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import org.opensim.modeling.*

% Apply the generic xml to the constructor
idTool = InverseDynamicsTool(genericSetupFileFullPath);

% Load the model and initialize
model = Model([inputDir '\' modelFileName]);
model.initSystem();

% Tell Tool to use the loaded model
idTool.setModel(model);

nTrials = size(motList,2);

% Loop through the trials
for trial= 1:nTrials;   
 
    % Get the name of the file for this trial
    motFile = motList{trial};
    
    % Create name of trial from .mot file name
    name = regexprep(motFile,'_ik.mot','');
    
    fullpath = ([inputDir '\' motFile]);

    % Get mot data to determine time range
    motData = Storage(fullpath);
    
    % Get initial and final time 
    initial_time = motData.getFirstTime();
    final_time = motData.getLastTime();    
    
    % Setup the idTool for this trial
    idTool.setName(name);
    idTool.setCoordinatesFileName(fullpath);
    idTool.setStartTime(initial_time);
    idTool.setEndTime(final_time);
    idTool.setOutputGenForceFileName([ 'inverse_dynamics_' name '.sto' ]);
    
    idTool.setResultsDir(outputDir);
    
    %External Load File
    % Create an external loads object
    extLoadsObject = ExternalLoads(model,genericExtLoadFullPath);
    
    fullpathGRFFile=[inputDir '\' name '.mot'];
    
    % Set the grf filename
    extLoadsObject.setDataFileName(fullpathGRFFile);
    
    % Set the model external loads file
    extLoadsObject.setExternalLoadsModelKinematicsFileName(fullpath);
    
    % Create name for a subject specific external loads xml
    extLoadsXml = [name '_' 'external_loads.xml'];
    
    % Print the external load xml file
    extLoadsObject.print([trialDir '\' extLoadsXml]);
        
    idTool.setExternalLoadsFileName([trialDir '\' extLoadsXml]);
    
    % Save the settings in a setup file
    outfile = [ 'setup_ID_' name '.xml' ];
    
    idTool.print([trialDir '\' outfile]);

    fprintf([ 'Performing ID on trial ' name '\n'])
      
    % Run ID
    idTool.run();
    
end