Muscles Moment extracting using python code

[Ali Khalilianmotamed Bonab]

To Whom it may concern,
I am trying to write a python code for simulating several subjects.

When I am working in GUI, I can easily use plot option to extract muscles moment, moment arm, etc. However, I do not know the procedure for extracting MuscleMoments using python code.
I would appreciate if you let me know How I can do this task.

Secondly, I want to run several subjects using python simultaneously. How it can be performed in python? To clarify, I do not want to do sequentially simulation for each subject.

Thirdly, When I am running each CMC simulation, It is automatically generating some files for me. Is it possible to change generated files format and save each simulation in a different directory?

Thanks for all the help,
Sincerely,
Ali.

[Dimitar Stanev]

You can calculate the moment arm after you position the model into the pose of interest and realize the state to position level. Please look at the following code, where I sample the moment arm of each muscle with respect to the coordinates that are spanned by the muscle

https://github.com/mitkof6/symbolic_mom ... rm.py#L257

Yes this is possible (see code below for performing SO in OpenSim v4.0). Please clarify what kind of analysis (IK, SO, ID, ...) do you want to run on python.

Code: Select all

def perform_so(model_file, ik_file, grf_file, grf_xml, reserve_actuators,
               results_dir):
    """Performs Static Optimization using OpenSim.

    Parameters
    ----------
    model_file: str
        OpenSim model (.osim)
    ik_file: str
        kinematics calculated from Inverse Kinematics
    grf_file: str
        the ground reaction forces
    grf_xml: str
        xml description containing how to apply the GRF forces
    reserve_actuators: str
        path to the reserve actuator .xml file
    results_dir: str
        directory to store the results
    """
    # model
    model = opensim.Model(model_file)

    # prepare external forces xml file
    name = os.path.basename(grf_file)[:-8]
    external_loads = opensim.ExternalLoads(model, grf_xml)
    external_loads.setExternalLoadsModelKinematicsFileName(ik_file)
    external_loads.setDataFileName(grf_file)
    external_loads.setLowpassCutoffFrequencyForLoadKinematics(6)
    external_loads.printToXML(results_dir + name + '.xml')

    # add reserve actuators
    force_set = opensim.ForceSet(model, reserve_actuators)
    force_set.setMemoryOwner(False)  # model will be the owner
    for i in range(0, force_set.getSize()):
        model.updForceSet().append(force_set.get(i))

    # construct static optimization
    motion = opensim.Storage(ik_file)
    static_optimization = opensim.StaticOptimization()
    static_optimization.setStartTime(motion.getFirstTime())
    static_optimization.setEndTime(motion.getLastTime())
    static_optimization.setUseModelForceSet(True)
    static_optimization.setUseMusclePhysiology(True)
    static_optimization.setActivationExponent(2)
    static_optimization.setConvergenceCriterion(0.0001)
    static_optimization.setMaxIterations(100)
    model.addAnalysis(static_optimization)

    # analysis
    analysis = opensim.AnalyzeTool(model)
    analysis.setName(name)
    analysis.setModel(model)
    analysis.setInitialTime(motion.getFirstTime())
    analysis.setFinalTime(motion.getLastTime())
    analysis.setLowpassCutoffFrequency(6)
    analysis.setCoordinatesFileName(ik_file)
    analysis.setExternalLoadsFileName(results_dir + name + '.xml')
    analysis.setLoadModelAndInput(True)
    analysis.setResultsDir(results_dir)
    analysis.run()
    so_force_file = results_dir + name + '_StaticOptimization_force.sto'
    so_activations_file = results_dir + name + \
                          '_StaticOptimization_activation.sto'
    return (so_force_file, so_activations_file)

The file format cannot be changed but you can set the result dir of the CMCTool.

[Ali Khalilianmotamed Bonab]

Thanks for your reply,
About your question for clarifying the tasks, I am trying to do RRA and CMC several times for each subjects.
Just in case for clarifying the idea for myself, In case of Calculating the Moment of each muscles during a gait cycle, I have to derive each muscle moment arm and multiply it with force generated by CMC.
Sincerely Yours,
Ali.

[Dimitar Stanev]

I am trying to do RRA and CMC several times for each subjects.

Unfortunately, I don't have python scripts for these two.

Just in case for clarifying the idea for myself, In case of Calculating the Moment of each muscles during a gait cycle, I have to derive each muscle moment arm and multiply it with force generated by CMC.

Yes tau = R * fm, but in CMC you also have the residual forces from the reserve actuators. You can perform inverse dynamics which is the result of what you want to calculate without getting into the trouble to calculate the moment arm and muscle forces.

[Ali Khalilianmotamed Bonab]

I just wrote this python code for RRA in Ubuntu. However, It is giving me a error :
Segmentation fault (core dumped)

Code: Select all

subject_01_Path = AbsPath + 'subject01/' ## Absolute Path of 1st subject
subject_01_RRA_Path = subject_01_Path + 'rra_multipleSteps/'  ## RRA Path
subject_01_Dataset = DatasetPathAbs + 'subject01/' ## Absolute Path of 1st subject
subject_01= opensim.Model(subject_01_Path + 'Subject_01.osim')
RRA = opensim.RRATool()
RRA.setModel(subject_01)
RRA.setDesiredKinematicsFileName(subject_01_Path + 'ik/Results_191/Run_20002.mot')
RRA.setLowpassCutoffFrequency(15)
RRA.setTaskSetFileName(subject_01_RRA_Path + 'gait2392_RRA_Tasks_v191.xml')
RRA.setOutputModelFileName(subject_01_Path + 'Subject_01.osim')
RRA.setAdjustedCOMBody('torso')
RRA.setAdjustCOMToReduceResiduals(True)
RRA.setReplaceForceSet(True)
RRA.setExternalLoadsFileName(subject_01_RRA_Path + 'ModifiedExternalForce.xml')
RRA.setInitialTime(0.199)
RRA.setFinalTime(0.962)
RRA.setMinDT(0.00000001)
RRA.setMaxDT(0.00001)
RRA.setMaximumNumberOfSteps(20000)
RRA.setErrorTolerance(0.00001)
RRA.setOutputPrecision(20)
MainDir = RRA.setResultsDir(subject_01_Dataset + 'RRA/Cycle_01')

RRA.run()

and Also in GUI there is a additional force set files which adds actuator to system. In python

Code: Select all

RRA.setForceSetFiles(subject_01_RRA_Path + 'gait2392_RRA_Actuators_v191.xml')

gives error :
TypeError: in method 'AbstractTool_setForceSetFiles', argument 2 of type 'OpenSim::Array< std::string > const &'

Could you please help me to figure out how I should fix this problems?
Sincerely,
Ali.

[Dimitar Stanev]

Code: Select all

arr = ArrayStr()
arr.append(subject_01_RRA_Path + 'gait2392_RRA_Actuators_v191.xml')
RRA.setForceSetFiles(arr)

[Ali Khalilianmotamed Bonab]

Thanks for the reply,
Is it going to solve my "CORE DUMB ERROR" also?
if it is, Could you please provide a brief explanation about the reason of this error?
Sincerely Yours,
Ali.