RRATool.h

/* -------------------------------------------------------------------------- *
 *                            OpenSim:  RRATool.h                             *
 * -------------------------------------------------------------------------- *
 * The OpenSim API is a toolkit for musculoskeletal modeling and simulation.  *
 * See http://opensim.stanford.edu and the NOTICE file for more information.  *
 * OpenSim is developed at Stanford University and supported by the US        *
 * National Institutes of Health (U54 GM072970, R24 HD065690) and by DARPA    *
 * through the Warrior Web program.                                           *
 *                                                                            *
 * Copyright (c) 2005-2012 Stanford University and the Authors                *
 * Author(s): Frank C. Anderson                                               *
 * Contributor(s): Ayman Habib, Frank C. Anderson                             *
 *                                                                            *
 * Licensed under the Apache License, Version 2.0 (the "License"); you may    *
 * not use this file except in compliance with the License. You may obtain a  *
 * copy of the License at http://www.apache.org/licenses/LICENSE-2.0.         *
 *                                                                            *
 * Unless required by applicable law or agreed to in writing, software        *
 * distributed under the License is distributed on an "AS IS" BASIS,          *
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.   *
 * See the License for the specific language governing permissions and        *
 * limitations under the License.                                             *
 * -------------------------------------------------------------------------- */

//
// This software, originally developed by Realistic Dynamics, Inc., was
// transferred to Stanford University on November 1, 2006.
//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#ifndef OPENSIM_RRATool_h__
#define OPENSIM_RRATool_h__

#include "osimToolsDLL.h"
#include <OpenSim/Simulation/Model/AbstractTool.h>


#ifdef SWIG
	#ifdef OSIMTOOLS_API
		#undef OSIMTOOLS_API
		#define OSIMTOOLS_API
	#endif
#endif

namespace OpenSim {

class ForceSet;
class ControlSet;
class Storage;
//=============================================================================
//=============================================================================
/**
 * An abstract class for specifying the interface for an investigation.
 *
 * @author Frank C. Anderson
 * @version 1.0
 */
class OSIMTOOLS_API RRATool: public AbstractTool {
OpenSim_DECLARE_CONCRETE_OBJECT(RRATool, AbstractTool);

//=============================================================================
// MEMBER VARIABLES
//=============================================================================
private:
	/** Name of the file containing the desired kinematic
	trajectories. */
	PropertyStr _desiredPointsFileNameProp;
	std::string &_desiredPointsFileName;

    /** Name of the file containing the desired kinematic trajectories. */ 		 
    PropertyStr _desiredKinematicsFileNameProp; 		 
    std::string &_desiredKinematicsFileName;

   /** Name of the file containing the tracking tasks. */  	 	 
    PropertyStr _taskSetFileNameProp; 		 
    std::string &_taskSetFileName; 		 

      /** Name of the file containing the constraints on the controls. */
	PropertyStr _constraintsFileNameProp;
	std::string &_constraintsFileName;

	/** Low-pass cut-off frequency for filtering the desired kinematics. A negative
	value results in no filtering.  The default value is -1.0, so no filtering. */
	PropertyDbl _lowpassCutoffFrequencyProp;
	double &_lowpassCutoffFrequency;
	/** Time window */
	double _targetDT;
	/** Preferred optimizer algorithm. */
	PropertyStr _optimizerAlgorithmProp;
	std::string &_optimizerAlgorithm;
	/** Perturbation size used by the optimizer to compute numerical derivatives. */
	PropertyDbl _numericalDerivativeStepSizeProp;
	double &_numericalDerivativeStepSize;
	/** Convergence criterion for the optimizer. */
	PropertyDbl _optimizationConvergenceToleranceProp;
	double &_optimizationConvergenceTolerance;

	/** Flag indicating whether or not to make an adjustment in the center of
	mass of a body to reduced DC offsets in MX and MZ. */
	PropertyBool _adjustCOMToReduceResidualsProp;
	bool &_adjustCOMToReduceResiduals;
	/** Initial time for computing average residuals used to adjust COM. */
	PropertyDbl _initialTimeForCOMAdjustmentProp;
	double &_initialTimeForCOMAdjustment;
	/** Final time for computing average residuals used to adjust COM. */
	PropertyDbl _finalTimeForCOMAdjustmentProp;
	double &_finalTimeForCOMAdjustment;
	/** Name of the body whose center of mass is adjusted. */
	PropertyStr _adjustedCOMBodyProp;
	std::string &_adjustedCOMBody;
	/** Name of the output model file containing adjustments to anthropometry
	made to reduce average residuals. This file is written if the property
	adjust_com_to_reduce_residuals is set to true. */
	PropertyStr _outputModelFileProp;
	std::string &_outputModelFile;

