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Merge branch 'master' into v40
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‎MATLAB/matlab_tool_v4.0/.gitignore‎

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*.log
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*.asv

‎MATLAB/matlab_tool_v4.0/MFD matlab tool v4.0 update notes (K. Song WUSTL).pdf‎

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‎MATLAB/matlab_tool_v4.0/TEST_plugin.m‎

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%-------------------------------------------------------------------------%
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% Copyright (c) 2019 Modenese L. %
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% Author: Luca Modenese %
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% email: l.modenese@imperial.ac.uk %
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% ----------------------------------------------------------------------- %
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% Load Library
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import org.opensim.modeling.*;
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% verification
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osimModel_name = '../_test_data/MFD_tests/testModel.osim';
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IK_mot_file = '../_test_data/MFD_tests/testKinematics_file.mot';
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results_directory = '../_test_data/MFD_tests';
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bodyOfInterest_name = 'MovingBody';
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bodyExpressResultsIn_name = [];
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effective_attachm = 'false';
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print_attachm = 'true';
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vis_on = 'true';
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N_frame_test = 5;
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% validated_results_folder = '../_test_data/MFD_tests/validated_res';
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res_anatAttach_local = getMuscleForceDirection(osimModel_name,...
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IK_mot_file,...
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results_directory,...
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bodyOfInterest_name,...
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bodyExpressResultsIn_name,...
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effective_attachm,...
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print_attachm,...
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vis_on,...
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N_frame_test);
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% res_effectAttach_local = getMuscleForceDirection(osimModel_name,...
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% IK_mot_file,...
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% results_directory,...
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% bodyOfInterest_name,...
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% bodyExpressResultsIn_name,...
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% 'true',...
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% print_attachm,...
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% vis_on,...
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% []);
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%
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% res_effectAttach_ground = getMuscleForceDirection(osimModel_name,...
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% IK_mot_file,...
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% results_directory,...
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% bodyOfInterest_name,...
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% 'ground',...
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% 'true',...
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% print_attachm,...
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% vis_on,...
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% []);
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%
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% res_anatAttach_ground = getMuscleForceDirection(osimModel_name,...
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% IK_mot_file,...
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% results_directory,...
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% bodyOfInterest_name,...
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% 'ground',...
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% 'false',...
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% print_attachm,...
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% vis_on,...
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% []);
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% res_anatAttach_local
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% res_anatAttach_ground
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% res_effectAttach_ground
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% res_effectAttach_local
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%
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% res_anatAttach_local_val = sto2Mat(fullfile(validated_results_folder,'LOCAL_ANATOM_MuscleForceDirection_vectors.sto'));
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%
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% res_anatAttach_ground.rowheaders
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% res_effectAttach_ground
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% res_effectAttach_local
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%--------------------------------------------------------------------------
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% %% test 1: simple arm26 model
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% osimModel_name = '../_test_data/Arm26/arm26.osim';
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% IK_mot_file = '../_test_data/Arm26/elbow_flexion.mot';
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% results_directory = '../_test_data/Arm26';
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% bodyOfInterest_name = 'r_humerus';
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% bodyExpressResultsIn_name = [];
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% effective_attachm = 'true';
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% print_attachm = 'true';
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% vis_on = 'true';
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% N_frame_test = 5;
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%
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% muscleLinesOfActionStruct = getMuscleForceDirection(osimModel_name,...
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% IK_mot_file,...
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% results_directory,...
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% bodyOfInterest_name,...
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% bodyExpressResultsIn_name,...
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% effective_attachm,...
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% print_attachm,...
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% vis_on,...
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% N_frame_test);
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%
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%
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%--------------------------------------------------------------------------
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%% test 2: gait2392 model
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osimModel_name = '../_test_data/gait2392/subject01.osim';
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IK_mot_file = '../_test_data/gait2392/subject01_walk1_ik.mot';
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results_directory = '../_test_data/gait2392';
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bodyOfInterest_name = 'femur_r';
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bodyExpressResultsIn_name = [];
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effective_attachm = 'true';
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print_attachm = 'true';
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vis_on = 'true';
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N_frame_test = 5;
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muscleLinesOfActionStruct = getMuscleForceDirection(osimModel_name,...
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IK_mot_file,...
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results_directory,...
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bodyOfInterest_name,...
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bodyExpressResultsIn_name,...
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effective_attachm,...
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print_attachm,...
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vis_on,...
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N_frame_test);

‎MATLAB/matlab_tool_v4.0/_dev_deal_withMuscleWrap.m‎

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%-------------------------------------------------------------------------%
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% Copyright (c) 2019 Modenese L. %
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% Author: Luca Modenese %
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% email: l.modenese@imperial.ac.uk %
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% ----------------------------------------------------------------------- %
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clear;clc
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import org.opensim.modeling.*
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% TO DO: add the possibility of following states
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%%%%%%%%%%%%% SET UP %%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% General model
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ModelFile = 'arm26.osim';
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% read model
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osimModel = Model(ModelFile);
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muscles = osimModel.getMuscles();
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aOsimMuscleNameSet = 'all';%{'BRA'};
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% setting which muscles will be followed
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muscleNames = ArrayStr;
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if strcmp(aOsimMuscleNameSet,'all')
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% getmuscles
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muscles.getNames(muscleNames);
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else
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% assign given muscle names to the set to be analyzed
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for n_mn = 1:length( aOsimMuscleNameSet )
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muscleNames.append(aOsimMuscleNameSet{n_mn})
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end
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end
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for n_mus = 0:muscleNames.getSize()-1
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% current muscle
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curr_muscle = muscles.get(muscleNames.getitem(n_mus));
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% EXTRACTING THE WRAPPING POINTS
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si = osimModel.initSystem();
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% get the geometry path for the current state
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PathpointArray = curr_muscle.getGeometryPath().getCurrentPath(si);
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% normal pathpoints attached to bodies
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ModelPathpoint = curr_muscle.getGeometryPath().getPathPointSet();
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% check if there are wrapping points
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NrOfWrappingPoints = PathpointArray.getSize()-ModelPathpoint.getSize();
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% header
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display(['Muscle ',char(curr_muscle.getName()), ' (',num2str(NrOfWrappingPoints),' wrapping points)']);
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for n_p = 0:PathpointArray.getSize()-1
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% get the coordinates of the current pathpoint
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curr_point_loc_OS = Vec3(PathpointArray.getitem(n_p).getLocation);
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curr_point_loc = [curr_point_loc_OS.get(0),curr_point_loc_OS.get(1),curr_point_loc_OS.get(2)];
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% body where the body is attached to
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display(['Point ',num2str(n_p+1), ' attached to body ',char(PathpointArray.getitem(n_p).getBodyName())]);
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display([num2str(curr_point_loc_OS.get(0)),' ',num2str(curr_point_loc_OS.get(1)),' ',num2str(curr_point_loc_OS.get(2))])
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end
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display('-----------------------------------');
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end

‎MATLAB/matlab_tool_v4.0/getBodyorGround.m‎

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function Body = getBodyorGround(osimModel,BodyName)
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%-------------------------------------------------------------------------%
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% getBodyorGround gets a Body or Ground by name from an OpenSim model %
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% (version 4.0 and up). %
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% %
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% INPUTS: %
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% - osimModel: the OpenSim model object. %
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% - BodyName: name pf body to get, a character string. %
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% %
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% OUTPUTS: %
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% - Body: target PhysicalFrame object, either a Body or Ground. %
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% %
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% code edition log: %
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% 18 Sep 2019: created for OpenSim 4.0 model Body/Ground format (KS). %
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% ----------------------------------------------------------------------- %
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% Author: Ke Song (Washington University in St. Louis) %
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% E-mail: ksong23@wustl.edu %
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% ----------------------------------------------------------------------- %
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% load Library
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import org.opensim.modeling.*;
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% get name of Ground in model
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osimGroundName = char(osimModel.getGround.getName());
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% get Ground or Body based on name
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if strcmp(BodyName,osimGroundName)
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Body = osimModel.getGround(); %Ground
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else
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Body = osimModel.getBodySet.get(BodyName);
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end
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end

