Gait3d Class Reference

The class describes the Gait3d model. More...

Inheritance diagram for Gait3d:

Public Member Functions
function	extractControl (in obj, in type, in controlname)
	Function to obtain index of contol with a specific type (and name)
function	extractState (in obj, in type, in statename)
	Function to obtain index of state with a specific type (and name)
function	Gait3d (in opensimfile)
	Constructor setting default Gait3d object.
function	getCoP (in obj, in grf)
	Function to calculate the center of pressure.
function	getDynamics (in obj, in x, in xdot, in u)
	Function computing implicit differential equation for 3D musculoskeletal model.
function	getErate_bhargava (in obj, in F_ce, in stim, in act, in l_ce, in v_ce, in t_stim)
	Model function to calculate the energy rate of a single time step using Bhargava et al.
function	getErate_Houdijk (in obj, in F_ce, in act, in l_ce, in v_ce)
	Model function to calculate the energy rate of a single time.
function	getErate_Lichtwark (in obj, in F_ce, in act, in l_ce, in v_ce, in t_stim)
	Model function to calculate the energy rate of a single time step using a continuous version of Lichtwark & Wilson's model.
function	getErate_margaria (in obj, in F_ce, in v_ce)
	Model function to calculate the energy rate of a single time step using Margaria's model.
function	getErate_Minetti (in obj, in act, in v_ce)
	Model function to calculate the energy rate of a single time.
function	getErate_uchida (in obj, in F_ce, in stim, in act, in l_ce, in v_ce)
	Model function to calculate the energy rate of a single time.
function	getErate_Umberger (in obj, in F_ce, in stim, in act, in l_ce, in v_ce)
	Model function to calculate the energy rate of a single time step with Umberger et al.
function	getEratec_bhargava (in obj, in F_ce, in stim, in act, in l_ce, in v_ce, in dFdx, in dFdxdot, in epsilon)
	Model function to calculate the energy rate of a single time step using a continuous version of Bhargava et al.
function	getEratec_Houdijk (in obj, in F_ce, in act, in l_ce, in v_ce, in dFdx, in dFdxdot, in epsilon)
	Model function to calculate the energy rate of a single time step using a continuous version of Houdijk et al.
function	getEratec_Lichtwark (in obj, in F_ce, in act, in l_ce, in v_ce, in dFdx, in dFdxdot, in epsilon)
	Model function to calculate the energy rate of a single time step using a continuous version of Lichtwark & Wilson's model.
function	getEratec_margaria (in obj, in F_ce, in v_ce, in dFdx, in dFdxdot, in epsilon)
	Model function to calculate the energy rate of a single time step using a continuous version of Margaria's model.
function	getEratec_Minetti (in obj, in act, in v_ce)
	Model function to calculate the energy rate of a single time step using Minetti's model.
function	getEratec_umberger (in obj, in F_ce, in stim, in act, in l_ce, in v_ce, in dFdx, in dFdxdot, in epsilon)
	Model function to calculate the energy rate of a single time step with the continuous version of Umberger et al.
function	getFkin (in obj, in q, in qdot)
	Function returns position and orientation of body segments, for the system in position q.
function	getGRF (in obj, in x)
	Function returns the ground reaction forces for the system in state x.
function	getJointmoments (in obj, in x, in u)
	Function returns joint moments, for the system in state x.
function	getLCE (in obj, in x)
	Function returns length of contractile element, for the system in state x.
function	getLdotCE (in obj, in xdot)
	Function returns length change of contractile element, for the system in state x.
function	getMetabolicRate_pernode (in obj, in x, in xdot, in u, in t_stim, in name, in getCont, in epsilon, in exponent)
	Model function to calculate metabolic cost of a movement.
function	getMuscleCEforces (in obj, in x, in xdot)
	Function returning muscle forces of CE for the system in state x.
function	getMuscleCEpower (in obj, in x, in xdot)
	Function returns power generated by muscle contractile elements, for the system in state x.
function	getMuscleforces (in obj, in x)
	Function returns muscle forces, for the system in state x.
function	getPassiveJointmoments (in obj, in x)
	Function returns passive joint moments, for the system in state x.
function	setbodymass (in obj, in bodymass)
	Function to set body mass, does not influence the.
function	setMuscles (in obj, in muscles)
	Function to set the muscles table.
function	setSegmentMass (in obj, in segmentName, in segmentMass)
	Function to set segment mass.
function	setSegments (in obj, in segmentTable)
	Function to set segment Table.
function	showMarker (in obj, in x, in markerTable, in measuredMean)
	Function to plot marker positions.
virtual	showStick (in obj, in x)
	Abstract function to show model as stick figure.
function	showStick (in obj, in x, in range, in plotFeet, in plotGRF, in plotCPs, in plotJointCOSYs, in az, in el)
	Function to show model as stick figure.
virtual	simuAccGyro (in obj, in data, in q, in qd, in qdd)
	Abstract function to simulate acceleration and gyroscope signals.
function	simuAccGyro (in obj, in variables, in q, in qd, in qdd, in idxSegment, in idxAcc, in idxGyro, in dlocalAll, in plocalAll)
	Matlab function to simulates sensors placed on 3D model.
function	simuMarker (in obj, in variables, in q, in idxSegment, in plocalAll, in dlocalAll)
	Matlab function to simulates markers placed on 3D model.

Static Public Member Functions
function	createRandomPerson (in obj, in symmusrand, in massratio, in lengthratio)
	Function to make MEX functions.
function	getMexFiles (in osimName, in clean, in rebuild_contact, in debugMode)
	Function to make MEX functions.

Public Attributes
Property	CPs
	Table: Contact points.
Property	dofs
	Table: Degrees of freedom (Range of Dofs should not be changed here.
Property	drag_coefficient
	Double: Air drag coefficient in N/(m/s)^2 (default: 0.2128)
Property	gravity
	Double array: Gravity vector in m/(s^2)
Constant Property	GRFNAMES = {'rightFx', 'rightFy', 'rightFz', 'rightMx', 'rightMy', 'rightMz', 'leftFx', 'leftFy', 'leftFz', 'leftMx', 'leftMy', 'leftMz' }
	Cell array with string: Gives the names for the GRF vector returned by getGRF()
Property	joints
	Table: Joints.
Property	markers
	Table: Markers (Containing also the CPs. Their names start with 'CP')
Property	mExtraScaleFactor
	Double: Scale factor for extra torques in Nm (default: 100 since we used this in previous simulations.
Property	muscles
	Table: Muscles.
Property	torques
	Table: Torque actuators.
Property	wind_speed
	Double: Wind speed in direction of +X in m/s (default: 0)

