C++ FunctionSet::get方法代码示例

/**
 * Set the velocity functions for the tasks.  Functions are set based on the
 * correspondence of the function and the task.  For example,
 * a task with the name "x" will search for a function or functions
 * with the name "x".  For tasks that require 3 functions, such
 * as CMC_Point tasks, the assumption is that there will be three
 * consecutive functions named "x" in the function set.  If the correct
 * number of functions is not found, the task is disabled.
 *
 * @param aFuncSet Function set.
 * @return Pointer to the previous function set.
 */
void CMC_TaskSet::
setFunctionsForVelocity(FunctionSet &aFuncSet)
{
    // LOOP THROUGH TRACK OBJECTS
    int i,j,iFunc=0;
    int nTrk;
    string name;
    Function *f[3];

    const CoordinateSet& coords = getModel()->getCoordinateSet(); 

    for(i=0;i<getSize();i++) {

        // OBJECT
        TrackingTask& ttask = get(i);

        // If CMC_Task process same way as pre 2.0.2
        if (dynamic_cast<CMC_Task*>(&ttask)==NULL) 
            continue;

        CMC_Task& task = dynamic_cast<CMC_Task&>(ttask);

        // NAME
        name = task.getName();
        if(name.empty()) continue;

        const Coordinate& coord = coords.get(name);

        // FIND FUNCTION(S)
        f[0] = f[1] = f[2] = NULL;
        nTrk = task.getNumTaskFunctions();
        iFunc = aFuncSet.getIndex(coord.getSpeedName(),iFunc);

        if (iFunc < 0){
            name = coord.getJoint().getName() + "/" + coord.getSpeedName();
            iFunc = aFuncSet.getIndex(name, iFunc);
            if (iFunc < 0){
                string msg = "CMC_TaskSet::setFunctionsForVelocity: function for task '";
                msg += name + " not found.";
                throw Exception(msg);
            }
        }

        for(j=0;j<nTrk;j++) {
            try {
                f[j] = &aFuncSet.get(iFunc);
            } catch(const Exception& x) {
                x.print(cout);
            }
            if(f[j]==NULL) break;
        }
        task.setTaskFunctionsForVelocity(f[0],f[1],f[2]);
    }
}

/**
 * This method creates a SimmMotionTrial instance with the markerFile and
 * timeRange parameters. It also creates a Storage instance with the
 * coordinateFile parameter. Then it updates the coordinates and markers in
 * the model, if specified. Then it does IK to fit the model to the static
 * pose. Then it uses the current model pose to relocate all non-fixed markers
 * according to their locations in the SimmMotionTrial. Then it writes the
 * output files selected by the user.
 *
 * @param aModel the model to use for the marker placing process.
 * @return Whether the marker placing process was successful or not.
 */
bool MarkerPlacer::processModel(Model* aModel, const string& aPathToSubject)
{
    if(!getApply()) return false;

    cout << endl << "Step 3: Placing markers on model" << endl;

    /* Load the static pose marker file, and average all the
     * frames in the user-specified time range.
     */
    MarkerData staticPose(aPathToSubject + _markerFileName);
    if (_timeRange.getSize()<2) 
        throw Exception("MarkerPlacer::processModel, time_range is unspecified.");

    staticPose.averageFrames(_maxMarkerMovement, _timeRange[0], _timeRange[1]);
    staticPose.convertToUnits(aModel->getLengthUnits());

    /* Delete any markers from the model that are not in the static
     * pose marker file.
     */
    aModel->deleteUnusedMarkers(staticPose.getMarkerNames());

    // Construct the system and get the working state when done changing the model
    SimTK::State& s = aModel->initSystem();
    
    // Create references and WeightSets needed to initialize InverseKinemaicsSolver
    Set<MarkerWeight> markerWeightSet;
    _ikTaskSet.createMarkerWeightSet(markerWeightSet); // order in tasks file
    MarkersReference markersReference(staticPose, &markerWeightSet);
    SimTK::Array_<CoordinateReference> coordinateReferences;

