combineCostsIntoVector.m

% This function is part of the NMSM Pipeline, see file for full license.
%
% Combines all tracking and penalization costs into a large vector
%
% (array of number, struct) -> (column vector of number)
% calculates the combined cost for the muscle tendon personalization module


function output = combineCostsIntoVector(costWeight, costs)
output = [ ...
    % Minimize joint moment tracking errors
    sqrt(costWeight(1)).* costs.momentMatching(:); ...  
    % Penalize difference of tact from set point
    sqrt(costWeight(2)).* costs.activationTimePenalty(:); ...
    % Penalize difference of Anonlin from set point
    sqrt(costWeight(3)).* costs.activationNonlinearityPenalty(:); ...
    % Penalize difference of lmo values from pre-calibrated values
    sqrt(costWeight(4)).* costs.optimalFiberLengthPenalty(:);... 
    % Penalize difference of lts values from pre-calibrated values
    sqrt(costWeight(5)).* costs.tendonSlackLengthPenalty(:);...    
    % Penalize difference of EMGScale from set point
    sqrt(costWeight(6)).* costs.emgScalePenalty(:);... 
    % Penalize change of lMtilda from pre-calibrated values
    sqrt(costWeight(7)).* costs.normalizedFiberLengthPenalty(:);...    
    % Penalize violation of lMtilda similarity between grouped muscles
    sqrt(costWeight(8)).* costs.normalizedFiberLengthGroupedSimilarity(:);...
    % Penalize violation of EMGScales similarity between grouped muscles
    sqrt(costWeight(9)).* costs.emgScaleGroupedSimilarity(:);...  
    % Penalize violation of tdelay similarity between grouped muscles
    sqrt(costWeight(10)).*costs.tdelayGroupedSimilarity(:);... 
    % Minimize passive force
    sqrt(costWeight(11)).*costs.minPassiveForce(:);...            
    ];
end