calcResidualMuscleActivationCost.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 = calcResidualMuscleActivationCost(synxModeledValues, ...
    modeledValues, experimentalData, costTerm)
errorCenter = valueOrAlternate(costTerm, "errorCenter", 0);
maximumAllowableError = valueOrAlternate(costTerm, "maxAllowableError", 0.3);
cost = calcDeviationCostTerm(...
    synxModeledValues.muscleActivations(:, setdiff(1 : ...
    size(synxModeledValues.muscleActivations, 2), ...
    [experimentalData.synergyExtrapolation.missingEmgChannelGroups{:}]), :) - ...
    modeledValues.muscleActivations(:, setdiff(1 : ...
    size(synxModeledValues.muscleActivations, 2), ...
    [experimentalData.synergyExtrapolation.missingEmgChannelGroups{:}]), :), ...
    errorCenter, maximumAllowableError);
end