This class serves as a serializable ActiveForceLengthCurve, for use in muscle models. More...

#include <ActiveForceLengthCurve.h>

Inheritance diagram for OpenSim::ActiveForceLengthCurve:

Public Member Functions
	ActiveForceLengthCurve ()
	Default constructor creates an curve with the default property values, and assigns it a default name
	ActiveForceLengthCurve (double minActiveNormFiberLength, double transitionNormFiberLength, double maxActiveNormFiberLength, double shallowAscendingSlope, double minValue, const std::string &muscleName)
	Constructs a C2 continuous active force length curve.
double	getMinActiveFiberLength () const
double	getTransitionFiberLength () const
double	getMaxActiveFiberLength () const
double	getShallowAscendingSlope () const
double	getMinValue () const
void	setMinActiveFiberLength (double minActiveNormFiberLength)
void	setTransitionFiberLength (double transitionNormFiberLength)
void	setMaxActiveFiberLength (double maxActiveNormFiberLength)
void	setShallowAscendingSlope (double shallowAscendingSlope)
void	setMinValue (double minValue)
double	calcValue (double normFiberLength) const
	Calculates the value of the curve evaluated at 'normFiberLength'.
double	calcDerivative (double normFiberLength, int order) const
	Calculates the derivative of the active force length multiplier w.r.t.
SimTK::Vec2	getCurveDomain () const
	This function returns a SimTK::Vec2 that contains in its 0th element the lowest value of the curve domain, and in its 1st element the highest value in the curve domain of the curve.
void	printMuscleCurveToCSVFile (const std::string &path) const
	This function will generate a csv file with a name that matches the curve name (e.g.
Property declarations
These are the serializable properties associated with this class.
	OpenSim_DECLARE_PROPERTY (min_norm_active_fiber_length, double,"normalized fiber length which the steep ascending limb starts")
	OpenSim_DECLARE_PROPERTY (transition_norm_fiber_length, double,"normalized fiber length which the steep ascending limb transitions"" to the shallow ascending limb")
	OpenSim_DECLARE_PROPERTY (max_norm_active_fiber_length, double,"normalized fiber length which the descending limb ends")
	OpenSim_DECLARE_PROPERTY (shallow_ascending_slope, double,"slope of the shallow ascending limb")
	OpenSim_DECLARE_PROPERTY (minimum_value, double,"minimum value of the active force length curve")
Public Member Functions inherited from OpenSim::ModelComponent
	ModelComponent ()
	Default constructor.
	ModelComponent (const std::string &aFileName, bool aUpdateFromXMLNode=true) SWIG_DECLARE_EXCEPTION
	Construct ModelComponent from an XML file.
	ModelComponent (SimTK::Xml::Element &aNode)
	Construct ModelComponent from a specific node in an XML document.
	ModelComponent (const ModelComponent &source)
	Construct ModelComponent with its contents copied from another ModelComponent; this is a deep copy so nothing is shared with the source after the copy.
virtual	~ModelComponent ()
	Destructor is virtual to allow concrete model component cleanup.
ModelComponent &	operator= (const ModelComponent &aModelComponent)
	Assignment operator to copy contents of an existing component.
const Model &	getModel () const
	Get a const reference to the Model this component is part of.
Model &	updModel ()
	Get a modifiable reference to the Model this component is part of.
virtual void	updateDisplayer (const SimTK::State &s)
	In case the ModelComponent has a visual representation (VisualObject), override this method to update it.
virtual int	getNumStateVariables () const
	Get the number of "Continuous" state variables maintained by the ModelComponent and its specified subcomponents.
virtual Array< std::string >	getStateVariableNames () const
	Get the names of "continuous" state variables maintained by the ModelComponent and its subcomponents.
virtual SimTK::SystemYIndex	getStateVariableSystemIndex (const std::string &stateVariableName) const
	Get the System Index of a state variable allocated by this ModelComponent.
int	getModelingOption (const SimTK::State &state, const std::string &name) const
	Get a ModelingOption flag for this ModelComponent by name.
void	setModelingOption (SimTK::State &state, const std::string &name, int flag) const
	Set the value of a ModelingOption flag for this ModelComponent.
double	getStateVariable (const SimTK::State &state, const std::string &name) const
	Get the value of a state variable allocated by this ModelComponent.
void	setStateVariable (SimTK::State &state, const std::string &name, double value) const
	Set the value of a state variable allocated by this ModelComponent by name.
double	getDiscreteVariable (const SimTK::State &state, const std::string &name) const
	Get the value of a discrete variable allocated by this ModelComponent by name.
void	setDiscreteVariable (SimTK::State &state, const std::string &name, double value) const
	Set the value of a discrete variable allocated by this ModelComponent by name.
template<typename T >
const T &	getCacheVariable (const SimTK::State &state, const std::string &name) const
	Get the value of a cache variable allocated by this ModelComponent by name.
template<typename T >
T &	updCacheVariable (const SimTK::State &state, const std::string &name) const
	Obtain a writable cache variable value allocated by this ModelComponent by name.
void	markCacheVariableValid (const SimTK::State &state, const std::string &name) const
	After updating a cache variable value allocated by this ModelComponent, you can mark its value as valid, which will not change until the realization stage falls below the minimum set at the time the cache variable was created.
void	markCacheVariableInvalid (const SimTK::State &state, const std::string &name) const
	Mark a cache variable value allocated by this ModelComponent as invalid.
bool	isCacheVariableValid (const SimTK::State &state, const std::string &name) const
	Enables the to monitor the validity of the cache variable value using the returned flag.
template<typename T >
void	setCacheVariable (const SimTK::State &state, const std::string &name, T &value) const
	Set cache variable value allocated by this ModelComponent by name.
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 \c true if any 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

