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RRATool.cpp
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RRATool.cpp
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/* -------------------------------------------------------------------------- *
* OpenSim: RRATool.cpp *
* -------------------------------------------------------------------------- *
* 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 *
* Contributor(s): Frank C. Anderson, Eran Guendelman, Chand T. John *
* *
* 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. *
* -------------------------------------------------------------------------- */
#include "RRATool.h"
#include "AnalyzeTool.h"
#include <OpenSim/Common/XMLDocument.h>
#include <OpenSim/Common/IO.h>
#include <OpenSim/Common/GCVSplineSet.h>
#include <OpenSim/Simulation/Model/Model.h>
#include <OpenSim/Simulation/Model/BodySet.h>
#include "VectorFunctionForActuators.h"
#include <OpenSim/Simulation/Manager/Manager.h>
#include <OpenSim/Simulation/Control/ControlLinear.h>
#include <OpenSim/Simulation/Control/ControlSet.h>
#include <OpenSim/Simulation/Model/CMCActuatorSubsystem.h>
#include <OpenSim/Analyses/Actuation.h>
#include <OpenSim/Analyses/Kinematics.h>
#include <OpenSim/Analyses/InverseDynamics.h>
#include <OpenSim/Simulation/SimbodyEngine/Joint.h>
#include "ForwardTool.h"
#include <OpenSim/Common/DebugUtilities.h>
#include "CMC.h"
#include "CMC_TaskSet.h"
#include "ActuatorForceTarget.h"
#include "ActuatorForceTargetFast.h"
using namespace std;
using namespace SimTK;
using namespace OpenSim;
//=============================================================================
// CONSTRUCTOR(S) AND DESTRUCTOR
//=============================================================================
//_____________________________________________________________________________
/**
* Destructor.
*/
RRATool::~RRATool()
{
}
//_____________________________________________________________________________
/**
* Default constructor.
*/
RRATool::RRATool() :
AbstractTool(),
_desiredPointsFileName(_desiredPointsFileNameProp.getValueStr()),
_desiredKinematicsFileName(_desiredKinematicsFileNameProp.getValueStr()),
_taskSetFileName(_taskSetFileNameProp.getValueStr()),
_constraintsFileName(_constraintsFileNameProp.getValueStr()),
_lowpassCutoffFrequency(_lowpassCutoffFrequencyProp.getValueDbl()),
_optimizerAlgorithm(_optimizerAlgorithmProp.getValueStr()),
_numericalDerivativeStepSize(_numericalDerivativeStepSizeProp.getValueDbl()),
_optimizationConvergenceTolerance(_optimizationConvergenceToleranceProp.getValueDbl()),
_adjustCOMToReduceResiduals(_adjustCOMToReduceResidualsProp.getValueBool()),
_initialTimeForCOMAdjustment(_initialTimeForCOMAdjustmentProp.getValueDbl()),
_finalTimeForCOMAdjustment(_finalTimeForCOMAdjustmentProp.getValueDbl()),
_adjustedCOMBody(_adjustedCOMBodyProp.getValueStr()),
_outputModelFile(_outputModelFileProp.getValueStr()),
_verbose(_verboseProp.getValueBool())
{
setNull();
}
//_____________________________________________________________________________
/**
* Construct from an XML property file.
*
* @param aFileName File name of the XML document.
*/
RRATool::RRATool(const string &aFileName, bool aLoadModel) :
AbstractTool(aFileName, false),
_desiredPointsFileName(_desiredPointsFileNameProp.getValueStr()),
_desiredKinematicsFileName(_desiredKinematicsFileNameProp.getValueStr()),
_taskSetFileName(_taskSetFileNameProp.getValueStr()),
_constraintsFileName(_constraintsFileNameProp.getValueStr()),
_lowpassCutoffFrequency(_lowpassCutoffFrequencyProp.getValueDbl()),
_optimizerAlgorithm(_optimizerAlgorithmProp.getValueStr()),
_numericalDerivativeStepSize(_numericalDerivativeStepSizeProp.getValueDbl()),
_optimizationConvergenceTolerance(_optimizationConvergenceToleranceProp.getValueDbl()),
_adjustCOMToReduceResiduals(_adjustCOMToReduceResidualsProp.getValueBool()),
_initialTimeForCOMAdjustment(_initialTimeForCOMAdjustmentProp.getValueDbl()),
_finalTimeForCOMAdjustment(_finalTimeForCOMAdjustmentProp.getValueDbl()),
_adjustedCOMBody(_adjustedCOMBodyProp.getValueStr()),
_outputModelFile(_outputModelFileProp.getValueStr()),
_verbose(_verboseProp.getValueBool())
{
setNull();
updateFromXMLDocument();
if(aLoadModel){
loadModel(aFileName, &_originalForceSet);
// Append to or replace model forces with those (i.e. actuators) specified by the analysis
updateModelForces(*_model, aFileName);
setModel(*_model);
setToolOwnsModel(true);
}
}
//_____________________________________________________________________________
/**
* Copy constructor.
*
* Copy constructors for all Tools do not copy the Object's DOMnode
* and XMLDocument. The reason for this is that for the
* object and all its derived classes to establish the correct connection
* to the XML document nodes, the the object would need to reconstruct based
* on the XML document not the values of the object's member variables.
*
* There are three proper ways to generate an XML document for a Tool:
*
* 1) Construction based on XML file (@see Tool(const char *aFileName)).
* In this case, the XML document is created by parsing the XML file.
*
* 2) Construction by Tool(const XMLDocument *aDocument).
* This constructor explictly requests construction based on an
* XML document that is held in memory. In this way the proper connection
* between an object's node and the corresponding node within the XML
* document is established.
* This constructor is a copy constructor of sorts because all essential
* Tool member variables should be held within the XML document.
* The advantage of this style of construction is that nodes
* within the XML document, such as comments that may not have any
* associated Tool member variable, are preserved.
*
* 3) A call to generateXMLDocument().
* This method generates an XML document for the Tool from scratch.
* Only the essential document nodes are created (that is, nodes that
* correspond directly to member variables.).
*
* @param aTool Object to be copied.
* @see Tool(const XMLDocument *aDocument)
* @see Tool(const char *aFileName)
* @see generateXMLDocument()
*/
RRATool::
RRATool(const RRATool &aTool) :
AbstractTool(aTool),
_desiredPointsFileName(_desiredPointsFileNameProp.getValueStr()),
_desiredKinematicsFileName(_desiredKinematicsFileNameProp.getValueStr()),
_taskSetFileName(_taskSetFileNameProp.getValueStr()),
_constraintsFileName(_constraintsFileNameProp.getValueStr()),
_lowpassCutoffFrequency(_lowpassCutoffFrequencyProp.getValueDbl()),
_optimizerAlgorithm(_optimizerAlgorithmProp.getValueStr()),
_numericalDerivativeStepSize(_numericalDerivativeStepSizeProp.getValueDbl()),
_optimizationConvergenceTolerance(_optimizationConvergenceToleranceProp.getValueDbl()),
_adjustCOMToReduceResiduals(_adjustCOMToReduceResidualsProp.getValueBool()),
_initialTimeForCOMAdjustment(_initialTimeForCOMAdjustmentProp.getValueDbl()),
_finalTimeForCOMAdjustment(_finalTimeForCOMAdjustmentProp.getValueDbl()),
_adjustedCOMBody(_adjustedCOMBodyProp.getValueStr()),
_outputModelFile(_outputModelFileProp.getValueStr()),
_verbose(_verboseProp.getValueBool())
{
setNull();
*this = aTool;
}
//_____________________________________________________________________________
/**
* Set all member variables to their null or default values.
*/
void RRATool::
setNull()
{
setupProperties();
_desiredPointsFileName = "";
_desiredKinematicsFileName = "";
_taskSetFileName = "";
_constraintsFileName = "";
_lowpassCutoffFrequency = -1.0;
//_lowpassCutoffFrequencyForLoadKinematics = -1.0;
_optimizerAlgorithm = "ipopt";
_numericalDerivativeStepSize = 1.0e-4;
_optimizationConvergenceTolerance = 1.0e-5;
_adjustedCOMBody = "";
_adjustCOMToReduceResiduals = false;
_initialTimeForCOMAdjustment = -1;
_finalTimeForCOMAdjustment = -1;
_outputModelFile = "";
_adjustKinematicsToReduceResiduals=true;
_verbose = false;
_targetDT = .001;
_replaceForceSet = false; // default should be false for Forward.
}
//_____________________________________________________________________________
/**
* Give this object's properties their XML names and add them to the property
* list held in class Object (@see OpenSim::Object).
*/
void RRATool::setupProperties()
{
string comment;
comment = "Motion (.mot) or storage (.sto) file containing the desired point trajectories.";
_desiredPointsFileNameProp.setComment(comment);
_desiredPointsFileNameProp.setName("desired_points_file");
_propertySet.append( &_desiredPointsFileNameProp );
comment = "Motion (.mot) or storage (.sto) file containing the desired kinematic trajectories.";
_desiredKinematicsFileNameProp.setComment(comment);
_desiredKinematicsFileNameProp.setName("desired_kinematics_file");
_propertySet.append( &_desiredKinematicsFileNameProp );
comment = "File containing the tracking tasks. Which coordinates are tracked and with what weights are specified here.";
_taskSetFileNameProp.setComment(comment);
_taskSetFileNameProp.setName("task_set_file");
_propertySet.append( &_taskSetFileNameProp );
comment = "DEPRECATED File containing the constraints on the controls.";
_constraintsFileNameProp.setComment(comment);
_constraintsFileNameProp.setName("constraints_file");
_propertySet.append( &_constraintsFileNameProp );
comment = "Low-pass cut-off frequency for filtering the desired kinematics.";
comment += " A negative value results in no filtering. The default value is -1.0, so no filtering.";
_lowpassCutoffFrequencyProp.setComment(comment);