Protected Member Functions
function	computeMomentArms (in obj, in range_muscleMoment, in examine, in name)
	Function to generate muscle length polynomials from Opensim muscle paths.
function	getCoM (in obj, in x)
	Function to calculate the center of mass.
function	getDynamicsCPOffset (in obj, in x, in xdot, in u, in CPYOffset)
	Function computing implicit differential equation for 3D musculoskeletal model which allows an adaption of the CP position.
function	initMex (in obj)
	Initialize model mex file.
function	initModel (in obj)
	Function to initialize model with default parameters.
virtual	initModel (in obj, in vargin)
	Abstract function to initialize with default parameters.
function	loadMomentArms (in obj)
	Function to load or compute moment arms.
function	loadOsimFile (in obj, in osimfile)
	Function to load the content from the opensim file.
function	update_constraints (in obj)
	Function defining the table Gait3d.constraints.
function	update_controls (in obj)
	Function defining the table Gait3d.controls.
function	update_idxControls (in obj)
	Function defining Model.hidxControls.
function	update_idxForward (in obj)
	Function defining Model.idxForward.
function	update_idxForwardAll (in obj)
	Function defining Model.idxForwardAll.
function	update_idxSideward (in obj)
	Function defining Model.idxSideward.
function	update_idxSidewardAll (in obj)
	Function defining Model.idxSidewardAll.
function	update_idxStates (in obj)
	Function defining Model.hidxStates.
function	update_idxSymmetry (in obj)
	Function defining Gait3d.idxSymmetry.
function	update_idxTorqueDof (in obj)
	Function defining Model.idxTorqueDof.
function	update_idxUpward (in obj)
	Function defining Model.idxUpward.
function	update_mexParameter (in obj, in src, in evnt)
	Function performed to update the parameter of the mex and the tables.
function	update_states (in obj)
	Function defining the table Gait3d.states.

Static Protected Member Functions
static function	plotgrf (in F, in CoP, in color)
	Function used in showStick() to plot GRFs.
function	readOsim (in osimfile)
	Function to load OpenSim model in Matlab as structure.

Protected Attributes
Property	bodyheight
Property	bodymass
	Double: Bodymass in kg (Is computed by summing up all body mass except talus.
Property	constraints
	Table: Information on constraints implemented in the mex and here.
Property	controls
	Table: Information on controls of the model.
Property	hdlMEX
	Handle: MEX function of the model for dynamics etc.
Property	idxForward
	Double array: Indices for forward translation.
Property	idxForwardAll
	Double array: Indices for forward translation, speed, position of contact points and force at contact points.
Property	idxSideward
	Double array: Indices for sideward translation.
Property	idxSidewardAll
	Double array: Indices for sideward translation, speed, position of contact points and force at contact points.
Property	idxSymmetry
	Struct: Double arrays with indices for symmetry to map right to left.
Property	idxTorqueDof
	Double array: Indices of dofs of torque actuators.
Property	idxUpward
	Double array: Indices for upward translation.
Property	init
	Double: Showing if the mex model is initialized.
Property	nConstraints
	Double: Number of constraints (height of Model.constraints)
Property	nControls
	Double: Number of controls (height of Model.controls)
Property	nCPs
	Double: Number of contact points (height of Model.CPs)
Property	nDofs
	Double: Number of degree of freedoms (height of Model.dofs)
Property	nJoints
	Double: Number of joints (height of Model.joints)
Property	nMarkers
	Double: Number of markers (height of Gait3d.markers)
Property	nMus
	Double: Number of muscles (height of Model.muscles)
Property	nSegments
	Double: Number of segments (height of Model.segments)
Property	nStates
	Double: Number of states (height of Model.states)
Property	nTor
	Double: Number of torque actuators (height of Model.torques)
Property	osim
	Struct: Information (name, file, modified, sha256) on opensim model.
Property	segments
	Table: Segments (Segment properties should not be changed)
Property	states
	Table: Information on states of the model.

Detailed Description

The class describes the Gait3d model.

• The model is based on Sam Hamner's running model: https://simtk.org/home/runningsim
• The code describes the basic Gait3d model
• The model is defined by the .osim file. Scaling must be done previously on the .osim file.
• Currently only the following models can be used
  • '3D Gait Model with Simple Arms'
  • '3D Gait Model with Simple Arms and Pelvis Rotation-Obliquity-Tilt Sequence'
  • 'gait24dof22musc'

Examples

/home/runner/work/BioMAC-Sim-Toolbox/BioMAC-Sim-Toolbox/ExampleScripts/+IntroductionExamples/script3D.m.

Constructor & Destructor Documentation

Gait3d()

function Gait3d

(

in

opensimfile

)

Constructor setting default Gait3d object.

Initializes the model and builds and initializes the mex function. The mex functions can be also build with other options if Gait3d.getMexFiles(osimName) is called before the constructor is called.

Sets a new default for Gait3d.mExtraScaleFactor: 10 Nm

The standard model can be called using:

Gait3d('gait3d.osim')

The osim file must be in the matlab path.

Parameters

opensimfile

String: Opensim file with path, name and extension

Return values

obj	Gait3d class object

Member Function Documentation

computeMomentArms()

function computeMomentArms ( in  obj, in  range_muscleMoment, in  examine, in  name  )

protected

Function to generate muscle length polynomials from Opensim muscle paths.

For each muscle, the generalized coordinates are moved through their entire range, in a specified number of steps (currently 6). So for a muscle that spans 4 dofs, we will examine 6^4 = 1296 poses. For each pose, the Opensim API is used to obtain the moment arms of the muscle. Also the API is used to obtain the muscle-tendon length when all generalized coordinates are zero.

Stepwise regression is done on the moment arm data to produce the best set of polynomial terms. The addition of terms stops when one of the following is true:

1. RMS difference between moment arms from Opensim and polynomial, relative to the largest moment arm, is less than "relerror" (currently 0.05)
2. Adding another term would decrease the RMS difference by less than "minerrorchange" (currently 0.01)
3. The maximum number of terms (currently 40) has been reached.

The examine option is intended for model developers to inspect the polynomials and make sure they are good enough. When regenerating polynomials for a model that has already been tested, the examine and name options should not be used.

Saves results at strrep(which(settings.osimfile), '.osim', '_momentarms.mat')

Parameters

obj	Gait3d class object
range_muscleMoment	Table: Ranges of DOFs which were used to fit polynomials
examine	(optional, default 0) when 1: plots results for each muscle and pauses for inspection
name	(optional) name of the muscle that should be processed (when missing, all are done)

Return values

momentarm_model

Struct: Resulting polynomials which are also saved at strrep(which(settings.osimfile), '.osim', '_momentarms.mat')

createRandomPerson()

function createRandomPerson ( in  obj, in  symmusrand, in  massratio, in  lengthratio  )

static

Function to make MEX functions.

Creates a musculoskeletal model with random parameters

Parameters

symmusrand	double matrix: matrix with random numbers that will be used to randomze muscle parameters
massratio	(optional) ratio to be used for randomizing the mass of the body
lengthratio	(optional) ratio to be used for randomizing the length of the body

extractControl()

function extractControl ( in  obj, in  type, in  controlname  )

inherited

Function to obtain index of contol with a specific type (and name)

Parameters

obj	Model class object
type	String: Type of the control
controlname	(optional) String or cell array of strings: Name of the control

Return values

iControl

Double array: Indices in Model.controls matching type (and name)

extractState()

function extractState ( in  obj, in  type, in  statename  )

inherited

Function to obtain index of state with a specific type (and name)

Parameters

obj	Model class object
type	String: Type of the state
statename	(optional) String or cell array of strings: Name of the state

Return values

iState

Double array: Indices in Model.states matching type (and name)

getCoM()

function getCoM ( in  obj, in  x  )

protected

Function to calculate the center of mass.

It solves the center of pressure (CoM) coordinates from the locations of the individual centers of mass

Parameters

obj	Model class object
x	Double vector: state of system

Return values

CoM	Double vector: x, y, z location of center of mass

getCoP()

function getCoP ( in  obj, in  grf  )

inherited

Function to calculate the center of pressure.

It solves the center of pressure (COP) coordinates from: COP x F + Ty = M, where COP is a point in the XZ plane and Ty is the "free moment" on the Y axis. expand the equation:

1. COPy * Fz - COPz * Fy + 0 = Mx
2. COPz * Fx - COPx * Fz + Ty = My
3. COPx * Fy - COPy * Fx + 0 = Mz

Use COPy = 0, to get COPx = Mz / Fy and COPz = -Mx / Fy

For 2D, COPz will be 0.

Parameters

obj	Model class object
grf	Double vector: Ground contact vector containing Fx, Fy, Fz, Mx, My, Mz (right), and Fx, Fy, Fz, Mx, My, Mz (left) (12)

Return values

CoP_r	Double vector: Center of pressure in x, y and z direction for right foot (3)
CoP_l	Double vector: Center of pressure in x, y and z direction for left foot (3)

getDynamics()

function getDynamics ( in  obj, in  x, in  xdot, in  u  )

virtual

Function computing implicit differential equation for 3D musculoskeletal model.

This function calls the mex file of gait3d.c: [f, dfdx, dfdxdot, dfdumus, dfdMextra] = obj.hdlMEX('Dynamics',x,xdot,umus,Mextra);

with the neural excitation umus and the extra torques Mextra.

The dynamic residuals will be between fmin and fmax when inputs satisfy system dynamics : fmin <= f(x,dx/dt,umus,Mextra) <= fmax

The last four outputs are optional and some computation time is saved if you do not request all of them.

Parameters

obj	Gait3d class object
x	Double array: State of the model (Gait3d.nStates x 1)
xdot	Double array: State derivatives (Gait3d.nStates x 1)
u	Double array: Controls of the model (Gait3d.nControls x 1)

Return values

f	Double array: Dynamic residuals (Gait3d.nConstraints x 1)
dfdx	(optional) Double matrix: Transpose of Jacobian matrix df/dx (Gait3d.nStates x Gait3d.nConstraints)
dfdxdot	(optional) Double matrix: Transpose of Jacobian matrix df/dxdot (Gait3d.nStates x Gait3d.nConstraints)
dfdu	(optional) Double matrix: Transpose of Jacobian matrix df/du (Gait3d.nControls x Gait3d.nConstraints)

Reimplemented from Model.

getDynamicsCPOffset()

function getDynamicsCPOffset ( in  obj, in  x, in  xdot, in  u, in  CPYOffset  )

protected

Function computing implicit differential equation for 3D musculoskeletal model which allows an adaption of the CP position.

I calls Gait3d.getDynamics() and then overrights the entries to allow apply a vertical shift to the CP position.

Parameters

obj	Gait3d_CPOffset class object
x	Double array: State of the model (Gait3d.nStates x 1)
xdot	Double array: State derivatives (Gait3d.nStates x 1)
u	Double array: Controls of the model (Gait3d.nControls x 1)
CPYOffset	Double: Vertical offset of original CP positions applied to all CPs

Return values

f	Double array: Dynamic residuals (Gait3d.nConstraints x 1)
dfdx	(optional) Double matrix: Transpose of Jacobian matrix df/dx (Gait3d.nStates x Gait3d.nConstraints)
dfdxdot	(optional) Double matrix: Transpose of Jacobian matrix df/dxdot (Gait3d.nStates x Gait3d.nConstraints)
dfdu	(optional) Double matrix: Transpose of Jacobian matrix df/du (Gait3d.nControls x Gait3d.nConstraints)
dfdCPYOffset	(optional) Double matrix: Transpose of Jacobian matrix df/dCPYOffset (1 x Gait3d.nConstraints)

getErate_bhargava()

function getErate_bhargava ( in  obj, in  F_ce, in  stim, in  act, in  l_ce, in  v_ce, in  t_stim  )

inherited

Model function to calculate the energy rate of a single time step using Bhargava et al.

's model

Function to calculate the energy rate at a single time step using a continuous version of Bhargava et al.'s model. Model paper: Bhargava et al., J Biomech, 2004

Inputs are muscle states of the specific muscle that is considered.

Parameters

obj	Model object
F_ce	Force in the contractile element
stim	Stimulation of the muscle (between 0 and 1)
act	Activation level of the muscle (between 0 and 1)
l_ce	Normalized length of the contractile element
v_ce	Normalized velocity of the contractile element
t_stim	Duration of stimulation of muscle

The output of getEratec_bhargava.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	The energy expenditure during the current time step

getErate_Houdijk()

function getErate_Houdijk ( in  obj, in  F_ce, in  act, in  l_ce, in  v_ce  )

inherited

Model function to calculate the energy rate of a single time.

Function to calculate the energy rate at a single time step using Houdijk et al.'s model. Houdijk et al., J Biomech, 2006. The paper desription is not optimal, see comments

Inputs are muscle parameters of the specific muscle that is considered. Inputs are muscle states of the specific muscle that is considered.

Parameters

obj	Model object
F_ce	Force in the contractile element
act	Activation level of the muscle (between 0 and 1)
l_ce	Normalized length of the contractile element
v_ce	Normalized velocity of the contractile element

The output of getErate_Houdijk.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	The energy expenditure during the current time step
w	Muscle work during the current time step

getErate_Lichtwark()

function getErate_Lichtwark ( in  obj, in  F_ce, in  act, in  l_ce, in  v_ce, in  t_stim  )

inherited

Model function to calculate the energy rate of a single time step using a continuous version of Lichtwark & Wilson's model.

Function to calculate the energy rate at a single time step using Lichtwark & Wilson's model, described in the supplement of Lichtwark & Wilson, J Biomech, 2007. The exception in gamma (line 68), which is according to Lichtwark & Wilson, J Exp Biol, 2005, because results were better in the 2019 comparison paper

Inputs are muscle parameters of the specific muscle that is considered.

Parameters

obj	Model object
F_ce	Force in the contractile element
act	Activation level of the muscle (between 0 and 1)
l_ce	Normalized length of the contractile element
v_ce	Normalized velocity of the contractile element
t_stim	Duration of stimulation of muscle

The output of getErate_Lichtwark.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	The energy expenditure during the current time step

getErate_margaria()

function getErate_margaria ( in  obj, in  F_ce, in  v_ce  )

inherited

Model function to calculate the energy rate of a single time step using Margaria's model.

Function to calculate the energy rate at a single time step using Margaria's model: 25 % efficient during shortening, 120% during lengthening. Margaria, Int Z Angew Physiol Einschl Arbeitsphysiol, 1968

Inputs are muscle parameters of the specific muscle that is considered.

Parameters

obj	Model object
F_ce	Force in the contractile element
v_ce	Normalized velocity of the contractile element

The output of getErate_margaria.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	is the energy expenditure during the current time step

getErate_Minetti()

function getErate_Minetti ( in  obj, in  act, in  v_ce  )

inherited

Model function to calculate the energy rate of a single time.