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 Member Functions inherited from OpenSim::ModelComponent
virtual void	connectToModel (Model &model)
	Perform any necessary initializations required to connect the component into the Model, and check for error conditions.
virtual void	addToSystem (SimTK::MultibodySystem &system) const
	Add appropriate Simbody elements (if needed) to the System corresponding to this component and specify needed state resources.
virtual void	initStateFromProperties (SimTK::State &state) const
	Transfer property values or other state-independent initial values into this component's state variables in the passed-in state argument.
virtual void	setPropertiesFromState (const SimTK::State &state)
	Update this component's property values to match the specified State, if the component has created any state variable that is intended to correspond to a property.
virtual SimTK::Vector	computeStateVariableDerivatives (const SimTK::State &s) const
	If a model component has allocated any continuous state variables using the addStateVariable() method, then computeStateVariableDerivatives() must be implemented to provide time derivatives for those states.
virtual void	generateDecorations (bool fixed, const ModelDisplayHints &hints, const SimTK::State &state, SimTK::Array_< SimTK::DecorativeGeometry > &appendToThis) const
	Optional method for generating arbitrary display geometry that reflects this ModelComponent at the specified state.
void	includeAsSubComponent (ModelComponent *aComponent)
	Include another ModelComponent as a Subcomponent of this ModelComponent.
void	addModelingOption (const std::string &optionName, int maxFlagValue) const
	Add a modeling option (integer flag stored in the State) for use by this ModelComponent.
void	addStateVariable (const std::string &stateVariableName, SimTK::Stage invalidatesStage=SimTK::Stage::Dynamics) const
	Add a continuous system state variable belonging to this ModelComponent, and assign a name by which to refer to it.
void	addDiscreteVariable (const std::string &discreteVariableName, SimTK::Stage invalidatesStage) const
	Add a system discrete variable belonging to this ModelComponent, give it a name by which it can be referenced, and declare the lowest Stage that should be invalidated if this variable's value is changed.
template<class T >
void	addCacheVariable (const std::string &cacheVariableName, const T &variablePrototype, SimTK::Stage dependsOnStage) const
	Add a state cache entry belonging to this ModelComponent to hold calculated values that must be automatically invalidated when certain state values change.
const int	getStateIndex (const std::string &name) const
	Get the index of a ModelComponent's continuous state variable in the Subsystem for allocations.
const SimTK::DiscreteVariableIndex	getDiscreteVariableIndex (const std::string &name) const
	Get the index of a ModelComponent's discrete variable in the Subsystem for allocations.
const SimTK::CacheEntryIndex	getCacheVariableIndex (const std::string &name) const
	Get the index of a ModelComponent's cache variable in the Subsystem for allocations.
Protected Attributes inherited from OpenSim::ModelComponent
Model *	_model
	The model this component belongs to.
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

This class serves as a serializable ActiveForceLengthCurve, for use in muscle models.

Author: Matt Millard

Constructor & Destructor Documentation

OpenSim::ActiveForceLengthCurve::ActiveForceLengthCurve ( )

 Default constructor creates an curve with the default property values,

and assigns it a default name

OpenSim::ActiveForceLengthCurve::ActiveForceLengthCurve	(	double	minActiveNormFiberLength,
		double	transitionNormFiberLength,
		double	maxActiveNormFiberLength,
		double	shallowAscendingSlope,
		double	minValue,
		const std::string &	muscleName
	)

Constructs a C2 continuous active force length curve.

The active force length curve requries 5 different properties and a name in order to construct a curve:

Parameters

minActiveNormFiberLength	The normalized fiber length where the steep ascending limb of the active force length curve transitions to the minimumValue and has a first and second derivative of 0.
transitionNormFiberLength	The normalized fiber length where the steep ascending limb transitions to the shallow ascending limb.
maxActiveNormFiberLength	The normalized fiber length where the descending limb transitions to the minimum value and has a first and second derivative of 0.
shallowAscendingSlope	The slope of the shallow ascending limb.
minValue	The minimum value of the active force length curve. Note that if you are using an equilibrium model that this value must be greater than 0, as a value of 0 will cause a singularity in the muscle dynamic equations.
muscleName	The name of the muscle this curve belongs to. This name is used to create the name of this curve, which is formed simply by appending "_ActiveForceLengthCurve" to the string in muscleName. This name is used for making intelligible error messages and also for naming the XML version of this curve when it is serialized.

Conditions:

    0 < minActiveFiberLength < transitionFiberLength < maxActiveFiberLength 
    0 <= shallowAscendingSlope < 1/(1-transitionFiberLength) 
    0 <= minimumValue

Computational Costs

    ~20,500 flops

Default Parameter Values

The default parameters have been chosen so that the resulting curve closely matches the active force length curve for human sarcomeres as documented by Nigg and Herzog. The descending limb has been adjusted to match the in-vitro human fiber data reported by Gollapudi and Lin. The default shoulder value is set to a rather high value of 0.1. This relatively large value is in place to ensure that muscle model dynamic equations with an active-force-length singularity do not take an unreasonable amount of time to simulate (simulation time grows inversely as the value of the active force length curve approaches 0). Muscle model formulations that do not have this singularity (for example the Millard2012AccelerationMuscle) do, and should set the `minValue' to be 0.

    minActiveNormFiberLength ....... 0.4441
    transitionNormFiberLength ...... 0.6259
    maxActiveNormFiberLength ....... 1.8123
    shallowAscendingSlope .......... 0.8616
    minValue ....................... 0.1

Example

ActiveForceLengthCurve falCurve3(0.5, 0.75,1.5,0.75,0.01,"soleus");
double falVal  = falCurve3.calcValue(1.0);
double dfalVal = falCurve3.calcDerivative(1.0,1);

References

Gollapudi, S.K., and Lin, D.C.(2009) Experimental determination of sarcomere
force-length relationship in type-1 human skeletal muscle fibers. 
J.Biomechanics, 42, 2011-2016. 

Nigg, BM., and Herzog, W. Biomechanics of the Musculo-skeletal System. 
Wiley 1994. ISBN 0 471 94444 0

Member Function Documentation

double OpenSim::ActiveForceLengthCurve::calcDerivative	(	double	normFiberLength,
		int	order
	)		const

Calculates the derivative of the active force length multiplier w.r.t.

normalized fiber length. Note that if the curve is out of date it is rebuilt (which will cost ~20,500 flops).

Parameters

normFiberLength	: the normalized length of the muscle fiber
order	: the order of the derivative. Only values of 0,1 and 2 are acceptable.

Returns: the derivative active force length curve w.r.t. normalized fiber length

Computational Costs

    x in curve domain  : ~391 flops
    x in linear section:   ~2 flops

double OpenSim::ActiveForceLengthCurve::calcValue ( double normFiberLength ) const

Calculates the value of the curve evaluated at 'normFiberLength'.

Note that if the curve is out of date it is rebuilt (at a cost of ~20,500 flops).

Parameters

normFiberLength : the normalized length of the muscle fiber

Returns: the value of the active force length curve

Computational Costs

    x in curve domain  : ~282 flops
    x in linear section:   ~5 flops

SimTK::Vec2 OpenSim::ActiveForceLengthCurve::getCurveDomain ( ) const

This function returns a SimTK::Vec2 that contains in its 0th element the lowest value of the curve domain, and in its 1st element the highest value in the curve domain of the curve.

Outside of this domain the curve is approximated using linear extrapolation. Note that if the curve is out of date is rebuilt (which will cost ~20,500 flops).

Returns: The minimum and maximum value of the domain, x, of the curve y(x). Within this range y(x) is a curve, outside of this range the function y(x) is a C2 (continuous to the second derivative) linear extrapolation

double OpenSim::ActiveForceLengthCurve::getMaxActiveFiberLength ( ) const

Returns: the normalized fiber length where the active force length descending limb transitions to the minimum activation value and simultaneously achives a first and second derivative of 0

double OpenSim::ActiveForceLengthCurve::getMinActiveFiberLength ( ) const

Returns: the normalized fiber length where the active force length steep ascending limb transitions to the minimum activation value and simultaneously achives a first and second derivative of 0

double OpenSim::ActiveForceLengthCurve::getMinValue ( ) const

Returns: the minimum active force length value permitted in the simulation. This value must be non-zero for an equilibrium model.

double OpenSim::ActiveForceLengthCurve::getShallowAscendingSlope ( ) const

Returns: the slope of the shallow ascending limb (d active_force_length/d normalized_fiber_length)

double OpenSim::ActiveForceLengthCurve::getTransitionFiberLength ( ) const

Returns: the normalized fiber length where the steep ascending limb transitions to the shallow ascending limb of the active force length curve.

OpenSim::ActiveForceLengthCurve::OpenSim_DECLARE_PROPERTY	(	min_norm_active_fiber_length	,
		double	,
		"normalized fiber length which the steep ascending limb starts"
	)

OpenSim::ActiveForceLengthCurve::OpenSim_DECLARE_PROPERTY	(	transition_norm_fiber_length	,
		double	,
		"normalized fiber length which the steep ascending limb transitions"" to the shallow ascending limb"
	)

OpenSim::ActiveForceLengthCurve::OpenSim_DECLARE_PROPERTY	(	max_norm_active_fiber_length	,
		double	,
		"normalized fiber length which the descending limb ends"
	)

OpenSim::ActiveForceLengthCurve::OpenSim_DECLARE_PROPERTY	(	shallow_ascending_slope	,
		double	,
		"slope of the shallow ascending limb"
	)

OpenSim::ActiveForceLengthCurve::OpenSim_DECLARE_PROPERTY	(	minimum_value	,
		double	,
		"minimum value of the active force length curve"
	)

void OpenSim::ActiveForceLengthCurve::printMuscleCurveToCSVFile ( const std::string & path ) const

This function will generate a csv file with a name that matches the curve name (e.g.

"bicepfemoris_fiberActiveForceLengthCurve.csv"); Note that if the curve is out of date is rebuilt (which will cost ~20,500 flops).

Parameters

path	The full path to the location. Note '/' slashes must be used, and do not put a '/' after the last folder.

The file will contain the following columns:

Col# 1, 2,     3,       4,  
     x, y, dy/dx, d2y/dx2,

The curve will be sampled from its linear extrapolation region (the region less than minActiveFiberLength), through the curve, out to the other linear extrapolation region (the region greater than maxActiveFiberLength). The width of each linear extrapolation region is 10% of the entire range of x, or 0.1*(x1-x0).

The curve is sampled quite densely: the active force length has 500+20 rows

Computational Costs

     ~487,000 flops

Example To read the csv file with a header in from Matlab, you need to use csvread set so that it will ignore the header row. This is accomplished by using the extra two numerical arguments for csvread to tell the function to begin reading from the 1st row, and the 0th index (csvread is 0 indexed). This is necessary to skip reading in the text header

 data=csvread('bicepfemoris_fiberActiveForceLengthCurve.csv',1,0);

void OpenSim::ActiveForceLengthCurve::setMaxActiveFiberLength ( double maxActiveNormFiberLength )

Parameters

maxActiveNormFiberLength The normalized fiber length where the descending limb transitions to the minimum value and has a first and second derivative of 0.