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StaticOptimization_GH.cpp
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StaticOptimization_GH.cpp
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/* -------------------------------------------------------------------------- *
* OpenSim: StaticOptimization_GH.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 *
* Author(s): Jeffrey A. Reinbolt *
* *
* 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. *
* -------------------------------------------------------------------------- */
//=============================================================================
// INCLUDES
//=============================================================================
#include <iostream>
#include <string>
#include <OpenSim/Common/IO.h>
#include <OpenSim/Simulation/Model/Model.h>
#include <OpenSim/Simulation/SimbodyEngine/SimbodyEngine.h>
#include <OpenSim/Simulation/Model/BodySet.h>
#include <OpenSim/Simulation/Model/CoordinateSet.h>
#include <OpenSim/Simulation/Model/ForceSet.h>
#include <OpenSim/Simulation/Model/Muscle.h>
#include <OpenSim/Common/GCVSplineSet.h>
#include <OpenSim/Actuators/CoordinateActuator.h>
#include <OpenSim/Simulation/Control/ControlSet.h>
#include <SimTKmath.h>
#include <SimTKlapack.h>
#include "StaticOptimization_GH.h"
#include "StaticOptimization_GHTarget.h"
#include <OpenSim/Simulation/Model/ActivationFiberLengthMuscle.h>
using namespace OpenSim;
using namespace std;
//=============================================================================
// CONSTRUCTOR(S) AND DESTRUCTOR
//=============================================================================
//_____________________________________________________________________________
/**
* Destructor.
*/
StaticOptimization_GH::~StaticOptimization_GH()
{
deleteStorage();
delete _modelWorkingCopy;
if(_ownsForceSet) delete _forceSet;
delete _forceReporter;
}
//_____________________________________________________________________________
/**
*/
StaticOptimization_GH::StaticOptimization_GH(Model *aModel) :
Analysis(aModel),
_useModelForceSet(_useModelForceSetProp.getValueBool()),
_activationExponent(_activationExponentProp.getValueDbl()),
_useMusclePhysiology(_useMusclePhysiologyProp.getValueBool()),
_GHstabTransitionParam(_GHstabTransitionParamProp.getValueDbl()),
_atheta(_athetaProp.getValueDbl()),
_aphi(_aphiProp.getValueDbl()),
_convergenceCriterion(_convergenceCriterionProp.getValueDbl()),
_maximumIterations(_maximumIterationsProp.getValueInt()),
_modelWorkingCopy(NULL),
_numCoordinateActuators(0),
_forceReporter(0)
{
setNull();
if(aModel) setModel(*aModel);
else allocateStorage();
}
// Copy constrctor and virtual copy
//_____________________________________________________________________________
/**
* Copy constructor.
*
*/
StaticOptimization_GH::StaticOptimization_GH(const StaticOptimization_GH &aStaticOptimization_GH):
Analysis(aStaticOptimization_GH),
_useModelForceSet(_useModelForceSetProp.getValueBool()),
_activationExponent(_activationExponentProp.getValueDbl()),
_useMusclePhysiology(_useMusclePhysiologyProp.getValueBool()),
_GHstabTransitionParam(_GHstabTransitionParamProp.getValueDbl()),
_atheta(_athetaProp.getValueDbl()),
_aphi(_aphiProp.getValueDbl()),
_convergenceCriterion(_convergenceCriterionProp.getValueDbl()),
_maximumIterations(_maximumIterationsProp.getValueInt()),
_modelWorkingCopy(NULL),
_numCoordinateActuators(aStaticOptimization_GH._numCoordinateActuators)
{
setNull();
// COPY TYPE AND NAME
*this = aStaticOptimization_GH;
_forceReporter = 0;
}
//=============================================================================
// OPERATORS
//=============================================================================
//-----------------------------------------------------------------------------
// ASSIGNMENT
//-----------------------------------------------------------------------------
//_____________________________________________________________________________
/**
* Assign this object to the values of another.
*
* @return Reference to this object.
