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OpenSim::MuscleFirstOrderActivationDynamicModel Class Reference

This is a muscle modeling utility class that computes the time derivative of activation using a first-order dynamic model. More...

#include <MuscleFirstOrderActivationDynamicModel.h>

Inheritance diagram for OpenSim::MuscleFirstOrderActivationDynamicModel:
OpenSim::Object

Public Member Functions

 MuscleFirstOrderActivationDynamicModel ()
 The default constructor creates an activation dynamic model with the default property values and assigns it a default name.
 MuscleFirstOrderActivationDynamicModel (double tauActivation, double tauDeactivation, double minActivation, const std::string &muscleName)
 Creates an activation dynamic model using the provided parameters.
void ensureModelUpToDate ()
double getActivationTimeConstant () const
double getDeactivationTimeConstant () const
double getMinimumActivation () const
double getMaximumActivation () const
bool setActivationTimeConstant (double activationTimeConstant)
bool setDeactivationTimeConstant (double deactivationTimeConstant)
bool setMinimumActivation (double minimumActivation)
double clampActivation (double activation) const
double calcDerivative (double activation, double excitation) const
 Calculates the time derivative of activation.
Property declarations

These are the serializable properties associated with this class.

 OpenSim_DECLARE_PROPERTY (activation_time_constant, double,"Activation time constant in seconds")
 OpenSim_DECLARE_PROPERTY (deactivation_time_constant, double,"Deactivation time constant in seconds")
 OpenSim_DECLARE_PROPERTY (minimum_activation, double,"Lower bound on activation")
- 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

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 Member Functions inherited from OpenSim::Object
 Object ()
 The default constructor is only for use by constructors of derived types.
 Object (const std::string &fileName, bool aUpdateFromXMLNode=true) SWIG_DECLARE_EXCEPTION
 Constructor from a file, to be called from other constructors that take a file as input.
 Object (const Object &source)
 Copy constructor is invoked automatically by derived classes with default copy constructors; otherwise it must be invoked explicitly.
 Object (SimTK::Xml::Element &aElement)
 Construct the base class portion of an Object from a given Xml element that describes this Object.
template<class T >
PropertyIndex addProperty (const std::string &name, const std::string &comment, const T &value)
 Define a new single-value property of known type T, with the given name, associated comment, and initial value.
template<class T >
PropertyIndex addOptionalProperty (const std::string &name, const std::string &comment)
 Add an optional property, meaning it can contain either no value or a single value.
template<class T >
PropertyIndex addOptionalProperty (const std::string &name, const std::string &comment, const T &value)
 Add an optional property, meaning it can contain either no value or a single value.
template<class T >
PropertyIndex addListProperty (const std::string &name, const std::string &comment, int minSize, int maxSize)
 Define a new list-valued property of known type T, with the given name, associated comment, minimum (==0) and maximum (>0) allowable list lengths, and a zero-length initial value.
template<class T , template< class > class Container>
PropertyIndex addListProperty (const std::string &name, const std::string &comment, int minSize, int maxSize, const Container< T > &valueList)
 Define a new list-valued property as above, but assigning an initial value via some templatized container class that supports size() and indexing.
PropertyIndex getPropertyIndex (const std::string &name) const
 Look up a property by name and return its PropertyIndex if it is found.
template<class T >
PropertyIndex getPropertyIndex () const
 Look up an unnamed property by the type of object it contains, and return its PropertyIndex if it is found.
void updateFromXMLDocument ()
 Use this method only if you're deserializing from a file and the object is at the top level; that is, primarily in constructors that take a file name as input.
void setDocument (XMLDocument *doc)
 Unconditionally set the XMLDocument associated with this object.
const XMLDocumentgetDocument () const
 Get a const pointer to the document (if any) associated with this object.
XMLDocumentupdDocument ()
 Get a writable pointer to the document (if any) associated with this object.
- Protected Attributes inherited from OpenSim::Object
PropertySet _propertySet
 OBSOLETE: Property_Deprecated set for serializable member variables of this and derived classes.

Detailed Description

This is a muscle modeling utility class that computes the time derivative of activation using a first-order dynamic model.

This activation model is a modification of those used by Thelen (2003) and Winters (1995). The time derivative of activation ( $da/dt$) is calculated as follows:

\[ \frac{da}{dt} = \frac{u-a}{\tau(u,a)} \]

where $u$ is excitation, $a$ is activation, and $\tau(u,a)$ is a variable time constant:

\[ \tau(u,a) = t_{\rm{act}} (0.5 + 1.5a) \quad {\rm{if}}\ u > a \]

\[ \tau(u,a) = t_{\rm{deact}} / (0.5 + 1.5a) \quad {\rm{otherwise}} \]

Since equilibrium muscle models typically have a numerical singularity in their state equations when activation is zero, we apply a lower activation bound ( $a_{\rm{min}}$) to both activation and excitation.

Parameters
tauActivationActivation time constant. A typical value is 0.010 s (10 ms).
tauDeactivationDeactivation time constant. A typical value is 0.040 s (40 ms).
minActivationThe minimum permissible activation. To avoid a numerical singularity at a = 0, this value is typically set to between 0.01 and 0.1 for use with an equilibrium muscle model.
muscleNameThe name of the muscle to which this activation dynamic model belongs. This string is used for reporting meaningful error messages.

Conditions

tauActivation > 0
tauDeactivation > 0
0 <= minActivation < 1

Default Parameter Values

tauActivation ...... 0.010
tauDeactivation .... 0.040
minActivation ...... 0.01

Note that this object should be updated through the set methods provided. These set methods will take care of rebuilding the object correctly. If you modify the properties directly, the object will not be rebuilt, and upon calling any function, an exception will be thrown because the object is out-of-date with its properties.

References

  • Thelen, D.G. (2003) Adjustment of muscle mechanics model parameters to simulate dynamic contractions in older adults. ASME Journal of Biomechanical Engineering 125(1):70–77.
  • Winters, J.M. (1995) An improved muscle-reflex actuator for use in large-scale neuromusculoskeletal models. Annals of Biomedical Engineering 23(4):359–374.
Author
Matt Millard

Constructor & Destructor Documentation

OpenSim::MuscleFirstOrderActivationDynamicModel::MuscleFirstOrderActivationDynamicModel ( )

The default constructor creates an activation dynamic model with the default property values and assigns it a default name.

OpenSim::MuscleFirstOrderActivationDynamicModel::MuscleFirstOrderActivationDynamicModel ( double  tauActivation,
double  tauDeactivation,
double  minActivation,
const std::string &  muscleName 
)

Creates an activation dynamic model using the provided parameters.

Member Function Documentation

double OpenSim::MuscleFirstOrderActivationDynamicModel::calcDerivative ( double  activation,
double  excitation 
) const

Calculates the time derivative of activation.

double OpenSim::MuscleFirstOrderActivationDynamicModel::clampActivation ( double  activation) const
Returns
Activation clamped to the range [minActivation, 1.0].
void OpenSim::MuscleFirstOrderActivationDynamicModel::ensureModelUpToDate ( )
double OpenSim::MuscleFirstOrderActivationDynamicModel::getActivationTimeConstant ( ) const
Returns
The activation time constant (in seconds).
double OpenSim::MuscleFirstOrderActivationDynamicModel::getDeactivationTimeConstant ( ) const
Returns
The deactivation time constant (in seconds).
double OpenSim::MuscleFirstOrderActivationDynamicModel::getMaximumActivation ( ) const
Returns
The upper bound on activation.
double OpenSim::MuscleFirstOrderActivationDynamicModel::getMinimumActivation ( ) const
Returns
The lower bound on activation.
OpenSim::MuscleFirstOrderActivationDynamicModel::OpenSim_DECLARE_PROPERTY ( activation_time_constant  ,
double  ,
"Activation time constant in seconds"   
)
OpenSim::MuscleFirstOrderActivationDynamicModel::OpenSim_DECLARE_PROPERTY ( deactivation_time_constant  ,
double  ,
"Deactivation time constant in seconds"   
)
OpenSim::MuscleFirstOrderActivationDynamicModel::OpenSim_DECLARE_PROPERTY ( minimum_activation  ,
double  ,
"Lower bound on activation"   
)
bool OpenSim::MuscleFirstOrderActivationDynamicModel::setActivationTimeConstant ( double  activationTimeConstant)
Parameters
activationTimeConstantThe activation time constant (in seconds).
Returns
A boolean indicating whether the value was set.
bool OpenSim::MuscleFirstOrderActivationDynamicModel::setDeactivationTimeConstant ( double  deactivationTimeConstant)
Parameters
deactivationTimeConstantThe deactivation time constant (in seconds).
Returns
A boolean indicating whether the value was set.
bool OpenSim::MuscleFirstOrderActivationDynamicModel::setMinimumActivation ( double  minimumActivation)
Parameters
minimumActivationThe lower bound on activation.
Returns
A boolean indicating whether the value was set.

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