processRawEmgFile.m

% This function is part of the NMSM Pipeline, see file for full license.
%
% Produce a new processed EMG file using RCNL's protocol for turning a
% matrix of double of EMG data into processed EMG data.
%
% (2D Array of double, 1D Array of double, string, struct) -> (None)
% Processes the input EMG data by RCNL's protocol


function processRawEmgFile(emgFilename, filterOrder, highPassCutoff, ...
    lowPassCutoff, processedEmgFileName)
emgStorage = org.opensim.modeling.Storage(emgFilename);
timePoints = findTimeColumn(emgStorage);
columnNames = getStorageColumnNames(emgStorage);
rawData = storageToDoubleMatrix(emgStorage);

processedData = processEmg( ...
                            rawData, ...
                            timePoints, ...
                            struct( ...
                                "filterOrder", filterOrder, ...
                                "highPassCutoff", highPassCutoff, ...
                                "lowPassCutoff", lowPassCutoff ...
                                ));

writeToSto(columnNames, timePoints, processedData, processedEmgFileName);
end