | -0.039496 0.919321 0.391521 14 | -0.740014 -0.398208 0.542043 15 | 0.272477 -0.766924 0.581019 16 | 0.302514 -0.788904 0.534898 17 | 0.289927 -0.025192 0.956717 18 | 0.187781 -0.695542 0.693513 19 | 0.542471 0.495205 0.678600 20 | 0.816589 0.469746 0.335442 21 | 0.758921 0.651023 0.014417 22 | 0.275945 0.902133 0.331678 23 | -0.916764 0.231952 -0.325179 24 | -0.255015 0.961583 -0.101617 25 | -0.459553 0.671144 -0.581702 26 | -0.750053 0.366918 -0.550265 27 | 0.174452 0.931814 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0.130264 87 | 0.239338 -0.907714 -0.344635 88 | -0.268015 0.438983 -0.857591 89 | -0.711139 0.522322 -0.470597 90 | 91 | 92 | 93 | 94 | -0.006227 -0.005999 -0.019078 95 | -0.008368 -0.012117 -0.013576 96 | -0.002791 -0.010802 -0.013712 97 | -0.001091 -0.006372 -0.017515 98 | -0.009177 -0.009207 -0.017151 99 | -0.006400 -0.005650 -0.020172 100 | -0.003519 -0.005579 -0.019102 101 | -0.009708 -0.014488 -0.015533 102 | -0.007909 -0.012536 -0.014026 103 | -0.007617 -0.012699 -0.014688 104 | -0.000987 -0.010584 -0.014097 105 | -0.000494 -0.012897 -0.016195 106 | 0.001978 -0.010222 -0.015438 107 | 0.003013 -0.010693 -0.016508 108 | -0.000791 -0.005790 -0.020325 109 | -0.001689 -0.005491 -0.019841 110 | -0.009096 -0.011887 -0.020008 111 | -0.005218 -0.005167 -0.020918 112 | -0.004644 -0.005772 -0.022469 113 | -0.006913 -0.007970 -0.022782 114 | -0.002003 -0.005135 -0.020423 115 | -0.010015 -0.014486 -0.019839 116 | -0.010097 -0.016565 -0.018456 117 | -0.009056 -0.017487 -0.020225 118 | 0.002216 -0.010920 -0.015356 119 | 0.002385 -0.011413 -0.015601 120 | 0.003258 -0.016033 -0.020187 121 | 0.003239 -0.012300 -0.017176 122 | 0.003476 -0.011808 -0.017776 123 | 0.002814 -0.011144 -0.015953 124 | -0.000745 -0.006716 -0.023729 125 | 0.002424 -0.016092 -0.027901 126 | -0.001315 -0.005069 -0.021285 127 | 0.003732 -0.015708 -0.020432 128 | -0.007653 -0.011263 -0.022316 129 | -0.008356 -0.012954 -0.021333 130 | -0.003552 -0.005604 -0.022888 131 | -0.002989 -0.005079 -0.022427 132 | -0.002607 -0.004869 -0.021445 133 | -0.004808 -0.009255 -0.025027 134 | -0.006451 -0.011171 -0.024242 135 | -0.009092 -0.016033 -0.022175 136 | -0.007076 -0.016816 -0.023808 137 | -0.008198 -0.018093 -0.021001 138 | -0.006940 -0.018561 -0.021244 139 | 0.004109 -0.019388 -0.022363 140 | -0.003027 -0.020575 -0.022666 141 | -0.002104 -0.005485 -0.023104 142 | 0.001621 -0.014616 -0.027841 143 | -0.001692 -0.007977 -0.025261 144 | 0.003153 -0.017429 -0.027982 145 | 0.002323 -0.018405 -0.028242 146 | 0.002073 -0.016547 -0.028148 147 | 0.003779 -0.020365 -0.026713 148 | 0.004536 -0.021513 -0.024183 149 | -0.005184 -0.013940 -0.023544 150 | -0.000978 -0.011626 -0.027022 151 | -0.003518 -0.012404 -0.025346 152 | -0.004869 -0.020067 -0.022683 153 | -0.004911 -0.016507 -0.025546 154 | -0.002708 -0.021179 -0.023933 155 | -0.002433 -0.019899 -0.028090 156 | 0.004300 -0.022027 -0.023604 157 | 0.003804 -0.022214 -0.023276 158 | -0.002635 -0.021163 -0.023152 159 | 0.002064 -0.022265 -0.023175 160 | 0.001685 -0.017078 -0.028214 161 | -0.000290 -0.014894 -0.027606 162 | 0.003351 -0.020710 -0.027076 163 | 0.000956 -0.021507 -0.025801 164 | -0.000378 -0.020255 -0.028184 165 | 0.000936 -0.017747 -0.028623 166 | 