%-------------------------------------------------------------------------%

% Copyright (c) 2019 Modenese L., Ceseracciu, E., Reggiani M., Lloyd, D.G.%

%                                                                         %

% Licensed under the Apache License, Version 2.0 (the "License");         %

% you may not use this file except in compliance with the License.        %

% You may obtain a copy of the License at                                 %

% http://www.apache.org/licenses/LICENSE-2.0.                             %

%                                                                         % 

% Unless required by applicable law or agreed to in writing, software     %

% distributed under the License is distributed on an "AS IS" BASIS,       %

% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or         %

% implied. See the License for the specific language governing            %

% permissions and limitations under the License.                          %

%                                                                         %

%    Author: Luca Modenese, August 2014                                   %

%                            revised for paper May 2015                   %

%    email:    l.modenese@imperial.ac.uk                                  % 

% ----------------------------------------------------------------------- %

%

% Script optimizing muscle parameters for the Example 2 described in 

% Modenese L, Ceseracciu E, Reggiani M, Lloyd DG (2015). "Estimation of 

% musculotendon parameters for scaled and subject specific musculoskeletal 

% models using an optimization technique" Journal of Biomechanics (submitted)

% The script performes a sensitivity study from which the Figures of the

% papers are then produced. 

% The script: 

% 1) optimizes muscle parameters varying the number of points used in the

%    optimization from 5 to 15 per degree of freedom. Optimized models and

%    optimization log are saved in the folder "Example2>OptimModels"

% 2) evaluates the results of the optimization in terms of muscle

%   parameters variation and muscle mapping metrics (and saves structures

%   summarizing the results in the folder "Example2>Results"

clear;clc;close all

% importing OpenSim libraries

import org.opensim.modeling.*

% importing muscle optimizer's functions

addpath(genpath('./Functions_MusOptTool'))

%========= USERS SETTINGS =======

% select case to simulate: 1 or 2

example_nr = 2;

% evaluations

N_eval_set = 5:15;

%================================

%=========== INITIALIZING FOLDERS AND FILES =============

% getting example details

[case_id, osimModel_ref_file, osimModel_targ_file] = getExampleInfo(example_nr);

% folders used by the script

refModel_folder         = ['./',case_id,'/MSK_Models'];

targModel_folder        = refModel_folder;

OptimizedModel_folder   = ['./',case_id,'/OptimModels'];% folder for storing optimized model

Results_folder          = ['./',case_id,'/Results'];

log_folder              = OptimizedModel_folder;

checkFolder(OptimizedModel_folder);% creates results folder is not existing

checkFolder(Results_folder);

% model files with paths

osimModel_ref_filepath   = fullfile(refModel_folder,osimModel_ref_file);

osimModel_targ_filepath  = fullfile(targModel_folder,osimModel_targ_file);

% reference model for calculating results metrics

osimModel_ref = Model(osimModel_ref_filepath);

for N_eval = N_eval_set;

    %====== MUSCLE OPTIMIZER ========

    % optimizing target model based on reference model fro N_eval points per

    % degree of freedom

    [osimModel_opt, SimsInfo{N_eval}] = optimMuscleParams(osimModel_ref_filepath, osimModel_targ_filepath, N_eval, log_folder);

    %====== PRINTING OPT MODEL =======

    % setting the output folder

    if strcmp(OptimizedModel_folder,'') || isempty(OptimizedModel_folder)

        OptimizedModel_folder = targModel_folder;

    end

    % printing the optimized model

    osimModel_opt.print(fullfile(OptimizedModel_folder, char(osimModel_opt.getName())));

    %====== SAVING RESULTS ===========

    % variation in muscle parameters

    Results_MusVarMetrics = assessMuscleParamVar(osimModel_ref, osimModel_opt, N_eval);

    % assess muscle mapping in terms of RMSE, max error

    % RMSE, errors etc evaluated at n_Metrics points between reference and

    % optimized model

    n_Metrics = 10;

    Results_MusMapMetrics = assessMuscleMapping(osimModel_ref,  osimModel_opt,N_eval, n_Metrics);

    % move results mat file to result folder

    movefile('./*.mat',Results_folder)

end

% save simulations infos

save([Results_folder,'./SimsInfo'],'SimsInfo');

% removing functions from path 

rmpath(genpath('./Functions_MusOptTool'));