Reference values to be achieved for specified Markers that will be used via optimization and/or tracking. More...

Inheritance diagram for OpenSim::MarkersReference:

OpenSim Properties, Sockets, Outputs, Inputs
Properties (single-value)
std::string	marker_file
	"Marker file(e.g. .trc) containing the time history of observations of " "marker positions." More...

Set< MarkerWeight >	marker_weights
	"Set of marker weights identified by marker name with weight being a " "positive scalar." More...

double	default_weight
	"Default weight for a marker." More...

Public Member Functions
	MarkersReference ()

	MarkersReference (const std::string &markerFileName, const Set< MarkerWeight > &markerWeightSet, Units modelUnits=Units(Units::Meters))
	Convenience load markers from a file. More...

	MarkersReference (const TimeSeriesTable_< SimTK::Vec3 > &markerData, const Set< MarkerWeight > &markerWeightSet, Units units=Units(Units::Meters))
	Form a Reference from TimeSeriesTable and corresponding marker weights. More...

virtual	~MarkersReference ()

void	initializeFromMarkersFile (const std::string &markerFile, const Set< MarkerWeight > &markerWeightSet, Units modelUnits=Units(Units::Meters))
	Initialize this MarkersReference from data in a markerFile such that it corresponds to the markers that have weights. More...

int	getNumRefs () const override
	get the number of referettes (individual signals) in this Reference. More...

SimTK::Vec2	getValidTimeRange () const override
	get the time range for which the MarkersReference values are valid, based on the loaded marker data. More...

const SimTK::Array_< std::string > &	getNames () const override
	get the names of the markers serving as references More...

void	getValuesAtTime (double time, SimTK::Array_< SimTK::Vec3 > &values) const override
	get the value of the MarkersReference More...

void	getWeights (const SimTK::State &s, SimTK::Array_< double > &weights) const override
	get the speed value of the MarkersReference More...

const TimeSeriesTable_< SimTK::Vec3 > &	getMarkerTable () const
	get the marker trajectories in a table More...

double	getSamplingFrequency () const

const Set< MarkerWeight > &	getMarkerWeightSet () const

Set< MarkerWeight > &	updMarkerWeightSet ()

void	setMarkerWeightSet (const Set< MarkerWeight > &markerWeights)
	Set the marker weights from a set of MarkerWeights. More...

void	setDefaultWeight (double weight)

size_t	getNumFrames () const

Property-related functions
const std::string &	get_marker_file () const
	Get the value of the marker_file property. More...

std::string &	upd_marker_file ()
	Get a writable reference to the marker_file property. More...

void	set_marker_file (const std::string &value)
	Set the value of the marker_file property. More...

const Set< MarkerWeight > &	get_marker_weights () const
	Get the value of the marker_weights property. More...

Set< MarkerWeight > &	upd_marker_weights ()
	Get a writable reference to the marker_weights property. More...

void	set_marker_weights (const Set< MarkerWeight > &value)
	Set the value of the marker_weights property. More...

const double &	get_default_weight () const
	Get the value of the default_weight property. More...

double &	upd_default_weight ()
	Get a writable reference to the default_weight property. More...

void	set_default_weight (const double &value)
	Set the value of the default_weight property. More...

Public Member Functions inherited from OpenSim::Reference_< SimTK::Vec3 >
virtual	~Reference_ ()

	Reference_ ()

	Reference_ (std::string name)

virtual SimTK::Array_< double >	getWeights (const SimTK::State &s) const

virtual bool	hasNext () const
	Indicate whether this Reference can provide discretized data or not. More...

virtual SimTK::Array_< SimTK::Vec3 >	getValues (double time) const

Public Member Functions inherited from OpenSim::Object
virtual	~Object ()
	Virtual destructor for cleanup. More...

bool	isEqualTo (const Object &aObject) const
	Equality operator wrapper for use from languages not supporting operator overloading. More...

Object &	operator= (const Object &aObject)
	Copy assignment copies he base class fields, including the properties. More...

virtual bool	operator== (const Object &aObject) const
	Determine if two objects are equal. More...

virtual bool	operator< (const Object &aObject) const
	Provide an ordering for objects so they can be put in sorted containers. More...

void	setName (const std::string &name)
	Set the name of the Object. More...

const std::string &	getName () const
	Get the name of this Object. More...

void	setDescription (const std::string &description)
	Set description, a one-liner summary. More...

const std::string &	getDescription () const
	Get description, a one-liner summary. More...

const std::string &	getAuthors () const
	Get Authors of this Object. More...

void	setAuthors (const std::string &authors)
	Set Authors of this object. More...

const std::string &	getReferences () const
	Get references or publications to cite if using this object. More...

void	setReferences (const std::string &references)
	Set references or publications to cite if using this object. More...

int	getNumProperties () const
	Determine how many properties are stored with this Object. More...

const AbstractProperty &	getPropertyByIndex (int propertyIndex) const
	Get a const reference to a property by its index number, returned as an AbstractProperty. More...

AbstractProperty &	updPropertyByIndex (int propertyIndex)
	Get a writable reference to a property by its index number, returned as an AbstractProperty. More...

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. More...

const AbstractProperty &	getPropertyByName (const std::string &name) const
	Get a const reference to a property by its name, returned as an AbstractProperty. More...

AbstractProperty &	updPropertyByName (const std::string &name)
	Get a writable reference to a property by its name, returned as an AbstractProperty. More...

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. More...

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. More...

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. More...

bool	isObjectUpToDateWithProperties () const
	Returns `true` if no property's value has changed since the last time setObjectIsUpToDateWithProperties() was called. More...

void	readObjectFromXMLNodeOrFile (SimTK::Xml::Element &objectElement, int versionNumber)
	We're given an XML element from which we are to populate this Object. More...

virtual void	updateFromXMLNode (SimTK::Xml::Element &objectElement, int versionNumber)
	Use this method to deserialize an object from a SimTK::Xml::Element. More...

void	updateXMLNode (SimTK::Xml::Element &parent, const AbstractProperty *prop=nullptr) const
	Serialize this object into the XML node that represents it. More...

bool	getInlined () const
	Inlined means an in-memory Object that is not associated with an XMLDocument. More...

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. More...

std::string	getDocumentFileName () const
	If there is a document associated with this object then return the file name maintained by the document. More...

int	getDocumentFileVersion () const
	If there is a document associated with this object then return its version number. More...

void	setAllPropertiesUseDefault (bool aUseDefault)

bool	print (const std::string &fileName) const
	Write this Object into an XML file of the given name; conventionally the suffix to use is ".osim". More...

std::string	dump () const
	dump the XML representation of this Object into an std::string and return it. More...

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. More...

const std::string &	toString () const
	Wrapper to be used on Java side to display objects in tree; this returns just the object's name. More...

PropertySet &	getPropertySet ()
	OBSOLETE: Get a reference to the PropertySet maintained by the Object. More...

const PropertySet &	getPropertySet () const

Auto-generated functions
static MarkersReference *	safeDownCast (OpenSim::Object *obj)
	For use in MATLAB and Python to access the concrete class. More...

static const std::string &	getClassName ()
	This returns "MarkersReference". More...

MarkersReference *	clone () const override
	Create a new heap-allocated copy of the concrete object to which this Object refers. More...

const std::string &	getConcreteClassName () const override
	Returns the class name of the concrete Object-derived class of the actual object referenced by this Object, as a string. More...

Additional Inherited Members
Static Public Member Functions inherited from OpenSim::Reference_< SimTK::Vec3 >
static Reference_ *	safeDownCast (OpenSim::Object *obj)
	For use in MATLAB and Python to access the concrete class. More...

static const std::string &	getClassName ()
	This returns "Reference__<T>_". More...

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. More...

static void	renameType (const std::string &oldTypeName, const std::string &newTypeName)
	Support versioning by associating the current Object type with an old name. More...

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. More...

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*. More...

static Object *	newInstanceOfType (const std::string &concreteClassName)
	Create a new instance of the concrete Object type whose class name is given as concreteClassName. More...

static void	getRegisteredTypenames (Array< std::string > &typeNames)
	Retrieve all the typenames registered so far. More...

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. More...

static bool	PrintPropertyInfo (std::ostream &os, const std::string &classNameDotPropertyName, bool printFlagInfo=true)
	Dump formatted property information to a given output stream, useful for creating a "help" facility for registered objects. More...

static bool	PrintPropertyInfo (std::ostream &os, const std::string &className, const std::string &propertyName, bool printFlagInfo=true)
	Same as the other signature but the class name and property name are provided as two separate strings. More...

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. More...

static const std::string &	getClassName ()
	Return the name of this class as a string; i.e., "Object". More...

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. More...

static bool	getSerializeAllDefaults ()
	Report the value of the "serialize all defaults" flag. More...

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. More...

static void	setDebugLevel (int newLevel)
	Set the amount of logging output. More...

static int	getDebugLevel ()
	Get the current setting of debug level. More...

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. More...

static void	RegisterType (const Object &defaultObject)
	OBSOLETE alternate name for registerType(). More...

static void	RenameType (const std::string &oldName, const std::string &newName)
	OBSOLETE alternate name for renameType(). More...

Detailed Description

Reference values to be achieved for specified Markers that will be used via optimization and/or tracking.

Also contains a weighting that identifies the relative importance of achieving one marker's reference relative to another.

Author: Ajay Seth

Examples:: exampleMarkerTracking.cpp, and exampleMarkerTracking10DOF.m.

Constructor & Destructor Documentation

◆ MarkersReference() [1/3]

OpenSim::MarkersReference::MarkersReference ( )

◆ MarkersReference() [2/3]

OpenSim::MarkersReference::MarkersReference	(	const std::string &	markerFileName,
		const Set< MarkerWeight > &	markerWeightSet,
		Units	modelUnits = `Units(Units::Meters)`
	)

Convenience load markers from a file.

See below.

◆ MarkersReference() [3/3]

OpenSim::MarkersReference::MarkersReference	(	const TimeSeriesTable_< SimTK::Vec3 > &	markerData,
		const Set< MarkerWeight > &	markerWeightSet,
		Units	units = `Units(Units::Meters)`
	)

Form a Reference from TimeSeriesTable and corresponding marker weights.

The marker weights are used to initialize the weightings of the markers provided by the Reference. Marker weights are associated to markers by name. If a markerWeightSet is provided, then only those markers listed in the set are tracked, otherwise all the markerData table that correspond with model markers are tracked with the default weighting. The TimeSeriesTable should contain the key 'Units', representing units of the columns, as table metadata. In absence of 'Units' metadata, columns are assumed to be of units 'meters'.

◆ ~MarkersReference()

virtual OpenSim::MarkersReference::~MarkersReference ( )

inlinevirtual

Member Function Documentation

◆ clone()

MarkersReference* OpenSim::MarkersReference::clone ( ) const

inlineoverridevirtual

Create a new heap-allocated copy of the concrete object to which this Object refers.

It is up to the caller to delete the returned object when no longer needed. Every concrete object deriving from Object implements this pure virtual method automatically, via the declaration macro it invokes (e.g., OpenSim_DECLARE_CONCRETE_OBJECT()). Note that the concrete class overrides modify the return type to be a pointer to the concrete object; that still overrides the base class method because the return type is covariant with (that is, derives from) Object.

Implements OpenSim::Reference_< SimTK::Vec3 >.

◆ get_default_weight()

const double& OpenSim::MarkersReference::get_default_weight ( ) const

inline

Get the value of the default_weight property.

◆ get_marker_file()

const std::string& OpenSim::MarkersReference::get_marker_file ( ) const

inline

Get the value of the marker_file property.

◆ get_marker_weights()

const Set<MarkerWeight>& OpenSim::MarkersReference::get_marker_weights ( ) const

inline

Get the value of the marker_weights property.

◆ getClassName()

static const std::string& OpenSim::MarkersReference::getClassName ( )

inlinestatic

This returns "MarkersReference".

See getConcreteClassName() if you want the class name of the underlying concrete object instead.

◆ getConcreteClassName()

const std::string& OpenSim::MarkersReference::getConcreteClassName ( ) const

inlineoverridevirtual

Returns the class name of the concrete Object-derived class of the actual object referenced by this Object, as a string.

This is the string that is used as the tag for this concrete object in an XML file. Every concrete class derived from Object automatically overrides this method via the declaration macro it uses. See getClassName() to get the class name of the referencing (possibly abstract) class rather than the concrete object.

See also: getClassName()

Implements OpenSim::Reference_< SimTK::Vec3 >.

◆ getMarkerTable()

const TimeSeriesTable_<SimTK::Vec3>& OpenSim::MarkersReference::getMarkerTable ( ) const

get the marker trajectories in a table

◆ getMarkerWeightSet()

const Set<MarkerWeight>& OpenSim::MarkersReference::getMarkerWeightSet ( ) const

inline

◆ getNames()

const SimTK::Array_<std::string>& OpenSim::MarkersReference::getNames ( ) const

overridevirtual

get the names of the markers serving as references

Implements OpenSim::Reference_< SimTK::Vec3 >.

◆ getNumFrames()

size_t OpenSim::MarkersReference::getNumFrames ( ) const

◆ getNumRefs()

int OpenSim::MarkersReference::getNumRefs ( ) const

overridevirtual

get the number of referettes (individual signals) in this Reference.

All return arrays are guaranteed to be this length

Implements OpenSim::Reference_< SimTK::Vec3 >.

◆ getSamplingFrequency()

double OpenSim::MarkersReference::getSamplingFrequency ( ) const

◆ getValidTimeRange()

SimTK::Vec2 OpenSim::MarkersReference::getValidTimeRange ( ) const

overridevirtual

get the time range for which the MarkersReference values are valid, based on the loaded marker data.

Reimplemented from OpenSim::Reference_< SimTK::Vec3 >.

◆ getValuesAtTime()

void OpenSim::MarkersReference::getValuesAtTime	(	double	time,
		SimTK::Array_< SimTK::Vec3 > &	values
	)		const

overridevirtual

get the value of the MarkersReference

Implements OpenSim::Reference_< SimTK::Vec3 >.