_lowpassCutoffFrequencyProp.setName("lowpass_cutoff_frequency");
_propertySet.append( &_lowpassCutoffFrequencyProp );
comment = "Preferred optimizer algorithm (currently support \"ipopt\" or \"cfsqp\", "
"the latter requiring the osimFSQP library.";
_optimizerAlgorithmProp.setComment(comment);
_optimizerAlgorithmProp.setName("optimizer_algorithm");
_propertySet.append( &_optimizerAlgorithmProp );
comment = "Step size used by the optimizer to compute numerical derivatives. "
"A value between 1.0e-4 and 1.0e-8 is usually appropriate.";
_numericalDerivativeStepSizeProp.setComment(comment);
_numericalDerivativeStepSizeProp.setName("numerical_derivative_step_size");
_propertySet.append( &_numericalDerivativeStepSizeProp );
comment = "Convergence criterion for the optimizer. The smaller this value, the deeper the convergence. "
"Decreasing this number can improve a solution, but will also likely increase computation time.";
_optimizationConvergenceToleranceProp.setComment(comment);
_optimizationConvergenceToleranceProp.setName("optimization_convergence_tolerance");
_propertySet.append( &_optimizationConvergenceToleranceProp );
comment = "Flag (true or false) indicating whether or not to make an adjustment "
"in the center of mass of a body to reduced DC offsets in MX and MZ. "
"If true, a new model is writen out that has altered anthropometry.";
_adjustCOMToReduceResidualsProp.setComment(comment);
_adjustCOMToReduceResidualsProp.setName("adjust_com_to_reduce_residuals");
_propertySet.append( &_adjustCOMToReduceResidualsProp );
comment = "Initial time used when computing average residuals in order to adjust "
"the body's center of mass. If both initial and final time are set to "
"-1 (their default value) then the main initial and final time settings will be used.";
_initialTimeForCOMAdjustmentProp.setComment(comment);
_initialTimeForCOMAdjustmentProp.setName("initial_time_for_com_adjustment");
_propertySet.append( &_initialTimeForCOMAdjustmentProp );
comment = "Final time used when computing average residuals in order to adjust "
"the body's center of mass.";
_finalTimeForCOMAdjustmentProp.setComment(comment);
_finalTimeForCOMAdjustmentProp.setName("final_time_for_com_adjustment");
_propertySet.append( &_finalTimeForCOMAdjustmentProp );
comment = "Name of the body whose center of mass is adjusted. "
"The heaviest segment in the model should normally be chosen. "
"For a gait model, the torso segment is usually the best choice.";
_adjustedCOMBodyProp.setComment(comment);
_adjustedCOMBodyProp.setName("adjusted_com_body");
_propertySet.append( &_adjustedCOMBodyProp );
comment = "Name of the output model file (.osim) 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. If a name is not specified, "
"the model is written out to a file called adjusted_model.osim.";
_outputModelFileProp.setComment(comment);
_outputModelFileProp.setName("output_model_file");
_propertySet.append( &_outputModelFileProp );
comment = "True-false flag indicating whether or not to turn on verbose printing for cmc.";
_verboseProp.setComment(comment);
_verboseProp.setName("use_verbose_printing");
_propertySet.append( &_verboseProp );
}
//=============================================================================
// OPERATORS
//=============================================================================
//_____________________________________________________________________________
/**
* Assignment operator.
*
* @return Reference to this object.
*/
RRATool& RRATool::
operator=(const RRATool &aTool)
{
// BASE CLASS
AbstractTool::operator=(aTool);
// MEMEBER VARIABLES
_desiredPointsFileName = aTool._desiredPointsFileName;
_desiredKinematicsFileName = aTool._desiredKinematicsFileName;
_taskSetFileName = aTool._taskSetFileName;
_constraintsFileName = aTool._constraintsFileName;
_lowpassCutoffFrequency = aTool._lowpassCutoffFrequency;
_targetDT = aTool._targetDT;
_numericalDerivativeStepSize = aTool._numericalDerivativeStepSize;
_optimizationConvergenceTolerance = aTool._optimizationConvergenceTolerance;
_optimizerAlgorithm = aTool._optimizerAlgorithm;
_adjustedCOMBody = aTool._adjustedCOMBody;
_outputModelFile = aTool._outputModelFile;
_adjustCOMToReduceResiduals = aTool._adjustCOMToReduceResiduals;
_initialTimeForCOMAdjustment = aTool._initialTimeForCOMAdjustment;
_finalTimeForCOMAdjustment = aTool._finalTimeForCOMAdjustment;
_verbose = aTool._verbose;
return(*this);
}
//=============================================================================
// GET AND SET
//=============================================================================
//=============================================================================
// RUN
//=============================================================================
//_____________________________________________________________________________
/**
* Run the investigation.
*/
bool RRATool::run()
{
cout<<"Running tool "<<getName()<<".\n";
// CHECK FOR A MODEL
if(_model==NULL) {
string msg = "ERROR- A model has not been set.";
cout<<endl<<msg<<endl;
throw(Exception(msg,__FILE__,__LINE__));
}
// OUTPUT DIRECTORY
// Do the maneuver to change then restore working directory
// so that the parsing code behaves prope()rly if called from a different directory
string saveWorkingDirectory = IO::getCwd();
string directoryOfSetupFile = IO::getParentDirectory(getDocumentFileName());
IO::chDir(directoryOfSetupFile);
try {
// SET OUTPUT PRECISION
IO::SetPrecision(_outputPrecision);
// CHECK PROPERTIES FOR ERRORS/INCONSISTENCIES
if(_adjustCOMToReduceResiduals) {
if(_adjustedCOMBody == "")
throw Exception("RRATool: ERROR- "+_adjustCOMToReduceResidualsProp.getName()+" set to true but "+
_adjustedCOMBodyProp.getName()+" not set",__FILE__,__LINE__);
else if (_model->getBodySet().getIndex(_adjustedCOMBody) == -1)
throw Exception("RRATool: ERROR- Body '"+_adjustedCOMBody+"' specified in "+
_adjustedCOMBodyProp.getName()+" not found",__FILE__,__LINE__);
}
bool externalLoads = createExternalLoads(_externalLoadsFileName, *_model);
CMC_TaskSet taskSet(_taskSetFileName);
cout<<"\n\n taskSet size = "<<taskSet.getSize()<<endl<<endl;
CMC* controller = new CMC(_model,&taskSet); // Need to make it a pointer since Model takes ownership
controller->setName( "CMC" );
controller->setActuators(_model->updActuators());
_model->addController(controller );
controller->setDisabled(false);
controller->setUseCurvatureFilter(false);
controller->setTargetDT(.001);
controller->setCheckTargetTime(true);
//Make sure system is uptodate with model (i.e. added actuators, etc...)
SimTK::State& s = _model->initSystem();
_model->getMultibodySystem().realize(s, Stage::Position );
taskSet.setModel(*_model);
_model->equilibrateMuscles(s);
// ---- INPUT ----
// DESIRED POINTS AND KINEMATICS
if(_desiredPointsFileName=="" && _desiredKinematicsFileName=="") {
cout<<"ERROR- a desired points file and desired kinematics file were not specified.\n\n";
IO::chDir(saveWorkingDirectory);
return false;
}
Storage *desiredPointsStore=NULL;
bool desiredPointsFlag = false;
if(_desiredPointsFileName=="") {
cout<<"\n\nWARN- a desired points file was not specified.\n\n";
} else {
cout<<"\n\nLoading desired points from file "<<_desiredPointsFileName<<" ...\n";
desiredPointsStore = new Storage(_desiredPointsFileName);
desiredPointsFlag = true;
}
Storage *desiredKinStore=NULL;
bool desiredKinFlag = false;
if(_desiredKinematicsFileName=="") {
cout<<"\n\nWARN- a desired kinematics file was not specified.\n\n";
} else {
cout<<"\n\nLoading desired kinematics from file "<<_desiredKinematicsFileName<<" ...\n";
desiredKinStore = new Storage();
loadQStorage( _desiredKinematicsFileName, *desiredKinStore );
desiredKinFlag = true;
}
// ---- INITIAL AND FINAL TIME ----
// NOTE: important to do this before padding (for filtering)
// Initial Time
if(desiredPointsFlag) {
double ti = desiredPointsStore->getFirstTime();
if(_ti<ti) {
cout<<"\nThe initial time set for the cmc run precedes the first time\n";
cout<<"in the desired points file "<<_desiredPointsFileName<<".\n";
cout<<"Resetting the initial time from "<<_ti<<" to "<<ti<<".\n\n";
_ti = ti;
}
// Final time
double tf = desiredPointsStore->getLastTime();
if(_tf>tf) {
cout<<"\n\nWARN- The final time set for the cmc run is past the last time stamp\n";
cout<<"in the desired points file "<<_desiredPointsFileName<<".\n";
cout<<"Resetting the final time from "<<_tf<<" to "<<tf<<".\n\n";
_tf = tf;
}
}
// Initial Time
if(desiredKinFlag) {
double ti = desiredKinStore->getFirstTime();
if(_ti<ti) {
cout<<"\nThe initial time set for the cmc run precedes the first time\n";
cout<<"in the desired kinematics file "<<_desiredKinematicsFileName<<".\n";
cout<<"Resetting the initial time from "<<_ti<<" to "<<ti<<".\n\n";
_ti = ti;
}
// Final time
double tf = desiredKinStore->getLastTime();
if(_tf>tf) {
cout<<"\n\nWARN- The final time set for the cmc run is past the last time stamp\n";
cout<<"in the desired kinematics file "<<_desiredKinematicsFileName<<".\n";
cout<<"Resetting the final time from "<<_tf<<" to "<<tf<<".\n\n";
_tf = tf;
}
}
// Filter
// Eran: important to filter *before* calling formCompleteStorages because we need the
// constrained coordinates (e.g. tibia-patella joint angle) to be consistent with the
// filtered trajectories
if(desiredPointsFlag) {
desiredPointsStore->pad(60);
desiredPointsStore->print("desiredPoints_padded.sto");
if(_lowpassCutoffFrequency>=0) {
int order = 50;
cout<<"\n\nLow-pass filtering desired points with a cutoff frequency of ";
cout<<_lowpassCutoffFrequency<<"...";
desiredPointsStore->lowpassFIR(order,_lowpassCutoffFrequency);
} else {
cout<<"\n\nNote- not filtering the desired points.\n\n";
}
}
if(desiredKinFlag) {
desiredKinStore->pad(60);
if (_verbose) desiredKinStore->print("desiredKinematics_padded.sto");
if(_lowpassCutoffFrequency>=0) {
int order = 50;
cout<<"\n\nLow-pass filtering desired kinematics with a cutoff frequency of ";
cout<<_lowpassCutoffFrequency<<"...\n\n";
desiredKinStore->lowpassFIR(order,_lowpassCutoffFrequency);
} else {
cout<<"\n\nNote- not filtering the desired kinematics.\n\n";
}
}
// TASK SET
if(_taskSetFileName=="") {
cout<<"ERROR- a task set was not specified\n\n";
IO::chDir(saveWorkingDirectory);
return false;
}
_model->printDetailedInfo(s, cout);
int nq = _model->getNumCoordinates();
int nu = _model->getNumSpeeds();
int na = _model->getActuators().getSize();
// Form complete storage objects for the q's and u's
// This means filling in unspecified generalized coordinates and
// setting constrained coordinates to their valid values.
