This class serves as a serializable FiberCompressiveForceLengthCurve, which is used to ensure that the fiber cannot generate force at, nor shorten beyond a minimum normalized length. More...

Inheritance diagram for OpenSim::FiberCompressiveForceLengthCurve:

Public Member Functions
	FiberCompressiveForceLengthCurve ()
	Default constructor creates an object with a default name that doesn't yet define a curve. More...

	FiberCompressiveForceLengthCurve (double normLengthAtZeroForce, double stiffnessAtZeroLength, double curviness, const std::string &muscleName)
	Constructs a C2 continuous compressive fiber force length curve. More...

double	getNormLengthAtZeroForce () const

double	getStiffnessAtZeroLengthInUse () const

double	getCurvinessInUse () const

void	setNormLengthAtZeroForce (double aNormLengthAtZeroForce)

void	setOptionalProperties (double aStiffnessAtZeroLength, double aCurviness)

bool	isFittedCurveBeingUsed () const

double	calcValue (double aNormLength) const
	Calculates the value of the curve evaluated at the desired normalized fiber length. More...

double	calcValue (const SimTK::Vector &x) const override
	Implement the generic OpenSim::Function interface. More...

double	calcDerivative (double aNormLength, int order) const
	Calculates the derivative of the fiber force length curve w.r.t. More...

double	calcIntegral (double aNormLength) const

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. More...

void	printMuscleCurveToCSVFile (const std::string &path)
	This function will generate a csv file with a name that matches the curve name (e.g. More...

void	ensureCurveUpToDate ()

Property declarations
These are the serializable properties associated with this class.
	OpenSim_DECLARE_PROPERTY (norm_length_at_zero_force, double,"Normalized fiber length at zero force")

	OpenSim_DECLARE_OPTIONAL_PROPERTY (stiffness_at_zero_length, double,"Fiber stiffness at zero length")

	OpenSim_DECLARE_OPTIONAL_PROPERTY (curviness, double,"Fiber curve bend, from linear to maximum bend (0-1)")

Public Member Functions inherited from OpenSim::Function
	Function ()

	Function (const Function &aFunction)

virtual	~Function ()

virtual void	init (Function *aFunction)

Function &	operator= (const Function &aFunction)

virtual double	calcDerivative (const std::vector< int > &derivComponents, const SimTK::Vector &x) const
	Calculate a partial derivative of this function at a particular point. More...

virtual int	getArgumentSize () const
	Get the number of components expected in the input vector. More...

virtual int	getMaxDerivativeOrder () const
	Get the maximum derivative order this Function object can calculate. More...

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

virtual Object *	clone () const =0
	Create a new heap-allocated copy of the concrete object to which this Object refers. More...

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. More...

virtual const VisibleObject *	getDisplayer () const
	Methods to support making the object displayable in the GUI or Visualizer Implemented only in few objects. More...

virtual VisibleObject *	updDisplayer ()
	get Non const pointer to VisibleObject 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, call this method in your constructor if needed. 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...

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. 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...

virtual void	updateXMLNode (SimTK::Xml::Element &parent)
	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...

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". More...

std::string	dump (bool dumpName=false)
	dump the XML representation of this Object into an std::string and return it. More...

void	clearObjectIsUpToDateWithProperties ()
	For testing or debugging purposes, manually clear the "object is up to date with respect to properties" flag. 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

Additional Inherited Members
Static Public Member Functions inherited from OpenSim::Function
static Function *	makeFunctionOfType (Function *aFunction, const std::string &aNewTypeName)

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 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. More...

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. 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 debug level to get verbose output. More...

static int	getDebugLevel ()
	Get 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...

Static Public Attributes inherited from OpenSim::Object
static const std::string	DEFAULT_NAME
	Name used for default objects when they are serialized. More...

Protected Member Functions inherited from OpenSim::Function
void	resetFunction ()
	This should be called whenever this object has been modified. More...

Protected Member Functions inherited from OpenSim::Object
	Object ()
	The default constructor is only for use by constructors of derived types. More...

	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. More...

	Object (const Object &source)
	Copy constructor is invoked automatically by derived classes with default copy constructors; otherwise it must be invoked explicitly. More...

	Object (SimTK::Xml::Element &aElement)
	Construct the base class portion of an Object from a given Xml element that describes this Object. More...

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. More...

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. More...

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. More...

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. More...

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. More...

PropertyIndex	getPropertyIndex (const std::string &name) const
	Look up a property by name and return its PropertyIndex if it is found. More...

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. More...

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. More...

void	setDocument (XMLDocument *doc)
	Unconditionally set the XMLDocument associated with this object. More...

const XMLDocument *	getDocument () const
	Get a const pointer to the document (if any) associated with this object. More...

XMLDocument *	updDocument ()
	Get a writable pointer to the document (if any) associated with this object. More...

Protected Attributes inherited from OpenSim::Function
SimTK::Function *	_function

Protected Attributes inherited from OpenSim::Object
PropertySet	_propertySet
	OBSOLETE: Property_Deprecated set for serializable member variables of this and derived classes. More...

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. More...

#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. More...

#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>. More...

#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. More...

Detailed Description

This class serves as a serializable FiberCompressiveForceLengthCurve, which is used to ensure that the fiber cannot generate force at, nor shorten beyond a minimum normalized length.

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

Author: Matt Millard

Constructor & Destructor Documentation

OpenSim::FiberCompressiveForceLengthCurve::FiberCompressiveForceLengthCurve ( )

Default constructor creates an object with a default name that doesn't yet define a curve.

OpenSim::FiberCompressiveForceLengthCurve::FiberCompressiveForceLengthCurve	(	double	normLengthAtZeroForce,
		double	stiffnessAtZeroLength,
		double	curviness,
		const std::string &	muscleName
	)

Constructs a C2 continuous compressive fiber force length curve.

This curve is used in the fiber model as a means of ensuring that the fiber cannot generate a tensile force at, nor shorten beyond, some minimum length. Details to appear in Millard et al. 2012.

Parameters

normLengthAtZeroForce	The normalized fiber length at which the compressive element begins to engage. Normalized length is defined as length_norm = l/l0, where l is the length of the fiber, and l0 is the resting length of the fiber.
stiffnessAtZeroLength	This is the stiffness of the compressive elastic force length spring when the fiber reaches a normalized length of 0.
curviness	A dimensionless parameter between [0-1] that controls how the curve is drawn: 0 will create a curve that is very close to a straight line segment while a value of 1 will create a curve that smoothly fills the corner formed by the linear extrapolation of 'stiffnessAtZeroLength' and the x axis as shown in the figure.
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 "_FiberCompressiveForceLengthCurve" 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:

        normLengthAtZeroForce > 0
        stiffnessAtZeroLength < -1/normLengthAtZeroForce
        0 <= curviness <= 1

Computational Costs

        ~174,100 flops

Default Parameter Values

         normLengthAtZeroForce   = 0.6 
         stiffnessAtZeroLength   = -8.4, 
         curviness               = 0.5)

Example:

Member Function Documentation

double OpenSim::FiberCompressiveForceLengthCurve::calcDerivative	(	double	aNormLength,
		int	order
	)		const

Calculates the derivative of the fiber force length curve w.r.t.

to the normalized fiber length.

Parameters

aNormLength	The normalized fiber length used to evaluate the compressive fiber force length curve for the corresponding normalized force. Here aNormLength = l/l0, where l is the length of the fiber and l0 is the resting length of the fiber. Thus normalized length of 1.0 means the fiber is at its resting length.
order	the order of the derivative. Only values of 0,1 and 2 are acceptable.

Returns: the derivative of the normalized fiber 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::FiberCompressiveForceLengthCurve::calcIntegral ( double aNormLength ) const

Parameters

aNormLength Here aNormLength = l/l0, where l is the length of the fiber and l0 is the resting length of the fiber. Thus normalized length of 1.0 means the fiber is at its resting length.

Returns: Computes the normalized area under the curve. For this curve, this quantity corresponds to the normalized potential energy stored in the fiber compressive force length spring - simply multiply this quantity by the number of NormForce*NormDistance (where NormForce corresponds to the number of Newtons that 1 normalized force corresponds to, and NormDistance is the distance in meters that a normalized value of 1 corresponds to) to obtain the potental energy stored in the fiber in units of Joules.

Computational Costs

    x in curve domain  : ~13 flops
    x in linear section: ~19 flops

double OpenSim::FiberCompressiveForceLengthCurve::calcValue ( double aNormLength ) const

Calculates the value of the curve evaluated at the desired normalized fiber length.

Parameters

aNormLength The normalized fiber length used to evaluate the fiber compressive force length curve for the corresponding normalized force. Here aNormLength = l/l0, where l is the length of the fiber and l0 is the resting length of the fiber. Thus normalized length of 1.0 means the fiber is at its resting length.

Returns: the value of the normalized force generated by the fiber

Computational Costs

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

double OpenSim::FiberCompressiveForceLengthCurve::calcValue ( const SimTK::Vector & x ) const

inlineoverridevirtual

Implement the generic OpenSim::Function interface.

Reimplemented from OpenSim::Function.

References OVERRIDE_11.

void OpenSim::FiberCompressiveForceLengthCurve::ensureCurveUpToDate ( )

SimTK::Vec2 OpenSim::FiberCompressiveForceLengthCurve::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.

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::FiberCompressiveForceLengthCurve::getCurvinessInUse ( ) const

Returns: A dimensionless parameter between [0-1] that controls how the curve is drawn: 0 will create a curve that is very close to a straight line segment while a value of 1 will create a curve that smoothly fills the corner formed by the linear extrapolation of 'stiffnessAtOneNormForce' and the x axis as shown in the figure. If this optional property is not specified, a suitable value will be calculated and used instead.

double OpenSim::FiberCompressiveForceLengthCurve::getNormLengthAtZeroForce ( ) const

Returns: The normalized fiber length at which the compressive element begins to engage. Normalized length is defined as length_norm = l/l0, where l is the length of the fiber, and l0 is the resting length of the fiber.

double OpenSim::FiberCompressiveForceLengthCurve::getStiffnessAtZeroLengthInUse ( ) const

Returns: This is the stiffness of the compressive elastic force length spring when the fiber reaches a normalized length of 0. If this optional property is not specified, a suitable value will be calculated and used instead.

bool OpenSim::FiberCompressiveForceLengthCurve::isFittedCurveBeingUsed ( ) const

Returns: true if the optional properties are empty and the fitted curve is being used. This function returns false if the optional properties are filled and are being used to construct the curve.

OpenSim::FiberCompressiveForceLengthCurve::OpenSim_DECLARE_OPTIONAL_PROPERTY	(	stiffness_at_zero_length	,
		double	,
		"Fiber stiffness at zero length"
	)

OpenSim::FiberCompressiveForceLengthCurve::OpenSim_DECLARE_OPTIONAL_PROPERTY	(	curviness	,
		double	,
		"Fiber curve	bend,
		from linear to maximum bend(0-1)"
	)

OpenSim::FiberCompressiveForceLengthCurve::OpenSim_DECLARE_PROPERTY	(	norm_length_at_zero_force	,
		double	,
		"Normalized fiber length at zero force"
	)

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

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

"bicepfemoris_FiberCompressiveForceLengthCurve.csv"); This function is not const to permit the curve to be rebuilt if it is out of date with its properties.

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 with normalized fiber velocities < -1), through the curve, out to the other linear extrapolation region (the region with normalized fiber velocities > 1). 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: there are 200+20 rows

Computational Costs

     ~194,800 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_fiberCompressiveForceLengthCurve.csv',1,0);

void OpenSim::FiberCompressiveForceLengthCurve::setNormLengthAtZeroForce ( double aNormLengthAtZeroForce )

Parameters

aNormLengthAtZeroForce Sets the normalized fiber length at which the compressive element begins to engage. Normalized length is defined as length_norm = l/l0, where l is the length of the fiber, and l0 is the resting length of the fiber. This length must be greater than 0.

Cost The curve is rebuilt at a cost of ~174,100 flops

void OpenSim::FiberCompressiveForceLengthCurve::setOptionalProperties	(	double	aStiffnessAtZeroLength,
		double	aCurviness
	)

Parameters

aStiffnessAtZeroLength	Sets the stiffness of the compressive elastic force length spring when the fiber reaches a normalized length of 0. This stiffness must be less than -1/normLengthAtZeroForce
aCurviness	A dimensionless parameter between [0-1] that controls how the curve is drawn: 0 will create a curve that is very close to a straight line segment while a value of 1 will create a curve that smoothly fills the corner formed by the linear extrapolation of 'stiffnessAtOneNormForce' and the x axis as shown in the figure. Cost The curve is rebuilt at a cost of ~174,100 flops

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

OpenSim/Actuators/FiberCompressiveForceLengthCurve.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation