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

% Copyright (c) 2019 Modenese L.                                          %

%                                                                         %

% 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.                             %

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% 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            %

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%                                                                         %

%    Author:   Luca Modenese                                              %

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

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

% This script converts a .sto file generated by OpenSim analyses in a

% matlab structure "MatStruct" with fields "colheaders" and "data".

% This is a convenient script to robustly read OpenSim files.

%

% INPUTS:

%           - Storage_file: a .sto file, including path, e.g. from static

%           optimization or JointReaction analysis.

% OUTPUTS:

%           -MatStruct: matlab structure with the following fields:

%               a) MatStruct.colheaders: cell array of headers of the

%                                           .sto file.

%               b) MatStruct.data: matrix containing the data that

%                                        were stored in the input file.

%

%

% written: 2014/2015 (Griffith University)

% last modified: 

% 26 Jun 2017: comments (LM)

% 29 Nov 2018: changed name - added to MFD Matlab version.

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

function MatStruct = sto2Mat(storage_file)

% OpenSim suggested settings

import org.opensim.modeling.*

OpenSimObject.setDebugLevel(3);

% read storage file

openSimStorage = Storage(storage_file);

% extract time column and place it in time array

timeColumn = ArrayDouble();

openSimStorage.getTimeColumn(timeColumn);

for n_t = 0:timeColumn.getSize-1

    time_vec(n_t+1,1) = timeColumn.getitem(n_t);

end

% converting labels

OSLabelsArray = openSimStorage.getColumnLabels;

for n_lab = 0:OSLabelsArray.getSize-1

    MatStruct.colheaders{n_lab+1} = char(OSLabelsArray.get(n_lab));

end

% converting data

dataColumn = ArrayDouble();

ind = 0;

while openSimStorage.getDataColumn(ind, dataColumn)

    for n_d = 0:dataColumn.getSize-1

        StorageData(n_d+1,ind+1) = dataColumn.getitem(n_d);

    end

    ind = ind+1;

end

MatStruct.data = [time_vec, StorageData];

% checking that dimensionality of data and colheaders are consistent

n_diff = size(MatStruct.colheaders,2)-size(MatStruct.data,2);

% if not consistent let the user decide what to do

if n_diff>0

    answ = menu(['In the conversion from storage to MATLAB structure ',num2str(n_diff),' more header(s) than data were found. Removing extra headers (y) or stop (n).'], 'Yes','No');

    if answ == 1

        MatStruct.colheaders = MatStruct.colheaders(1:size(MatStruct.data,2));

    elseif answ == 2

        error('Please check your sto files manually.');

    end

end

end