processMuscleAnalysis.m

% This function is part of the NMSM Pipeline, see file for full license.
%
% This function takes an OpenSim Model, the file name of the .mot/.sto of
% the IK results, the list of coordinates of interest, and the 'prefix' of
% the trial (i.e. squat, gait, stair-step) and processes the data correctly
% to be used by the MuscleTendonPersonalization.
%
% The muscle length and moments are calculated and placed in a folder
% named 'prefix' in the current working directory.
%
% (Model, string, Array of string, string) -> (None)
% processes MuscleAnalysis in preparation for MuscleTendonPersonalization


function processMuscleAnalysis(model, motionFileName, coordinates, prefix)
import org.opensim.modeling.MuscleAnalysis
import org.opensim.modeling.Storage
state = model.initSystem();
muscleAnalysis = MuscleAnalysis(model);
muscleAnalysis.setStatesStore(Storage(motionFileName));
muscleAnalysis.setCoordinates(stringArrayToArrayStr(coordinates));
muscleAnalysis.setComputeMoments(true);
muscleAnalysis.begin(state);
mkdir(prefix);
muscleAnalysis.printResults(prefix, fullfile(pwd, prefix));
removeUnneededFiles(fullfile(pwd, prefix), prefix);
end

function removeUnneededFiles(directory, prefix)
files = dir(directory);
for i=1:length(files)
    if(~files(i).isdir && contains(files(i).name, prefix))
        if(~(contains(files(i).name, "_MomentArm") || ...
                contains(files(i).name, "_Length")))
            delete(fullfile(directory, files(i).name))
        end
    end
end
end