Function to calculate the energy rate at a single time step using Minetti's model. Based on: Minetti & Alexander, J Theor Biol, 1997. Uses muscle-level work instead of torque-level

Inputs are muscle parameters of the specific muscle that is considered.

Parameters

obj	Model object
act	activation level of the muscle (between 0 and 1)
v_ce	current velocity of the contractile element

The output of getErate_Minetti is a double which is equal to the energy rate

Return values

Edot	is the energy expenditure during the current time step

getErate_uchida()

function getErate_uchida ( in  obj, in  F_ce, in  stim, in  act, in  l_ce, in  v_ce  )

inherited

Model function to calculate the energy rate of a single time.

Function to calculate the energy rate at a single time step using Uchida's model: Uchida et al., PLOS ONE, 2016

Inputs are muscle states of the specific muscle that is considered

Parameters

obj	Model class object
F_ce	Double vector: Muscle force of CE returned by obj.getMuscleCEforces(x) (Model.nMus x 1)
stim	Double vector: Stimulation of muscles = neural excitation u (Model.nMus x 1)
act	Double vector: Activation of muscles a (Model.nMus x 1)
l_ce	Double vector: Length of contractile element of muscles s (Model.nMus x 1)
v_ce	Double vector: Velocity of contractile element of muscles (Model.nMus x 1)

The output of getErate_uchida.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	Double vector: Energy expenditure during one time step (energy rate) in W (Model.nMus x 1)
w_ce	Double vector: Mechanical work rate of contractile element in W/kg (normalized to muscle mass) (Model.nMus x 1)
h_sl	Double vector: Heat rate due to shortening and lengthening of muscles in W/kg (normalized to muscle mass) (Model.nMus x 1)
h_am	Double vector: Heat rate from the activation of muscles and its maintenance in W/kg (normalized to muscle mass) (Model.nMus x 1)

getErate_Umberger()

function getErate_Umberger ( in  obj, in  F_ce, in  stim, in  act, in  l_ce, in  v_ce  )

inherited

Model function to calculate the energy rate of a single time step with Umberger et al.

's model. Ross Miller's code was also used as a reference.

Function to calculate the energy rate at a single time step using Umberger's model. It uses the 2010 version (no negative work): Umberger, J R Soc Interface, 2010 2003 (original) Version: Umberger et al., "A model of human muscle energy expenditure," Computer methods in biomechanics and biomedical engineering, vol. 6, no. 2, pp. 99–111, 2003.

Inputs are muscle states of the specific muscle that is considered

Parameters

obj	Gait2dc class object
F_ce	Double vector: Muscle force of CE returned by Model.getMuscleCEforces(x) (Model.nMus x 1)
stim	Double vector: Stimulation of muscles = neural excitation u (Model.nMus x 1)
act	Double vector: Activation of muscles a (Model.nMus x 1)
l_ce	Double vector: Length of contractile element of muscles s (Model.nMus x 1)
v_ce	Double vector: Velocity of contractile element of muscles (Model.nMus x 1)

The output of getErate_Umberger.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	Double vector: Energy expenditure during one time step (energy rate) in W (Model.nMus x 1)
w_ce	Double vector: Mechanical work rate of contractile element in W/kg (normalized to muscle mass) (Model.nMus x 1)
h_sl	Double vector: Heat rate due to shortening and lengthening of muscles in W/kg (normalized to muscle mass) (Model.nMus x 1)
h_am	Double vector: Heat rate from the activation of muscles and its maintenance in W/kg (normalized to muscle mass) (Model.nMus x 1)

getEratec_bhargava()

function getEratec_bhargava ( in  obj, in  F_ce, in  stim, in  act, in  l_ce, in  v_ce, in  dFdx, in  dFdxdot, in  epsilon  )

inherited

Model function to calculate the energy rate of a single time step using a continuous version of Bhargava et al.

's model

Function to calculate the energy rate at a single time step using a continuous version of Bhargava et al.'s model. Line 60, phi, was chosen based on graphs of phi as a function of t_stim, since t_stim cannot be differentiated. Model paper: bhargava et al., J Biomech, 2004

Inputs are muscle states of the specific muscle that is considered.

Parameters

obj	Model object
F_ce	Force in the contractile element
stim	Stimulation of the muscle (between 0 and 1)
act	Activation level of the muscle (between 0 and 1)
l_ce	Normalized length of the contractile element
v_ce	Normalized velocity of the contractile element
dFdx	Derivative of CE forces with respect to the state
dFdxdot	Derivative of CE forces with respect to the state derivative
epsilon	Measure of the nonlinearity of the continuous functions

The output of getEratec_bhargava.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	The energy expenditure during the current time step
dEdot	The gradient of Edot with respect to all states and inputs

getEratec_Houdijk()

function getEratec_Houdijk ( in  obj, in  F_ce, in  act, in  l_ce, in  v_ce, in  dFdx, in  dFdxdot, in  epsilon  )

inherited

Model function to calculate the energy rate of a single time step using a continuous version of Houdijk et al.

's model

Function to calculate the energy rate at a single time step using a continuous version of Houdijk et al.'s model. Houdijk et al., J Biomech, 2006.

Inputs are muscle parameters of the specific muscle that is considered. Inputs are muscle states of the specific muscle that is considered.

Parameters

obj	Model object
F_ce	Force in the contractile element
act	Activation level of the muscle (between 0 and 1)
l_ce	Normalized length of the contractile element
v_ce	Normalized velocity of the contractile element
dFdx	Derivative of CE forces with respect to the state
dFdxdot	Derivative of CE forces with respect to the state derivative
epsilon	Measure of the nonlinearity of the continuous functions

The output of getEratec_Houdijk.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	The energy expenditure during the current time step
dEdot	The gradient of Edot with respect to all states and inputs%

getEratec_Lichtwark()

function getEratec_Lichtwark ( in  obj, in  F_ce, in  act, in  l_ce, in  v_ce, in  dFdx, in  dFdxdot, in  epsilon  )

inherited

Model function to calculate the energy rate of a single time step using a continuous version of Lichtwark & Wilson's model.

Function to calculate the energy rate at a single time step using a continuous version of Lichtwark & Wilson's model, described in the supplement of Lichtwark & Wilson, J Biomech, 2007.

Inputs are muscle parameters of the specific muscle that is considered.

Parameters

obj	Model object
F_ce	Force in the contractile element
act	Activation level of the muscle (between 0 and 1)
l_ce	Normalized length of the contractile element
v_ce	Normalized velocity of the contractile element
dFdx	Derivative of CE forces with respect to the state
dFdxdot	Derivative of CE forces with respect to the state derivative
epsilon	Measure of the nonlinearity of the continuous functions

The output of getEratec_Lichtwark.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	The energy expenditure during the current time step
dEdot	The gradien

getEratec_margaria()

function getEratec_margaria ( in  obj, in  F_ce, in  v_ce, in  dFdx, in  dFdxdot, in  epsilon  )

inherited

Model function to calculate the energy rate of a single time step using a continuous version of Margaria's model.

Function to calculate the energy rate at a single time step using a continuous version of Margaria's model: 25 % efficient during shortening, 120% during lengthening. Margaria, Int Z Angew Physiol Einschl Arbeitsphysiol, 1968

Inputs are muscle parameters of the specific muscle that is considered.

