parseSelectMomentArms.m

% This function is part of the NMSM Pipeline, see file for full license.
%
% () -> ()
% 


function cells = parseSelectMomentArms(directories, coordinateNames, muscleNames)
import org.opensim.modeling.Storage
firstTrial = parseSpecificMuscleAnalysisCoordinates(directories(1), ...
    coordinateNames, muscleNames);
cells = zeros([length(directories) size(firstTrial)]);
cells(1, :, :, :) = firstTrial;
for i=2:length(directories)
    cells(i, :, :, :) = parseSpecificMuscleAnalysisCoordinates(directories(i), ...
        coordinateNames, muscleNames);
end
end

function cells = parseSpecificMuscleAnalysisCoordinates(inputDirectory, ...
    coordinateNames, muscleNames)
import org.opensim.modeling.Storage
coordFileNames = findSpecificMuscleAnalysisCoordinateFiles(inputDirectory, coordinateNames);
firstFile = storageToDoubleMatrix(Storage(coordFileNames(1)));
columnNames = getStorageColumnNames(Storage(coordFileNames(1)));
cells = zeros([length(coordFileNames) size(firstFile)]);
cells(1, :, :) = firstFile;
for i=2:length(coordFileNames)
    cells(i, :, :) = storageToDoubleMatrix(Storage(coordFileNames(i)));
end
cells = findSpecificMusclesInData(cells, columnNames, muscleNames);
end

function names = findSpecificMuscleAnalysisCoordinateFiles(directory, coordinateNames)
files = dir(directory);
names = string([]);
for i=1:length(coordinateNames)
    for j=1:length(files)
        if(contains(files(j).name, strcat("MomentArm_", ...
                coordinateNames(i)', ".sto")))
            names(end+1) = fullfile(directory, files(j).name);
        end
    end
end
end