    // Load the coordinate data
    // create CoordinateReferences for Coordinate Tasks
    FunctionSet *coordFunctions = NULL;
    bool haveCoordinateFile = false;
    if(_coordinateFileName != "" && _coordinateFileName != "Unassigned"){
        Storage coordinateValues(aPathToSubject + _coordinateFileName);
        aModel->getSimbodyEngine().convertDegreesToRadians(coordinateValues);
        haveCoordinateFile = true;
        coordFunctions = new GCVSplineSet(5,&coordinateValues);
    }
    
    int index = 0;
    for(int i=0; i< _ikTaskSet.getSize(); i++){
        IKCoordinateTask *coordTask = dynamic_cast<IKCoordinateTask *>(&_ikTaskSet[i]);
        if (coordTask && coordTask->getApply()){
            CoordinateReference *coordRef = NULL;
            if(coordTask->getValueType() == IKCoordinateTask::FromFile){
                index = coordFunctions->getIndex(coordTask->getName(), index);
                if(index >= 0){
                    coordRef = new CoordinateReference(coordTask->getName(),coordFunctions->get(index));
                }
            }
            else if((coordTask->getValueType() == IKCoordinateTask::ManualValue)){
                Constant reference(Constant(coordTask->getValue()));
                coordRef = new CoordinateReference(coordTask->getName(), reference);
            }
            else{ // assume it should be held at its current/default value
                double value = aModel->getCoordinateSet().get(coordTask->getName()).getValue(s);
                Constant reference = Constant(value);
                coordRef = new CoordinateReference(coordTask->getName(), reference);
            }

            if(coordRef == NULL)
                throw Exception("MarkerPlacer: value for coordinate "+coordTask->getName()+" not found.");

            // We have a valid coordinate reference so now set its weight according to the task
            coordRef->setWeight(coordTask->getWeight());
            coordinateReferences.push_back(*coordRef);      
        }           
    }
    double constraintWeight = std::numeric_limits<SimTK::Real>::infinity();

    InverseKinematicsSolver ikSol(*aModel, markersReference,
                                  coordinateReferences, constraintWeight);
    ikSol.assemble(s);

    // Call realize Position so that the transforms are updated and  markers can be moved correctly
    aModel->getMultibodySystem().realize(s, SimTK::Stage::Position);
    // Report marker errors to assess the quality 
    int nm = markerWeightSet.getSize();
    SimTK::Array_<double> squaredMarkerErrors(nm, 0.0);
    SimTK::Array_<Vec3> markerLocations(nm, Vec3(0));
    double totalSquaredMarkerError = 0.0;
    double maxSquaredMarkerError = 0.0;
    int worst = -1;
    // Report in the same order as the marker tasks/weights
    ikSol.computeCurrentSquaredMarkerErrors(squaredMarkerErrors);
    for(int j=0; j<nm; ++j){
//.........这里部分代码省略.........

/**
 * Run the inverse Dynamics tool.
 */
bool InverseDynamicsTool::run()
{
	bool success = false;
	bool modelFromFile=true;
	try{
		//Load and create the indicated model
		if (!_model) 
			_model = new Model(_modelFileName);
		else
			modelFromFile = false;
		_model->printBasicInfo(cout);

		cout<<"Running tool " << getName() <<".\n"<<endl;

		// Do the maneuver to change then restore working directory 
		// so that the parsing code behaves properly if called from a different directory.
		string saveWorkingDirectory = IO::getCwd();
		string directoryOfSetupFile = IO::getParentDirectory(getDocumentFileName());
		IO::chDir(directoryOfSetupFile);

		const CoordinateSet &coords = _model->getCoordinateSet();
		int nq = _model->getNumCoordinates();

