File List

Here is a list of all files with brief descriptions:

[detail level 12345678]

▼ BioMAC-Sim-Toolbox
▼ docs
▼ Doxygen
pages
▼ ExampleScripts
▼ +ExoPaper
exoWalking.m
standing2D.m	Function to specify the optimization problem for 2D standing
walking2D_exo.m
walking2D_fixedsteprate.m	Function to specify the optimization problem for 2D running
▼ +IMUTracking2D
move2D_IMU.m	Function to set up optimal control problem to simulate walking or running from inertial sensor data
scriptIMU2D.m	Script to show how we can run simulations tracking inertial sensor data
standing2D.m
▼ +IntroductionExamples
running2D.m	Function to specify the optimization problem for 2D running
running3D.m	Function to specify the optimization problem for 3D running
script2D.m	Script to start working with the Bio-Sim-Toolbox for 2D models
script3D.m	Script to start working with the Bio-Sim-Toolbox for 3D models
scriptPlotting.m	Script to show how to work with the toolbox's plotting options
standing2D.m	Function to specify the optimization problem for 2D standing
standing3D.m	Function to specify the optimization problem for 3D standing
▼ +MarkerTracking3D
run_motion_angle.m	Function to do simulation with angle tracking
run_motion_marker.m	Function to do simulation with marker tracking
run_standing_angle.m	Function to do standing simulation with angle tracking
run_standing_marker.m	Function to do standing simulation with marker tracking
scriptMarkerTracking.m	Example script for marker tracking (in 3D)
setup_motion_angle.m	Function to setup motion problem with angle tracking
setup_motion_marker.m	Function to setup motion problem with marker tracking
setup_standing_angle.m	Function to setup standing problem with angle tracking
setup_standing_marker.m	Function to setup standing problem with marker tracking
▼ +Treadmill
script2D.m	Script to show how to simulate a treadmill and with the 2D OpenSim model
walking2D.m
▼ src
▼ HelperFunctions
addLegend.m	Function to add the legend for a plot
calculateCMC.m	Function to caluclate the Coefficient of Multiple Correlation
calculateCORR.m	Function to caluclate the Pearson correlation coefficient
calculateMeasures.m	Function to caluclate the error and performance measures for a simVarTable
calculateOLP.m	Function to caluclate the OLP Regression
calculateRelativeRMSE.m	Function to calculate Relative RMSE
calculateRMSE.m	Function to calculate RMSE
callPdflatex.m	Function to call pdflatex
compareElements.m	Function to find differences between two elements
convertUnit.m	Function to convert unit of a variables table or simVarTable
getStancePhase.m	Function to get the stance phase from vertical GRF
getSubfigurePosition.m	Function to get the position of a subfigure
myvecnorm.m	Function to compute the norm of a vector
plotStancePhase.m	Function to plot a shaded area to indicate the stance phase
plotVariable.m	Function to plot the mean and optional also plus minus SD
plotVarTable.m	Function to plot all variables within a variables table
plotVarType.m	Function to plot one type of variable of a variables table
readMot.m	Function to read data to a .mot file
readSto.m	Function to read data to a .sto file
saveLaTeXDocument.m	Function to save a text body within a LaTeX document
setLegendBelowSubfigures.m	Function to position a legend centered below all subfigures
tableToLaTeX.m	Function to convert a matlab table to a table formated in LaTeX
writeControlXML.m	Function to write controls to a .xml file
writeIMUcsv.m	Function to write IMU data to a .csv file
writeMarkerTrc.m	Function to write marker data to a .trc file
writeMotSto.m	Function to write data to a .mot or .sto file
▼ model
► @Model
getCoP.m	Model function to calculate the center of pressure
getErate_bhargava.m	Model function to calculate the energy rate of a single time step with Bhargava et al
getErate_Houdijk.m	Model function to calculate the energy rate of a single time step with Houdijk et al
getErate_Lichtwark.m	Model function to calculate the energy rate of a single time step with Lichtwark and Wilson's model
