Diff of /MATLAB/private/sto2Mat.m [000000] .. [b87f69]

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+%-------------------------------------------------------------------------%
+% 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.                             %
+%                                                                         % 
+% 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                                              %
+%    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
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