Storage *qStore=NULL;
Storage *uStore=NULL;
if(desiredKinFlag) {
_model->getMultibodySystem().realize(s, Stage::Time );
_model->getSimbodyEngine().formCompleteStorages(s, *desiredKinStore,qStore,uStore);
if(qStore->isInDegrees()){
_model->getSimbodyEngine().convertDegreesToRadians(*qStore);
_model->getSimbodyEngine().convertDegreesToRadians(*uStore);
}
}
// Adjust COM to reduce residuals (formerly RRA pass 1) if requested
string massAdjMsg;
if(desiredKinFlag) {
if(_adjustCOMToReduceResiduals) {
massAdjMsg = adjustCOMToReduceResiduals(s, *qStore,*uStore);
// If not adjusting kinematics, we don't proceed with CMC, and just stop here.
if(!_adjustKinematicsToReduceResiduals) {
cout << "No kinematics adjustment requested." << endl;
delete qStore;
delete uStore;
writeAdjustedModel();
IO::chDir(saveWorkingDirectory);
return true;
}
}
}
// Spline
GCVSplineSet *posSet=NULL;
if(desiredPointsFlag) {
cout<<"\nConstructing function set for tracking desired points...\n\n";
posSet = new GCVSplineSet(5,desiredPointsStore);
Storage *velStore=posSet->constructStorage(1);
GCVSplineSet velSet(5,velStore);
delete velStore; velStore=NULL;
// Print acc for debugging
if (_verbose) {
Storage *accStore=posSet->constructStorage(2);
accStore->print("desiredPoints_splinefit_accelerations.sto");
delete accStore; accStore=NULL;
}
}
GCVSplineSet *qSet=NULL;
GCVSplineSet *uSet=NULL;
GCVSplineSet *uDotSet=NULL;
if(desiredKinFlag) {
cout<<"\nConstructing function set for tracking desired kinematics...\n\n";
qSet = new GCVSplineSet(5,qStore);
delete qStore; qStore = NULL;
uSet = new GCVSplineSet(5,uStore);
delete uStore; uStore=NULL;
Storage *dudtStore = uSet->constructStorage(1);
uDotSet = new GCVSplineSet(5,dudtStore);
// Print dudt for debugging
if (_verbose) {
dudtStore->print("desiredKinematics_splinefit_accelerations.sto");
}
delete dudtStore; dudtStore=NULL;
}
// ANALYSES
addNecessaryAnalyses();
GCVSplineSet *qAndPosSet=NULL;
qAndPosSet = new GCVSplineSet();
if(desiredPointsFlag) {
int nps=posSet->getSize();
for(int i=0;i<nps;i++) {
qAndPosSet->adoptAndAppend(&posSet->get(i));
}
}
if(desiredKinFlag) {
int nqs=qSet->getSize();
for(int i=0;i<nqs;i++) {
qAndPosSet->adoptAndAppend(&qSet->get(i));
}
}
if (taskSet.getDataFileName()!=""){
// Add functions from data files to track states
Storage stateStorage(taskSet.getDataFileName());
GCVSplineSet* stateFuntcions = new GCVSplineSet(3, &stateStorage);
for (int i=0; i< stateFuntcions->getSize(); i++)
qAndPosSet->cloneAndAppend(stateFuntcions->get(i));
}
taskSet.setFunctions(*qAndPosSet);
taskSet.setFunctionsForVelocity(*uSet);
taskSet.setFunctionsForAcceleration(*uDotSet);
// CONSTRAINTS ON THE CONTROLS
ControlSet *controlConstraints = NULL;
if(_constraintsFileName!="") {
controlConstraints = new ControlSet(_constraintsFileName);
cout << "WARNING: Using DEPRECATED Control Constrails file "<< _constraintsFileName <<
" in RRA, generally unnecessary.\nSupport will be dropped in the future." << endl;
}
// ---- INITIAL STATES ----
Array<double> q(0.0,nq);
Array<double> u(0.0,nu);
if(desiredKinFlag) {
cout<<"Using the generalized coordinates specified in "<<_desiredKinematicsFileName;
cout<<" to set the initial configuration.\n" << endl;
qSet->evaluate(q,0,_ti);
uSet->evaluate(u,0,_ti);
} else {
cout<<"Using the generalized coordinates specified as zeros ";
cout<<" to set the initial configuration.\n" << endl;
}
for(int i=0;i<nq;i++) s.updQ()[i] = q[i];
for(int i=0;i<nu;i++) s.updU()[i] = u[i];
// Actuator force predictor
// This requires the trajectories of the generalized coordinates
// to be specified.
string rraControlName;
CMCActuatorSystem actuatorSystem;
CMCActuatorSubsystem cmcActSubsystem(actuatorSystem, _model);
cmcActSubsystem.setCoordinateTrajectories(qSet);
actuatorSystem.realizeTopology();
// initialize the actuator states
SimTK::State& actuatorSystemState = actuatorSystem.updDefaultState();
SimTK::Vector &actSysZ = actuatorSystemState.updZ();
const SimTK::Vector &modelZ = _model->getForceSubsystem().getZ(s);
int nra = actSysZ.size();
int nrm = modelZ.size();
assert(nra == nrm);
actSysZ = modelZ;
VectorFunctionForActuators *predictor =
new VectorFunctionForActuators(&actuatorSystem, _model, &cmcActSubsystem);
controller->setActuatorForcePredictor(predictor);
controller->updTaskSet().setFunctions(*qAndPosSet);
// Optimization target
OptimizationTarget *target = NULL;
if(false) {
target = new ActuatorForceTargetFast(s, na,controller);
} else {
target = new ActuatorForceTarget(na,controller);
}
target->setDX(_numericalDerivativeStepSize);
// Pick optimizer algorithm
SimTK::OptimizerAlgorithm algorithm = SimTK::InteriorPoint;
if(IO::Uppercase(_optimizerAlgorithm) == "CFSQP") {
if(!SimTK::Optimizer::isAlgorithmAvailable(SimTK::CFSQP)) {
std::cout << "CFSQP optimizer algorithm unavailable. Will try to use IPOPT instead." << std::endl;
algorithm = SimTK::InteriorPoint;
} else {
std::cout << "Using CFSQP optimizer algorithm." << std::endl;
algorithm = SimTK::CFSQP;
}
} else if(IO::Uppercase(_optimizerAlgorithm) == "IPOPT") {
std::cout << "Using IPOPT optimizer algorithm." << std::endl;
algorithm = SimTK::InteriorPoint;
} else {
throw Exception("RRATool: ERROR- Unrecognized optimizer algorithm: '"+_optimizerAlgorithm+"'",__FILE__,__LINE__);
}
SimTK::Optimizer *optimizer = new SimTK::Optimizer(*target, algorithm);
controller->setOptimizationTarget(target, optimizer);
cout<<"\nSetting optimizer print level to "<< (_verbose?4:0) <<".\n";
optimizer->setDiagnosticsLevel(_verbose?4:0);
cout<<"Setting optimizer convergence tolerance to "<<_optimizationConvergenceTolerance<<".\n";
optimizer->setConvergenceTolerance(_optimizationConvergenceTolerance);
cout<<"Setting optimizer maximum iterations to "<<2000<<".\n";
optimizer->setMaxIterations(2000);
optimizer->useNumericalGradient(false); // Use our own central difference approximations
optimizer->useNumericalJacobian(false);
if(algorithm == SimTK::InteriorPoint) {
// Some IPOPT-specific settings
optimizer->setLimitedMemoryHistory(500); // works well for our small systems
optimizer->setAdvancedBoolOption("warm_start",true);
optimizer->setAdvancedRealOption("obj_scaling_factor",1);
optimizer->setAdvancedRealOption("nlp_scaling_max_gradient",100);
}
if(_verbose) cout<<"\nSetting cmc controller to use verbose printing."<<endl;
else cout<<"\nSetting cmc controller to not use verbose printing."<<endl;
controller->setUseVerbosePrinting(_verbose);
controller->setCheckTargetTime(true);
// ---- SIMULATION ----
//
// Manager
RungeKuttaMersonIntegrator integrator(_model->getMultibodySystem());
integrator.setMaximumStepSize(_maxDT);
integrator.setMinimumStepSize(_minDT);
integrator.setAccuracy(_errorTolerance);
Manager manager(*_model, integrator);
_model->setAllControllersEnabled( true );
manager.setSessionName(getName());
manager.setInitialTime(_ti);
manager.setFinalTime(_tf-_targetDT-SimTK::Zero);
// Initialize integrand controls using controls read in from file (which specify min/max control values)
initializeControlSetUsingConstraints(NULL,controlConstraints, controller->updControlSet());
// Initial auxilliary states
time_t startTime,finishTime;
struct tm *localTime;
double elapsedTime;
if( s.getNZ() > 0) { // If there are actuator states (i.e. muscles dynamics)
cout<<"\n\n\n";
cout<<"================================================================\n";
cout<<"================================================================\n";
cout<<"Computing initial values for muscles states (activation, length)\n";
time(&startTime);
localTime = localtime(&startTime);
cout<<"Start time = "<<asctime(localTime);
cout<<"\n================================================================\n";
try {
controller->computeInitialStates(s,_ti);
}
catch(const Exception& x) {
// TODO: eventually might want to allow writing of partial results
x.print(cout);
IO::chDir(saveWorkingDirectory);
return false;
}
catch(...) {
// TODO: eventually might want to allow writing of partial results
IO::chDir(saveWorkingDirectory);
// close open files if we die prematurely (e.g. Opt fail)
return false;
}
time(&finishTime);
cout<<endl;
// copy the final states from the last integration
s.updY() = cmcActSubsystem.getCompleteState().getY();
cout<<"-----------------------------------------------------------------\n";
cout<<"Finished computing initial states:\n";
cout<<"-----------------------------------------------------------------\n";
cout<<"=================================================================\n";
localTime = localtime(&startTime);
cout<<"Start time = "<<asctime(localTime);
localTime = localtime(&finishTime);