		FunctionSet *coordFunctions = NULL;
		//Storage *coordinateValues = NULL;

		if(hasCoordinateValues()){
			if(_lowpassCutoffFrequency>=0) {
				cout<<"\n\nLow-pass filtering coordinates data with a cutoff frequency of "<<_lowpassCutoffFrequency<<"..."<<endl<<endl;
				_coordinateValues->pad(_coordinateValues->getSize()/2);
				_coordinateValues->lowpassIIR(_lowpassCutoffFrequency);
				if (getVerboseLevel()==Debug) _coordinateValues->print("coordinateDataFiltered.sto");
			}
			// Convert degrees to radian if indicated
			if(_coordinateValues->isInDegrees()){
				_model->getSimbodyEngine().convertDegreesToRadians(*_coordinateValues);
			}
			// Create differentiable splines of the coordinate data
			coordFunctions = new GCVSplineSet(5, _coordinateValues);

			//Functions must correspond to model coordinates and their order for the solver
			for(int i=0; i<nq; i++){
				if(coordFunctions->contains(coords[i].getName())){
					coordFunctions->insert(i,coordFunctions->get(coords[i].getName()));
				}
				else{
					coordFunctions->insert(i,new Constant(coords[i].getDefaultValue()));
					std::cout << "InverseDynamicsTool: coordinate file does not contain coordinate " << coords[i].getName() << " assuming default value" << std::endl;
				}
			}
			if(coordFunctions->getSize() > nq){
				coordFunctions->setSize(nq);
			}
		}
		else{
			IO::chDir(saveWorkingDirectory);
			throw Exception("InverseDynamicsTool: no coordinate file found.");

		}

		bool externalLoads = createExternalLoads(_externalLoadsFileName, *_model, _coordinateValues);
		// Initialize the the model's underlying computational system and get its default state.
		SimTK::State& s = _model->initSystem();

		// Exclude user-specified forces from the dynamics for this analysis
		disableModelForces(*_model, s, _excludedForces);

		double first_time = _coordinateValues->getFirstTime();
		double last_time = _coordinateValues->getLastTime();

		// Determine the starting and final time for the Tool by comparing to what data is available
		double start_time = ( first_time > _timeRange[0]) ? first_time : _timeRange[0];
		double final_time = ( last_time < _timeRange[1]) ? last_time : _timeRange[1];
		int start_index = _coordinateValues->findIndex(start_time);
		int final_index = _coordinateValues->findIndex(final_time);

		// create the solver given the input data
		InverseDynamicsSolver ivdSolver(*_model);

		const clock_t start = clock();

		int nt = final_index-start_index+1;
		
		Array_<double> times(nt, 0.0);
		for(int i=0; i<nt; i++){
			times[i]=_coordinateValues->getStateVector(start_index+i)->getTime();
		}

		// Preallocate results
		Array_<Vector> genForceTraj(nt, Vector(nq, 0.0));

		// solve for the trajectory of generlized forces that correspond to the coordinate
		// trajectories provided
		ivdSolver.solve(s, *coordFunctions, times, genForceTraj);


		success = true;
//.........这里部分代码省略.........

/**
 * This method creates a SimmMotionTrial instance with the markerFile and
 * timeRange parameters. It also creates a Storage instance with the
 * coordinateFile parameter. Then it updates the coordinates and markers in
 * the model, if specified. Then it does IK to fit the model to the static
 * pose. Then it uses the current model pose to relocate all non-fixed markers
 * according to their locations in the SimmMotionTrial. Then it writes the
 * output files selected by the user.
 *
 * @param aModel the model to use for the marker placing process.
 * @return Whether the marker placing process was successful or not.
 */
bool MarkerPlacer::processModel(Model* aModel,
        const string& aPathToSubject) const {

    if(!getApply()) return false;

    cout << endl << "Step 3: Placing markers on model" << endl;

    if (_timeRange.getSize()<2) 
        throw Exception("MarkerPlacer::processModel, time_range is unspecified.");