getErate_margaria.m	Model function to calculate the energy rate of a single time step with Margaria's model
getErate_Minetti.m	Model function to calculate the energy rate of a single time step with Minetti and Alexander's model
getErate_uchida.m	Model function to calculate the energy rate of a single time step with Uchida et al
getErate_Umberger.m	Model function to calculate the energy rate of a single time step with Umberger et al
getEratec_bhargava.m	Model function to calculate the energy rate of a single time step with the continuous version of Bhargava et al
getEratec_Houdijk.m	Model function to calculate the energy rate of a single time step with the continuous version of Houdijk et al
getEratec_Lichtwark.m	Model function to calculate the energy rate of a single time step with the continuous version of Lichtwark and Wilson's model
getEratec_margaria.m	Model function to calculate the energy rate of a single time step with the continuous version of Margaria's model
getEratec_Minetti.m	Model function to calculate the energy rate of a single time step with the continuous version of Minetti and Alexander's model
getEratec_umberger.m	Model function to calculate the energy rate of a single time step with the continuous version of Umberger et al
getMetabolicRate_pernode.m	Model function to calculate metabolic cost of a movement
Model.m	Matlab class (abstract) describing a musculoskeletal model
► gait2d_osim
► @Gait2d_osim
computeMomentArms.m	Gait2d_osim function to generate muscle length polynomials from Opensim muscle paths
Gait2d_osim.m	Matlab class describing the Gait2d_osim model
getMexFiles.m	Gait2d_osim function to make MEX functions
readOsim.m	Gait2d_osim function to load OpenSim model in Matlab as structure
scaleOsim.m	Gait2d_osim function to scale OpenSim model in Matlab
simuMarker.m	Gait2d_osim function to simulates markers placed on 2D model
► c_files
► contact
clean_contact_2d.c
contact_2d_raw.c
gait2d_osim_contact.h
► gait10dof18musc
clean_gait10dof18musc.c
create_alfile_gait10dof18musc.m
gait10dof18musc.c
gait10dof18musc.h
gait10dof18musc_FK_raw.c
gait10dof18musc_multibody.h
gait10dof18musc_NoDer_raw.c
gait10dof18musc_raw.c
► gait2d_osim
clean_gait2d_osim.c
create_alfile_gait2d_osim.m
gait2d_osim.c
gait2d_osim.h
gait2d_osim_FK_raw.c
gait2d_osim_multibody.h
gait2d_osim_NoDer_raw.c
gait2d_osim_raw.c
► gait2dc
► @Gait2dc
Gait2dc.m	Matlab class describing the Gait2dc model
getCoM.m	Gait2dc function to calculate the center of mass
getFootAngle.m	Gait2dc function to calculate the angle between foot and ground
getMexFiles.m	Gait2dc function to make MEX functions
getRandomParticipant.m	Gait2dc function to generate a participant with random muscle parameters
getSameRandomParticipant.m	Gait2dc function to generate a participant with repeatable random muscle parameters
readParameter.m	Gait2dc function to read parameter matrix into tables
scaleParameters.m	Gait2dc function to scale the parameters defined in the excelfile
simuAccGyro.m	Gait2dc function to simulate acceleration and gyroscope signals
simuMarker.m	Gait2dc function to simulates markers placed on 2D model
► @Gait2dc_Exo
Gait2dc_Exo.m	Gait2dc class describing the Gait2dc_Exo model
► c_files
autolevclean.c	MEX function to extract clean C source code from C files generated by Autolevs
contact_al.c
gait2dc.c	C source code for the MEX function gait2dc.mex32
gait2dc.h	Header file defining the data structure that holds model parameters
gait2dc.m	Matlab script documenting the use of the MEX function gait2dc.mex32
gait2dc_acc_al.c
gait2dc_dyn_al.c
gait2dc_FK_al.c
gait2dc_stick_al.c
► gait3d
► @Gait3d
computeMomentArms.m	Gait3d function to generate muscle length polynomials from Opensim muscle paths
createRandomPerson.m	Gait3d function to create random musculoskeletal parameters
Gait3d.m	Matlab class describing the Gait3d model
getCoM.m	Gait3d function to calculate the center of pressure
getDynamicsCPOffset.m	Gait3d computing implicit differential equation for 3D musculoskeletal model which allows an adaption of the CP position
getMexFiles.m	Gait3d function to make MEX functions
readOsim.m	Gait3d function to load OpenSim model in Matlab as structure
simuAccGyro.m	Gait3d function to simulates sensors placed on 3D model
simuMarker.m	Gait3d function to simulates markers placed on 2D model
► c_files
► contact
contact_3d_raw.c
gait3d_clean_contact.c
gait3d_contact.h
► gait3d_pelvis213
clean_gait3d_pelvis213.c
create_alfile_gait3d_pelvis213.m
gait3d_pelvis213.c
gait3d_pelvis213.h
gait3d_pelvis213_FK_raw.c
gait3d_pelvis213_multibody.h
gait3d_pelvis213_NoDer_raw.c
gait3d_pelvis213_raw.c
► gait3d_pelvis213_torque
clean_gait3d_pelvis213_torque.c
create_alfile_gait3d_pelvis213_torque.m
gait3d_pelvis213_torque.c
gait3d_pelvis213_torque.h
gait3d_pelvis213_torque_FK_raw.c
gait3d_pelvis213_torque_multibody.h
gait3d_pelvis213_torque_NoDer_raw.c
gait3d_pelvis213_torque_raw.c
▼ problem
► @Collocation
checkXScaling.m	Collocation function to check the scaling withing X
Collocation.m	Matlab class for defining an optimal control of musculoskeletal model
comFixConstraint.m	Collocation function to fix center of mass motion
cotTerm.m	Collocation function to compute cost of transport from states
curveConstraint_pelvis213.m	Collocation function to compute the periodicity constraint for curved running
durationConstraint.m	Collocation function to compute duration constraint
dynamicConstraints.m	Collocation function to compute dynamic constraint
dynamicsFirstNodeConstraint.m	Collocation function to constrain the first node
effortTermMuscles.m	Collocation function to compute effort of the muscles from states vector
effortTermMusclesAct.m	Collocation function to compute effort of the muscles from states vector
effortTermTorques.m	Collocation function to compute effort of the torques from states vector
equilibriumConstraints.m	Collocation function to compute dynamic constraint for standing
equilibriumConstraintsCPOffset.m	Collocation function to compute dynamic constraint for standing with a vertical offset of the contact points
extractData.m	Collocation function to extract simulated and tracked data of the problem
fromStandingConstraint.m	Collocation function to find walking/running from standing
getCEPower.m	Collocation function to compute the CE Power over the whole movemenent
getComMotion.m	Collocation function to compuate center of mass motion
getComMotionDeriv.m	Collocation function to compuate center of mass motion
getMetabolicCost.m	Collocation function to calculate metabolic cost of a movement
getSimData.m	Collocation function to extract simulated variables
getStepLength.m	Collocation function to compute step length
getStimTime.m	Collocation function to calculate the stimulation time for one gait cycle
headStabTerm.m	Head Stabilistation Term from Veerkamp, 2021
impactTerm.m	Foot-Ground Impact Term from Veerkamp, 2021
jointAccelerationTerm.m	Collocation function to compute the joint acceleration from states vector
kneeExtTerm.m	Knee extension / kneeinj Term from Veerkamp, 2021
maximizeSpeed.m
metabolicRateTerm.m
metabolicTerm.m
passiveMomentTerm.m	Collocation function to compute term minimizing passive torques
periodicityConstraint.m	Collocation function to compute periodicity constraint
plotMeanSimVarTable.m	Collocation function to plot the mean and SD of multiple simulation variable tables
plotMultSimVarTables.m	Collocation function to plot the content of multiple simulation variable tables
plotStickSlider.m	Collocation function to create plot stick figure with slider
regTerm.m	Collocation function to compute regularization term
report.m	Collocation function to report a current state vector of the problem
resampleInitialContact.m	Function to shift the result.X vector to start with an initial contact
speedConstraint.m	Collocation function to compute speed constraint
trackAcc.m	Collocation function to track accelerometer data
trackAngles.m	Collocation function to track angles
trackDuration.m	Collocation function to track duration of the gait cycle
trackGRF.m	Collocation function to track ground reaction forces
trackGyro.m	Collocation function to track gyroscope data
trackMarker.m	Collocation function to track marker data
trackSpeed.m	Collocation function to track speed of the gait cycle
trackTranslations.m	Collocation function to track translations
trackTranslationsAndAngles.m	Collocation function to track translations and angles in one term
translationSpeedConstraint.m	Collocation function to compute a constraint based on speed and translation
writeMotionToOsim.m	Collocation function to write motion from a solution X to OpenSim files
writeMovie.m	Collocation function to create a movie of a simulation result
writeMovieCurvedRunning.m	Collocation function to create a movie of a simulation result for curved running
► @Collocation_Exo
Collocation_Exo.m	Matlab class describing collocation using the exoskeleton
dynamicConstraints.m	Collocation_Exo function to compute dynamic constraint
► @Collocation_NN
Collocation_NN.m	Class for python import
dynamicConstraints.m	Collocation function to compute dynamic constraint
► @Collocation_stoch
Collocation_stoch.m	Matlab class for defining an optimal control of musculoskeletal model
dynamicConstraints.m	Collocation_stoch function to compute dynamic constraint
Problem.m	Matlab class (abstract) for defining an optimization problem
▼ result
► @Result
report.m	Result function to create graphical report from a result
Result.m	Matlab class for defining an optimization result
▼ solver
IPOPT.m	Matlab class to call the IPOPT optimization software
Solver.m	Matlab class (abstract) a solver inherits from
▼ tests
Gait2d_osimTest.m	Maltab m-file containing test class for class Gait3d
Gait2dcTest.m	Maltab m-file containing test class for class Gait2dc
Gait3dTest.m	Maltab m-file containing test class for class Gait3d
ModelTest.m	Maltab m-file containing abstract test class for class Model
▼ Toolboxes
► gif_v1.0
gif.m
gif_documentation.m
► matlab2tikz-matlab2tikz-v1.1.0-0-g816f875
► src
► dev
formatWhitespace.m
► private
errorUnknownEnvironment.m
getEnvironment.m
guitypes.m
isAxis3D.m
isVersionBelow.m
m2tstrjoin.m
m2tUpdater.m
versionArray.m
versionString.m
cleanfigure.m
figure2dot.m
m2tInputParser.m
matlab2tikz.m
► test
► examples
example_bar_plot.m
example_quivers.m
► private
calculateMD5Hash.m
cleanFiles.m
countNumberOfErrors.m
emptyStage.m
emptyStatus.m
errorHandler.m
errorHasOccurred.m
execute_hash_stage.m
execute_plot_stage.m
execute_save_stage.m
execute_tikz_stage.m
execute_type_stage.m
fillStruct.m
getEnvironment.m
getStagesFromStatus.m
hashTableName.m
hasTestFailed.m
initializeGlobalState.m
loadHashTable.m
m2troot.m
m2tstrjoin.m
OSVersion.m
restoreGlobalState.m
splitPassFailSkippedTests.m
splitUnreliableTests.m
StreamMaker.m
testMatlab2tikz.m
VersionControlIdentifier.m
► suites
► private
getEnvironment.m
herrorbar.m
isEnvironment.m
isMATLAB.m
isOctave.m
isVersionBelow.m
versionCompare.m
ACID.m
issues.m
testPatches.m
testSurfshader.m
codeReport.m
compareTimings.m
makeLatexReport.m
makeTapReport.m
makeTravisReport.m
runMatlab2TikzTests.m
saveHashTable.m
testGraphical.m
testHeadless.m
▼ trackingData
► @TrackingData
correctGyroSum.m	TrackingData function to set the sum of a periodic gyro signal to 0
correctVariance.m	TrackingData function to prevent small variances of the variables
extractData.m	TrackingData function to extract only specific data from the TrackingData object
inclineGRF.m	TrackingData function to incline force plates
mirrorMovement.m
preprocessData.m	TrackingData function to preprocess tracking data
resampleData.m	TrackingData function to resample tracking data
takeMeanAndVar.m	TrackingData function to compute the mean and variance of several data sets
TrackingData.m	Matlab class to define tracking data
trimData.m	TrackingData function to trim tracking data
useHalfGaitCycleData.m	TrackingData cut the tracking data such that only half is used
writeMotionToOsim.m	TrackingData function to write motion from tracking data object to OpenSim files