Parameters

obj	Model object
F_ce	Force in the contractile element
v_ce	Normalized velocity of the contractile element
dFdx	Derivative of CE forces with respect to the state
dFdxdot	Derivative of CE forces with respect to the state derivative
epsilon	Measure of the nonlinearity of the continuous functions

The output of getEratec_margaria.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	is the energy expenditure during the current time step
dEdot	is the gradient of Edot with respect to all states and inputs

getEratec_Minetti()

function getEratec_Minetti ( in  obj, in  act, in  v_ce  )

inherited

Model function to calculate the energy rate of a single time step using Minetti's model.

No discsontinuities here, so it is the same as the original model.

Function to calculate the energy rate at a single time step using Minetti's model. Based on: Minetti & Alexander, J Theor Biol, 1997. Uses muscle-level work instead of torque-level

Inputs are muscle parameters of the specific muscle that is considered.

Parameters

obj	Model object
act	activation level of the muscle (between 0 and 1)
v_ce	current velocity of the contractile element

The output of getEratec_Minetti.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	is the energy expenditure during the current time step
dEdot	is the gradient of Edot with respect to all states and inputs

getEratec_umberger()

function getEratec_umberger ( in  obj, in  F_ce, in  stim, in  act, in  l_ce, in  v_ce, in  dFdx, in  dFdxdot, in  epsilon  )

inherited

Model function to calculate the energy rate of a single time step with the continuous version of Umberger et al.

's model

Function to calculate the energy rate at a single time step using a continuous version of Umberger's model. This one is published in Koelewijn, Dorscky et al., Comp Meth Biomed Biomech Eng, 2016, and uses the 2010 version (no negative work): Umberger, J R Soc Interface, 2010

Inputs are muscle states of the specific muscle that is considered.

Parameters

obj	Model object
F_ce	Force in the contractile element
stim	Stimulation of the muscle (between 0 and 1)
act	Activation level of the muscle (between 0 and 1)
l_ce	Normalized length of the contractile element
v_ce	Normalized velocity of the contractile element
dFdx	Derivative of CE forces with respect to the state
dFdxdot	Derivative of CE forces with respect to the state derivative
epsilon	Measure of the nonlinearity of the continuous functions

The output of getEratec_umberger.m is a double which is equal to the energy rate of the time step in W/kg

Return values

Edot	The energy expenditure during the current time step
dEdot	The gradient of Edot with respect to all states and inputs

getFkin()

function getFkin	(	in	obj,
		in	q,
		in	qdot
	)

Function returns position and orientation of body segments, for the system in position q.

Needed for tracking of marker trajectories, and for 3D visualization of the model. This function calls the mex file of gait3d.c [FK, dFKdq,dFKdotdq] = obj.hdlMEX('Fkin', q, qdot);

The order the following for each segment:

'p1', 'p2', 'p3', 'R11', 'R12', 'R13', 'R21', 'R22', 'R23', 'R31', 'R32', 'R33'

p can be obtained by:

p = FK((idxCurSegment-2)*12 + (1:3));

R can be obtained by:

R = reshape(FK((idxCurSegment-2)*12 + (4:12)), 3, 3)';

Parameters

obj	Gait3d class object
q	Double array: Generalized coordinates (elements of states with type 'q') (Gait3d.nDofs x 1)
qdot	(optional) Double array: Generalized velocities (elements of states with type 'qdot') (Gait3d.nDofs x 1)

Return values

FK	Double array: position (3) and orientation (3x3, stored row-wise) of nSegments-1. Segments are the bodies in the .osim model, not including ground. ((Gait3d.nSegments-1) * 12)
dFKdq	(optional) Double matrix: Jacobian of FK with respect to q ((Gait3d.nSegments-1) * 12 x Gait3d.nDofs)
dFKdotdq	(optional) Double matrix: Jacobian of dFK/dt with respect to q ((Gait3d.nSegments-1) * 12 x Gait3d.nDofs)

getGRF()

function getGRF ( in  obj, in  x  )

virtual

Function returns the ground reaction forces for the system in state x.

This function calls the mex file of gait3d.c: [grf, dgrfdx] = obj.hdlMEX('GRF', x);

Parameters

obj	Gait3d class object
x	Double array: State of the model (Gait3d.nStates x 1)

Return values

grf	Double array (12x1) containing: right Fx, Fy, Fz (in bodyweight) right Mx, My, Mz (in bodyweight*m) left Fx, Fy, Fz (in bodyweight) left Mx, My, Mz (in bodyweight*m)
dgrfdx	(optional) Double matrix: Transpose of Jacobian matrix dgrf/dx (Gait3d.nStates x 12)

Reimplemented from Model.

getJointmoments()

function getJointmoments ( in  obj, in  x, in  u  )

virtual

Function returns joint moments, for the system in state x.

This includes passive joint moments and muscle moments and extra moments (e.g. arms).

Parameters

obj	Gait3d class object
x	Double array: State of the model (Gait3d.nStates x 1)
u	(optional) Double array: Controls of the model which are only needed if you want to apply extra moments (i.e. arm torques) (Gait3d.nControls x 1)

Return values

M	Double array: Moment/force for each DOF (Gait3d.nDofs x 1)
dMdx	(optional) Double matrix: Transpose of Jacobian matrix dM/dx (Gait3d.nStates x Gait3d.nDofs)
dMdu	(optional) Double matrix: Transpose of Jacobian matrix dM/du (Gait3d.nControls x Gait3d.nDofs)

Reimplemented from Model.

getLCE()

function getLCE	(	in	obj,
		in	x
	)

Function returns length of contractile element, for the system in state x.

This function obtaines L_CE from s using the equations which are also implemented in the c code.

Parameters

obj	Gait3d class object
x	Double array: State of the model (Gait3d.nStates x 1)

Return values

L_CE	Double array: CE length (m) of each muscle (Gait3d.nMus x 1)

getLdotCE()

function getLdotCE	(	in	obj,
		in	xdot
	)

Function returns length change of contractile element, for the system in state x.

This function obtaines Ldot_CE from sdot using the equations which are also implemented in the c code.

Parameters

obj	Gait3d class object
xdot	Double array: State derivatives (Gait3d.nStates x 1)

Return values

Ldot_CE

Double array: CE length change (m/s) of each muscle (Gait3d.nMus x 1)

getMetabolicRate_pernode()

function getMetabolicRate_pernode ( in  obj, in  x, in  xdot, in  u, in  t_stim, in  name, in  getCont, in  epsilon, in  exponent  )

inherited

Model function to calculate metabolic cost of a movement.

Function to calculate the metabolic cost of a movement. Seven different models are currently implemented

Parameters

obj	Model object
x	Double vector: States of the current node
xdot	Double vector: Derivatives of states
u	Double vector: Controls of the current node
t_stim	Double vector: how long each muscle was already stimulated
name	(optional) String: name of the model that is being used. Options are umberger, lichtwark, bhargava, margaria, minetti, houdijk, and uchida
getCont	(optional) Boolean: If true, get the continuous version which is needed if we use the output for simulation. (default: 0)
epsilon	(optional) double parameter: Measure of nonlinearity of model, which is only used in the continuous model version. Default 0.
exponent	(optional) integer: if metabolic cost is the objective, this number allows to minimize the square, cube, or nth-power of metabolic cost. Default is 1

Return values

Edot	Double vector: Energy expenditure during one time step (energy rate) in W (Model.nMus x 1)
dEdotdx	Double vector: Derivative of Edot w.r.t to x (Model.nStates x 1)
dEdotdu	Double vector: Derivative of Edot w.r.t to u (Model.nControls x 1)
dEdotdT	Double: Derivative of Edot w.r.t to T

getMexFiles()

function getMexFiles ( in  osimName, in  clean, in  rebuild_contact, in  debugMode  )

static

Function to make MEX functions.

Generates Autolev source file for model and builds the MEX function

Parameters

osimName	String: Name of Opensim model. See lines 30-41 for supported models
rebuild_contact	(optional) Bool: If true, enforce rebuilding contact_raw.c (default: 0)
debugMode	(optional) Bool: If true, code will be compiled in debug mode and not optimized. (default: 0)

Return values

name_MEX

String: Name of the mex function which has to be called

getMuscleCEforces()

function getMuscleCEforces ( in  obj, in  x, in  xdot  )

virtual

Function returning muscle forces of CE for the system in state x.

This function calls the mex file of gait3d.c: [forces] = obj.hdlMEX('MuscleCEforces', x);

Parameters

obj	Gait3d class object
x	Double array: State of the model (Gait3d.nStates x 1)
xdot	Double array: State derivatives (Gait3d.nStates x 1)

Return values

forcesCE	Double array: Muscle forces of CE (in N) (Gait3d.nMus x 1)
dforcesCEdx	Double array: Transpose of Jacobian matrix d force / d x (Gait3d.nStates x Gait3d.nMus)
dforcesCEdxdot	Double array: Transpose of Jacobian matrix d force / d xdot (Gait3d.nStates x Gait3d.nMus)

Reimplemented from Model.

getMuscleCEpower()

function getMuscleCEpower ( in  obj, in  x, in  xdot  )

virtual

Function returns power generated by muscle contractile elements, for the system in state x.

xdot must be the state derivatives, such that the muscle balance equations are satisfied It is up to the user to ensure that the muscle contraction balance f(x,xdot)=0 when this function is used.

Parameters

obj	Gait3d class object
x	Double array: State of the model (Gait3d.nStates x 1)
xdot	Double array: State derivatives (Gait3d.nStates x 1)

Return values

powers	Double array: CE power output (W) of each muscle (Gait3d.nMus x 1)
conDynRes	Double array: Contraction dynamics residuals (Gait3d.nMus x 1)

Reimplemented from Model.

getMuscleforces()

function getMuscleforces ( in  obj, in  x  )

virtual

Function returns muscle forces, for the system in state x.

This function calls the mex file of gait3d.c: [forces, lengths, momentarms] = obj.hdlMEX('Muscleforces', x);

Parameters

obj	Gait3d class object
x	Double array: State of the model (Gait3d.nStates x 1)

Return values

forces	Double array: Muscle forces (N) (Gait3d.nMus x 1)
lengths	(optional) Double array: Muscle-tendon lengths (m) (Gait3d.nMus x 1)
momentarms	(optional) Double matrix: Muscle moment arms (m) (Gait3d.nMus x Gait3d.nDofs)

Reimplemented from Model.

getPassiveJointmoments()

function getPassiveJointmoments	(	in	obj,
		in	x
	)

Function returns passive joint moments, for the system in state x.

This function returns the passive joint moments due to ligaments

Parameters

obj	Gait3d class object
x	Double array: State of the model (Gait3d.nStates x 1)

Return values

M	Double array: Passive moment for each DOF (Gait3d.nDofs x 1)
dMdx	(optional) Double matrix: Transpose of Jacobian matrix dM/dx (Gait3d.nStates x Gait3d.nDofs)

initMex()

function initMex ( in  obj )

protectedvirtual

Initialize model mex file.

This function calls the mex file of gait3d.c [info] = obj.hdlMEX('Initialize', model)

This initializes the model. This is required before anything is done with the model.

Input: model Struct containing model parameters.

Output: info Struct with information about the size of the model, fields: Nx Number of state variables: 2* Gait3d.nDofs + 2* Gait3d.nMuscles + 9* Gait3d.nCPs Nf Number of functions returned by the Dynamics function fmin,fmax Lower and upper bounds for dynamics residuals f Bodyweight Sum of weights of all segments. This is used to set bodymass

Parameters

obj	Gait3d class object

Reimplemented from Model.

initModel() [1/2]

function initModel ( in  obj )

protected

Function to initialize model with default parameters.

Initialize contact points and stiffness of dofs

Parameters

obj	Gait3d class object

initModel() [2/2]

virtual initModel ( in  obj, in  vargin  )

protectedvirtualinherited

Abstract function to initialize with default parameters.

Reimplemented in Gait2dc.

loadMomentArms()

function loadMomentArms ( in  obj )

protected

Function to load or compute moment arms.

Loads moment arms save in the file strrep(obj.osim.file,'.osim','_momentarms.mat'). If there is not such a file, the moment arms will be computed and saved.

We define here also the ranges of the dofs used to get the muscle moments and the ones used to get the passive moments:

• range_muscleMoment: They were manually tune to result in good polynomials.
• range_passiveMoment: By default, they are equal to the ranges used for the muscle moments. But for the arms, we smaller the range of the osim file by 2 degrees at each boundary (e.g. range_osim = [-90, 90], range_passiveMoment = [-88, 88])

Parameters

obj	Gait3d class object

loadOsimFile()

function loadOsimFile ( in  obj, in  osimfile  )

protected

Function to load the content from the opensim file.

Calls readOsim() if there is no .mat file corresponding to the requested osimfile. Therefore it searches for a file called strrep(osimfile, '.osim', '.mat') and checks the sha code to see weather the .mat file is still up to date with the opensim file.

Parameters

obj	Gait3d class object
osimfile	String: Filename of opensim file including path and extension

plotgrf()

static function plotgrf ( in  F, in  CoP, in  color  )

staticprotected

Function used in showStick() to plot GRFs.

Plots a ground reaction force vector represented by 3D force and CoP.

Parameters

F	Double array: Force (3 x 1)
CoP	Double array: Center of pressure in x, y, z coordinates (3 x 1)
color	String: Color (e.g. color = 'r')

readOsim()

function readOsim ( in  osimfile )

staticprotected

Function to load OpenSim model in Matlab as structure.

Saves the model struct using strrep(osimfile, '.osim', '.mat').

Parameters

osimfile

String: Filename of opensim file including path and extension

Return values

model

Struct: Parameters of OpenSim model

setbodymass()

function setbodymass ( in  obj, in  bodymass  )

inherited

Function to set body mass, does not influence the.

Parameters

obj	Model class object
segmentTable	Double: bodymass

setMuscles()

function setMuscles ( in  obj, in  muscles  )

inherited

Function to set the muscles table.

Parameters

obj	Model class object
segmentTable	Table: muscles

setSegmentMass()

function setSegmentMass ( in  obj, in  segmentName, in  segmentMass  )

inherited

Function to set segment mass.

Parameters

obj	Model class object
segmentName	String: Name of the segment
segmentMass	Double: Mass of the segment in kg

setSegments()

function setSegments ( in  obj, in  segmentTable  )

inherited

Function to set segment Table.