◆ getWeights()

void OpenSim::MarkersReference::getWeights	(	const SimTK::State &	s,
		SimTK::Array_< double > &	weights
	)		const

overridevirtual

get the speed value of the MarkersReference

get the acceleration value of the MarkersReference get the weighting (importance) of meeting this MarkersReference in the same order as names

Implements OpenSim::Reference_< SimTK::Vec3 >.

◆ initializeFromMarkersFile()

void OpenSim::MarkersReference::initializeFromMarkersFile	(	const std::string &	markerFile,
		const Set< MarkerWeight > &	markerWeightSet,
		Units	modelUnits = `Units(Units::Meters)`
	)

Initialize this MarkersReference from data in a markerFile such that it corresponds to the markers that have weights.

If weights is empty Set, all corresponding markers are tracked at default reference weight. See setDefaultWeight()

◆ safeDownCast()

static MarkersReference* OpenSim::MarkersReference::safeDownCast ( OpenSim::Object * obj )

inlinestatic

For use in MATLAB and Python to access the concrete class.

Example: cObj = MarkersReference.safeDownCast(obj). This is equivalent to dynamic_cast<MarkersReference*>(obj) in C++.

◆ set_default_weight()

void OpenSim::MarkersReference::set_default_weight ( const double & value )

inline

Set the value of the default_weight property.

◆ set_marker_file()

void OpenSim::MarkersReference::set_marker_file ( const std::string & value )

inline

Set the value of the marker_file property.

◆ set_marker_weights()

void OpenSim::MarkersReference::set_marker_weights ( const Set< MarkerWeight > & value )

inline

Set the value of the marker_weights property.

◆ setDefaultWeight()

void OpenSim::MarkersReference::setDefaultWeight ( double weight )

◆ setMarkerWeightSet()

void OpenSim::MarkersReference::setMarkerWeightSet ( const Set< MarkerWeight > & markerWeights )

Set the marker weights from a set of MarkerWeights.

As of OpenSim 4.0 the input set is const and a copy of the Set is used internally. Therefore, subsequent changes to the Set of MarkerWeights will have no effect on the marker weights associated with this Reference.

◆ upd_default_weight()

double& OpenSim::MarkersReference::upd_default_weight ( )

inline

Get a writable reference to the default_weight property.

◆ upd_marker_file()

std::string& OpenSim::MarkersReference::upd_marker_file ( )

inline

Get a writable reference to the marker_file property.

◆ upd_marker_weights()

Set<MarkerWeight>& OpenSim::MarkersReference::upd_marker_weights ( )

inline

Get a writable reference to the marker_weights property.

◆ updMarkerWeightSet()

Set<MarkerWeight>& OpenSim::MarkersReference::updMarkerWeightSet ( )

inline

OpenSim Property, Socket, Output, Input Documentation

◆ default_weight

double OpenSim::MarkersReference::default_weight

"Default weight for a marker."

This property appears in XML files under the tag <default_weight>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.

See also: get_default_weight(), upd_default_weight(), set_default_weight()

◆ marker_file

std::string OpenSim::MarkersReference::marker_file

"Marker file(e.g. .trc) containing the time history of observations of " "marker positions."

This property appears in XML files under the tag <marker_file>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.

See also: get_marker_file(), upd_marker_file(), set_marker_file()

◆ marker_weights

Set<MarkerWeight> OpenSim::MarkersReference::marker_weights

"Set of marker weights identified by marker name with weight being a " "positive scalar."

This property appears in XML files under the tag <marker_weights>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.

See also: get_marker_weights(), upd_marker_weights(), set_marker_weights()

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

OpenSim/Simulation/MarkersReference.h

OpenSim Properties, Sockets, Outputs, Inputs

Public Member Functions

Auto-generated functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MarkersReference() [1/3]

◆ MarkersReference() [2/3]

◆ MarkersReference() [3/3]

◆ ~MarkersReference()

Member Function Documentation

◆ clone()

◆ get_default_weight()

◆ get_marker_file()

◆ get_marker_weights()

◆ getClassName()

◆ getConcreteClassName()

◆ getMarkerTable()

◆ getMarkerWeightSet()

◆ getNames()

◆ getNumFrames()

◆ getNumRefs()

◆ getSamplingFrequency()

◆ getValidTimeRange()

◆ getValuesAtTime()

◆ getWeights()

◆ initializeFromMarkersFile()

◆ safeDownCast()

◆ set_default_weight()

◆ set_marker_file()

◆ set_marker_weights()

◆ setDefaultWeight()

◆ setMarkerWeightSet()

◆ upd_default_weight()

◆ upd_marker_file()

◆ upd_marker_weights()

◆ updMarkerWeightSet()

OpenSim Property, Socket, Output, Input Documentation

◆ default_weight

◆ marker_file

◆ marker_weights