	/** Flag indicating whether or not to adjust the kinematics in order to reduce residuals. */
	bool _adjustKinematicsToReduceResiduals;
	/** Flag for turning on and off verbose printing. */
	PropertyBool _verboseProp;
	bool &_verbose;

	ForceSet _originalForceSet;

//=============================================================================
// METHODS
//=============================================================================
	//--------------------------------------------------------------------------
	// CONSTRUCTION
	//--------------------------------------------------------------------------
public:
	virtual ~RRATool();
	RRATool();
	RRATool(const std::string &aFileName, bool aLoadModel=true) SWIG_DECLARE_EXCEPTION;
	RRATool(const RRATool &aObject);

private:
	void setNull();
	void setupProperties();

	//--------------------------------------------------------------------------
	// OPERATORS
	//--------------------------------------------------------------------------
public:
#ifndef SWIG
	RRATool&
		operator=(const RRATool &aRRATool);
#endif

	//--------------------------------------------------------------------------
	// GET AND SET
	//--------------------------------------------------------------------------

	const std::string &getDesiredPointsFileName() { return _desiredPointsFileName; }
	void setDesiredPointsFileName(const std::string &aFileName) { _desiredPointsFileName = aFileName; }

	const std::string &getDesiredKinematicsFileName() { return _desiredKinematicsFileName; }
	void setDesiredKinematicsFileName(const std::string &aFileName) { _desiredKinematicsFileName = aFileName; }

    const std::string &getConstraintsFileName() { return _constraintsFileName; }  	 	 
    void setConstraintsFileName(const std::string &aFileName) { _constraintsFileName = aFileName; } 		 
  		 
    const std::string &getTaskSetFileName() { return _taskSetFileName; } 		 
    void setTaskSetFileName(const std::string &aFileName) { _taskSetFileName = aFileName; }

	const std::string &getOutputModelFileName() { return _outputModelFile; }
	void setOutputModelFileName(const std::string &aFileName) { _outputModelFile = aFileName; }

	bool getAdjustCOMToReduceResiduals() { return _adjustCOMToReduceResiduals; }
	void setAdjustCOMToReduceResiduals(bool aAdjust) { _adjustCOMToReduceResiduals = aAdjust; }

	const std::string &getAdjustedCOMBody() { return _adjustedCOMBody; }
	void setAdjustedCOMBody(const std::string &aBody) { _adjustedCOMBody = aBody; }

	double getLowpassCutoffFrequency() const { return _lowpassCutoffFrequency; }
	void setLowpassCutoffFrequency(double aLowpassCutoffFrequency) { _lowpassCutoffFrequency = aLowpassCutoffFrequency; }

	// External loads get/set
	const std::string &getExternalLoadsFileName() const { return _externalLoadsFileName; }
	void setExternalLoadsFileName(const std::string &aFileName) { _externalLoadsFileName = aFileName; }

	//--------------------------------------------------------------------------
	// INTERFACE
	//--------------------------------------------------------------------------
	virtual bool run() SWIG_DECLARE_EXCEPTION;

	//--------------------------------------------------------------------------
	// UTILITY
	//--------------------------------------------------------------------------
	Storage &getForceStorage();

	void setOriginalForceSet(const ForceSet &aForceSet);

	virtual void updateFromXMLNode(SimTK::Xml::Element& aNode, int versionNumber=-1);
#ifndef SWIG

	void initializeControlSetUsingConstraints(const ControlSet *aRRAControlSet,const ControlSet *aControlConstraints, ControlSet& rControlSet );
	std::string adjustCOMToReduceResiduals(SimTK::State& s, const Storage &qStore, const Storage &uStore);
	std::string adjustCOMToReduceResiduals(const OpenSim::Array<double> &aFAve,const OpenSim::Array<double> &aMAve);
	void addNecessaryAnalyses();
	void writeAdjustedModel();

	static void computeAverageResiduals(const Storage &aForceStore,OpenSim::Array<double> &rFAve,OpenSim::Array<double> &rMAve);
	static void computeAverageResiduals(SimTK::State& s, Model &aModel,double aTi,double aTf,const Storage &aStatesStore,OpenSim::Array<double>& rFAve,OpenSim::Array<double>& rMAve);
#endif
//=============================================================================
};	// END of class RRATool
//=============================================================================
//=============================================================================

}; // end namespace

#endif  // OPENSIM_RRATool_h__