0.004065 -0.021356 -0.025394 167 | 0.003565 -0.021688 -0.025807 168 | 0.004235 -0.022046 -0.024398 169 | -0.002814 -0.015117 -0.023811 170 | -0.001664 -0.013749 -0.026419 171 | -0.003015 -0.016826 -0.027882 172 | -0.002162 -0.018023 -0.028592 173 | 0.003819 -0.022497 -0.023781 174 | 0.003651 -0.022426 -0.024456 175 | -0.000637 -0.016111 -0.028194 176 | -0.002091 -0.015488 -0.026291 177 | 178 | 179 | 180 | 181 | 0 1 2 182 | 3 0 2 183 | 0 4 1 184 | 5 4 0 185 | 0 3 6 186 | 6 5 0 187 | 1 4 7 188 | 2 1 8 189 | 8 1 7 190 | 2 8 9 191 | 2 10 3 192 | 10 2 11 193 | 9 11 2 194 | 3 12 13 195 | 3 13 14 196 | 3 14 15 197 | 3 15 6 198 | 10 12 3 199 | 7 4 16 200 | 16 4 5 201 | 17 18 5 202 | 17 5 6 203 | 19 16 5 204 | 19 5 18 205 | 17 6 20 206 | 20 6 15 207 | 16 21 7 208 | 21 22 7 209 | 9 8 7 210 | 22 9 7 211 | 22 23 9 212 | 9 23 11 213 | 10 24 12 214 | 11 25 10 215 | 10 25 24 216 | 23 26 11 217 | 27 25 11 218 | 27 11 26 219 | 24 13 12 220 | 14 13 28 221 | 28 13 29 222 | 29 13 24 223 | 30 14 31 224 | 32 14 30 225 | 32 20 14 226 | 20 15 14 227 | 14 33 31 228 | 33 14 28 229 | 16 19 34 230 | 35 21 16 231 | 34 35 16 232 | 36 18 17 233 | 37 36 17 234 | 17 38 37 235 | 17 20 38 236 | 18 39 19 237 | 36 39 18 238 | 40 34 19 239 | 39 40 19 240 | 38 20 32 241 | 41 22 21 242 | 35 41 21 243 | 23 22 41 244 | 23 42 43 245 | 23 44 26 246 | 41 42 23 247 | 23 43 44 248 | 25 29 24 249 | 25 27 29 250 | 45 33 26 251 | 44 46 26 252 | 26 33 27 253 | 45 26 46 254 | 29 27 28 255 | 33 28 27 256 | 30 47 32 257 | 30 31 48 258 | 47 30 49 259 | 49 30 48 260 | 31 50 51 261 | 48 31 52 262 | 31 51 52 263 | 50 31 33 264 | 38 32 47 265 | 50 33 53 266 | 54 53 33 267 | 54 33 45 268 | 34 55 35 269 | 55 34 40 270 | 55 41 35 271 | 47 36 37 272 | 49 36 47 273 | 39 36 49 274 | 38 47 37 275 | 56 39 49 276 | 56 40 39 277 | 40 57 55 278 | 56 57 40 279 | 41 55 42 280 | 58 43 42 281 | 42 55 59 282 | 60 58 42 283 | 61 60 42 284 | 59 61 42 285 | 43 58 44 286 | 58 46 44 287 | 45 62 54 288 | 63 62 45 289 | 46 63 45 290 | 64 65 46 291 | 65 63 46 292 | 64 46 58 293 | 66 67 48 294 | 66 48 52 295 | 48 56 49 296 | 48 67 56 297 | 51 50 68 298 | 53 68 50 299 | 68 69 51 300 | 51 66 52 301 | 70 51 69 302 | 71 51 70 303 | 66 51 71 304 | 54 72 53 305 | 68 53 73 306 | 53 72 73 307 | 62 74 54 308 | 74 72 54 309 | 75 59 55 310 | 75 55 57 311 | 76 57 56 312 | 67 76 56 313 | 76 75 57 314 | 60 64 58 315 | 59 77 61 316 | 75 77 59 317 | 61 70 60 318 | 64 60 65 319 | 70 69 60 320 | 69 65 60 321 | 77 78 61 322 | 61 78 70 323 | 63 79 62 324 | 79 74 62 325 | 79 63 65 326 | 69 80 65 327 | 80 79 65 328 | 67 66 71 329 | 81 76 67 330 | 67 71 81 331 | 68 73 69 332 | 69 73 80 333 | 71 70 78 334 | 78 81 71 335 | 73 72 80 336 | 74 80 72 337 | 79 80 74 338 | 77 75 82 339 | 82 75 76 340 | 81 82 76 341 | 77 82 81 342 | 78 77 81 343 | 344 | 345 | 3 6 9 12 15 18 21 24 27 30 33 36 39 42 45 48 51 54 57 60 63 66 69 72 75 78 81 84 87 90 93 96 99 102 105 108 111 114 117 120 123 126 129 132 135 138 141 144 147 150 153 156 159 162 165 168 171 174 177 180 183 186 189 192 195 198 201 204 207 210 213 216 219 222 225 228 231 234 237 240 243 246 249 252 255 258 261 264 267 270 273 276 279 282 285 288 291 294 297 300 303 306 309 312 315 318 321 324 327 330 333 336 339 342 345 348 351 354 357 360 363 366 369 372 375 378 381 384 387 390 393 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Author: Scott Uhlrich, Stanford 2 | % University, 2020. Please cite: 3 | % Uhlrich SD, Jackson RW, Seth A, Kolesar JA, Delp SL, 2021. 4 | % Muscle coordination retraining inspired by musculoskeletal simulations: a study on reducing joint loading. 5 | % bioRxiv. doi: https://doi.org/10.1101/2020.12.30.424841. 6 | 7 | function [] = MAIN_StaticOptimizationAPI() 8 | % This main loop allows you to run StaticOptimizationAPI.m 9 | 10 | clear all; close all; format compact; clc; fclose all; 11 | 12 | % % Path to the data and utility functions. No need to change this, unless 13 | % you rearrange the folder structure, differently from github. 14 | baseDir = [pwd '\TestData\'] ; % Base Directory to base results directory. 15 | addpath(genpath('Utilities')) 16 | 17 | % % % Fill Path names 18 | INPUTS.trialname = 'walking_baseline1' ; 19 | INPUTS.forceFilePath = [baseDir '\walking_baseline1_forces.mot'] ; % Full path of forces file 20 | INPUTS.ikFilePath = [baseDir '\results_ik.sto'] ; % Full path of IK file 21 | INPUTS.idFilePath = [baseDir '\results_id.sto'] ; % Full path of ID file 22 | INPUTS.emgFilePath = [baseDir '\EMG_allMuscles.sto'] ; % location of *.mot file with normalized EMG (if using EMG) 23 | INPUTS.outputFilePath = [baseDir '\results_SO\'] ; % full path for SO & JRA outputs 24 | INPUTS.modelDir = [baseDir] ; % full path to folder where model is 25 | INPUTS.modelName = 'Rajagopal_scaled_Sub1_gasAvoid.osim' ; % model file name 26 | geometryPath = [baseDir '\Geometry'] ; % full path to geometry folder for Model. If pointing to Geometry folder in OpenSim install, leave this field blank: [] 27 | 28 | % % % Set time for simulation % % % 29 | INPUTS.startTime = 10.9 ; 30 | INPUTS.endTime = 11.7 ; 31 | 32 | INPUTS.leg = 'l' ; % If deleteContralateralMuscles flag is true, actuates this leg 33 | % with muscles and contralateral leg with coordinate actuators 34 | % only. If deleteContralateralMuscles flag is false, 35 | % this input doesn't matter. 36 | 37 | % Flags 38 | 39 | % % Load up the INPUTS structure for static optimization parameters that are constant across all 40 | % trials and subjects 41 | INPUTS.filtFreq = 6 ; % Lowpass filter frequency for IK coordinates. -1 if no filtering 42 | 43 | % Flags 44 | INPUTS.appendActuators = true ; % Append reserve actuators at all coordinates? 45 | INPUTS.appendForces = true ; % True if you want to append grfs? 46 | INPUTS.deleteContralateralMuscles = false ; % replace muscles on contralateral leg with powerful reserve actuators (makes SO faster) 47 | INPUTS.useEmgRatios = false ; % true if you want to track EMG ratios defined in INPUTS.emgRatioPairs 48 | INPUTS.useEqualMuscles = false ; % true if you want to constrain INPUTS.equalMuscles muscle pairs to be equivalent 49 | INPUTS.useEmgConstraints = false ; % true if you want to constrain muscle activations to follow EMG input INPUTS.emgConstrainedMuscles 50 | INPUTS.changePassiveForce = false ; % true if want to turn passive forces off 51 | INPUTS.ignoreTendonCompliance = false ; % true if making all tendons rigid 52 | 53 | 54 | % Degrees of Freedom to ignore (patellar coupler