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/**
* \brief Performs inverse dynamics given a IK motion and externally applied
* forces. Results are stored in the provided result directory as
* subjectName_id.sto.
*/
class OactivePipeline_API InverseDynamicsModule {
public:
    struct Parameters {
        std::string subjectName;
        OpenSim::Model model;
        std::string inverseKinematicsMotion;
        std::string groundReactionXMLTemplate;
        std::string groundReactionForces;
        std::string resultsDir;
    };
    InverseDynamicsModule(Parameters& parameters);
    void run();
private:
    Parameters parameters;
};

InverseDynamicsModule::InverseDynamicsModule(Parameters& parameters)
    : parameters(parameters) {
}

void InverseDynamicsModule::run() {
    string tempExternalLoadsXML = parameters.resultsDir +
        parameters.subjectName + "_external_loads.xml";
    // prepare external loads
    ExternalLoads externalLoads(parameters.model,
                                parameters.groundReactionXMLTemplate);
    // update template
    externalLoads.setExternalLoadsModelKinematicsFileName(
        parameters.inverseKinematicsMotion);
    externalLoads.setDataFileName(parameters.groundReactionForces);
    externalLoads.setLowpassCutoffFrequencyForLoadKinematics(6);
    externalLoads.print(tempExternalLoadsXML);

    // ID tool
    InverseDynamicsTool id;
    id.setModel(parameters.model);
    Storage motion(parameters.inverseKinematicsMotion);
    id.setStartTime(motion.getFirstTime());
    id.setEndTime(motion.getLastTime());
    id.setCoordinatesFileName(parameters.inverseKinematicsMotion);
    // let createExternalLoads handle the creation of the external loads (internally)
    id.setExternalLoadsFileName(tempExternalLoadsXML);
    id.setOutputGenForceFileName(parameters.subjectName + "_id.sto");
    id.setResultsDir(parameters.resultsDir);
    // if muscles are not excluded then the results are wrong (very high)
    Array<string> forcesToExclude;
    forcesToExclude.append("Muscles");
    id.setExcludedForces(forcesToExclude);
    id.setLowpassCutoffFrequency(6);
    id.run();
}

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    // perform ID
    InverseDynamicsModule::Parameters idParameters{
    	"subject01_walk1",
    	model,
    	subjectDir + "results_cpp/subject01_walk1_ik.mot" ,
    	subjectDir + "subject01_walk1_grf.xml",
    	subjectDir + "subject01_walk1_grf.mot",
    	subjectDir + "results_cpp/"
    };
    InverseDynamicsModule id(idParameters);
    id.run();