calcNormalizedFiberLengthDeviationCost.m

% This function is part of the NMSM Pipeline, see file for full license.
%
% (Array of number, struct) -> (Array of number)
% returns the cost for all rounds of the Muscle Tendon optimization


function cost = calcNormalizedFiberLengthDeviationCost(modeledValues, ...
    experimentalData, costTerm)
errorCenter = valueOrAlternate(costTerm, "errorCenter", 0);
maximumAllowableError = valueOrAlternate(costTerm, "maxAllowableError", 0.1);
normalizedFiberLengthMagnitudeDeviation = calcMagnitudeDeviations( ...
    modeledValues.normalizedFiberLength, ...
    experimentalData.normalizedFiberLength);
normalizedFiberLengthMagnitudeDeviationCost = calcDeviationCostTerm( ...
    normalizedFiberLengthMagnitudeDeviation, errorCenter, ...
    maximumAllowableError);
normalizedFiberLengthShapeDeviation = calcShapeDeviations( ...
    modeledValues.normalizedFiberLength, ...
    experimentalData.normalizedFiberLength);
normalizedFiberLengthShapeDeviationCost = calcDeviationCostTerm( ...
    normalizedFiberLengthShapeDeviation, errorCenter, ...
    maximumAllowableError);
cost = normalizedFiberLengthMagnitudeDeviationCost + ...
    normalizedFiberLengthShapeDeviationCost;
end