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API
4.4
For C++ developers
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API
4.4
For C++ developers
|
Umberger2010MuscleMetabolicsProbe is a Probe ModelComponent for computing the net metabolic energy rate of a set of Muscles in the model during a simulation. More...
Inheritance diagram for OpenSim::Umberger2010MuscleMetabolicsProbe:OpenSim Properties, Sockets, Outputs, Inputs | |
Properties (single-value) | |
Default value = true | |
| bool | activation_maintenance_rate_on |
| "Specify whether activation & maintenance heat rate is to be calculated (true/false)." More... | |
| bool | shortening_rate_on |
| "Specify whether shortening heat rate is to be calculated (true/false)." More... | |
| bool | basal_rate_on |
| "Specify whether basal heat rate is to be calculated (true/false)." More... | |
| bool | mechanical_work_rate_on |
| "Specify whether mechanical work rate is to be calculated (true/false)." More... | |
| bool | enforce_minimum_heat_rate_per_muscle |
| "Specify whether the total heat rate for a muscle will be clamped to a " "minimum value of 1.0 W/kg (true/false)." More... | |
| double | aerobic_factor |
| "Aerobic scale factor (S=1.0 for primarily anaerobic conditions and S=1.5 " "for primarily aerobic conditions. See Umberger et al., (2003)." More... | |
| double | basal_coefficient |
| "Basal metabolic coefficient." More... | |
| double | basal_exponent |
| "Basal metabolic exponent." More... | |
| double | muscle_effort_scaling_factor |
| "Scale the excitation and activation values used by the probe to " "compensate for solutions with excessive coactivation (e.g., when a " "suboptimal tracking strategy is used)." More... | |
| bool | use_Bhargava_recruitment_model |
| "Specify whether the recruitment model described by Bhargava et al. " "(2004) will used to determine the slow-twitch fiber ratio " "(true/false). Disable to use the model as published in Umberger " "(2010)." More... | |
| bool | include_negative_mechanical_work |
| "Specify whether negative mechanical work will be included in Wdot and " "a coefficient of 4.0 will be used to calculate alpha_L (true/false). " "Disable to use the model as published in Umberger (2010)." More... | |
| bool | forbid_negative_total_power |
| "Specify whether the total power for each muscle must remain positive " "(true/false). Disable to use the model as published in Umberger " "(2010)." More... | |
| bool | report_total_metabolics_only |
| "If set to false, the individual muscle metabolics, basal rate, and " "total summation will be reported. If set to true, only the total " "summation will be reported." More... | |
Properties (unnamed) | |
| Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet | Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet |
| "A set containing, for each muscle, the parameters " "required to calculate muscle metabolic power." More... | |
| OpenSim Properties, Sockets, Outputs, Inputs inherited from OpenSim::Probe | |
| bool | enabled |
| "Flag indicating whether the Probe is Enabled." More... | |
| std::string | probe_operation |
| "The operation to perform on the probe input value: " "'value'(no operation, just return the probe value), 'integrate', " "'differentiate', 'minimum', 'minabs', 'maximum', 'maxabs'." More... | |
| double | gain |
| "Constant gain to scale the probe output by." More... | |
| double | initial_conditions_for_integration |
| "Array of initial conditions to be specified if the 'integrate' operation is " "selected. Note that the size of initial conditions must be the same size as " "the data being integrated, otherwise an exception will be thrown." More... | |
| SimTK::Vector | probe_outputs |
| Provides the value of getProbeOutputs() and is available at stage SimTK::Stage::Report . More... | |
| OpenSim Properties, Sockets, Outputs, Inputs inherited from OpenSim::Component | |
| Component | components |
| "List of components that this component owns and serializes." More... | |
Public Member Functions | |
| Umberger2010MuscleMetabolicsProbe () | |
| Default constructor. More... | |
| Umberger2010MuscleMetabolicsProbe (const bool activation_maintenance_rate_on, const bool shortening_rate_on, const bool basal_rate_on, const bool work_rate_on) | |
| Convenience constructor. More... | |
| virtual SimTK::Vector | computeProbeInputs (const SimTK::State &state) const override |
| Compute muscle metabolic power. More... | |
| int | getNumProbeInputs () const override |
| Returns the number of probe inputs in the vector returned by computeProbeInputs(). More... | |
| virtual OpenSim::Array< std::string > | getProbeOutputLabels () const override |
| Returns the column labels of the probe values for reporting. More... | |
Property-related functions | |
| const bool & | get_activation_maintenance_rate_on () const |
| Get the value of the activation_maintenance_rate_on property. More... | |
| bool & | upd_activation_maintenance_rate_on () |
| Get a writable reference to the activation_maintenance_rate_on property. More... | |
| void | set_activation_maintenance_rate_on (const bool &value) |
| Set the value of the activation_maintenance_rate_on property. More... | |
| const bool & | get_shortening_rate_on () const |
| Get the value of the shortening_rate_on property. More... | |
| bool & | upd_shortening_rate_on () |
| Get a writable reference to the shortening_rate_on property. More... | |
| void | set_shortening_rate_on (const bool &value) |
| Set the value of the shortening_rate_on property. More... | |
| const bool & | get_basal_rate_on () const |
| Get the value of the basal_rate_on property. More... | |
| bool & | upd_basal_rate_on () |
| Get a writable reference to the basal_rate_on property. More... | |
| void | set_basal_rate_on (const bool &value) |
| Set the value of the basal_rate_on property. More... | |
| const bool & | get_mechanical_work_rate_on () const |
| Get the value of the mechanical_work_rate_on property. More... | |
| bool & | upd_mechanical_work_rate_on () |
| Get a writable reference to the mechanical_work_rate_on property. More... | |
| void | set_mechanical_work_rate_on (const bool &value) |
| Set the value of the mechanical_work_rate_on property. More... | |
| const bool & | get_enforce_minimum_heat_rate_per_muscle () const |
| Get the value of the enforce_minimum_heat_rate_per_muscle property. More... | |
| bool & | upd_enforce_minimum_heat_rate_per_muscle () |
| Get a writable reference to the enforce_minimum_heat_rate_per_muscle property. More... | |
| void | set_enforce_minimum_heat_rate_per_muscle (const bool &value) |
| Set the value of the enforce_minimum_heat_rate_per_muscle property. More... | |
| const double & | get_aerobic_factor () const |
| Get the value of the aerobic_factor property. More... | |
| double & | upd_aerobic_factor () |
| Get a writable reference to the aerobic_factor property. More... | |
| void | set_aerobic_factor (const double &value) |
| Set the value of the aerobic_factor property. More... | |
| const double & | get_basal_coefficient () const |
| Get the value of the basal_coefficient property. More... | |
| double & | upd_basal_coefficient () |
| Get a writable reference to the basal_coefficient property. More... | |
| void | set_basal_coefficient (const double &value) |
| Set the value of the basal_coefficient property. More... | |
| const double & | get_basal_exponent () const |
| Get the value of the basal_exponent property. More... | |
| double & | upd_basal_exponent () |
| Get a writable reference to the basal_exponent property. More... | |
| void | set_basal_exponent (const double &value) |
| Set the value of the basal_exponent property. More... | |
| const double & | get_muscle_effort_scaling_factor () const |
| Get the value of the muscle_effort_scaling_factor property. More... | |
| double & | upd_muscle_effort_scaling_factor () |
| Get a writable reference to the muscle_effort_scaling_factor property. More... | |
| void | set_muscle_effort_scaling_factor (const double &value) |
| Set the value of the muscle_effort_scaling_factor property. More... | |
| const bool & | get_use_Bhargava_recruitment_model () const |
| Get the value of the use_Bhargava_recruitment_model property. More... | |
| bool & | upd_use_Bhargava_recruitment_model () |
| Get a writable reference to the use_Bhargava_recruitment_model property. More... | |
| void | set_use_Bhargava_recruitment_model (const bool &value) |
| Set the value of the use_Bhargava_recruitment_model property. More... | |
| const bool & | get_include_negative_mechanical_work () const |
| Get the value of the include_negative_mechanical_work property. More... | |
| bool & | upd_include_negative_mechanical_work () |
| Get a writable reference to the include_negative_mechanical_work property. More... | |
| void | set_include_negative_mechanical_work (const bool &value) |
