simtk.org

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for i= 1:no_data_set
    %% ===================== Call files and folders ======================== %%
    % ----------- Specify results file for current iteration
    data_set_no = sprintf('_%d',i);
    results_folder_current = append(results_folder_base, data_set_no); % create a name for folder which will contain results for current iteration
    mkdir([path2mot results_folder_4_batch results_folder_current{1}])  % create folder for results of current iteration

    % ----------- Load relevant .mot file
    file_no = sprintf('_%d',i);
    CurrentMotFile = [path2mot results_folder_4_batch NameNoExt file_no '.mot']; % path to .mot file
    [~, CurrentMotFileName, extension] = fileparts(CurrentMotFile);    % Create the storage object from the input .mot file
    CurrentMotStor = STOFileAdapter().read(CurrentMotFile);
    % get labels from mot file
    MotTableLabels = CurrentMotStor.getColumnLabels; 
    forceslabels = cell(CurrentMotStor.getNumColumns(),1);
    for i = 0 : CurrentMotStor.getNumColumns() -1 
        forceslabels{i+1,1} = char(MotTableLabels.get(i)); 
    end
    
    %% ========================== OpenSim Model ============================ %%
    % @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ %    
    % Load a model
    % path to model defined outside of loop
    myModel = Model(path2model);
    % initiate model
    myModel.initSystem();
    % ------------------ Get various model components ---------------------- %
    % ------------------------- Bodies
    bodySet = myModel.getBodySet();
    nBodies = bodySet.getSize;
    % ------------------------- Joints
    jointSet = myModel.getJointSet();
    nJoints = jointSet.getSize;
    
    % ------------------------- Muscles
    muscSet = myModel.getMuscles();
    nMuscles = muscSet.getSize;
    % nameMusc = myModel.getStateVariableNames();
    
    % ------------------------- Ground
    gnd = myModel.getGround();
    
    % ------------------------- Actuators
    actSet = myModel.getActuators();
    nact = actSet.getSize;
    
    % ------------------------- Forces
    forceSet = myModel.getForceSet();
    %

    %% ===================== Set External Loads ======================== %%
    % @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ %
    
    % define application of external loads
    LowpassFilt = -1;

    % ---------------- External force
    %
    % externalforce placed within externalload, 
    extforce = ExternalForce();
    extforce.setName(CurrentMotFileName);
    % Identify force and point columns
    forceIDIndex = find( contains(forceslabels,'_vx'));
    pointIDIndex = find( contains(forceslabels,'_px'));
    %
    extforce.set_applied_to_body('top_pot');
    extforce.set_force_expressed_in_body('ground');
    extforce.set_point_expressed_in_body('ground');
    extforce.set_force_identifier(strrep(forceslabels{forceIDIndex},'x','')); 
    extforce.set_point_identifier(strrep(forceslabels{pointIDIndex},'x','')); 
    %
    % ---------------- External load
    %
    extload = ExternalLoads();
    extload.setName(CurrentMotFileName);
    extload.setDataFileName(CurrentMotFile); % provide path to .mot file
    extload.cloneAndAppend(extforce); % add the external force to the external load
    extload.setLowpassCutoffFrequencyForLoadKinematics(LowpassFilt);
    % Create external load xml file
    extLoadsXml = [CurrentMotFileName '_' 'external_loads.xml'];
    % Print the external load xml file
    extload.print([path2mot results_folder_4_batch results_folder_current{1} '\' extLoadsXml]); % must go into an already existing folder
    %
    %
    %% ------------- Set-up of ForwardTool through Matlab -------------- %%
    %
    % setup options 
    
    errorTol = 1.0000000000000001e-05;
    maxIntergratorSteps = 20000;
    minStepSize = 1e-08;
    maxStepSize = 1;
    outputPrecision = 8;
    timeStart = 0;
    timeEnd = 1.24;

    % Apply to forward tool
    ft = ForwardTool(); 
    ft.setName(['set-up_' CurrentMotFileName]); % name of forward tool
    ft.setModel(myModel); % model
    ft.setModelFilename([char(myModel.getName) '_' CurrentMotFileName]); % name model
    ft.setReplaceForceSet(0) % specified force sets are appended 
    % apply set up options
    ft.setStartTime(timeStart);
    ft.setFinalTime(timeEnd);   
    ft.setErrorTolerance(errorTol);
    ft.setMaximumNumberOfSteps(maxIntergratorSteps);
    ft.setMinDT(minStepSize);
    ft.setMaxDT(maxStepSize);
    ft.setOutputPrecision(outputPrecision);
    ft.setSolveForEquilibrium(0); % very important when muscles are involved
    % set the external load of the current loop, this should make no
    % difference as there are no muscles in the model, simulations have
    % shown this is the case
    ft.setExternalLoads(extload); 
    % specify output directory
    ft.setResultsDir([path2mot results_folder_4_batch results_folder_current{1}]) % folder for results, it will be automatically created MotFilePath results_folder_4_batch
    % print out .xml file of forward tool
    FT_SetUp_Xml = [CurrentMotFileName '_' 'SetUp.xml']; 
    ft.print([path2mot results_folder_4_batch results_folder_current{1} '\' FT_SetUp_Xml]); % Write this Object into an XML file of the given name
    %
    % ----------------
    %
    %% ---------------------- Prepare Analysis ------------------------- %%
    % Necessary to define the analysis 
    %
    % ------------------------- Add point kinematics analysis
    %
    % Add analysis for a point in L3
    pk1 = PointKinematics();
    myModel.addAnalysis(pk1);
    pk1.setInDegrees(1)
    pk1.setBody(bodySet.get(1));
    pk1.setRelativeToBody(gnd)
    pk1.setPointName('centre_of_DIC_point_L3')
    pk1.setPoint(Vec3(-0.0395074751100576,0.0471332730104978,0.00651529708770742));
    % Add analysis for a point in L2
    pk2 = PointKinematics();
    myModel.addAnalysis(pk2);
    pk2.setInDegrees(1)
    pk2.setBody(bodySet.get(2));
    pk2.setRelativeToBody(gnd)
    pk2.setPointName('centre_of_DIC_point_L2')
    pk2.setPoint(Vec3(-0.0436541829436566,0.0862211168263703,0.0112360325795324));
    %
    % ------------------------- Add body kinematics
    bk = BodyKinematics();
    bk.setModel(myModel)
    bk.setInDegrees(1)
    bk.setExpressResultsInLocalFrame(1);
    myModel.addAnalysis(bk);
    %
    % --------------------------- Run simulation ---------------------------- %
    %
    myModel.initSystem();
    ft.run();
    clear myModel extload extforce ft pk1 pk2 bk
end

Code: Select all

% ---------------- Define the external force, specifies the body the force is applied to, the reference frames and should be able to also specify the mot file using the command data_source_name (I couldn't)
% externalforce placed within externalload
extforce = ExternalForce ();
% specify the column headings that contains the force magnitude and point of application data 
% specify the body to apply forces to 
% pecify reference frames

% ---------------- External load
extload = ExternalLoads();
% I had problems setting the .mot file in the external force so added it here, a .mot file can contain multiple force sets, you specify which is applied to which body in the external force above
extload.setDataFileName(paths.path2loading);
% this adds the external force to the external load, which then applied the load in the simulation/analysis
extload.cloneAndAppend(extforce);