constraints, etc.) during moment matching constraint 55 | INPUTS.fixedDOFs = {'knee_angle_r_beta','knee_angle_l_beta'} ; 56 | 57 | % EMG file 58 | INPUTS.emgRatioPairs = {} ; % nPairs x 2 cell for muscle names whos ratios you want to constrain with EMG. Can leave off '_[leg]' if you want it to apply to both 59 | INPUTS.equalMuscles = {} ; % nPairs x 2 cell of muscles for whom you want equal activations 60 | INPUTS.emgConstrainedMuscles = {} ; % nMuscles x 1 cell of muscles for which you want activation to track EMG. Can leave off '_[leg]' if you want it to apply to both 61 | 62 | INPUTS.emgSumThreshold = 0 ; % If sum of emg pairs is less than this it won't show up in the constraint or cost (wherever you put it) 63 | 64 | % Weights for reserves, muscles. The weight is in 65 | % the cost function as sum(w*(whatever^2)), so the weight is not squared. 66 | INPUTS.reserveActuatorWeights = 1 ; 67 | INPUTS.muscleWeights = 1 ; 68 | INPUTS.ipsilateralActuatorStrength = 1 ; 69 | INPUTS.contralateralActuatorStrength = 100 ; 70 | INPUTS.weightsToOverride = {} ; % Overrides the general actuator weight for muscles or reserves. 71 | % Can be a partial name. Eg. 'hip_rotation' will change hip_rotation_r and hip_rotation_l 72 | % or 'gastroc' to override the weight for the right and left gastroc muscles 73 | INPUTS.overrideWeights = [] ; % A column vector the same size as weights 74 | INPUTS.prescribedActuationCoords = {} ; % A column cell with coordinates (exact name) that will be prescribed from ID moments eg. 'knee_adduction_r' 75 | % The muscles will not aim to balance the moment at this DOF, 76 | % but their contribution to the moment will be computed at the 77 | % end of the optimization step, and the remaining moment generated by 78 | % the reserve actuator 79 | 80 | 81 | % External Forces Definitions 82 | INPUTS.externalForceName = {'GRF_r','GRF_l'} ; % nForces x 1 cell 83 | INPUTS.applied_to_body = {'calcn_r','calcn_l'} ; 84 | INPUTS.force_expressed_in_body = {'ground','ground'} ; 85 | INPUTS.force_identifier = {'ground_force_v','1_ground_force_v'} ; 86 | INPUTS.point_expressed_in_body = {'ground','ground'} ; 87 | INPUTS.point_identifier = {'ground_force_p','1_ground_force_p'} ; 88 | 89 | % Joint Reaction Fields 90 | INPUTS.jRxn.inFrame = 'child' ; 91 | INPUTS.jRxn.onBody = 'child' ; 92 | INPUTS.jRxn.jointNames = ['all'] ; 93 | 94 | INPUTS.passiveForceStrains = [3 4] ; % Default = [0,.7] this is strain at zero force and strain at 1 norm force in Millard model 95 | % This only matters if ignorePassiveForces = true 96 | 97 | % % % % % END OF USER INPUTS % % % % %% % % % %% % % % %% % % % %% % % % % 98 | 99 | 100 | if ~isempty(INPUTS.overrideWeights) 101 | disp('YOU ARE OVERRIDING SOME ACTUATOR WEIGHTS'); 102 | end 103 | 104 | if ~isempty(geometryPath) 105 | org.opensim.modeling.ModelVisualizer.addDirToGeometrySearchPaths(geometryPath) 106 | end 107 | 108 | % Run it! 109 | StaticOptimizationAPIVectorized(INPUTS) ; % Run StaticOptimizationAPI 110 | 111 | % Save this script in the folder to reference settings 112 | FileNameAndLocation=[mfilename('fullpath')]; 113 | newbackup=[INPUTS.outputFilePath 'API_staticOpt_settings.m']; 114 | currentfile=strcat(FileNameAndLocation, '.m'); 115 | copyfile(currentfile,newbackup); 116 | 117 | end % Main 118 | 119 | -------------------------------------------------------------------------------- /TestData/results_SO/JrxnSetup.