| Set the value of the include_negative_mechanical_work property. More... | |
| const bool & | get_forbid_negative_total_power () const |
| Get the value of the forbid_negative_total_power property. More... | |
| bool & | upd_forbid_negative_total_power () |
| Get a writable reference to the forbid_negative_total_power property. More... | |
| void | set_forbid_negative_total_power (const bool &value) |
| Set the value of the forbid_negative_total_power property. More... | |
| const bool & | get_report_total_metabolics_only () const |
| Get the value of the report_total_metabolics_only property. More... | |
| bool & | upd_report_total_metabolics_only () |
| Get a writable reference to the report_total_metabolics_only property. More... | |
| void | set_report_total_metabolics_only (const bool &value) |
| Set the value of the report_total_metabolics_only property. More... | |
| const Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet & | get_Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet () const |
| Get the value of the Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet property. More... | |
| Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet & | upd_Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet () |
| Get a writable reference to the Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet property. More... | |
| void | set_Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet (const Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet &value) |
| Set the value of the Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet property. More... | |
| Public Member Functions inherited from OpenSim::Probe | |
| Probe () | |
| void | reset (SimTK::State &s) |
| Reset (initialize) the underlying Probe SimTK::Measure. More... | |
| int | getNumInternalMeasureStates () const |
| Get the number of states in the underlying SimTK::Measure. More... | |
| bool | isEnabled () const |
| Returns true if the Probe is enabled and false if the probe is disabled. More... | |
| void | setEnabled (bool enabled) |
| Set the Probe as enabled (true) or disabled (false). More... | |
| std::string | getOperation () const |
| Return the operation being performed on the probe value. More... | |
| void | setOperation (std::string probe_operation) |
| Set the operation being performed on the probe value. More... | |
| SimTK::Vector | getInitialConditions () const |
| Return the initial conditions (when the probe_operation is set to 'integrate'). More... | |
| void | setInitialConditions (SimTK::Vector initial_conditions_for_integration) |
| Set the initial conditions (when the probe_operation is set to 'integrate'). More... | |
| double | getGain () const |
| Return the gain to apply to the probe output. More... | |
| void | setGain (double gain) |
| Set the gain to apply to the probe output. More... | |
| SimTK::Vector | getProbeOutputs (const SimTK::State &state) const |
| Returns the values of the probe after the operation has been performed. More... | |
| void | updateFromXMLNode (SimTK::Xml::Element &node, int versionNumber) override |
| Handle a change in XML syntax for Sockets. More... | |
| const bool & | get_enabled () const |
| Get the value of the enabled property. More... | |
| bool & | upd_enabled () |
| Get a writable reference to the enabled property. More... | |
| void | set_enabled (const bool &value) |
| Set the value of the enabled property. More... | |
| const std::string & | get_probe_operation () const |
| Get the value of the probe_operation property. More... | |
| std::string & | upd_probe_operation () |
| Get a writable reference to the probe_operation property. More... | |
| void | set_probe_operation (const std::string &value) |
| Set the value of the probe_operation property. More... | |
| const double & | get_initial_conditions_for_integration (int i) const |
| Get the value of the i-th element of the initial_conditions_for_integration property. More... | |
| double & | upd_initial_conditions_for_integration (int i) |
| Get a writable reference to the i-th element of the initial_conditions_for_integration property. More... | |
| void | set_initial_conditions_for_integration (int i, const double &value) |
| Set the value of the i-th element of initial_conditions_for_integration property. More... | |
| int | append_initial_conditions_for_integration (const double &value) |
| Append an element to the initial_conditions_for_integration property. More... | |
| const double & | get_gain () const |
| Get the value of the gain property. More... | |
| double & | upd_gain () |
| Get a writable reference to the gain property. More... | |
| void | set_gain (const double &value) |
| Set the value of the gain property. More... | |
| void | assign (Object &aObject) override |
| This allows copy assignment in the Java GUI. More... | |
| Public Member Functions inherited from OpenSim::ModelComponent | |
| ModelComponent () | |
| Default constructor. More... | |
| ModelComponent (const std::string &aFileName, bool aUpdateFromXMLNode=true) | |
| Construct ModelComponent from an XML file. More... | |
| ModelComponent (SimTK::Xml::Element &aNode) | |
| Construct ModelComponent from a specific node in an XML document. More... | |
| virtual | ~ModelComponent () |
| Destructor is virtual to allow concrete model component cleanup. More... | |
| void | connectToModel (Model &model) |
| Connect this ModelComponent to its aggregate- a Model. More... | |
| const Model & | getModel () const |
| Get a const reference to the Model this component is part of. More... | |
| Model & | updModel () |
| Get a modifiable reference to the Model this component is part of. More... | |
| bool | hasModel () const |
| Does this ModelComponent have a Model associated with it? More... | |
| void | preScale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Perform any computations that must occur before ModelComponent::scale() is invoked on all ModelComponents in the Model. More... | |
| void | scale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Scale the ModelComponent. More... | |
| void | postScale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Perform any computations that must occur after ModelComponent::scale() has been invoked on all ModelComponents in the Model. More... | |
| void | assign (Object &aObject) override |
| This allows copy assignment in the Java GUI. More... | |
| Public Member Functions inherited from OpenSim::Component | |
| Component () | |
| Default constructor. More... | |
| Component (const std::string &aFileName, bool aUpdateFromXMLNode=true) | |
| Construct Component from an XML file. More... | |
| Component (SimTK::Xml::Element &aNode) | |
| Construct Component from a specific node in an XML document. More... | |
| Component (const Component &)=default | |
| Use default copy constructor and assignment operator. More... | |
| Component & | operator= (const Component &)=default |
| virtual | ~Component ()=default |
| Destructor is virtual to allow concrete Component to cleanup. More... | |
| 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 Component at the specified state. More... | |
| const SimTK::MultibodySystem & | getSystem () const |
| Get the underlying MultibodySystem that this component is connected to. More... | |
| bool | hasSystem () const |
| Check if this component has an underlying MultibodySystem. More... | |
| bool | isComponentInOwnershipTree (const Component *component) const |
| Does the provided component already exist anywhere in the ownership tree (not just subcomponents of this component)? More... | |
| void | addComponent (Component *subcomponent) |
| Add a Component (as a subcomponent) of this component. More... | |
| template<typename T = Component> | |
| ComponentList< const T > | getComponentList () const |
| Get an iterator through the underlying subcomponents that this component is composed of. More... | |
| template<typename T = Component> | |
| ComponentList< T > | updComponentList () |
| Similar to getComponentList(), except the resulting list allows one to modify the components. More... | |
| template<typename T = Component> | |
| unsigned | countNumComponents () const |
| Uses getComponentList<T>() to count the number of underlying subcomponents of the specified type. More... | |
| std::string | getAbsolutePathString () const |
| Get the complete (absolute) pathname for this Component to its ancestral Component, which is the root of the tree to which this Component belongs. More... | |
| ComponentPath | getAbsolutePath () const |
| Return a ComponentPath of the absolute path of this Component. More... | |
| std::string | getRelativePathString (const Component &wrt) const |
| Get the relative path of this Component with respect to another Component, as a string. More... | |
| ComponentPath | getRelativePath (const Component &wrt) const |
