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OpenSim::MuscleAnalysis Class Reference

A class for recording and computting basic quantities (length, shortening velocity, tendon length, ...) for muscles during a simulation. More...

#include <MuscleAnalysis.h>

Inheritance diagram for OpenSim::MuscleAnalysis:
OpenSim::Analysis OpenSim::Object

Classes

struct  private

Public Member Functions

 MuscleAnalysis (Model *aModel=0)
 MuscleAnalysis (const std::string &aFileName)
 MuscleAnalysis (const MuscleAnalysis &aObject)
virtual ~MuscleAnalysis ()
MuscleAnalysisoperator= (const MuscleAnalysis &aMuscleAnalysis)
virtual void setModel (Model &aModel)
 set pointer to model to be analyzed.
void setStorageCapacityIncrements (int aIncrement)
StoragegetPennationAngleStorage () const
StoragegetMuscleTendonLengthStorage () const
StoragegetFiberLengthStorage () const
StoragegetNormalizedFiberLengthStorage () const
StoragegetTendonLengthStorage () const
StoragegetFiberVelocityStorage () const
StoragegetNormalizedFiberVelocityStorage () const
StoragegetPennationAngularVelocityStorage () const
StoragegetForceStorage () const
StoragegetFiberForceStorage () const
StoragegetActiveFiberForceStorage () const
StoragegetPassiveFiberForceStorage () const
StoragegetActiveFiberForceAlongTendonStorage () const
StoragegetPassiveFiberForceAlongTendonStorage () const
StoragegetFiberActivePowerStorage () const
StoragegetFiberPassivePowerStorage () const
StoragegetTendonPowerStorage () const
StoragegetMusclePowerStorage () const
void setMuscles (Array< std::string > &aMuscles)
void setCoordinates (Array< std::string > &aCoordinates)
void setComputeMoments (bool aTrueFalse)
bool getComputeMoments () const
const ArrayPtrs
< StorageCoordinatePair > & 
getMomentArmStorageArray () const
virtual int begin (SimTK::State &s)
virtual int step (const SimTK::State &s, int setNumber)
virtual int end (SimTK::State &s)
virtual int printResults (const std::string &aBaseName, const std::string &aDir="", double aDT=-1.0, const std::string &aExtension=".sto")
 Print the results of the analysis.
void allocateStorageObjects ()
 Intended for use only by GUI that holds one MuscleAnalysis and keeps changing attributes to generate various plots For all other use cases, the code handles the allocation/deallocation of resources internally.
- Public Member Functions inherited from OpenSim::Analysis
 Analysis (Model *aModel=0)
 Default constructor.
 Analysis (const std::string &aFileName, bool aUpdateFromXMLNode=true)
 Construct an object from file.
 Analysis (const Analysis &aAnalysis)
 Copy constructor.
virtual ~Analysis ()
Analysisoperator= (const Analysis &aAnalysis)
 Assignment operator.
virtual void setStatesStore (const Storage &aStatesStore)
 set states storage for analysis.
void setOn (bool aTrueFalse)
bool getOn () const
void setStartTime (double aStartTime)
double getStartTime () const
void setEndTime (double aEndTime)
double getEndTime () const
void setInDegrees (bool aTrueFalse)
 Set whether or not to write the output of angles in degrees.
bool getInDegrees () const
virtual bool proceed (int aStep=0)
void setStepInterval (int aStepInterval)
int getStepInterval () const
void setColumnLabels (const Array< std::string > &aLabels)
 Set the column labels for this analysis.
const Array< std::string > & getColumnLabels () const
void setStorageInterval (int aInterval)
int getStorageInterval () const
virtual ArrayPtrs< Storage > & getStorageList ()
void setPrintResultFiles (bool aToWrite)
bool getPrintResultFiles () const
- Public Member Functions inherited from OpenSim::Object
virtual ~Object ()
 Virtual destructor for cleanup.
virtual Objectclone () const =0
 Create a new heap-allocated copy of the concrete object to which this Object refers.
virtual const std::string & getConcreteClassName () const =0
 Returns the class name of the concrete Object-derived class of the actual object referenced by this Object, as a string.
virtual const VisibleObjectgetDisplayer () const
 Methods to support making the object displayable in the GUI or Visualizer Implemented only in few objects.
virtual VisibleObjectupdDisplayer ()
 get Non const pointer to VisibleObject
bool isEqualTo (const Object &aObject) const
 Equality operator wrapper for use from languages not supporting operator overloading.
Objectoperator= (const Object &aObject)
 Copy assignment copies he base class fields, including the properties.
virtual bool operator== (const Object &aObject) const