cout<<"Finish time = "<<asctime(localTime);
elapsedTime = difftime(finishTime,startTime);
cout<<"Elapsed time = "<<elapsedTime<<" seconds.\n";
cout<<"=================================================================\n";
} else {
cmcActSubsystem.setCompleteState( s );
actuatorSystemState.updTime() = _ti;
s.updTime() = _ti;
actuatorSystem.realize(actuatorSystemState, Stage::Time );
controller->setTargetDT(1.0e-8);
controller->computeControls( s, controller->updControlSet() );
controller->setTargetDT(_targetDT);
}
manager.setInitialTime(_ti);
// ---- INTEGRATE ----
cout<<"\n\n\n";
cout<<"================================================================\n";
cout<<"================================================================\n";
cout<<"Using CMC to track the specified kinematics\n";
cout<<"Integrating from "<<_ti<<" to "<<_tf<<endl;
s.updTime() = _ti;
controller->setTargetTime( _ti );
time(&startTime);
localTime = localtime(&startTime);
cout<<"Start time = "<<asctime(localTime);
cout<<"================================================================\n";
_model->getMultibodySystem().realize(s, Stage::Acceleration );
controller->updTaskSet().computeAccelerations(s);
cmcActSubsystem.setCompleteState( s );
// Set output file names so that files are flushed regularly in case we fail
IO::makeDir(getResultsDir()); // Create directory for output in case it doesn't exist
manager.getStateStorage().setOutputFileName(getResultsDir() + "/" + getName() + "_states.sto");
try {
manager.integrate(s);
}
catch(const Exception& x) {
// TODO: eventually might want to allow writing of partial results
x.print(cout);
IO::chDir(saveWorkingDirectory);
// close open files if we die prematurely (e.g. Opt fail)
manager.getStateStorage().print(getResultsDir() + "/" + getName() + "_states.sto");
return false;
}
catch(...) {
// TODO: eventually might want to allow writing of partial results
IO::chDir(saveWorkingDirectory);
// close open files if we die prematurely (e.g. Opt fail)
manager.getStateStorage().print(getResultsDir() + "/" + getName() + "_states.sto");
return false;
}
time(&finishTime);
cout<<"----------------------------------------------------------------\n";
cout<<"Finished tracking the specified kinematics\n";
if( _verbose ){
std::cout << "states= " << s.getY() << std::endl;
}
cout<<"=================================================================\n";
localTime = localtime(&startTime);
cout<<"Start time = "<<asctime(localTime);
localTime = localtime(&finishTime);
cout<<"Finish time = "<<asctime(localTime);
elapsedTime = difftime(finishTime,startTime);
cout<<"Elapsed time = "<<elapsedTime<<" seconds.\n";
cout<<"================================================================\n\n\n";
// ---- RESULTS -----
printResults(getName(),getResultsDir()); // this will create results directory if necessary
controller->updControlSet().print(getResultsDir() + "/" + getName() + "_controls.xml");
_model->printControlStorage(getResultsDir() + "/" + getName() + "_controls.sto");
manager.getStateStorage().print(getResultsDir() + "/" + getName() + "_states.sto");
/*
Storage statesDegrees(manager.getStateStorage());
_model->getSimbodyEngine().convertRadiansToDegrees(statesDegrees);
statesDegrees.setWriteSIMMHeader(true);
statesDegrees.print(getResultsDir() + "/" + getName() + "_states_degrees.mot");
*/
controller->getPositionErrorStorage()->print(getResultsDir() + "/" + getName() + "_pErr.sto");
stringstream adjQMsg;
if(_model->getAnalysisSet().getIndex("Actuation") != -1) {
Actuation& actuation = (Actuation&)_model->getAnalysisSet().get("Actuation");
Array<double> FAve(0.0,3),MAve(0.0,3);
Storage *forceStore = actuation.getForceStorage();
computeAverageResiduals(*forceStore,FAve,MAve);
adjQMsg << "************************************************************" << endl;
adjQMsg << "* Final Average Residuals *" << endl;
adjQMsg << "************************************************************" << endl;
adjQMsg << "* After "<<_adjustedCOMBody<<" COM and Kinematics adjustments:"<< endl;
adjQMsg << "* FX="<<FAve[0]<<" FY="<<FAve[1]<<" FZ="<<FAve[2]<<endl;
adjQMsg << "* MX="<<MAve[0]<<" MY="<<MAve[1]<<" MZ="<<MAve[2]<<endl;
adjQMsg << "************************************************************\n" << endl;
// Write the average residuals (DC offsets) out to a file
ofstream residualFile((getResultsDir() + "/" + getName() + "_avgResiduals.txt").c_str());
residualFile << "Average Residuals:\n\n";
residualFile << "FX average = " << FAve[0] << "\n";
residualFile << "FY average = " << FAve[1] << "\n";
residualFile << "FZ average = " << FAve[2] << "\n";
residualFile << "MX average = " << MAve[0] << "\n";
residualFile << "MY average = " << MAve[1] << "\n";
residualFile << "MZ average = " << MAve[2] << "\n";
residualFile.close();
}
// Write new model file
if(_adjustCOMToReduceResiduals) writeAdjustedModel();
cout << massAdjMsg << adjQMsg.str() << endl;
//_model->removeController(controller); // So that if this model is from GUI it doesn't double-delete it.