*/
StaticOptimization_GH& StaticOptimization_GH::
operator=(const StaticOptimization_GH &aStaticOptimization_GH)
{
// BASE CLASS
Analysis::operator=(aStaticOptimization_GH);
_modelWorkingCopy = aStaticOptimization_GH._modelWorkingCopy;
_numCoordinateActuators = aStaticOptimization_GH._numCoordinateActuators;
_useModelForceSet = aStaticOptimization_GH._useModelForceSet;
_activationExponent=aStaticOptimization_GH._activationExponent;
_convergenceCriterion=aStaticOptimization_GH._convergenceCriterion;
_maximumIterations=aStaticOptimization_GH._maximumIterations;
_GHstabTransitionParam = aStaticOptimization_GH._GHstabTransitionParam;
_atheta = aStaticOptimization_GH._atheta;
_aphi = aStaticOptimization_GH._aphi;
_useMusclePhysiology=aStaticOptimization_GH._useMusclePhysiology;
_forceReporter = aStaticOptimization_GH._forceReporter;
return(*this);
}
//_____________________________________________________________________________
/**
* SetNull().
*/
void StaticOptimization_GH::setNull()
{
setAuthors("Dimitra Blana");
setupProperties();
// OTHER VARIABLES
_useModelForceSet = true;
_activationStorage = NULL;
_ownsForceSet = false;
_forceSet = NULL;
_activationExponent=2;
_useMusclePhysiology=true;
_numCoordinateActuators = 0;
_GHstabTransitionParam = 0.01;
_atheta = 0.7744;
_aphi = 0.6728;
_convergenceCriterion = 1e-4;
_maximumIterations = 100;
_forceReporter = 0;
setName("StaticOptimization_GH");
}
//_____________________________________________________________________________
/**
* Connect properties to local pointers.
*/
void StaticOptimization_GH::
setupProperties()
{
_useModelForceSetProp.setComment("If true, the model's own force set will be used in the static optimization computation. "
"Otherwise, inverse dynamics for coordinate actuators will be computed for all unconstrained degrees of freedom.");
_useModelForceSetProp.setName("use_model_force_set");
_propertySet.append(&_useModelForceSetProp);
_activationExponentProp.setComment(
"A double indicating the exponent to raise activations to when solving static optimization. ");
_activationExponentProp.setName("activation_exponent");
_propertySet.append(&_activationExponentProp);
_useMusclePhysiologyProp.setComment(
"If true muscle force-length curve is observed while running optimization.");
_useMusclePhysiologyProp.setName("use_muscle_physiology");
_propertySet.append(&_useMusclePhysiologyProp);
_GHstabTransitionParamProp.setComment(
"Transition parameter used to determine the shape of the GH stability curve in the cost function");
_GHstabTransitionParamProp.setName("GH_stability_transition_parameter");
_propertySet.append(&_GHstabTransitionParamProp);
_athetaProp.setName("theta_at_glenoid_rim");
_athetaProp.setComment("Angle along the major axis of the ellipse representing the glenoid fossa.");
_propertySet.append(&_athetaProp);
_aphiProp.setName("phi_at_glenoid_rim");
_aphiProp.setComment("Angle along the minor axis of the ellipse representing the glenoid fossa.");
_propertySet.append(&_aphiProp);
_convergenceCriterionProp.setComment(
"Value used to determine when the optimization solution has converged");
_convergenceCriterionProp.setName("optimizer_convergence_criterion");
_propertySet.append(&_convergenceCriterionProp);
_maximumIterationsProp.setComment(
"An integer for setting the maximum number of iterations the optimizer can use at each time. ");
_maximumIterationsProp.setName("optimizer_max_iterations");
_propertySet.append(&_maximumIterationsProp);
}
//=============================================================================
// CONSTRUCTION METHODS
//=============================================================================
//_____________________________________________________________________________
/**
* Construct a description for the static optimization files.
*/
void StaticOptimization_GH::
constructDescription()
{
string descrip = "This file contains static optimization results.\n\n";
setDescription(descrip);
}
//_____________________________________________________________________________
/**
* Construct column labels for the static optimization files.
*/
void StaticOptimization_GH::
constructColumnLabels()
{
Array<string> labels;
labels.append("time");
if(_model)
for (int i = 0; i < _forceSet->getActuators().getSize(); i++) labels.append(_forceSet->getActuators().get(i).getName());
setColumnLabels(labels);
}
//_____________________________________________________________________________
/**
* Allocate storage for the static optimization.
*/
void StaticOptimization_GH::
allocateStorage()
{
_activationStorage = new Storage(1000,"Static Optimization GH");
_activationStorage->setDescription(getDescription());
_activationStorage->setColumnLabels(getColumnLabels());
}
//=============================================================================
// DESTRUCTION METHODS
//=============================================================================
//_____________________________________________________________________________
/**
* Delete storage objects.
*/
void StaticOptimization_GH::
deleteStorage()
{
delete _activationStorage; _activationStorage = NULL;
}
//=============================================================================
// GET AND SET
//=============================================================================
//_____________________________________________________________________________
/**
* Set the model for which the static optimization is to be computed.
*
* @param aModel Model pointer
*/
void StaticOptimization_GH::
setModel(Model& aModel)
{
Analysis::setModel(aModel);
}
//-----------------------------------------------------------------------------
// STORAGE
//-----------------------------------------------------------------------------
//_____________________________________________________________________________
/**
* Get the activation storage.
*
* @return Activation storage.
*/
Storage* StaticOptimization_GH::
getActivationStorage()
{
return(_activationStorage);
}
//_____________________________________________________________________________
/**
* Get the force storage.
*
* @return Force storage.
*/
Storage* StaticOptimization_GH::
getForceStorage()
{
if (_forceReporter)
return(&_forceReporter->updForceStorage());
else
return NULL;
}
//-----------------------------------------------------------------------------
// STORAGE CAPACITY
//-----------------------------------------------------------------------------
//_____________________________________________________________________________
/**
* Set the capacity increments of all storage instances.
*
* @param aIncrement Increment by which storage capacities will be increased
* when storage capacities run out.
*/
void StaticOptimization_GH::
setStorageCapacityIncrements(int aIncrement)
{
_activationStorage->setCapacityIncrement(aIncrement);
}
//=============================================================================
// ANALYSIS
//=============================================================================
//_____________________________________________________________________________
/**
* Record the results.
*/
int StaticOptimization_GH::
record(const SimTK::State& s)
{
if(!_modelWorkingCopy) return -1;
// Set model to whatever defaults have been updated to from the last iteration
SimTK::State& sWorkingCopy = _modelWorkingCopy->updWorkingState();
sWorkingCopy.setTime(s.getTime());
_modelWorkingCopy->initStateWithoutRecreatingSystem(sWorkingCopy);
// update Q's and U's
sWorkingCopy.setQ(s.getQ());
sWorkingCopy.setU(s.getU());
_modelWorkingCopy->getMultibodySystem().realize(sWorkingCopy, SimTK::Stage::Velocity);
//_modelWorkingCopy->equilibrateMuscles(sWorkingCopy);
const Set<Actuator>& acts = _modelWorkingCopy->getActuators();
int na = acts.getSize();
