API  4.3
For MATLAB, Python, Java, and C++ users
OpenSim::MarkersReference Class Reference

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< MarkerWeightmarker_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...
 
Objectoperator= (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 AbstractPropertygetPropertyByIndex (int propertyIndex) const
 Get a const reference to a property by its index number, returned as an AbstractProperty. More...
 
AbstractPropertyupdPropertyByIndex (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 AbstractPropertygetPropertyByName (const std::string &name) const
 Get a const reference to a property by its name, returned as an AbstractProperty. More...
 
AbstractPropertyupdPropertyByName (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...
 
PropertySetgetPropertySet ()
 OBSOLETE: Get a reference to the PropertySet maintained by the Object. More...
 
const PropertySetgetPropertySet () const
 

Auto-generated functions

static MarkersReferencesafeDownCast (OpenSim::Object *obj)
 For use in MATLAB and Python to access the concrete class. More...
 
static const std::string & getClassName ()
 This returns "MarkersReference". More...
 
MarkersReferenceclone () 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 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. 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 ObjectnewInstanceOfType (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 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. 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 ObjectSafeCopy (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: