calcMinimumNormalizedFiberLengthDeviationCost.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 = calcMinimumNormalizedFiberLengthDeviationCost( ...
    modeledValues, experimentalData, costTerm)
errorCenter = valueOrAlternate(costTerm, "errorCenter", 0);
maximumAllowableError = valueOrAlternate(costTerm, "maxAllowableError", 0.3);
minNormalizedFiberLength = min(modeledValues.normalizedFiberLength, [], 3);
for i = 1 : size(experimentalData.muscleTendonLength,1)
for ii = 1 : length(experimentalData.muscleNames)
    if minNormalizedFiberLength(i, ii) < experimentalData.minNormalizedMuscleFiberLength 
        minNormalizedFiberLengthError(i, ii) = ...
            minNormalizedFiberLength(i, ii) - ...
            experimentalData.minNormalizedMuscleFiberLength;
    else
        minNormalizedFiberLengthError(i, ii) = 0;
    end
end 
end

cost = calcDeviationCostArray(...
    minNormalizedFiberLengthError, errorCenter, maximumAllowableError);
end