} catch(const Exception& x) {
// TODO: eventually might want to allow writing of partial results
x.print(cout);
IO::chDir(saveWorkingDirectory);
// close open files if we die prematurely (e.g. Opt fail)
return false;
}
IO::chDir(saveWorkingDirectory);
return true;
}
//=============================================================================
// UTILITY
//=============================================================================
void RRATool::
writeAdjustedModel()
{
if(_outputModelFile=="") {
cerr<<"Warning: A name for the output model was not set.\n";
cerr<<"Specify a value for the property "<<_outputModelFileProp.getName();
cerr<<" in the setup file.\n";
if (getDocument()){
string directoryOfSetupFile = IO::getParentDirectory(getDocumentFileName());
_outputModelFile = directoryOfSetupFile+"adjusted_model.osim";
}
else{
cerr<<"Writing to adjusted_model.osim ...\n\n";
_outputModelFile = "adjusted_model.osim";
}
cerr<<"Writing to " <<_outputModelFile << " ...\n\n";
}
// Set the model's actuator set back to the original set. e.g. in RRA1
// we load the model but replace its (muscle) actuators with torque actuators.
// So we need to put back the muscles before writing out the adjusted model.
// NOTE: use operator= so actuator groups are properly copied over
_model->updForceSet() = _originalForceSet;
// CMC was added as a model controller, now remove before printing out
int c = _model->updControllerSet().getIndex("CMC");
_model->updControllerSet().remove(c);
_model->print(_outputModelFile);
}
//_____________________________________________________________________________
/**
* Compute the average residuals.
*
* @param rFAve The computed average force residuals. The size of rFAve is
* set to 3.
* @param rMAve The computed average moment residuals. The size of rMAve is
* set to 3.
*/
void RRATool::
computeAverageResiduals(const Storage &aForceStore,OpenSim::Array<double> &rFAve,OpenSim::Array<double> &rMAve)
{
int iFX, iFY, iFZ, iMX, iMY, iMZ;
// COMPUTE AVERAGE
int size = aForceStore.getSmallestNumberOfStates();
Array<double> ave(0.0);
ave.setSize(size);
aForceStore.computeAverage(size,&ave[0]);
// GET INDICES
iFX = aForceStore.getStateIndex("FX");
iFY = aForceStore.getStateIndex("FY");
iFZ = aForceStore.getStateIndex("FZ");
iMX = aForceStore.getStateIndex("MX");
iMY = aForceStore.getStateIndex("MY");
iMZ = aForceStore.getStateIndex("MZ");
//cout << "storage = " << aForceStore.getName() << endl;
//cout << "computeAverageResiduals size=" << size << " ave=" << ave << endl;
//cout << "indexs=" << iFX << " " << iFY << " " << iFZ << " " << iMX << " " << iMY << " " << iMZ << endl;
// GET AVE FORCES
if(iFX>=0) rFAve[0] = ave[iFX];
if(iFY>=0) rFAve[1] = ave[iFY];
if(iFZ>=0) rFAve[2] = ave[iFZ];
// GET AVE MOMENTS
if(iMX>=0) rMAve[0] = ave[iMX];
if(iMY>=0) rMAve[1] = ave[iMY];
if(iMZ>=0) rMAve[2] = ave[iMZ];
//cout << "forces= " << rFAve << endl;
//cout << "moments=" << rMAve << endl;
}
string RRATool::
adjustCOMToReduceResiduals(SimTK::State& s, const Storage &qStore, const Storage &uStore)
{
// Create a states storage from q's and u's
Storage *statesStore = AnalyzeTool::createStatesStorageFromCoordinatesAndSpeeds(*_model, qStore, uStore);
double ti = _ti;
double tf = _tf;
if(_initialTimeForCOMAdjustment!=-1 || _finalTimeForCOMAdjustment!=-1) {
ti = _initialTimeForCOMAdjustment;
tf = _finalTimeForCOMAdjustment;