int nacc = _accelerationIndices.getSize();
// IPOPT
_numericalDerivativeStepSize = 0.0001;
_optimizerAlgorithm = "ipopt";
_printLevel = 0;
//_optimizationConvergenceTolerance = 1e-004;
//_maxIterations = 2000;
// Optimization target
_modelWorkingCopy->setAllControllersEnabled(false);
StaticOptimization_GHTarget target(sWorkingCopy,_modelWorkingCopy,na,nacc,_useMusclePhysiology);
target.setStatesStore(_statesStore);
target.setStatesSplineSet(_statesSplineSet);
target.setActivationExponent(_activationExponent);
target.setGHstabTransitionParam(_GHstabTransitionParam);
target.setatheta(_atheta);
target.setaphi(_aphi);
target.setDX(_numericalDerivativeStepSize);
// Pick optimizer algorithm
SimTK::OptimizerAlgorithm algorithm = SimTK::InteriorPoint;
//SimTK::OptimizerAlgorithm algorithm = SimTK::CFSQP;
// Optimizer
SimTK::Optimizer *optimizer = new SimTK::Optimizer(target, algorithm);
// Optimizer options
//cout<<"\nSetting optimizer print level to "<<_printLevel<<".\n";
optimizer->setDiagnosticsLevel(_printLevel);
//cout<<"Setting optimizer convergence criterion to "<<_convergenceCriterion<<".\n";
optimizer->setConvergenceTolerance(_convergenceCriterion);
//cout<<"Setting optimizer maximum iterations to "<<_maximumIterations<<".\n";
optimizer->setMaxIterations(_maximumIterations);
optimizer->useNumericalGradient(true);
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",1);
}
// Parameter bounds
SimTK::Vector lowerBounds(na), upperBounds(na);
for(int i=0,j=0;i<acts.getSize();i++) {
Actuator& act = acts.get(i);
lowerBounds(j) = act.getMinControl();
upperBounds(j) = act.getMaxControl();
j++;
}
target.setParameterLimits(lowerBounds, upperBounds);
_parameters = 0; // Set initial guess to zeros
// Static optimization
_modelWorkingCopy->getMultibodySystem().realize(sWorkingCopy,SimTK::Stage::Velocity);
target.prepareToOptimize(sWorkingCopy, &_parameters[0]);
//LARGE_INTEGER start;
//LARGE_INTEGER stop;
//LARGE_INTEGER frequency;
//QueryPerformanceFrequency(&frequency);
//QueryPerformanceCounter(&start);
try {
target.setCurrentState( &sWorkingCopy );
optimizer->optimize(_parameters);
}
catch (const SimTK::Exception::Base& ex) {
cout << ex.getMessage() << endl;
cout << "OPTIMIZATION FAILED..." << endl;
cout << endl;
cout << "StaticOptimization_GH.record: WARN- The optimizer could not find a solution at time = " << s.getTime() << endl;
cout << endl;
double tolBounds = 1e-1;
bool weakModel = false;
string msgWeak = "The model appears too weak for static optimization.\nTry increasing the strength and/or range of the following force(s):\n";
for(int a=0;a<na;a++) {
Actuator* act = dynamic_cast<Actuator*>(&_forceSet->get(a));
if( act ) {
Muscle* mus = dynamic_cast<Muscle*>(&_forceSet->get(a));
if(mus==NULL) {
if(_parameters(a) < (lowerBounds(a)+tolBounds)) {
msgWeak += " ";
msgWeak += act->getName();
msgWeak += " approaching lower bound of ";
ostringstream oLower;
oLower << lowerBounds(a);
msgWeak += oLower.str();
msgWeak += "\n";
weakModel = true;
} else if(_parameters(a) > (upperBounds(a)-tolBounds)) {
msgWeak += " ";
msgWeak += act->getName();
msgWeak += " approaching upper bound of ";
ostringstream oUpper;
oUpper << upperBounds(a);
msgWeak += oUpper.str();
msgWeak += "\n";
weakModel = true;
}
} else {
if(_parameters(a) > (upperBounds(a)-tolBounds)) {
msgWeak += " ";
msgWeak += mus->getName();
msgWeak += " approaching upper bound of ";
ostringstream o;
o << upperBounds(a);
msgWeak += o.str();
msgWeak += "\n";
weakModel = true;
}
}
}
}
if(weakModel) cout << msgWeak << endl;
if(!weakModel) {
double tolConstraints = 1e-6;
bool incompleteModel = false;
string msgIncomplete = "The model appears unsuitable for static optimization.\nTry appending the model with additional force(s) or locking joint(s) to reduce the following acceleration constraint violation(s):\n";
SimTK::Vector constraints;
target.constraintFunc(_parameters,true,constraints);
const CoordinateSet& coordSet = _modelWorkingCopy->getCoordinateSet();
for(int acc=0;acc<nacc;acc++) {
if(fabs(constraints(acc)) > tolConstraints) {
const Coordinate& coord = coordSet.get(_accelerationIndices[acc]);
msgIncomplete += " ";
msgIncomplete += coord.getName();
msgIncomplete += ": constraint violation = ";
ostringstream o;
o << constraints(acc);
msgIncomplete += o.str();
msgIncomplete += "\n";
incompleteModel = true;
}
}
_forceReporter->step(sWorkingCopy, 1);
if(incompleteModel) cout << msgIncomplete << endl;
}
}
//QueryPerformanceCounter(&stop);
//double duration = (double)(stop.QuadPart-start.QuadPart)/(double)frequency.QuadPart;
//cout << "optimizer time = " << (duration*1.0e3) << " milliseconds" << endl;
target.printPerformance(sWorkingCopy, &_parameters[0]);
//update defaults for use in the next step
const Set<Actuator>& actuators = _modelWorkingCopy->getActuators();
for(int k=0; k < actuators.getSize(); ++k){
ActivationFiberLengthMuscle *mus = dynamic_cast<ActivationFiberLengthMuscle*>(&actuators[k]);
if(mus){
mus->setDefaultActivation(_parameters[k]);
// Don't send up red flags when the def
mus->setObjectIsUpToDateWithProperties();
}
}
_activationStorage->append(sWorkingCopy.getTime(),na,&_parameters[0]);
SimTK::Vector forces(na);
target.getActuation(const_cast<SimTK::State&>(sWorkingCopy), _parameters,forces);
_forceReporter->step(sWorkingCopy, 1);
return 0;
}
//_____________________________________________________________________________
/**
* This method is called at the beginning of an analysis so that any
* necessary initializations may be performed.
*
* This method is meant to be called at the begining of an integration
*
* @param s Current state .
*
* @return -1 on error, 0 otherwise.
*/
int StaticOptimization_GH::
begin(SimTK::State& s )
{
if(!proceed()) return(0);
// Make a working copy of the model
delete _modelWorkingCopy;
_modelWorkingCopy = _model->clone();
_modelWorkingCopy->initSystem();
// Replace model force set with only generalized forces
if(_model) {
SimTK::State& sWorkingCopyTemp = _modelWorkingCopy->updWorkingState();
// Update the _forceSet we'll be computing inverse dynamics for
if(_ownsForceSet) delete _forceSet;
if(_useModelForceSet) {
// Set pointer to model's internal force set
_forceSet = &_modelWorkingCopy->updForceSet();
_ownsForceSet = false;
} else {
ForceSet& as = _modelWorkingCopy->updForceSet();
// Keep a copy of forces that are not muscles to restore them back.
ForceSet* saveForces = as.clone();
// Generate an force set consisting of a coordinate actuator for every unconstrained degree of freedom
_forceSet = CoordinateActuator::CreateForceSetOfCoordinateActuatorsForModel(sWorkingCopyTemp,*_modelWorkingCopy,1,false);
_ownsForceSet = false;
_modelWorkingCopy->setAllControllersEnabled(false);
_numCoordinateActuators = _forceSet->getSize();
// Copy whatever forces that are not muscles back into the model
for(int i=0; i<saveForces->getSize(); i++){
const Force& f=saveForces->get(i);
if ((dynamic_cast<const Muscle*>(&saveForces->get(i)))==NULL)
as.append(saveForces->get(i).clone());
}
}
SimTK::State& sWorkingCopy = _modelWorkingCopy->initSystem();
// Set modeiling options for Actuators to be overriden
for(int i=0; i<_forceSet->getSize(); i++) {
Actuator* act = dynamic_cast<Actuator*>(&_forceSet->get(i));
if( act ) {
act->overrideForce(sWorkingCopy,true);
}
}
sWorkingCopy.setTime(s.getTime()); //Keep time in sync.