Parameters

obj	Model class object
segmentTable	Table: segmentTable

showMarker()

function showMarker	(	in	obj,
		in	x,
		in	markerTable,
		in	measuredMean
	)

Function to plot marker positions.

The motion in x and the matrix measured have to fit to each other. If you want to plot for example only a single node, markerTable.mean must be only the data of this single node.

You can use the function like this:

figure();
x = result.X(result.problem.idx.states(:, 1:result.problem.nNodes)); % get states
result.problem.model.showStick(x, [], 1, 0, 1); % plot stick figure
markerTable = result.problem.objectiveTerms(1).varargin{1}.variables; % assuming trackMarker is your first objective
markerMean = cell2mat(markerTable.mean')/1000; % extract and convert from mm to meter
result.problem.model.showMarker(x, markerTable, markerMean); % plot marker data

Parameters

obj	Gait3d class object
x	Double matrix: State vector of model for n time points (Gait3d.nStates x n)
markerTable	Table: Variables table specifying markers with at least the columns: type, name, segment, position, direction to call Gait3d.simuMarker.
measuredMean	(optional) Double matrix: Measured marker data in meter(!) which will be plotted as reference. The matrix must have the same number of time points as the state vector x. Further, the matrix columns must correspond to the rows of the markerTable in the same order to be able to match coordinates of the markers. (n x height(markerTable)) (default: empty)

showStick() [1/2]

virtual showStick ( in  obj, in  x  )

virtualinherited

Abstract function to show model as stick figure.

showStick() [2/2]

function showStick	(	in	obj,
		in	x,
		in	range,
		in	plotFeet,
		in	plotGRF,
		in	plotCPs,
		in	plotJointCOSYs,
		in	az,
		in	el
	)

Function to show model as stick figure.

Parameters

obj	Gait3d class object
x	Double matrice: State vector of model for n time points (Gait3d.nStates x n)
range	(optional) Double matrice: Defining the range of the figure with [xmin, xmax; ymin, ymax, zmin, zmax]. (3 x 2) (default: [pelvisX-1, pelvisX+1; -0.2, 2, pelvisZ-1, pelvisZ+1])
plotFeet	(optional) Integer: Defines if and how the feet are plotted (default: 0) 0: Toe segments are not plotted, 1: Toe segments are plotted using double the center of mass in x direction, 2: Feet segments are plotted using the predefined position of the CPs. In future, we could think of using the simulated positions saved in the states.
plotGRF	(optional) Bool: If true, it plots arrows for the GRFs (default: 0)
plotCPs	(optional) Bool: If true, it plots spheres for the CPs (default: 0)
plotJointCOSYs	(optional) Bool: If true, it plots the coordinate systems of the joints (default: 0)
az	(optional) Double: Azimuth for the view of the figure (view(az, el)). (default: 90)
el	(optional) Double: Elevation for the view of the figure (view(az, el)). (default: 0)

simuAccGyro() [1/2]

virtual simuAccGyro ( in  obj, in  data, in  q, in  qd, in  qdd  )

virtualinherited

Abstract function to simulate acceleration and gyroscope signals.

simuAccGyro() [2/2]

function simuAccGyro	(	in	obj,
		in	variables,
		in	q,
		in	qd,
		in	qdd,
		in	idxSegment,
		in	idxAcc,
		in	idxGyro,
		in	dlocalAll,
		in	plocalAll
	)

Matlab function to simulates sensors placed on 3D model.

Do not change "obj" or "variables" in this function! This will allow Matlab to "pass by reference" and avoid function call overhead.

Position has to given as X, Y and Z position of sensor in segment coordinate system in m.

Direction has to be given in axis definition, e.g [1, 0, 0].

Parameters

obj	Gait3d class object
variables	Table: Variable table containing the accelerometer and gyroscope data with at least the columns: type, name, segment, position, direction
q	Generalized coordinates (Gait3d.nDofs x 1)
qd	First derivatives of generalized coordinates (Gait3d.nDofs x 1)
qdd	Second derivatives of generalized coordinates (Gait3d.nDofs x 1) (use NaN to skip)
idxSegment	(optional) Double array: Indices of segments fitting to respective IMU (variables.nVars.all x 1) => It is faster to pass them than to recalculate each time.
idxAcc	(optional) Double array: Indices in variables that have type 'acc' (nAcc x 1) => It is faster to pass them than to recalculate each time.
idxGyro	(optional) Double array: Indices in variables that have type 'gyro' (nGyro x 1) => It is faster to pass them than to recalculate each time.
dlocalAll	(optional) Double matrix: Local direction of the IMU saved in variables (variables.nVars.all x 3) => It is faster to pass them than to extract them each time.
plocalAll	(optional) Double matrix: Local position of the IMU saved in variables (variables.nVars.all x 3) => It is faster to pass them than to extract them each time.

Return values

s	Simulated sensor signals (variables.nVars.all x 1)
ds_dq	Sparse Jacobian ds/dq (variables.nVars.all x Gait3d.nDofs)
ds_dqd	Sparse Jacobian ds/dqd (variables.nVars.all x Gait3d.nDofs)
ds_dqdd	Sparse Jacobian ds/dqdd (variables.nVars.all x Gait3d.nDofs)

simuMarker()

function simuMarker	(	in	obj,
		in	variables,
		in	q,
		in	idxSegment,
		in	plocalAll,
		in	dlocalAll
	)

Matlab function to simulates markers placed on 3D model.

Do not change "obj" or "variables" in this function! This will allow Matlab to "pass by reference" and avoid function call overhead.

Position has to given as X, Y, and Z position of marker in segment coordinate system in m. Direction has to be given in axis definition, e.g [1, 0, 0].

Parameters

obj	Gait3d class object
variables	Table: Variable table containing the marker data with at least the columns: type, name, segment, position, direction
q	Double array: Generalized coordinates (Gait3d.nDofs x 1)
idxSegment	(optional) Double array: Indices of segments fitting to respective markers (variables.nVars.all x 1) => It is faster to pass them than to recalculate each time.
plocalAll	(optional) Double matrix: Local position of the markers saved in variables (variables.nVars.all x 3) => It is faster to pass them than to extract them each time.
dlocalAll	(optional) Double matrix: Local direction of the markers saved in variables (variables.nVars.all x 3) => It is faster to pass them than to extract them each time.

Return values

m	Simulated marker signals in meter (variables.nVars.all x 1)
dm_dq	Sparse Jacobian dm/dq (variables.nVars.all x Gait3d.nDofs)

update_constraints()

function update_constraints ( in  obj )

protectedvirtual

Function defining the table Gait3d.constraints.

Table lists type, name, equation (string), fmin and fmax

The constraints are composed of Gait3d.nConstraints = 2* Gait3d.nDofs + 2* Gait3d.nMus + 13* Gait3d.nCPs)

• implicite differential equations: qdot-dq/dt = 0 (Gait3d.nDofs x 1)
• equations of motion from Autolev (Gait3d.nDofs x 1)
• muscle contraction dynamics (Gait3d.nMus x 1)
• muscle activation dynamics: da/dt - rate * (u-a) = 0 (Gait3d.nMus x 1)
• six equality constraints for contact points (Gait3d.nCPs*6 x 1)

Parameters

obj	Gait3d class object

Reimplemented from Model.

update_controls()

function update_controls ( in  obj )

protectedvirtual

Function defining the table Gait3d.controls.

Table lists type, name, xmin, xmax and xneutral

Parameters

obj	Gait3d class object

Reimplemented from Model.

update_idxControls()

function update_idxControls ( in  obj )

protectedinherited

Function defining Model.hidxControls.

Parameters

obj	Model class object

update_idxForward()

function update_idxForward ( in  obj )

protectedinherited

Function defining Model.idxForward.

Provides the indices of state variables that have forward translation. States have to be updated before!

Parameters

obj	Model class object

update_idxForwardAll()

function update_idxForwardAll ( in  obj )

protectedinherited

Function defining Model.idxForwardAll.

Provides the indices of state variables that have forward translation, speed, position of contact points and force at contact points. States and idxForward have to be updated before!

Parameters

obj	Model class object

update_idxSideward()

function update_idxSideward ( in  obj )

protectedinherited

Function defining Model.idxSideward.

Provides the indices of state variables that have sideward translation. States have to be updated before!

Parameters

obj	Model class object

update_idxSidewardAll()

function update_idxSidewardAll ( in  obj )

protectedinherited

Function defining Model.idxSidewardAll.

Provides the indices of state variables that have sideward translation, speed, position of contact points and force at contact points. States and idxSideward have to be updated before!

Parameters

obj	Model class object

update_idxStates()

function update_idxStates ( in  obj )

protectedinherited

Function defining Model.hidxStates.

Parameters

obj	Model class object

update_idxSymmetry()

function update_idxSymmetry ( in  obj )

protectedvirtual

Function defining Gait3d.idxSymmetry.

Parameters

obj	Gait3d class object

Reimplemented from Model.

update_idxTorqueDof()

function update_idxTorqueDof ( in  obj )

protectedinherited

Function defining Model.idxTorqueDof.

Searches for indices of dof which have torque actuators in Model.torques.

Parameters

obj	Model class object

update_idxUpward()

function update_idxUpward ( in  obj )

protectedinherited

Function defining Model.idxUpward.

Provides the indices of state variables that have upward translation. States have to be updated before!

Parameters

obj	Model class object

update_mexParameter()

function update_mexParameter ( in  obj, in  src, in  evnt  )

protectedvirtual

Function performed to update the parameter of the mex and the tables.

• Called with a PostSet event after set Gait3d.gravity, Gait3d.drag_coefficient, Gait3d.wind_speed, Gait3d.joints, Gait3d.muscles, Gait3d.CPs, Gait3d.dofs, Gait3d.segments.
• Reinitializes mex with new parameters.
• This function calls all the other update functions. If we would also add a listener for them, we could not ensure that they are called in the correct order!

Parameters

obj	Gait3d class object
src	meta.property: Object describing the source of the event
evnt	(optional) event.Propertyevent: Object describing the event

Reimplemented from Model.

update_states()

function update_states ( in  obj )

protectedvirtual

Function defining the table Gait3d.states.

Table lists type, name, xmin, xmax and xneutral

Todo:

Variables of contact points of neutral position shouldn't be zero.

Parameters

obj	Gait3d class object

Reimplemented from Model.

Member Data Documentation

bodyheight

Property bodyheight

protected

bodymass

Property bodymass

protected

Double: Bodymass in kg (Is computed by summing up all body mass except talus.

See gait3d.c)

Todo:

Is is not nice that the talus is missing in the computation of the bodyweight.

constraints

Property constraints

protectedinherited

Table: Information on constraints implemented in the mex and here.

controls

Property controls

protectedinherited

Table: Information on controls of the model.

CPs

Property CPs

inherited

Table: Contact points.

dofs

Property dofs

inherited

Table: Degrees of freedom (Range of Dofs should not be changed here.

Set the bounds of the Problem instead.)

drag_coefficient

Property drag_coefficient

inherited

Double: Air drag coefficient in N/(m/s)^2 (default: 0.2128)

gravity

Property gravity

inherited

Double array: Gravity vector in m/(s^2)

GRFNAMES

Constant Property GRFNAMES = {'rightFx', 'rightFy', 'rightFz', 'rightMx', 'rightMy', 'rightMz', 'leftFx', 'leftFy', 'leftFz', 'leftMx', 'leftMy', 'leftMz' }

inherited

Cell array with string: Gives the names for the GRF vector returned by getGRF()

hdlMEX

Property hdlMEX

protected

Handle: MEX function of the model for dynamics etc.

idxForward

Property idxForward

protectedinherited

Double array: Indices for forward translation.

idxForwardAll

Property idxForwardAll

protectedinherited

Double array: Indices for forward translation, speed, position of contact points and force at contact points.

idxSideward

Property idxSideward

protectedinherited

Double array: Indices for sideward translation.

idxSidewardAll

Property idxSidewardAll

protectedinherited

Double array: Indices for sideward translation, speed, position of contact points and force at contact points.

idxSymmetry

Property idxSymmetry

protectedinherited

Struct: Double arrays with indices for symmetry to map right to left.

idxTorqueDof

Property idxTorqueDof

protectedinherited

Double array: Indices of dofs of torque actuators.

idxUpward

Property idxUpward

protectedinherited

Double array: Indices for upward translation.

init

Property init

protectedinherited

Double: Showing if the mex model is initialized.

joints

Property joints

inherited

Table: Joints.

markers

Property markers

Table: Markers (Containing also the CPs. Their names start with 'CP')

mExtraScaleFactor

Property mExtraScaleFactor

inherited

Double: Scale factor for extra torques in Nm (default: 100 since we used this in previous simulations.

However, it's probably overwritten in the construction (see Gait3d.m)!)

muscles

Property muscles

inherited

Table: Muscles.

nConstraints

Property nConstraints

protectedinherited

Double: Number of constraints (height of Model.constraints)

nControls

Property nControls

protectedinherited

Double: Number of controls (height of Model.controls)

nCPs

Property nCPs

protectedinherited

Double: Number of contact points (height of Model.CPs)

nDofs

Property nDofs

protectedinherited

Double: Number of degree of freedoms (height of Model.dofs)

nJoints

Property nJoints

protectedinherited

Double: Number of joints (height of Model.joints)

nMarkers

Property nMarkers

protected

Double: Number of markers (height of Gait3d.markers)

nMus

Property nMus

protectedinherited

Double: Number of muscles (height of Model.muscles)

nSegments

Property nSegments

protectedinherited

Double: Number of segments (height of Model.segments)

nStates

Property nStates

protectedinherited

Double: Number of states (height of Model.states)

nTor

Property nTor

protectedinherited

Double: Number of torque actuators (height of Model.torques)

osim

Property osim

protected

Struct: Information (name, file, modified, sha256) on opensim model.

segments

Property segments

protectedinherited

Table: Segments (Segment properties should not be changed)

states

Property states

protectedinherited

Table: Information on states of the model.

torques

Property torques

inherited

Table: Torque actuators.

wind_speed

Property wind_speed

inherited

Double: Wind speed in direction of +X in m/s (default: 0)

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

• BioMAC-Sim-Toolbox/src/model/gait3d/@Gait3d/Gait3d.m