‎MATLAB/matlab_tool_v4.0/getCurrentMusclePathAsMat.m‎

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%-------------------------------------------------------------------------%
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% Copyright (c) 2019 Modenese L. %
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% %
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% Licensed under the Apache License, Version 2.0 (the "License"); %
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% you may not use this file except in compliance with the License. %
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% You may obtain a copy of the License at %
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% http://www.apache.org/licenses/LICENSE-2.0. %
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% %
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% Unless required by applicable law or agreed to in writing, software %
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% distributed under the License is distributed on an "AS IS" BASIS, %
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% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or %
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% implied. See the License for the specific language governing %
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% permissions and limitations under the License. %
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% %
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% Author: Luca Modenese, 2017 %
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% email: l.modenese@imperial.ac.uk %
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% ----------------------------------------------------------------------- %
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% Given a state, this script collects info about the path of a muscle.
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% Bodies of muscle attachments and point coordinates are made available as
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% a list and a matrix respectively.
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%
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% INPUTS:
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% - osimMuscle: an OpenSim model (API object).
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% - s: state, used to update the current muscle path and get
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% active conditional viapoints.
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%
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% OUTPUTS:
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% - mus_bodyset_list: matrix where each row is a muscle point and
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% columns are its [X Y Z] coordinates in the reference system of
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% the body they belong to (as in .osim file).
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% - mus_pointset_mat: cell array of body names, same length as
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% the PathPointSet, with the name of the Body for each point.
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%
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%
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% last modified:
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% 2017: created.
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% 26 Jun 2018: comments (LM)
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% 29 Nov 2018: renamed, recommented, modified, added to MFD Matlab version.
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% 18 Sep 2019: using getCurrentPath to recognize wrap points (KS).
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% ----------------------------------------------------------------------- %
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function [mus_bodyset_list, mus_pointset_mat] = getCurrentMusclePathAsMat(osimMuscle, s)
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% load libraries
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import org.opensim.modeling.*;
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% get geometry path point array (including wrap points) for current state
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curr_PathPointSet = osimMuscle.getGeometryPath().getCurrentPath(s);
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n_pp = 1;
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for n_p = 0:curr_PathPointSet.getSize-1
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% point under examination
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curr_point = curr_PathPointSet.get(n_p);
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attachBody = curr_point.getBodyName();
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% if pathpoint is conditional, then check if it is active
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if strcmp(char(curr_point.getConcreteClassName), 'ConditionalPathPoint')
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cond_viapoint = ConditionalPathPoint.safeDownCast(curr_point);
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% is it active?
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if cond_viapoint.isActive(s)
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% if yes add it to point set
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mus_pointset_mat(n_pp, 1:3) = [curr_point.getLocation(s).get(0), curr_point.getLocation(s).get(1), curr_point.getLocation(s).get(2)]; %#ok<*AGROW>
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mus_bodyset_list(n_pp) = {char(attachBody)};
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n_pp = n_pp+1;
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else
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continue
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end
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else
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% if not conditional add it
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mus_pointset_mat(n_pp, 1:3) = [curr_point.getLocation(s).get(0), curr_point.getLocation(s).get(1), curr_point.getLocation(s).get(2)];
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mus_bodyset_list(n_pp) = {char(attachBody)};
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n_pp = n_pp+1;
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end
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end
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end

‎MATLAB/matlab_tool_v4.0/getMatStructColumn.m‎

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%-------------------------------------------------------------------------%
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% Copyright (c) 2019 Modenese L. %
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% %
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% Licensed under the Apache License, Version 2.0 (the "License"); %
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% you may not use this file except in compliance with the License. %
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% You may obtain a copy of the License at %
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% http://www.apache.org/licenses/LICENSE-2.0. %
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% %
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% Unless required by applicable law or agreed to in writing, software %
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% distributed under the License is distributed on an "AS IS" BASIS, %
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% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or %
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% implied. See the License for the specific language governing %
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% permissions and limitations under the License. %
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% %
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% Author: Luca Modenese %
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% email: l.modenese@imperial.ac.uk %
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% ----------------------------------------------------------------------- %
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%
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% Function that allows to retrieve the value of a specified variable whose
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% name is specified in var_name.
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%
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% INPUTS
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% struct: is a structure with fields 'colheaders', the headers, and 'data'
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% that is a matrix of data.
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% var_name: the name of the variable to extract.
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%
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% OUTPUTS
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% var_value: the column of the matrix correspondent to the header specified
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% in input as var_name.
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%
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%
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% written: Luca Modenese, July 2014
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% last modified:
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% Header (February 2018, LM)
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% 29 Nov 2018: renamed, recommented, added to MFD Matlab version (LM).
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% ----------------------------------------------------------------------- %
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function var_value = getMatStructColumn(struct, var_name)
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% gets the index of the desired variable name in the colheaders of the
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% structure from where it will be extracted
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var_index = strncmp(struct.colheaders, var_name, length(var_name));
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if sum(var_index) == 0
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%error(['getValueColumnForHeader.m','. No header in structure is matching the name ''',var_name,'''.'])
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display(['getValueColumnForHeader.m','. No header in structure is matching the name ''',var_name,''''])
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var_value = [];
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return
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end
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% uses the index to retrieve the column of values for that variable.
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var_value = struct.data(:,var_index);
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end

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