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:

Classes
struct	private

Public Member Functions
	MuscleAnalysis (Model *aModel=0)
	MuscleAnalysis (const std::string &aFileName)
	MuscleAnalysis (const MuscleAnalysis &aObject)
virtual	~MuscleAnalysis ()
MuscleAnalysis &	operator= (const MuscleAnalysis &aMuscleAnalysis)
virtual void	setModel (Model &aModel)
	set pointer to model to be analyzed.
void	setStorageCapacityIncrements (int aIncrement)
Storage *	getPennationAngleStorage () const
Storage *	getMuscleTendonLengthStorage () const
Storage *	getFiberLengthStorage () const
Storage *	getNormalizedFiberLengthStorage () const
Storage *	getTendonLengthStorage () const
Storage *	getFiberVelocityStorage () const
Storage *	getNormalizedFiberVelocityStorage () const
Storage *	getPennationAngularVelocityStorage () const
Storage *	getForceStorage () const
Storage *	getFiberForceStorage () const
Storage *	getActiveFiberForceStorage () const
Storage *	getPassiveFiberForceStorage () const
Storage *	getActiveFiberForceAlongTendonStorage () const
Storage *	getPassiveFiberForceAlongTendonStorage () const
Storage *	getFiberActivePowerStorage () const
Storage *	getFiberPassivePowerStorage () const
Storage *	getTendonPowerStorage () const
Storage *	getMusclePowerStorage () 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 ()
Analysis &	operator= (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 Object *	clone () 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 VisibleObject *	getDisplayer () const
	Methods to support making the object displayable in the GUI or Visualizer Implemented only in few objects.
virtual VisibleObject *	updDisplayer ()
	get Non const pointer to VisibleObject
bool	isEqualTo (const Object &aObject) const
	Equality operator wrapper for use from languages not supporting operator overloading.
Object &	operator= (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 AbstractProperty &	getPropertyByIndex (int propertyIndex) const
	Get a const reference to a property by its index number, returned as an AbstractProperty.
AbstractProperty &	updPropertyByIndex (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 AbstractProperty &	getPropertyByName (const std::string &name) const
	Get a const reference to a property by its name, returned as an AbstractProperty.
AbstractProperty &	updPropertyByName (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.
PropertySet &	getPropertySet ()
	OBSOLETE: Get a reference to the PropertySet maintained by the Object.
const PropertySet &	getPropertySet () 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 Object *	getDefaultInstanceOfType (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 Object *	newInstanceOfType (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 Object *	makeObjectFromFile (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 Object *	SafeCopy (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
Related Functions inherited from OpenSim::Object
#define	OpenSim_DECLARE_CONCRETE_OBJECT(ConcreteClass, SuperClass)
	Macro to be included as the first line of the class declaration for any non-templatized, concrete class that derives from OpenSim::Object.
#define	OpenSim_DECLARE_ABSTRACT_OBJECT(ConcreteClass, SuperClass)
	Macro to be included as the first line of the class declaration for any still-abstract class that derives from OpenSim::Object.
#define	OpenSim_DECLARE_CONCRETE_OBJECT_T(ConcreteClass, TArg, SuperClass)
	Macro to be included as the first line of the class declaration for any templatized, concrete class that derives from OpenSim::Object, like Set<T>.
#define	OpenSim_DECLARE_ABSTRACT_OBJECT_T(ConcreteClass, TArg, SuperClass)
	Macro to be included as the first line of the class declaration for any templatized, still-abstract class that derives from OpenSim::Object.

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

aBaseName	Base name of file to which to print the data.
aDir	Directory name.
aDT	Time interval between results (linear interpolation is used). If not supplied as an argument or negative, all time steps are printed without interpolation.
aExtension	File 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:

• E:/Projects/OpenSimTrunk/OpenSim/Analyses/MuscleAnalysis.h