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | true 6 | 7 | 1 8 | 9 | Inf 10 | 11 | 1 12 | 13 | true 14 | 15 | 16 | 17 | ground_pelvis hip_r walker_knee_r patellofemoral_r ankle_r subtalar_r mtp_r hip_l walker_knee_l patellofemoral_l ankle_l subtalar_l mtp_l back 18 | 19 | child 20 | 21 | child 22 | 23 | 24 | -------------------------------------------------------------------------------- /Utilities/CostFunction.m: -------------------------------------------------------------------------------- 1 | function f = CostFunction(coeffs,params) ; 2 | % Runs model simulation for given coefficients, returns integration 3 | % coeffs = initial set of control values 4 | % params = optimization parameters; simulation parameters and 5 | % pointers to instantiated OpenSim objects. 6 | 7 | 8 | vars4Minimization = [1:params.nMuscles, (params.actuatorsForIDmatching + params.nMuscles)] ; % If actuator is on INPUTS.prescribedActuation Coords list, we don't want to minimize its control 9 | 10 | % Compute activation ratios act1/(act1+act2) 11 | 12 | % % Compute Cost Function 13 | activComponent = sum(params.weights(vars4Minimization) .* coeffs(vars4Minimization).^2) ; 14 | if params.useEmgRatios 15 | 16 | % Can put EMG tracking things in the cost function! 17 | % actRatios = coeffs(params.coeffRatioInds(:,1))'./(sum(coeffs(params.coeffRatioInds(:,:)))); 18 | % emgRatioComponent = sum(params.weights(params.nActuators+1:params.nActuators+params.nRatios)' .* (actRatios-params.emgRatio_step).^2) ; 19 | emgRatioComponent = 0 ; 20 | 21 | else 22 | emgRatioComponent = 0 ; 23 | end 24 | 25 | f = activComponent + emgRatioComponent ; 26 | % fprintf('activComponent is %.1f and emg component is %.1f \n',activComponent,emgRatioComponent) 27 | -------------------------------------------------------------------------------- /Utilities/DynamicsConstraint_accelerationMatching.m: -------------------------------------------------------------------------------- 1 | function [c ceq] = DynamicsConstraint(coeffs,params) ; 2 | % Runs model simulation for given coefficients, returns integration 3 | % coeffs = initial set of control values 4 | % params = optimization parameters; simulation parameters and 5 | % pointers to instantiated OpenSim objects. 6 | 7 | % import org.opensim.modeling.* 8 | 9 | % % Get a reference to the model and states 10 | osimModel = params.model ; 11 | state = params.state ; 12 | coords = params.coords ; 13 | muscles = params.muscles ; 14 | nActuators = params.nActuators ; 15 | nFreeCoords = params.nFreeCoords ; 16 | nMuscles = params.nMuscles ; 17 | coordVelNames = params.coordVelNames ; 18 | % stateVectorYMuscleInds = params.stateVectorYMuscleInds; 19 | % stateVectorY = params.stateVectorY ; 20 | controls = params.controls ; 21 | normalMuscInds = params.normalMuscleInds_ML ; 22 | 23 | % % % Set Muscle Activations by changing the state vector directly 24 | %This works the same as setActivation when there aren't reserve actuators. 25 | %But it gives a state error when I turn the reserves on. It was only 26 | %marginally (10%) faster using the arm26 model than setActivation. 27 | % for i = 1:nMuscles 28 | % stateVectorY.set(stateVectorYMuscleInds(i),coeffs(i)) 29 | % end 30 | % state.setY(stateVectorY) ; 31 | % osimModel.calcMassCenterVelocity(state) ; % This does realizeDynamics to re initialize position and velocity info for the state 32 | 33 | 34 | % Set coordinate actuator controls 35 | % Assumes you have all coordinates actuated with a coordinate actuator. 36 | % Also assumes coeffs matrix has all muscles first, then coord 37 | % actuators 38 | for i = muscles.getSize:nActuators-1 39 | controls.set(i, coeffs(i+1)) ; 40 | end 41 | osimModel.setControls(state,controls) ; 42 | 43 | % % Special Case Activation Equality Constraints 44 | nRatios = size(params.coeffRatioInds,1) ; 45 | nEquals = size(params.equalMuscleInds_ML,1) ; 46 | actConstraints = zeros(1,nRatios+nEquals) ; 47 | 48 | % % Special Case: Sets muscle activation ratios 49 | if params.useEmgRatios 50 | ineqDif = 0.02 ; % allow this much difference on either side 51 | actRatios = coeffs(params.coeffRatioInds(:,1))'./(sum(coeffs(params.coeffRatioInds(:,:)))); 52 | emgWeights = params.weights(nActuators+1:end) ; 53 | actConstraints(1:nRatios) = emgWeights.* (abs(actRatios-params.emgRatio_step)-ineqDif) ; 54 | end 55 | 56 | % % Special Case: Sets muscle activations of some muscles equal to each 57 | % other with some wiggle room 58 | if params.useEqualMuscles 59 | ineqDif = 0.02 ; % allow this much difference on either side 60 | actConstraints(nRatios+1:nRatios+nEquals) = ... 61 | abs((coeffs(params.equalMuscleInds_ML(:,2)) - ... 62 | coeffs(params.equalMuscleInds_ML(:,1)))') - ineqDif ; 63 | end 64 | 65 | % % % Set Muscle Activations the slow way 66 | for i = 1:nMuscles% (IMPROVE ME) this is really slow - it takes ~75% of the whole simulation time 67 | muscles.get(i-1).setActivation(state,coeffs(i)) ; 68 | end 69 | 70 | % % Equillibrate Muscles in Model 71 | osimModel.equilibrateMuscles(state); 72 | % % Get qdd_sim from model - only for the coordinate speeds 73 | osimModel.computeStateVariableDerivatives(state) ; % Osim3.3 gave back a vector here - no such luck in 4.0. 74 | 75 | qdd_sim = zeros(size(params.qddIK_step)) ; 76 | for i = 0:nFreeCoords-1 77 | % qdd_sim(i+1) = stateDerivs.get(params.coordVelIndicies_ML(i+1)-1) ; 78 | qdd_sim(i+1) = osimModel.getStateVariableDerivativeValue(state,coordVelNames{i+1}) ; 79 | end 80 | 81 | % %Compute differences in accelerations 82 | ceq= [qdd_sim-params.qddIK_step] ; 83 | c = actConstraints ; 84 | 85 | -------------------------------------------------------------------------------- /Utilities/DynamicsConstraint_momentMatching.m: -------------------------------------------------------------------------------- 1 | function [c ceq] = DynamicsConstraint(coeffs,params) ; 2 | % Runs model simulation for given coefficients, returns integration 3 | % coeffs = initial set of control values 4 | % params = optimization parameters; simulation parameters and 5 | % pointers to instantiated OpenSim objects. 6 | 7 | % import org.opensim.modeling.