 Determine if two objects are equal.
virtual bool operator< (const Object &aObject) const
 Provide an ordering for objects so they can be put in sorted containers.
void setName (const std::string &name)
 Set the name of the Object.
const std::string & getName () const
 Get the name of this Object.
void setDescription (const std::string &description)
 Set description, a one-liner summary.
const std::string & getDescription () const
 Get description, a one-liner summary.
const std::string & getAuthors () const
 Get Authors of this Object.
void setAuthors (const std::string &authors)
 Set Authors of this object, call this method in your constructor if needed.
const std::string & getReferences () const
 Get references or publications to cite if using this object.
void setReferences (const std::string &references)
 Set references or publications to cite if using this object.
int getNumProperties () const
 Determine how many properties are stored with this Object.
const AbstractPropertygetPropertyByIndex (int propertyIndex) const
 Get a const reference to a property by its index number, returned as an AbstractProperty.
AbstractPropertyupdPropertyByIndex (int propertyIndex)
 Get a writable reference to a property by its index number, returned as an AbstractProperty.
bool hasProperty (const std::string &name) const
 Return true if this Object has a property of any type with the given name, which must not be empty.
const AbstractPropertygetPropertyByName (const std::string &name) const
 Get a const reference to a property by its name, returned as an AbstractProperty.
AbstractPropertyupdPropertyByName (const std::string &name)
 Get a writable reference to a property by its name, returned as an AbstractProperty.
template<class T >
bool hasProperty () const
 Return true if this Object contains an unnamed, one-object property that contains objects of the given template type T.
template<class T >
const Property< T > & getProperty (const PropertyIndex &index) const
 Get property of known type Property<T> as a const reference; the property must be present and have the right type.
template<class T >
Property< T > & updProperty (const PropertyIndex &index)
 Get property of known type Property<T> as a writable reference; the property must be present and have the right type.
void setObjectIsUpToDateWithProperties ()
 When an object is initialized using the current values of its properties, it can set a flag indicating that it is up to date.
bool isObjectUpToDateWithProperties () const
 Returns true if no property's value has changed since the last time setObjectIsUpToDateWithProperties() was called.
void readObjectFromXMLNodeOrFile (SimTK::Xml::Element &objectElement, int versionNumber)
 We're given an XML element from which we are to populate this Object.
virtual void updateFromXMLNode (SimTK::Xml::Element &objectElement, int versionNumber)
 Use this method to deserialize an object from a SimTK::Xml::Element.
virtual void updateXMLNode (SimTK::Xml::Element &parent)
 Serialize this object into the XML node that represents it.
bool getInlined () const
 Inlined means an in-memory Object that is not associated with an XMLDocument.
void setInlined (bool aInlined, const std::string &aFileName="")
 Mark this as inlined or not and optionally provide a file name to associate with the new XMLDocument for the non-inline case.
std::string getDocumentFileName () const
 If there is a document associated with this object then return the file name maintained by the document.
void setAllPropertiesUseDefault (bool aUseDefault)
bool print (const std::string &fileName)
 Write this Object into an XML file of the given name; conventionally the suffix to use is ".osim".
std::string dump (bool dumpName=false)
 dump the XML representation of this Object into an std::string and return it.
void clearObjectIsUpToDateWithProperties ()
 For testing or debugging purposes, manually clear the "object is up to date with respect to properties" flag.
virtual bool isA (const char *type) const
 The default implementation returns true only if the supplied string is "Object"; each Object-derived class overrides this to match its own class name.
const std::string & toString () const
 Wrapper to be used on Java side to display objects in tree; this returns just the object's name.
PropertySetgetPropertySet ()
 OBSOLETE: Get a reference to the PropertySet maintained by the Object.
const PropertySetgetPropertySet () const

Public Attributes

PropertyStrArray _coordinateListProp
 List of generalized coordinates for which to compute moment arms.
PropertyBool _computeMomentsProp
 Compute moments and moment arms.
Storage_pennationAngleStore
 Pennation angle storage.
Storage_lengthStore
 Muscle-tendon length storage.
Storage_fiberLengthStore
 Fiber length storage.
Storage_normalizedFiberLengthStore
 Normalized fiber length storage.
Storage_tendonLengthStore
 Tendon length storage.
Storage_fiberVelocityStore
 Lengthening velocity of the muscle fibers.
Storage_normFiberVelocityStore
 Normalized lengthening velocity of the muscle fibers.
Storage_pennationAngularVelocityStore
 Angular velocity of the muscle fibers.
Storage_forceStore
 Force applied by the muscle.
Storage_fiberForceStore
 Force in the muscle fibers.
Storage_activeFiberForceStore
 Active force in the muscle fibers.
Storage_passiveFiberForceStore
 Passive force in the muscle fibers.
Storage_activeFiberForceAlongTendonStore
 Active force in the muscle fibers along tendon.
Storage_passiveFiberForceAlongTendonStore
 Passive force in the muscle fibers along tendon.
Storage_fiberActivePowerStore
 Fiber power.
Storage_fiberPassivePowerStore
Storage_tendonPowerStore
 Tendon power.
Storage_musclePowerStore
 Muscle actuator power.
Array< std::string > _muscleList
 Work array for holding the list of muscles.
Array< std::string > _coordinateList
 Work array for holding the list of coordinates.
bool _computeMoments
ArrayPtrs< StorageCoordinatePair > _momentArmStorageArray
 Array of active storage and coordinate pairs.
ArrayPtrs< Muscle_muscleArray
 Array of active muscles.
- Public Attributes inherited from OpenSim::Analysis
Model_model
const Storage_statesStore

Protected Member Functions

virtual int record (const SimTK::State &s)

Additional Inherited Members

- Static Public Member Functions inherited from OpenSim::Object
static void registerType (const Object &defaultObject)
 Register an instance of a class; if the class is already registered it will be replaced.
static void renameType (const std::string &oldTypeName, const std::string &newTypeName)
 Support versioning by associating the current Object type with an old name.
static const ObjectgetDefaultInstanceOfType (const std::string &concreteClassName)
 Return a pointer to the default instance of the registered (concrete) Object whose class name is given, or NULL if the type is not registered.
template<class T >
static bool isObjectTypeDerivedFrom (const std::string &concreteClassName)
 Return true if the given concrete object type represents a subclass of the template object type T, and thus could be referenced with a T*.
static ObjectnewInstanceOfType (const std::string &concreteClassName)
 Create a new instance of the concrete Object type whose class name is given as concreteClassName.
static void getRegisteredTypenames (Array< std::string > &typeNames)
 Retrieve all the typenames registered so far.
template<class T >
static void getRegisteredObjectsOfGivenType (ArrayPtrs< T > &rArray)
 Return an array of pointers to the default instances of all registered (concrete) Object types that derive from a given Object-derived type that does not have to be concrete.
static void PrintPropertyInfo (std::ostream &os, const std::string &classNameDotPropertyName)
 Dump formatted property information to a given output stream, useful for creating a "help" facility for registered objects.
static void PrintPropertyInfo (std::ostream &os, const std::string &className, const std::string &propertyName)
 Same as the other signature but the class name and property name are provided as two separate strings.
static ObjectmakeObjectFromFile (const std::string &fileName)
 Create an OpenSim object whose type is based on the tag at the root node of the XML file passed in.
static const std::string & getClassName ()
 Return the name of this class as a string; i.e., "Object".
static void setSerializeAllDefaults (bool shouldSerializeDefaults)
 Static function to control whether all registered objects and their properties are written to the defaults section of output files rather than only those values for which the default was explicitly overwritten when read in from an input file or set programmatically.
static bool getSerializeAllDefaults ()
 Report the value of the "serialize all defaults" flag.
static bool isKindOf (const char *type)
 Returns true if the passed-in string is "Object"; each Object-derived class defines a method of this name for its own class name.
static void setDebugLevel (int newLevel)
 Set the debug level to get verbose output.
static int getDebugLevel ()
 Get current setting of debug level.
static ObjectSafeCopy (const Object *aObject)
 Use the clone() method to duplicate the given object unless the pointer is null in which case null is returned.
static void RegisterType (const Object &defaultObject)
 OBSOLETE alternate name for registerType().
static void RenameType (const std::string &oldName, const std::string &newName)
 OBSOLETE alternate name for renameType().
- Static Public Attributes inherited from OpenSim::Object
static const std::string DEFAULT_NAME
 Name used for default objects when they are serialized.
- Protected Attributes inherited from OpenSim::Analysis
PropertyInt _stepIntervalProp
 Step interval.
int & _stepInterval
PropertyBool _onProp
 On, off flag.
bool & _on
PropertyDbl _startTimeProp
 Start time for the callback in normalized time.
double & _startTime
PropertyDbl _endTimeProp
 End time for the callback in normalized time.
double & _endTime
ArrayPtrs< Storage_storageList
bool _printResultFiles

Detailed Description

A class for recording and computting basic quantities (length, shortening velocity, tendon length, ...) for muscles during a simulation.

Author
Ajay Seth, Matthew Millard, Katherine Holzbaur, Frank C. Anderson
Version
1.0

Constructor & Destructor Documentation

OpenSim::MuscleAnalysis::MuscleAnalysis ( Model aModel = 0)
OpenSim::MuscleAnalysis::MuscleAnalysis ( const std::string &  aFileName)
OpenSim::MuscleAnalysis::MuscleAnalysis ( const MuscleAnalysis aObject)
virtual OpenSim::MuscleAnalysis::~MuscleAnalysis ( )
virtual

Member Function Documentation

void OpenSim::MuscleAnalysis::allocateStorageObjects ( )

Intended for use only by GUI that holds one MuscleAnalysis and keeps changing attributes to generate various plots For all other use cases, the code handles the allocation/deallocation of resources internally.

virtual int OpenSim::MuscleAnalysis::begin ( SimTK::State &  s)
virtual

Reimplemented from OpenSim::Analysis.

virtual int OpenSim::MuscleAnalysis::end ( SimTK::State &  s)
virtual

Reimplemented from OpenSim::Analysis.

Storage* OpenSim::MuscleAnalysis::getActiveFiberForceAlongTendonStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getActiveFiberForceStorage ( ) const
inline
bool OpenSim::MuscleAnalysis::getComputeMoments ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getFiberActivePowerStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getFiberForceStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getFiberLengthStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getFiberPassivePowerStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getFiberVelocityStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getForceStorage ( ) const
inline
const ArrayPtrs<StorageCoordinatePair>& OpenSim::MuscleAnalysis::getMomentArmStorageArray ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getMusclePowerStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getMuscleTendonLengthStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getNormalizedFiberLengthStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getNormalizedFiberVelocityStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getPassiveFiberForceAlongTendonStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getPassiveFiberForceStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getPennationAngleStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getPennationAngularVelocityStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getTendonLengthStorage ( ) const
inline
Storage* OpenSim::MuscleAnalysis::getTendonPowerStorage ( ) const
inline
MuscleAnalysis& OpenSim::MuscleAnalysis::operator= ( const MuscleAnalysis aMuscleAnalysis)
virtual int OpenSim::MuscleAnalysis::printResults ( const std::string &  aBaseName,
const std::string &  aDir = "",
double  aDT = -1.0,
const std::string &  aExtension = ".sto" 
)
virtual

Print the results of the analysis.