    /* Load the static pose marker file, and average all the
    * frames in the user-specified time range.
    */
    TimeSeriesTableVec3 staticPoseTable{aPathToSubject + _markerFileName};
    const auto& timeCol = staticPoseTable.getIndependentColumn();

    // Users often set a time range that purposely exceeds the range of
    // their data with the mindset that all their data will be used.
    // To allow for that, we have to narrow the provided range to data
    // range, since the TimeSeriesTable will correctly throw that the 
    // desired time exceeds the data range.
    if (_timeRange[0] < timeCol.front())
        _timeRange[0] = timeCol.front();
    if (_timeRange[1] > timeCol.back())
        _timeRange[1] = timeCol.back();

    const auto avgRow = staticPoseTable.averageRow(_timeRange[0],
                                                   _timeRange[1]);
    for(size_t r = staticPoseTable.getNumRows(); r-- > 0; )
        staticPoseTable.removeRowAtIndex(r);
    staticPoseTable.appendRow(_timeRange[0], avgRow);
    
    OPENSIM_THROW_IF(!staticPoseTable.hasTableMetaDataKey("Units"),
                     Exception,
                     "MarkerPlacer::processModel -- Marker file does not have "
                     "'Units'.");
    Units
    staticPoseUnits{staticPoseTable.getTableMetaData<std::string>("Units")};
    double scaleFactor = staticPoseUnits.convertTo(aModel->getLengthUnits());
    OPENSIM_THROW_IF(SimTK::isNaN(scaleFactor),
                     Exception,
                     "Model has unspecified units.");
    if(std::fabs(scaleFactor - 1) >= SimTK::Eps) {
        for(unsigned r = 0; r < staticPoseTable.getNumRows(); ++r)
            staticPoseTable.updRowAtIndex(r) *= scaleFactor;

        staticPoseUnits = aModel->getLengthUnits();
        staticPoseTable.removeTableMetaDataKey("Units");
        staticPoseTable.addTableMetaData("Units",
                                         staticPoseUnits.getAbbreviation());
    }
    
    MarkerData* staticPose = new MarkerData(aPathToSubject + _markerFileName);
    staticPose->averageFrames(_maxMarkerMovement, _timeRange[0], _timeRange[1]);
    staticPose->convertToUnits(aModel->getLengthUnits());

    /* Delete any markers from the model that are not in the static
     * pose marker file.
     */
    aModel->deleteUnusedMarkers(staticPose->getMarkerNames());

    // Construct the system and get the working state when done changing the model
    SimTK::State& s = aModel->initSystem();
    s.updTime() = _timeRange[0];
    
    // Create references and WeightSets needed to initialize InverseKinemaicsSolver
    Set<MarkerWeight> markerWeightSet;
    _ikTaskSet.createMarkerWeightSet(markerWeightSet); // order in tasks file
    // MarkersReference takes ownership of marker data (staticPose)
    MarkersReference markersReference(staticPoseTable, &markerWeightSet);
    SimTK::Array_<CoordinateReference> coordinateReferences;

    // Load the coordinate data
    // create CoordinateReferences for Coordinate Tasks
    FunctionSet *coordFunctions = NULL;
    // bool haveCoordinateFile = false;
    if(_coordinateFileName != "" && _coordinateFileName != "Unassigned"){
        Storage coordinateValues(aPathToSubject + _coordinateFileName);
        aModel->getSimbodyEngine().convertDegreesToRadians(coordinateValues);
        // haveCoordinateFile = true;
        coordFunctions = new GCVSplineSet(5,&coordinateValues);
    }
    
    int index = 0;
    for(int i=0; i< _ikTaskSet.getSize(); i++){
        IKCoordinateTask *coordTask = dynamic_cast<IKCoordinateTask *>(&_ikTaskSet[i]);
        if (coordTask && coordTask->getApply()){
            std::unique_ptr<CoordinateReference> coordRef{};
//.........这里部分代码省略.........