* 8 | 9 | % % Get a reference to the model and states 10 | 11 | % state = params.state ; 12 | % coords = params.coords ; 13 | % muscles = params.muscles ; 14 | nActuators = params.nActuators ; 15 | nFreeCoords = params.nFreeCoords ; 16 | nMuscles = params.nMuscles ; 17 | % coordVelNames = params.coordVelNames ; 18 | % stateVectorYMuscleInds = params.stateVectorYMuscleInds; 19 | % stateVectorY = params.stateVectorY ; 20 | controls = params.controls ; 21 | normalMuscInds = params.normalMuscleInds_ML ; 22 | 23 | % % % Set Muscle Activations by changing the state vector directly 24 | %This works the same as setActivation when there aren't reserve actuators. 25 | %But it gives a state error when I turn the reserves on. It was only 26 | %marginally (10%) faster using the arm26 model than setActivation. 27 | % for i = 1:nMuscles 28 | % stateVectorY.set(stateVectorYMuscleInds(i),coeffs(i)) 29 | % end 30 | % state.setY(stateVectorY) ; 31 | % osimModel.calcMassCenterVelocity(state) ; % This does realizeDynamics to re initialize position and velocity info for the state 32 | 33 | 34 | % Set coordinate actuator controls 35 | % Assumes you have all coordinates actuated with a coordinate actuator. 36 | % Also assumes coeffs matrix has all muscles first, then coord 37 | % actuators 38 | % for i = muscles.getSize:nActuators-1 39 | % controls.set(i, coeffs(i+1)) ; 40 | % end 41 | % osimModel.setControls(state,controls) ; 42 | 43 | % % Special Case Activation Equality Constraints 44 | nRatios = size(params.coeffRatioInds,1) ; 45 | nEquals = size(params.equalMuscleInds_ML,1) ; 46 | nConstrained = size(params.coeffEmgConstraintInds,1) ; 47 | actConstraints = zeros(nRatios+nEquals+nConstrained,1) ; 48 | 49 | % % Special Case: Sets muscle activation ratios 50 | if params.useEmgRatios 51 | ineqDif = 0.02 ; % allow this much difference on either side 52 | actRatios = coeffs(params.coeffRatioInds(:,1))'./(sum(coeffs(params.coeffRatioInds(:,:)))); 53 | emgWeights = params.weights(nActuators+1:end) ; 54 | actConstraints(1:nRatios,1) = emgWeights' .* abs(actRatios-params.emgRatio_step)-ineqDif ; 55 | end 56 | 57 | % % Special Case: Sets muscle activations of some muscles equal to each 58 | % other with some wiggle room 59 | if params.useEqualMuscles 60 | ineqDif = 0.02 ; % allow this much difference on either side 61 | actConstraints(nRatios+1:nRatios+nEquals,1) = ... 62 | abs((coeffs(params.equalMuscleInds_ML(:,2)) - ... 63 | coeffs(params.equalMuscleInds_ML(:,1)))') - ineqDif ; 64 | end 65 | 66 | % % Special Case: Sets muscle activations of some muscles equal input EMG 67 | % with some wiggle room 68 | if params.useEmgConstraints 69 | ineqDif = 0.02 ; % allow this much difference on either side 70 | actConstraints(nRatios+nEquals+1:nRatios+nEquals+nConstrained,1) = ... 71 | abs(coeffs(params.coeffEmgConstraintInds) - max(params.emgConstraints_step',0)) - ineqDif ; 72 | end 73 | 74 | % % Special Case: Make Sure Actuation of Prescribed Actuators equals ID 75 | % moment 76 | 77 | 78 | 79 | % % % Set Muscle Activations the slow way 80 | % for i = 1:nMuscles% (IMPROVE ME) this is really slow - it takes ~75% of the whole simulation time 81 | % muscles.get(i-1).setActivation(state,coeffs(i)) ; 82 | % end 83 | 84 | % % Compute Model Moments and match with ID moments 85 | MP = params.muscParams ; 86 | moments_sim_muscles = ((coeffs(1:nMuscles)' .* MP.activeForceMult + MP.passiveForce) .* MP.cosAlpha) * MP.momentArms ; 87 | moments_sim_actuators = coeffs(nMuscles+1:nMuscles+nFreeCoords)' .* MP.coordOptForce ; 88 | moments_sim = moments_sim_muscles + moments_sim_actuators ; 89 | matchingInds = params.actuatorsForIDmatching ; % only match with ID moments if not a prescribed actuation coordinate 90 | 91 | 92 | % %Compute differences in accelerations 93 | ceq= [moments_sim(matchingInds) - params.moments_ID(matchingInds)] ; 94 | c = actConstraints ; 95 | 96 | -------------------------------------------------------------------------------- /Utilities/getMuscleParams.m: -------------------------------------------------------------------------------- 1 | function OUT = getMuscleParams(params,coeffs_initial) ; 2 | % Pre-computes the following variables and stores in structure. 3 | % Note: state must be realized through velocity! 4 | % 5 | % passiveForce = 1 x nMuscles vector of passive muscle forces 6 | % activeForceMult = 1 x nMuscles vector containing sum of F_0_m*f_act(l)*f_act(v) 7 | % cosAlpha = 1 x nMuscles of cosine of pennation angle 8 | % momentArms = nMuscles x nFreeCoords of moment arms 9 | % coordOptForce = 1 x nFreeCoords of optimal force for coordinate actuators 10 | 11 | 12 | import org.opensim.modeling.* 13 | 14 | % Initialize Matricies 15 | OUT.passiveForce = zeros(1,params.nMuscles) ; 16 | OUT.activeForceMult = OUT.passiveForce ; 17 | OUT.cosAlpha = OUT.passiveForce ; 18 | OUT.momentArms = zeros(params.nMuscles,params.nFreeCoords) ; 19 | OUT.coordOptForce = zeros(1,params.nFreeCoords) ; 20 | 21 | if ~params.ignoreTendonCompliance 22 | % try % this is a hack for thelen muscle that doesn't equilibrate sometimes... 23 | for i = 0:params.nMuscles-1 24 | params.muscles.get(i).setActivation(params.state,coeffs_initial(i+1)) ; 25 | end 26 | params.model.equilibrateMuscles(params.state) ; 27 | % catch 28 | % warning('muscles didnt equilibrate - reduced activation 10% to try again') 29 | % for i = 0:params.nMuscles-1 30 | % params.muscles.get(i).setActivation(params.state,0.9*coeffs_initial(i+1)) ; 31 | % end 32 | % params.model.equilibrateMuscles(params.state) ; 33 | % end 34 | 35 | 36 | else % rigid tendon, still equilibrate Muscles (may be unneccesary) 37 | params.model.equilibrateMuscles(params.state) ; 38 | end 39 | 40 | for i = 1:params.nMuscles 41 | OUT.passiveForce(i) = max([params.muscles.get(i-1).getPassiveFiberForce(params.state),0]) ; 42 | OUT.activeForceMult(i) = params.muscles.get(i-1).getActiveForceLengthMultiplier(params.state)* ... 43 | params.muscles.get(i-1).getForceVelocityMultiplier(params.state)* ... 44 | params.muscles.get(i-1).getMaxIsometricForce ; 45 | OUT.cosAlpha(i) = params.muscles.get(i-1).getCosPennationAngle(params.state) ; 46 | for j = 1:params.nFreeCoords 47 | OUT.momentArms(i,j) = params.muscles.get(i-1).computeMomentArm(params.state,params.coords.get(params.freeCoordsNames{j})) ; 48 | end 49 | end 50 | 51 | for i = 1:params.nFreeCoords 52 | thisCoordActuator = CoordinateActuator.safeDownCast(params.actuators.get(params.nMuscles-1+i)) ; 53 | OUT.coordOptForce(i) = thisCoordActuator.get_optimal_force ; 54 | end 55 | 56 | 57 | 58 | 59 | --------------------------------------------------------------------------------