sWorkingCopy.setQ(s.getQ());
sWorkingCopy.setU(s.getU());
sWorkingCopy.setZ(s.getZ());
_modelWorkingCopy->getMultibodySystem().realize(s,SimTK::Stage::Velocity);
_modelWorkingCopy->equilibrateMuscles(sWorkingCopy);
// Gather indices into speed set corresponding to the unconstrained degrees of freedom (for which we will set acceleration constraints)
_accelerationIndices.setSize(0);
const CoordinateSet& coordSet = _model->getCoordinateSet();
for(int i=0; i<coordSet.getSize(); i++) {
const Coordinate& coord = coordSet.get(i);
if(!coord.isConstrained(sWorkingCopy)) {
_accelerationIndices.append(i);
}
}
int nf = _forceSet->getSize();
int nacc = _accelerationIndices.getSize();
if(nf < nacc)
throw(Exception("StaticOptimization_GH: ERROR- overconstrained system -- need at least as many forces as there are degrees of freedom.\n"));
// initialize forceReporter using modified set of Forces and state from corresponding model
delete _forceReporter;
_forceReporter = new ForceReporter(_modelWorkingCopy);
_forceReporter->begin(sWorkingCopy);
_forceReporter->updForceStorage().reset();
_parameters.resize(_forceSet->getActuators().getSize());
_parameters = 0;
}
_statesSplineSet=GCVSplineSet(5,_statesStore);
// DESCRIPTION AND LABELS
constructDescription();
constructColumnLabels();
deleteStorage();
allocateStorage();
// RESET STORAGE
_activationStorage->reset(s.getTime());
// RECORD
int status = 0;
if(_activationStorage->getSize()<=0) {
status = record(s);
const Set<Actuator>& fs = _modelWorkingCopy->getActuators();
for(int k=0;k<fs.getSize();k++) {
Actuator& act = fs.get(k);
cout << "Bounds for " << act.getName() << ": " << act.getMinControl()<< " to "<< act.getMaxControl() << endl;
}
}
return(status);
}
//_____________________________________________________________________________
/**
* This method is called to perform the analysis. It can be called during
* the execution of a forward integrations or after the integration by
* feeding it the necessary data.
*
* This method should be overriden in derived classes. It is
* included here so that the derived class will not have to implement it if
* it is not necessary.
*
* @param s Current state .
*
* @return -1 on error, 0 otherwise.
*/
int StaticOptimization_GH::
step(const SimTK::State& s, int stepNumber )
{
if(!proceed(stepNumber)) return(0);
record(s);
return(0);
}
//_____________________________________________________________________________
/**
* This method is called at the end of an analysis so that any
* necessary finalizations may be performed.
*
* @param s Current state
*
* @return -1 on error, 0 otherwise.
*/
int StaticOptimization_GH::
end( SimTK::State& s )
{
if(!proceed()) return(0);
record(s);
return(0);
}
//=============================================================================
// IO
//=============================================================================
//_____________________________________________________________________________
/**
* Print results.
*
* The file names are constructed as
* aDir + "/" + aBaseName + "_" + ComponentName + aExtension
*
* @param aDir Directory in which the results reside.
* @param aBaseName Base file name.
* @param aDT Desired time interval between adjacent storage vectors. Linear
* interpolation is used to print the data out at the desired interval.
* @param aExtension File extension.
*
* @return 0 on success, -1 on error.
*/
int StaticOptimization_GH::
printResults(const string &aBaseName,const string &aDir,double aDT,
const string &aExtension)
{
// ACTIVATIONS
Storage::printResult(_activationStorage,aBaseName+"_"+getName()+"_activation",aDir,aDT,aExtension);
// FORCES
Storage::printResult(getForceStorage(),aBaseName+"_"+getName()+"_force",aDir,aDT,aExtension);
// Make a ControlSet out of activations for use in forward dynamics
ControlSet cs(*_activationStorage);
std::string path = (aDir=="") ? "." : aDir;
std::string name = path + "/" + aBaseName+"_"+getName()+"_controls.xml";
cs.print(name);
return(0);
}