Parameters
aBaseNameBase name of file to which to print the data.
aDirDirectory name.
aDTTime interval between results (linear interpolation is used). If not supplied as an argument or negative, all time steps are printed without interpolation.
aExtensionFile extension if not the default ".sto".
Returns
-1 on error, 0 otherwise.

Reimplemented from OpenSim::Analysis.

virtual int OpenSim::MuscleAnalysis::record ( const SimTK::State &  s)
protectedvirtual
void OpenSim::MuscleAnalysis::setComputeMoments ( bool  aTrueFalse)
inline
void OpenSim::MuscleAnalysis::setCoordinates ( Array< std::string > &  aCoordinates)
virtual void OpenSim::MuscleAnalysis::setModel ( Model aModel)
virtual

set pointer to model to be analyzed.

Parameters
aModel

Reimplemented from OpenSim::Analysis.

void OpenSim::MuscleAnalysis::setMuscles ( Array< std::string > &  aMuscles)
void OpenSim::MuscleAnalysis::setStorageCapacityIncrements ( int  aIncrement)
virtual int OpenSim::MuscleAnalysis::step ( const SimTK::State &  s,
int  setNumber 
)
virtual

Reimplemented from OpenSim::Analysis.

Member Data Documentation

Storage* OpenSim::MuscleAnalysis::_activeFiberForceAlongTendonStore

Active force in the muscle fibers along tendon.

Storage* OpenSim::MuscleAnalysis::_activeFiberForceStore

Active force in the muscle fibers.

bool OpenSim::MuscleAnalysis::_computeMoments
PropertyBool OpenSim::MuscleAnalysis::_computeMomentsProp

Compute moments and moment arms.

Array<std::string> OpenSim::MuscleAnalysis::_coordinateList

Work array for holding the list of coordinates.

PropertyStrArray OpenSim::MuscleAnalysis::_coordinateListProp

List of generalized coordinates for which to compute moment arms.

Storage* OpenSim::MuscleAnalysis::_fiberActivePowerStore

Fiber power.

Storage* OpenSim::MuscleAnalysis::_fiberForceStore

Force in the muscle fibers.

Storage* OpenSim::MuscleAnalysis::_fiberLengthStore

Fiber length storage.

Storage* OpenSim::MuscleAnalysis::_fiberPassivePowerStore
Storage* OpenSim::MuscleAnalysis::_fiberVelocityStore

Lengthening velocity of the muscle fibers.

Storage* OpenSim::MuscleAnalysis::_forceStore

Force applied by the muscle.

Storage* OpenSim::MuscleAnalysis::_lengthStore

Muscle-tendon length storage.

ArrayPtrs<StorageCoordinatePair> OpenSim::MuscleAnalysis::_momentArmStorageArray

Array of active storage and coordinate pairs.

ArrayPtrs<Muscle> OpenSim::MuscleAnalysis::_muscleArray

Array of active muscles.

Array<std::string> OpenSim::MuscleAnalysis::_muscleList

Work array for holding the list of muscles.

This array

Storage* OpenSim::MuscleAnalysis::_musclePowerStore

Muscle actuator power.

Storage* OpenSim::MuscleAnalysis::_normalizedFiberLengthStore

Normalized fiber length storage.

Storage* OpenSim::MuscleAnalysis::_normFiberVelocityStore

Normalized lengthening velocity of the muscle fibers.

Storage* OpenSim::MuscleAnalysis::_passiveFiberForceAlongTendonStore

Passive force in the muscle fibers along tendon.

Storage* OpenSim::MuscleAnalysis::_passiveFiberForceStore

Passive force in the muscle fibers.

Storage* OpenSim::MuscleAnalysis::_pennationAngleStore

Pennation angle storage.

Storage* OpenSim::MuscleAnalysis::_pennationAngularVelocityStore

Angular velocity of the muscle fibers.

Storage* OpenSim::MuscleAnalysis::_tendonLengthStore

Tendon length storage.

Storage* OpenSim::MuscleAnalysis::_tendonPowerStore

Tendon power.


The documentation for this class was generated from the following file: