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OpenSim::FiberCompressiveForceLengthCurve Class Reference

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...

#include <FiberCompressiveForceLengthCurve.h>

Inheritance diagram for OpenSim::FiberCompressiveForceLengthCurve:
OpenSim::ModelComponent OpenSim::Object

Public Member Functions

 FiberCompressiveForceLengthCurve ()
 
 Default constructor creates an object with a default name that doesn't

yet define a curve.

 FiberCompressiveForceLengthCurve (double normLengthAtZeroForce, double stiffnessAtZeroLength, double curviness, const std::string &muscleName)
 Constructs a C2 continuous compressive fiber force length curve.
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.
double calcDerivative (double aNormLength, int order) const
 Calculates the derivative of the fiber force length curve w.r.t.
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.
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 (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::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.
ModelComponentoperator= (const ModelComponent &aModelComponent)
 Assignment operator to copy contents of an existing component.
const ModelgetModel () const
 Get a const reference to the Model this component is part of.
ModelupdModel ()
 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 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 \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.

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::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.

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.

fig_FiberCompressiveForceLengthCurve.png
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
normLengthAtZeroForceThe 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.
stiffnessAtZeroLengthThis is the stiffness of the compressive elastic force length spring when the fiber reaches a normalized length of 0.
curvinessA 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.
muscleNameThe 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. Note that if the curve is out of date it is rebuilt (at a cost of ~20,500 flops).

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
aNormLengthHere 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.

Note that if the curve is out of date it is rebuilt (at a cost of ~20,500 flops).

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
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. 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::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) const

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

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

Parameters
pathThe 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
aNormLengthAtZeroForceSets 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.
void OpenSim::FiberCompressiveForceLengthCurve::setOptionalProperties ( double  aStiffnessAtZeroLength,
double  aCurviness 
)
Parameters
aStiffnessAtZeroLengthSets 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
aCurvinessA 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.

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