| Get the relative path of this Component with respect to another Component. More... | |
| bool | hasComponent (const std::string &pathname) const |
| Query if there is a component (of any type) at the specified path name. More... | |
| template<class C = Component> | |
| bool | hasComponent (const std::string &pathname) const |
| Query if there is a component of a given type at the specified path name. More... | |
| template<class C = Component> | |
| const C & | getComponent (const std::string &pathname) const |
| Get a unique subcomponent of this Component by its path name and type 'C'. More... | |
| template<class C = Component> | |
| const C & | getComponent (const ComponentPath &pathname) const |
| const Component & | getComponent (const std::string &pathname) const |
| Similar to the templatized getComponent(), except this returns the component as the generic Component type. More... | |
| template<class C = Component> | |
| C & | updComponent (const std::string &name) |
| Get a writable reference to a subcomponent. More... | |
| template<class C = Component> | |
| C & | updComponent (const ComponentPath &name) |
| Component & | updComponent (const std::string &pathname) |
| Similar to the templatized updComponent(), except this returns the component as the generic Component type. More... | |
| unsigned | printComponentsMatching (const std::string &substring) const |
| Print a list to the console of all components whose absolute path name contains the given string. More... | |
| int | getNumStateVariables () const |
| Get the number of "continuous" state variables maintained by the Component and its subcomponents. More... | |
| Array< std::string > | getStateVariableNames () const |
| Get the names of "continuous" state variables maintained by the Component and its subcomponents. More... | |
| template<class C = Component> | |
| const C * | findComponent (const ComponentPath &pathToFind) const |
| Find a Component to which this Component is an ancestor—in other words, a Component that is directly owned by this Component or is owned by one of its sub-components, sub-sub-components, etc. More... | |
| template<class C = Component> | |
| const C * | findComponent (const std::string &pathToFind) const |
| Same as findComponent(const ComponentPath&), but accepting a string (a path or just a name) as input. More... | |
| const StateVariable * | traverseToStateVariable (const std::string &pathName) const |
| Get a StateVariable anywhere in the Component tree, given a StateVariable path. More... | |
| const StateVariable * | traverseToStateVariable (const ComponentPath &path) const |
| Get a StateVariable anywhere in the Component tree, given a StateVariable path. More... | |
| void | finalizeFromProperties () |
| Define a Component's internal data members and structure according to its properties. More... | |
| void | finalizeConnections (Component &root) |
| Satisfy the Component's connections specified by its Sockets and Inputs. More... | |
| void | clearConnections () |
| Disconnect/clear this Component from its aggregate component. More... | |
| void | addToSystem (SimTK::MultibodySystem &system) const |
| Have the Component add itself to the underlying computational System. More... | |
| void | initStateFromProperties (SimTK::State &state) const |
| Initialize Component's state variable values from its properties. More... | |
| void | setPropertiesFromState (const SimTK::State &state) |
| Set Component's properties given a state. More... | |
| int | getNumSockets () const |
| Get the number of Sockets in this Component. More... | |
| std::vector< std::string > | getSocketNames () |
| Collect and return the names of the sockets in this component. More... | |
| template<typename T > | |
| const T & | getConnectee (const std::string &name) const |
| Get the "connectee" object that the Component's Socket is bound to. More... | |
| const Object & | getConnectee (const std::string &name) const |
| Get the connectee as an Object. More... | |
| const AbstractSocket & | getSocket (const std::string &name) const |
| Get an AbstractSocket for the given socket name. More... | |
| AbstractSocket & | updSocket (const std::string &name) |
| Get a writable reference to the AbstractSocket for the given socket name. More... | |
| template<typename T > | |
| const Socket< T > & | getSocket (const std::string &name) const |
| Get a const reference to the concrete Socket provided by this Component by name. More... | |
| template<typename T > | |
| Socket< T > & | updSocket (const std::string &name) |
| Get a writable reference to the concrete Socket provided by this Component by name. More... | |
| void | printSubcomponentInfo () const |
| List all subcomponents by name and recurse into these components to list their subcomponents, and so on. More... | |
| void | printSocketInfo () const |
| List all the Sockets of this component and whether or not they are connected. More... | |
| void | printInputInfo () const |
| List all the inputs of this component and whether or not they are connected. More... | |
| template<typename C > | |
| void | printSubcomponentInfo () const |
| void | printOutputInfo (const bool includeDescendants=true) const |
| Print outputs of this component and optionally, those of all subcomponents. More... | |
| void | assign (Object &aObject) override |
| This allows copy assignment in the Java GUI. More... | |
| int | getNumInputs () const |
| Access the number of Inputs that this component has. More... | |
| int | getNumOutputs () const |
| Access the number of Outputs that this component has. More... | |
| std::vector< std::string > | getInputNames () const |
| Collect and return the names of Inputs in this component as an std::vector. More... | |
| std::vector< std::string > | getOutputNames () const |
| Collect and return the names of Outputs in this component as an std::vector. More... | |
| const AbstractInput & | getInput (const std::string &name) const |
| Get an Input provided by this Component by name. More... | |
| AbstractInput & | updInput (const std::string &name) |
| Get a writable reference to an Input provided by this Component by name. More... | |
| template<typename T > | |
| const Input< T > & | getInput (const std::string &name) const |
| Get a concrete Input that you can directly ask for its values. More... | |
| const AbstractOutput & | getOutput (const std::string &name) const |
| Get the Output provided by this Component by name. More... | |
| AbstractOutput & | updOutput (const std::string &name) |
| Get a writable reference to an Output provided by this Component by name. More... | |
| SimTK::IteratorRange< OutputConstIterator > | getOutputs () const |
| Iterate through all Outputs of this component. More... | |
| int | getModelingOption (const SimTK::State &state, const std::string &name) const |
| Get a ModelingOption flag for this Component by name. More... | |
| void | setModelingOption (SimTK::State &state, const std::string &name, int flag) const |
| Set the value of a ModelingOption flag for this Component. More... | |
| template<typename T > | |
| const T & | getInputValue (const SimTK::State &state, const std::string &name) const |
| Get the Input value that this component is dependent on. More... | |
| template<typename T > | |
| const T & | getOutputValue (const SimTK::State &state, const std::string &name) const |
| Get the Output value provided by this Component by name. More... | |
| double | getStateVariableValue (const SimTK::State &state, const std::string &name) const |
| Get the value of a state variable allocated by this Component. More... | |
| double | getStateVariableValue (const SimTK::State &state, const ComponentPath &path) const |
| Get the value of a state variable allocated by this Component. More... | |
| void | setStateVariableValue (SimTK::State &state, const std::string &name, double value) const |
| Set the value of a state variable allocated by this Component by name. More... | |
| SimTK::Vector | getStateVariableValues (const SimTK::State &state) const |
| Get all values of the state variables allocated by this Component. More... | |
| void | setStateVariableValues (SimTK::State &state, const SimTK::Vector &values) const |
| Set all values of the state variables allocated by this Component. More... | |
| double | getStateVariableDerivativeValue (const SimTK::State &state, const std::string &name) const |
| Get the value of a state variable derivative computed by this Component. More... | |
| double | getDiscreteVariableValue (const SimTK::State &state, const std::string &name) const |
| Get the value of a discrete variable allocated by this Component by name. More... | |
| void | setDiscreteVariableValue (SimTK::State &state, const std::string &name, double value) const |
| Set the value of a discrete variable allocated by this Component by name. More... | |
| template<class T > | |
| SimTK::CacheEntryIndex | getCacheVariableIndex (const CacheVariable< T > &cv) const |
| Get the index of a Component's cache variable in the Subsystem for allocations. More... | |
| SimTK::CacheEntryIndex | getCacheVariableIndex (const std::string &name) const |
| Get the index of a Component's cache variable in the Subsystem for allocations. More... | |
| template<class T > | |
| const T & | getCacheVariableValue (const SimTK::State &state, const std::string &name) const |
| Get the value of a cache variable allocated by this Component by name. More... | |
| template<class T > | |
| const T & | getCacheVariableValue (const SimTK::State &state, const CacheVariable< T > &cv) const |
| Get the value of a cache variable allocated by this Component. More... | |
| template<typename T > | |
| void | setCacheVariableValue (const SimTK::State &state, const std::string &k, T value) const |
Set the value of a cache variable, identified by name, to a new value and mark the cache variable as valid. More... | |
| template<typename T > | |
| void | setCacheVariableValue (const SimTK::State &state, const CacheVariable< T > &cv, T value) const |
| Set the value of a cache variable to a new value and mark the cache variable as valid. More... | |
| template<typename T > | |
| T & | updCacheVariableValue (const SimTK::State &state, const std::string &name) const |
Returns a mutable reference to the value of a cache variable identified by name. More... | |
| template<typename T > | |
| T & | updCacheVariableValue (const SimTK::State &state, const CacheVariable< T > &cv) const |
| Returns a mutable reference to the value of a cache variable. More... | |
| bool | isCacheVariableValid (const SimTK::State &state, const std::string &name) const |
Returns true if the cache variable, identified by name, is valid. More... | |
| template<class T > | |
| bool | isCacheVariableValid (const SimTK::State &state, const CacheVariable< T > &cv) const |
| Returns true if the cache variable is valid. More... | |
| void | markCacheVariableValid (const SimTK::State &state, const std::string &name) const |
Marks the value of a cache variable, identified by name, as valid. More... | |
| template<typename T > | |
| void | markCacheVariableValid (const SimTK::State &state, const CacheVariable< T > &cv) const |
| Marks the value of a cache variable as valid. More... | |
| void | markCacheVariableInvalid (const SimTK::State &state, const std::string &name) const |
Marks the value of a cache variable, identified by name, as invalid. More... | |
| template<class T > | |
| void | markCacheVariableInvalid (const SimTK::State &state, const CacheVariable< T > &cv) const |
| Marks the value of a cache variable as invalid. More... | |
| const Component & | getOwner () const |
| Access the owner of this Component. More... | |
| bool | hasOwner () const |
| (For advanced users) Check if this Component has an owner. More... | |
| const Component & | getRoot () const |
| Obtain the root Component, which is this component if it is orphaned. More... | |
| Public Member Functions inherited from OpenSim::Object | |
| virtual | ~Object () |
| Virtual destructor for cleanup. More... | |
| bool | isEqualTo (const Object &aObject) const |
| Equality operator wrapper for use from languages not supporting operator overloading. More... | |
| 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. 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... | |
| 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... | |
| void | updateXMLNode (SimTK::Xml::Element &parent, const AbstractProperty *prop=nullptr) const |
| Serialize this object into the XML node that represents it. More... | |
| bool | getInlined () const |
| Inlined means an in-memory Object that is not associated with an XMLDocument. More... | |
| void | setInlined (bool aInlined, const std::string &aFileName="") |
| Mark this as inlined or not and optionally provide a file name to associate with the new XMLDocument for the non-inline case. More... | |
| std::string | getDocumentFileName () const |
| If there is a document associated with this object then return the file name maintained by the document. More... | |
| int | getDocumentFileVersion () const |
| If there is a document associated with this object then return its version number. More... | |
| void | setAllPropertiesUseDefault (bool aUseDefault) |
| bool | print (const std::string &fileName) const |
| Write this Object into an XML file of the given name; conventionally the suffix to use is ".osim". More... | |
| std::string | dump () const |
| dump the XML representation of this Object into an std::string and return it. More... | |
| virtual bool | isA (const char *type) const |
| The default implementation returns true only if the supplied string is "Object"; each Object-derived class overrides this to match its own class name. More... | |
| const std::string & | toString () const |
| Wrapper to be used on Java side to display objects in tree; this returns just the object's name. More... | |
| PropertySet & | getPropertySet () |
| OBSOLETE: Get a reference to the PropertySet maintained by the Object. More... | |
| const PropertySet & | getPropertySet () const |
Public Types | |
| typedef Umberger2010MuscleMetabolicsProbe | Self |
| This typedef might be useful within the member functions of this class. More... | |
| typedef Probe | Super |
| Use this typedef to refer to the superclass of this class. More... | |
| typedef std::map< std::string, Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameter * > | MuscleMap |
| MuscleMap typedef. More... | |
| Public Types inherited from OpenSim::Probe | |
| typedef Probe | Self |
| This typedef might be useful within the member functions of this class. More... | |
| typedef ModelComponent | Super |
| Use this typedef to refer to the superclass of this class. More... | |
| Public Types inherited from OpenSim::ModelComponent | |
| typedef ModelComponent | Self |
| This typedef might be useful within the member functions of this class. More... | |
| typedef Component | Super |
| Use this typedef to refer to the superclass of this class. More... | |
| Public Types inherited from OpenSim::Component | |
| typedef Component | Self |
| This typedef might be useful within the member functions of this class. More... | |
| typedef Object | Super |
| Use this typedef to refer to the superclass of this class. More... | |
| typedef std::map< std::string, SimTK::ClonePtr< AbstractOutput > >::const_iterator | OutputConstIterator |
| Define OutputConstIterator for convenience. More... | |
Auto-generated functions | |
| static Umberger2010MuscleMetabolicsProbe * | safeDownCast (OpenSim::Object *obj) |
| For use in MATLAB and Python to access the concrete class. More... | |
| static const std::string & | getClassName () |
| This returns "Umberger2010MuscleMetabolicsProbe". More... | |
| void | assign (Object &aObject) override |
| This allows copy assignment in the Java GUI. More... | |
| Umberger2010MuscleMetabolicsProbe * | clone () const override |
| Create a new heap-allocated copy of the concrete object to which this Object refers. More... | |
| const std::string & | getConcreteClassName () const override |
| Returns the class name of the concrete Object-derived class of the actual object referenced by this Object, as a string. More... | |
Umberger2010MuscleMetabolicsProbe Interface | |
These accessor methods are to be used when setting up a new muscle metabolic analysis from the API. The basic operation is as follows: model.addProbe(myProbe); myProbe->addMuscle("muscleName1", ... ); myProbe->addMuscle("muscleName2", ... ); myProbe->addMuscle("muscleName3", ... ); myProbe->useProvidedMass("muscleName1", 1.2); // muscle1 mass = 1.2 kg myProbe->useCalculatedMass("muscleName2"); // muscle2 mass is based on muscle properties (below) myProbe->setDensity("muscleName2", 1100.0); // muscle2 density is 1100 kg/m^3 myProbe->setSpecificTension("muscleName2", 0.26e6); // muscle2 specific tension is 0.26e6 Pa myProbe->removeMuscle("muscleName3"); myProbe->setOperation("integrate") // See OpenSim::Probe for other operations
| |
| int | getNumMetabolicMuscles () const |
| Get the number of muscles being analyzed in the metabolic analysis. More... | |
| void | addMuscle (const std::string &muscleName, double ratio_slow_twitch_fibers) |
| Add a muscle and its parameters so that it can be included in the metabolic analysis. More... | |
| void | addMuscle (const std::string &muscleName, double ratio_slow_twitch_fibers, double muscle_mass) |
| Add a muscle and its parameters so that it can be included in the metabolic analysis. More... | |
| void | removeMuscle (const std::string &muscleName) |
| Remove a muscle from the metabolic analysis. More... | |
| void | useProvidedMass (const std::string &muscleName, double providedMass) |
| Set an existing muscle to use a provided muscle mass. More... | |
| void | useCalculatedMass (const std::string &muscleName) |
| Set an existing muscle to calculate its own mass. More... | |
| bool | isUsingProvidedMass (const std::string &muscleName) |
| Get whether the muscle mass is being explicitly provided. More... | |
| double | getMuscleMass (const std::string &muscleName) const |
| Get the muscle mass used in the metabolic analysis. More... | |
| double | getRatioSlowTwitchFibers (const std::string &muscleName) const |
| Get the ratio of slow twitch fibers for an existing muscle. More... | |
| void | setRatioSlowTwitchFibers (const std::string &muscleName, const double &ratio) |
| Set the ratio of slow twitch fibers for an existing muscle. More... | |
| double | getDensity (const std::string &muscleName) const |
| Get the density for an existing muscle (kg/m^3). More... | |
| void | setDensity (const std::string &muscleName, const double &density) |
| Set the density for an existing muscle (kg/m^3). More... | |
| double | getSpecificTension (const std::string &muscleName) const |
| Get the specific tension for an existing muscle (Pascals (N/m^2)). More... | |
| void | setSpecificTension (const std::string &muscleName, const double &specificTension) |
| Set the specific tension for an existing muscle (Pascals (N/m^2)). More... | |
Additional Inherited Members | |
| Static Public Member Functions inherited from OpenSim::Probe | |
| static Probe * | safeDownCast (OpenSim::Object *obj) |
| For use in MATLAB and Python to access the concrete class. More... | |
| static const std::string & | getClassName () |
| This returns "Probe". More... | |
| Static Public Member Functions inherited from OpenSim::ModelComponent | |
| static ModelComponent * | safeDownCast (OpenSim::Object *obj) |
| For use in MATLAB and Python to access the concrete class. More... | |
| static const std::string & | getClassName () |
| This returns "ModelComponent". More... | |
| Static Public Member Functions inherited from OpenSim::Component | |
| static Component * | safeDownCast (OpenSim::Object *obj) |
| For use in MATLAB and Python to access the concrete class. More... | |
| static const std::string & | getClassName () |
| This returns "Component". More... | |
| Static Public Member Functions inherited from OpenSim::Object | |
| static void | registerType (const Object &defaultObject) |
| Register an instance of a class; if the class is already registered it will be replaced. More... | |
| static void | renameType (const std::string &oldTypeName, const std::string &newTypeName) |
| Support versioning by associating the current Object type with an old name. More... | |
| static const 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 bool | PrintPropertyInfo (std::ostream &os, const std::string &classNameDotPropertyName, bool printFlagInfo=true) |
| Dump formatted property information to a given output stream, useful for creating a "help" facility for registered objects. More... | |
| static bool | PrintPropertyInfo (std::ostream &os, const std::string &className, const std::string &propertyName, bool printFlagInfo=true) |
| Same as the other signature but the class name and property name are provided as two separate strings. More... | |
| static 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 amount of logging output. More... | |
| static int | getDebugLevel () |
| Get the 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::Probe | |
| void | extendAddToSystem (SimTK::MultibodySystem &system) const override |
| Concrete probes may override; be sure to invoke Super::extendAddToSystem() at the beginning of the overriding method. More... | |
| Protected Member Functions inherited from OpenSim::ModelComponent | |
| const SimTK::Vec3 & | getScaleFactors (const ScaleSet &scaleSet, const Frame &frame) const |
| Get the scale factors corresponding to the base OpenSim::Body of the specified Frame. More... | |
| virtual void | extendPreScale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Perform any computations that must occur before ModelComponent::scale() is invoked on all ModelComponents in the Model. More... | |
| virtual void | extendScale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Scale the ModelComponent. More... | |
| virtual void | extendPostScale (const SimTK::State &s, const ScaleSet &scaleSet) |
| Perform any computations that must occur after ModelComponent::scale() has been invoked on all ModelComponents in the Model. More... | |
| void | extendFinalizeFromProperties () override |
| Perform any time-invariant calculations, data structure initializations, or other configuration based on the component's properties to form a functioning (but not yet connected) component. More... | |
| Protected Member Functions inherited from OpenSim::Component | |
| SimTK_DEFINE_UNIQUE_INDEX_TYPE (MemberSubcomponentIndex) | |
| template<class C = Component> | |
| MemberSubcomponentIndex | constructSubcomponent (const std::string &name) |
| Construct a subcomponent as a data member of this Component. More... | |
| template<class C = Component> | |
| const C & | getMemberSubcomponent (MemberSubcomponentIndex ix) const |
| template<class C = Component> | |
| C & | updMemberSubcomponent (MemberSubcomponentIndex ix) |
| void | adoptSubcomponent (Component *subcomponent) |
| Adopt a component as a subcomponent of this Component. More... | |
| size_t | getNumImmediateSubcomponents () const |
| Get the number of Subcomponents immediately owned by this Component. More... | |
| size_t | getNumMemberSubcomponents () const |
| Get the number of Subcomponents that are data members of this Component. More... | |
| size_t | getNumPropertySubcomponents () const |
| Get the number of Subcomponents that are properties of this Component. More... | |
| size_t | getNumAdoptedSubcomponents () const |
| Get the number of Subcomponents adopted by this Component. More... | |
| std::vector< SimTK::ReferencePtr< const Component > > | getImmediateSubcomponents () const |
| Access this Component's immediate subcomponents (not those owned by subcomponents) More... | |
| template<class C > | |
| const C * | traversePathToComponent (ComponentPath path) const |
| void | setNextSubcomponentInSystem (const Component &sub) const |
| Helper method to enable Component makers to specify the order of their subcomponents to be added to the System during addToSystem(). More... | |
| void | resetSubcomponentOrder () |
| resetSubcomponentOrder clears this Component's list of ordered subcomponents (but otherwise leaves subcomponents untouched). More... | |
| const Component & | get_components (int i) const |
| Get the value of the i-th element of the components property. More... | |
| Component & | upd_components (int i) |
| Get a writable reference to the i-th element of the components property. More... | |
| void | set_components (int i, const Component &value) |
| Set the value of the i-th element of components property. More... | |
| int | append_components (const Component &value) |
| Append an element to the components property. More... | |
| virtual void | extendAddComponent (Component *subcomponent) |
| Perform any secondary operations, e.g. More... | |
| void | initComponentTreeTraversal (const Component &root) const |
| Build the tree of Components from this component through its descendants. More... | |
| virtual void | extendAddToSystemAfterSubcomponents (SimTK::MultibodySystem &system) const |
| Add appropriate Simbody elements (if needed) to the System after your component's subcomponents have had a chance to add themselves to the system. More... | |
| virtual void | extendInitStateFromProperties (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. More... | |
| virtual void | extendSetPropertiesFromState (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. More... | |
| virtual void | 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. More... | |
| void | setStateVariableDerivativeValue (const SimTK::State &state, const std::string &name, double deriv) const |
| Set the derivative of a state variable by name when computed inside of this Component's computeStateVariableDerivatives() method. More... | |
| virtual void | extendRealizeTopology (SimTK::State &state) const |
| Obtain state resources that are needed unconditionally, and perform computations that depend only on the system topology. More... | |
| virtual void | extendRealizeModel (SimTK::State &state) const |
| Obtain and name state resources (like state variables allocated by an underlying Simbody component) that may be needed, depending on modeling options. More... | |
| virtual void | extendRealizeInstance (const SimTK::State &state) const |
| Perform computations that depend only on instance variables, like lengths and masses. More... | |
| virtual void | extendRealizeTime (const SimTK::State &state) const |
| Perform computations that depend only on time and earlier stages. More... | |
| virtual void | extendRealizePosition (const SimTK::State &state) const |
| Perform computations that depend only on position-level state variables and computations performed in earlier stages (including time). More... | |
| virtual void | extendRealizeVelocity (const SimTK::State &state) const |
| Perform computations that depend only on velocity-level state variables and computations performed in earlier stages (including position, and time). More... | |
| virtual void | extendRealizeDynamics (const SimTK::State &state) const |
| Perform computations (typically forces) that may depend on dynamics-stage state variables, and on computations performed in earlier stages (including velocity, position, and time), but not on other forces, accelerations, constraint multipliers, or reaction forces. More... | |
| virtual void | extendRealizeAcceleration (const SimTK::State &state) const |
| Perform computations that may depend on applied forces. More... | |
| virtual void | extendRealizeReport (const SimTK::State &state) const |
| Perform computations that may depend on anything but are only used for reporting and cannot affect subsequent simulation behavior. More... | |
| void | addModelingOption (const std::string &optionName, int maxFlagValue) const |
| Add a modeling option (integer flag stored in the State) for use by this Component. More... | |
| void | addStateVariable (const std::string &stateVariableName, const SimTK::Stage &invalidatesStage=SimTK::Stage::Dynamics, bool isHidden=false) const |
| Add a continuous system state variable belonging to this Component, and assign a name by which to refer to it. More... | |
| void | addStateVariable (Component::StateVariable *stateVariable) const |
| The above method provides a convenient interface to this method, which automatically creates an 'AddedStateVariable' and allocates resources in the SimTK::State for this variable. More... | |
| void | addDiscreteVariable (const std::string &discreteVariableName, SimTK::Stage invalidatesStage) const |
| Add a system discrete variable belonging to this Component, 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. More... | |
| SimTK::MultibodySystem & | updSystem () const |
| Get writable reference to the MultibodySystem that this component is connected to. More... | |
| int | getStateIndex (const std::string &name) const |
| Get the index of a Component's continuous state variable in the Subsystem for allocations. More... | |
| SimTK::SystemYIndex | getStateVariableSystemIndex (const std::string &stateVariableName) const |
| Get the System Index of a state variable allocated by this Component. More... | |
| const SimTK::DiscreteVariableIndex | getDiscreteVariableIndex (const std::string &name) const |
| Get the index of a Component's discrete variable in the Subsystem for allocations. More... | |
| template<typename T > | |
| PropertyIndex | constructSocket (const std::string &name, const std::string &propertyComment) |
| Construct a specialized Socket for this Component's dependence on another Component. More... | |
| template<typename T , typename CompType = Component> | |
| bool | constructOutput (const std::string &name, T(CompType::*const memFunc)(const SimTK::State &) const, const SimTK::Stage &dependsOn=SimTK::Stage::Acceleration) |
| Construct an output for a member function of the same component. More... | |
| template<typename T , typename CompType = Component> | |
| bool | constructOutput (const std::string &name, const T &(CompType::*const memFunc)(const SimTK::State &) const, const SimTK::Stage &dependsOn=SimTK::Stage::Acceleration) |
| This variant handles component member functions that return the output value by const reference (const T&). More... | |
| template<typename T , typename CompType > | |
| bool | constructListOutput (const std::string &name, T(CompType::*const memFunc)(const SimTK::State &, const std::string &channel) const, const SimTK::Stage &dependsOn=SimTK::Stage::Acceleration) |
| Construct an output that can have multiple channels. More... | |
| bool | constructOutputForStateVariable (const std::string &name) |
| Construct an Output for a StateVariable. More... | |
| template<typename T > | |
| PropertyIndex | constructInput (const std::string &name, bool isList, const std::string &propertyComment, const SimTK::Stage &requiredAtStage=SimTK::Stage::Instance) |
| Construct an Input (socket) for this Component's dependence on an Output signal. More... | |
| template<class T > | |
| CacheVariable< T > | addCacheVariable (std::string name, T variablePrototype, SimTK::Stage dependsOnStage) const |
| Add a state cache entry belonging to this Component to hold calculated values that must be automatically invalidated when certain state values change. More... | |
| void | setOwner (const Component &owner) |
| Set this Component's reference to its owning Component 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) | |
| 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... | |
| template<class T > | |
| void | checkPropertyValueIsPositive (const Property< T > &p) const |
| Throw an exception if any of the property's values are not positive. More... | |
| template<class T > | |
| void | checkPropertyValueIsInSet (const Property< T > &p, const std::set< T > &set) const |
| Throw an exception if any of the property's values are not in the provided set. More... | |
| template<class T > | |
| void | checkPropertyValueIsInRangeOrSet (const Property< T > &p, const T &lower, const T &upper, const std::set< T > &set) const |
| Throw an exception if any of the property's values are neither in the provided range nor in the provided set. 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... | |
| void | clearObjectIsUpToDateWithProperties () |
| For testing or debugging purposes, manually clear the "object is up to
date with respect to properties" flag. More... | |
| void | makeObjectNamesConsistentWithProperties () |
| Make sure the name of an object is consistent with its property type. 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... | |
| Static Protected Member Functions inherited from OpenSim::Component | |
| static void | prependComponentPathToConnecteePath (Component &subcomponent) |
| For internal use. More... | |
| Protected Attributes inherited from OpenSim::ModelComponent | |
| SimTK::ReferencePtr< Model > | _model |
| The model this component belongs to. More... | |
| Protected Attributes inherited from OpenSim::Object | |
| PropertySet | _propertySet |
| OBSOLETE: Property_Deprecated set for serializable member variables of this and derived classes. More... | |
| Static Protected Attributes inherited from OpenSim::ModelComponent | |
| static const SimTK::Vec3 | InvalidScaleFactors |
| Returned by getScaleFactors() if the ScaleSet does not contain scale factors for the base Body associated with the specified Frame. 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... | |
Umberger2010MuscleMetabolicsProbe is a Probe ModelComponent for computing the net metabolic energy rate of a set of Muscles in the model during a simulation.
The discussion here is based on the following papers:
Umberger, B. R. (2010). Stance and swing phase costs in human walking. J R Soc Interface 7, 1329-40.
Note that the equations below that describe the particular implementation of Umberger2010MuscleMetabolicsProbe may slightly differ from the equations described in the representative publications above. Note also that we define positive muscle velocity to indicate lengthening (eccentric contraction) and negative muscle velocity to indicate shortening (concentric contraction).
Muscle metabolic power (or rate of metabolic energy consumption) is equal to the rate at which heat is liberated plus the rate at which work is done:
Edot = Bdot + sumOfAllMuscles(Adot + Mdot + Sdot + Wdot).
This probe also uses muscle parameters stored in the MetabolicMuscle object for each muscle. The full set of all MetabolicMuscles (MetabolicMuscleSet) is a property of this probe:
The recruitment model described by Bhargava et al. (2004) is used to set the slow-twitch fiber ratio used in the calculations below. The ratio specified by the user indicates the composition of the muscle; this value is used only at full excitation (i.e., when all fibers are recruited). As excitation decreases from 1 to 0, the proportion of recruited fibers that are slow-twitch fibers increases from r to 1. See Bhargava, L.J., Pandy, M.G., Anderson, F.C. (2004) A phenomenological model for estimating metabolic energy consumption in muscle contraction. J Biomech 37:81-88 and Uchida et al. (2016). To assume a constant ratio of slow- and fast-twitch fiber recruitment, set the 'use_Bhargava_recruitment_model' property to false.
If basal_rate_on is set to true, then Bdot is calculated as follows:
Bdot = basal_coefficient * (m_body^basal_exponent)
If activation_maintenance_rate_on is set to true, then Adot+Mdot is calculated as follows:
Adot+Mdot = [128*(1-r) + 25] * A^0.6 * S , l_CE <= l_CE_opt
Adot+Mdot = (0.4*[128*(1-r) + 25] + 0.6*[128*(1-r) + 25]*F_CE_iso) * A^0.6 * S , l_CE > l_CE_opt
If shortening_rate_on is set to true, then Sdot is calculated as follows:
Sdot = m * (-[(alphaS_slow * v_CE_norm * r) + (alphaS_fast * v_CE_norm * (1-r))] * A^2 * S) , l_CE <= l_CE_opt & v_CE >= 0 (concentric / isometric contraction)
Sdot = m * (-[(alphaS_slow * v_CE_norm * r) + (alphaS_fast * v_CE_norm * (1-r))] * A^2 * S * F_iso) , l_CE > l_CE_opt & v_CE >= 0 (concentric / isometric contraction)
Sdot = m * (alphaL * v_CE_norm * A * S) , l_CE <= l_CE_opt & v_CE < 0 (eccentric contraction)
Sdot = m * (alphaL * v_CE_norm * A * S * F_CE_iso) , l_CE > l_CE_opt & v_CE < 0 (eccentric contraction)
If mechanical_work_rate_on is set to true, then Wdot is calculated as follows:
Wdot = -(F_CE * v_CE)
During eccentric contraction, the magnitude of the (negative) mechanical work rate can exceed that of the total (positive) heat rate, resulting in a flow of energy into the fiber. Experiments indicate that the chemical processes involved in fiber contraction cannot be reversed, and most of the energy that is absorbed during eccentric contraction (in increased cross-bridge potentials, for example) is eventually converted into heat. Thus, we increase Sdot (if necessary) to ensure Edot > 0 for each muscle. See Constable, J.K., Barclay, C.J., Gibbs, C.L. (1997) Energetics of lengthening in mouse and toad skeletal muscles. J Physiol 505:205-215 and Uchida et al. (2016). To allow muscles to have negative total power, set the 'forbid_negative_total_power' property to false.
Note that if enforce_minimum_heat_rate_per_muscle == true AND activation_maintenance_rate_on == shortening_rate_on == true, then the total heat rate (AMdot + Sdot) will be capped to a minimum value of 1.0 W/kg (Umberger(2003), page 104).
Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameter is an Object class that holds the metabolic parameters required to calculate metabolic power for a single muscle.
REQUIRED PROPERTIES
OPTIONAL PROPERTIES
| typedef std::map<std::string, Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameter*> OpenSim::Umberger2010MuscleMetabolicsProbe::MuscleMap |
MuscleMap typedef.
This typedef might be useful within the member functions of this class.
This is generated by the OpenSim_DECLARE_*_OBJECT macros.
Use this typedef to refer to the superclass of this class.
Avoid using the explicit type name of the superclass; this would introduce bugs if the superclass is changed.
This is generated by the OpenSim_DECLARE_*_OBJECT macros.
| OpenSim::Umberger2010MuscleMetabolicsProbe::Umberger2010MuscleMetabolicsProbe | ( | ) |
Default constructor.
| OpenSim::Umberger2010MuscleMetabolicsProbe::Umberger2010MuscleMetabolicsProbe | ( | const bool | activation_maintenance_rate_on, |
| const bool | shortening_rate_on, | ||
| const bool | basal_rate_on, | ||
| const bool | work_rate_on | ||
| ) |
Convenience constructor.
| void OpenSim::Umberger2010MuscleMetabolicsProbe::addMuscle | ( | const std::string & | muscleName, |
| double | ratio_slow_twitch_fibers | ||
| ) |
Add a muscle and its parameters so that it can be included in the metabolic analysis.
| void OpenSim::Umberger2010MuscleMetabolicsProbe::addMuscle | ( | const std::string & | muscleName, |
| double | ratio_slow_twitch_fibers, | ||
| double | muscle_mass | ||
| ) |
Add a muscle and its parameters so that it can be included in the metabolic analysis.
|
inlineoverride |
This allows copy assignment in the Java GUI.
| Exception | if the argument is not of type Umberger2010MuscleMetabolicsProbe. |
|
inlineoverridevirtual |
Create a new heap-allocated copy of the concrete object to which this Object refers.
It is up to the caller to delete the returned object when no longer needed. Every concrete object deriving from Object implements this pure virtual method automatically, via the declaration macro it invokes (e.g., OpenSim_DECLARE_CONCRETE_OBJECT()). Note that the concrete class overrides modify the return type to be a pointer to the concrete object; that still overrides the base class method because the return type is covariant with (that is, derives from) Object.
Implements OpenSim::Probe.
|
overridevirtual |
Compute muscle metabolic power.
Implements OpenSim::Probe.
|
inline |
Get the value of the activation_maintenance_rate_on property.
|
inline |
Get the value of the aerobic_factor property.
|
inline |
Get the value of the basal_coefficient property.
|
inline |
Get the value of the basal_exponent property.
|
inline |
Get the value of the basal_rate_on property.
|
inline |
Get the value of the enforce_minimum_heat_rate_per_muscle property.
|
inline |
Get the value of the forbid_negative_total_power property.
|
inline |
Get the value of the include_negative_mechanical_work property.
|
inline |
Get the value of the mechanical_work_rate_on property.
|
inline |
Get the value of the muscle_effort_scaling_factor property.
|
inline |
Get the value of the report_total_metabolics_only property.
|
inline |
Get the value of the shortening_rate_on property.
|
inline |
Get the value of the Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet property.
|
inline |
Get the value of the use_Bhargava_recruitment_model property.
|
inlinestatic |
This returns "Umberger2010MuscleMetabolicsProbe".
See getConcreteClassName() if you want the class name of the underlying concrete object instead.
This is generated by the OpenSim_DECLARE_*_OBJECT macros.
|
inlineoverridevirtual |
Returns the class name of the concrete Object-derived class of the actual object referenced by this Object, as a string.
This is the string that is used as the tag for this concrete object in an XML file. Every concrete class derived from Object automatically overrides this method via the declaration macro it uses. See getClassName() to get the class name of the referencing (possibly abstract) class rather than the concrete object.
Implements OpenSim::Probe.
| double OpenSim::Umberger2010MuscleMetabolicsProbe::getDensity | ( | const std::string & | muscleName | ) | const |
Get the density for an existing muscle (kg/m^3).
| double OpenSim::Umberger2010MuscleMetabolicsProbe::getMuscleMass | ( | const std::string & | muscleName | ) | const |
Get the muscle mass used in the metabolic analysis.
The value returned will depend on if the muscle mass is explicitly provided (i.e. isUsingProvidedMass = true), or if it is being automatically calculated from muscle data already present in the model (i.e. isUsingProvidedMass = true).
| int OpenSim::Umberger2010MuscleMetabolicsProbe::getNumMetabolicMuscles | ( | ) | const |
Get the number of muscles being analyzed in the metabolic analysis.
|
overridevirtual |
Returns the number of probe inputs in the vector returned by computeProbeInputs().
Implements OpenSim::Probe.
|
overridevirtual |
Returns the column labels of the probe values for reporting.
Currently uses the Probe name as the column label, so be sure to name your probe appropriately!
Implements OpenSim::Probe.
| double OpenSim::Umberger2010MuscleMetabolicsProbe::getRatioSlowTwitchFibers | ( | const std::string & | muscleName | ) | const |
Get the ratio of slow twitch fibers for an existing muscle.
| double OpenSim::Umberger2010MuscleMetabolicsProbe::getSpecificTension | ( | const std::string & | muscleName | ) | const |
Get the specific tension for an existing muscle (Pascals (N/m^2)).
| bool OpenSim::Umberger2010MuscleMetabolicsProbe::isUsingProvidedMass | ( | const std::string & | muscleName | ) |
Get whether the muscle mass is being explicitly provided.
True means that it is using the property 'provided_muscle_mass' False means that the muscle mass is being calculated from muscle properties.
| void OpenSim::Umberger2010MuscleMetabolicsProbe::removeMuscle | ( | const std::string & | muscleName | ) |
Remove a muscle from the metabolic analysis.
|
inlinestatic |
For use in MATLAB and Python to access the concrete class.
Example: cObj = Umberger2010MuscleMetabolicsProbe.safeDownCast(obj). This is equivalent to dynamic_cast<Umberger2010MuscleMetabolicsProbe*>(obj) in C++.
|
inline |
Set the value of the activation_maintenance_rate_on property.
|
inline |
Set the value of the aerobic_factor property.
|
inline |
Set the value of the basal_coefficient property.
|
inline |
Set the value of the basal_exponent property.
|
inline |
Set the value of the basal_rate_on property.
|
inline |
Set the value of the enforce_minimum_heat_rate_per_muscle property.
|
inline |
Set the value of the forbid_negative_total_power property.
|
inline |
Set the value of the include_negative_mechanical_work property.
|
inline |
Set the value of the mechanical_work_rate_on property.
|
inline |
Set the value of the muscle_effort_scaling_factor property.
|
inline |
Set the value of the report_total_metabolics_only property.
|
inline |
Set the value of the shortening_rate_on property.
|
inline |
Set the value of the Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet property.
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inline |
Set the value of the use_Bhargava_recruitment_model property.
| void OpenSim::Umberger2010MuscleMetabolicsProbe::setDensity | ( | const std::string & | muscleName, |
| const double & | density | ||
| ) |
Set the density for an existing muscle (kg/m^3).
| void OpenSim::Umberger2010MuscleMetabolicsProbe::setRatioSlowTwitchFibers | ( | const std::string & | muscleName, |
| const double & | ratio | ||
| ) |
Set the ratio of slow twitch fibers for an existing muscle.
| void OpenSim::Umberger2010MuscleMetabolicsProbe::setSpecificTension | ( | const std::string & | muscleName, |
| const double & | specificTension | ||
| ) |
Set the specific tension for an existing muscle (Pascals (N/m^2)).
|
inline |
Get a writable reference to the activation_maintenance_rate_on property.
|
inline |
Get a writable reference to the aerobic_factor property.
|
inline |
Get a writable reference to the basal_coefficient property.
|
inline |
Get a writable reference to the basal_exponent property.
|
inline |
Get a writable reference to the basal_rate_on property.
|
inline |
Get a writable reference to the enforce_minimum_heat_rate_per_muscle property.
|
inline |
Get a writable reference to the forbid_negative_total_power property.
|
inline |
Get a writable reference to the include_negative_mechanical_work property.
|
inline |
Get a writable reference to the mechanical_work_rate_on property.
|
inline |
Get a writable reference to the muscle_effort_scaling_factor property.
|
inline |
Get a writable reference to the report_total_metabolics_only property.
|
inline |
Get a writable reference to the shortening_rate_on property.
|
inline |
Get a writable reference to the Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet property.
|
inline |
Get a writable reference to the use_Bhargava_recruitment_model property.
| void OpenSim::Umberger2010MuscleMetabolicsProbe::useCalculatedMass | ( | const std::string & | muscleName | ) |
Set an existing muscle to calculate its own mass.
| void OpenSim::Umberger2010MuscleMetabolicsProbe::useProvidedMass | ( | const std::string & | muscleName, |
| double | providedMass | ||
| ) |
Set an existing muscle to use a provided muscle mass.
| bool OpenSim::Umberger2010MuscleMetabolicsProbe::activation_maintenance_rate_on |
"Specify whether activation & maintenance heat rate is to be calculated (true/false)."
This property appears in XML files under the tag <activation_maintenance_rate_on>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Umberger2010MuscleMetabolicsProbe::aerobic_factor |
"Aerobic scale factor (S=1.0 for primarily anaerobic conditions and S=1.5 " "for primarily aerobic conditions. See Umberger et al., (2003)."
This property appears in XML files under the tag <aerobic_factor>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Umberger2010MuscleMetabolicsProbe::basal_coefficient |
"Basal metabolic coefficient."
This property appears in XML files under the tag <basal_coefficient>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Umberger2010MuscleMetabolicsProbe::basal_exponent |
"Basal metabolic exponent."
This property appears in XML files under the tag <basal_exponent>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Umberger2010MuscleMetabolicsProbe::basal_rate_on |
"Specify whether basal heat rate is to be calculated (true/false)."
This property appears in XML files under the tag <basal_rate_on>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Umberger2010MuscleMetabolicsProbe::enforce_minimum_heat_rate_per_muscle |
"Specify whether the total heat rate for a muscle will be clamped to a " "minimum value of 1.0 W/kg (true/false)."
This property appears in XML files under the tag <enforce_minimum_heat_rate_per_muscle>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Umberger2010MuscleMetabolicsProbe::forbid_negative_total_power |
"Specify whether the total power for each muscle must remain positive " "(true/false). Disable to use the model as published in Umberger " "(2010)."
This property appears in XML files under the tag <forbid_negative_total_power>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Umberger2010MuscleMetabolicsProbe::include_negative_mechanical_work |
"Specify whether negative mechanical work will be included in Wdot and " "a coefficient of 4.0 will be used to calculate alpha_L (true/false). " "Disable to use the model as published in Umberger (2010)."
This property appears in XML files under the tag <include_negative_mechanical_work>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Umberger2010MuscleMetabolicsProbe::mechanical_work_rate_on |
"Specify whether mechanical work rate is to be calculated (true/false)."
This property appears in XML files under the tag <mechanical_work_rate_on>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| double OpenSim::Umberger2010MuscleMetabolicsProbe::muscle_effort_scaling_factor |
"Scale the excitation and activation values used by the probe to " "compensate for solutions with excessive coactivation (e.g., when a " "suboptimal tracking strategy is used)."
This property appears in XML files under the tag <muscle_effort_scaling_factor>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Umberger2010MuscleMetabolicsProbe::report_total_metabolics_only |
"If set to false, the individual muscle metabolics, basal rate, and " "total summation will be reported. If set to true, only the total " "summation will be reported."
This property appears in XML files under the tag <report_total_metabolics_only>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Umberger2010MuscleMetabolicsProbe::shortening_rate_on |
"Specify whether shortening heat rate is to be calculated (true/false)."
This property appears in XML files under the tag <shortening_rate_on>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
| Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet OpenSim::Umberger2010MuscleMetabolicsProbe::Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet |
"A set containing, for each muscle, the parameters " "required to calculate muscle metabolic power."
This property appears in XML files under the tag <Umberger2010MuscleMetabolicsProbe_MetabolicMuscleParameterSet>. This property was generated with the OpenSim_DECLARE_UNNAMED_PROPERTY macro; see Property to learn about the property system.
| bool OpenSim::Umberger2010MuscleMetabolicsProbe::use_Bhargava_recruitment_model |
"Specify whether the recruitment model described by Bhargava et al. " "(2004) will used to determine the slow-twitch fiber ratio " "(true/false). Disable to use the model as published in Umberger " "(2010)."
This property appears in XML files under the tag <use_Bhargava_recruitment_model>. This property was generated with the OpenSim_DECLARE_PROPERTY macro; see Property to learn about the property system.
1.8.13 