calcNormalizedFiberLengthMeanSimilarityCost.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 = calcNormalizedFiberLengthMeanSimilarityCost( ...
    modeledValues, experimentalData, costTerm)
errorCenter = valueOrAlternate(costTerm, "errorCenter", 0);
maximumAllowableError = valueOrAlternate(costTerm, "maxAllowableError", 0.1);
Ind = 1;
for i = 1:length(experimentalData.normalizedFiberLengthGroups)
normalizedFiberLengthSimilarity = ...
    abs(modeledValues.normalizedFiberLength(:, ...
    experimentalData.normalizedFiberLengthGroups{i}, :) - ...
    mean(modeledValues.normalizedFiberLength(:, ...
    experimentalData.normalizedFiberLengthGroups{i}, :),  2));
normalizedFiberLengthSimilarityCost(Ind : Ind + ...
    size(experimentalData.normalizedFiberLengthGroups{i}, 2) - 1) = ...
    log(sum(exp(500 * (normalizedFiberLengthSimilarity)), [1 3])) / 500;
Ind = Ind + size(experimentalData.normalizedFiberLengthGroups{i}, 2);
end

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