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Merged
modenaxe merged 4 commits into from
Feb 13, 2020
Merged

matlab_tool_v4.0 #1

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2 changes: 2 additions & 0 deletions matlab_tool_v4.0/.gitignore
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*.log
*.asv
Binary file added matlab_tool_v4.0/MFD matlab tool v4.0 update notes (K. Song WUSTL).pdf
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116 changes: 116 additions & 0 deletions matlab_tool_v4.0/TEST_plugin.m
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%-------------------------------------------------------------------------%
% Copyright (c) 2019 Modenese L. %
% Author: Luca Modenese %
% email: l.modenese@imperial.ac.uk %
% ----------------------------------------------------------------------- %
% Load Library
import org.opensim.modeling.*;

% verification
osimModel_name = '../_test_data/MFD_tests/testModel.osim';
IK_mot_file = '../_test_data/MFD_tests/testKinematics_file.mot';
results_directory = '../_test_data/MFD_tests';
bodyOfInterest_name = 'MovingBody';
bodyExpressResultsIn_name = [];
effective_attachm = 'false';
print_attachm = 'true';
vis_on = 'true';
N_frame_test = 5;

% validated_results_folder = '../_test_data/MFD_tests/validated_res';

res_anatAttach_local = getMuscleForceDirection(osimModel_name,...
IK_mot_file,...
results_directory,...
bodyOfInterest_name,...
bodyExpressResultsIn_name,...
effective_attachm,...
print_attachm,...
vis_on,...
N_frame_test);

% res_effectAttach_local = getMuscleForceDirection(osimModel_name,...
% IK_mot_file,...
% results_directory,...
% bodyOfInterest_name,...
% bodyExpressResultsIn_name,...
% 'true',...
% print_attachm,...
% vis_on,...
% []);
%
% res_effectAttach_ground = getMuscleForceDirection(osimModel_name,...
% IK_mot_file,...
% results_directory,...
% bodyOfInterest_name,...
% 'ground',...
% 'true',...
% print_attachm,...
% vis_on,...
% []);
%
% res_anatAttach_ground = getMuscleForceDirection(osimModel_name,...
% IK_mot_file,...
% results_directory,...
% bodyOfInterest_name,...
% 'ground',...
% 'false',...
% print_attachm,...
% vis_on,...
% []);


% res_anatAttach_local
% res_anatAttach_ground
% res_effectAttach_ground
% res_effectAttach_local
%
% res_anatAttach_local_val = sto2Mat(fullfile(validated_results_folder,'LOCAL_ANATOM_MuscleForceDirection_vectors.sto'));
%
% res_anatAttach_ground.rowheaders
% res_effectAttach_ground
% res_effectAttach_local
%--------------------------------------------------------------------------
% %% test 1: simple arm26 model
% osimModel_name = '../_test_data/Arm26/arm26.osim';
% IK_mot_file = '../_test_data/Arm26/elbow_flexion.mot';
% results_directory = '../_test_data/Arm26';
% bodyOfInterest_name = 'r_humerus';
% bodyExpressResultsIn_name = [];
% effective_attachm = 'true';
% print_attachm = 'true';
% vis_on = 'true';
% N_frame_test = 5;
%
% muscleLinesOfActionStruct = getMuscleForceDirection(osimModel_name,...
% IK_mot_file,...
% results_directory,...
% bodyOfInterest_name,...
% bodyExpressResultsIn_name,...
% effective_attachm,...
% print_attachm,...
% vis_on,...
% N_frame_test);
%
%
%--------------------------------------------------------------------------
%% test 2: gait2392 model
osimModel_name = '../_test_data/gait2392/subject01.osim';
IK_mot_file = '../_test_data/gait2392/subject01_walk1_ik.mot';
results_directory = '../_test_data/gait2392';
bodyOfInterest_name = 'femur_r';
bodyExpressResultsIn_name = [];
effective_attachm = 'true';
print_attachm = 'true';
vis_on = 'true';
N_frame_test = 5;

muscleLinesOfActionStruct = getMuscleForceDirection(osimModel_name,...
IK_mot_file,...
results_directory,...
bodyOfInterest_name,...
bodyExpressResultsIn_name,...
effective_attachm,...
print_attachm,...
vis_on,...
N_frame_test);
65 changes: 65 additions & 0 deletions matlab_tool_v4.0/_dev_deal_withMuscleWrap.m
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%-------------------------------------------------------------------------%
% Copyright (c) 2019 Modenese L. %
% Author: Luca Modenese %
% email: l.modenese@imperial.ac.uk %
% ----------------------------------------------------------------------- %

clear;clc
import org.opensim.modeling.*

% TO DO: add the possibility of following states
%%%%%%%%%%%%% SET UP %%%%%%%%%%%%%%%%%%%%%%%%%%%%
% General model
ModelFile = 'arm26.osim';
% read model
osimModel = Model(ModelFile);
muscles = osimModel.getMuscles();
aOsimMuscleNameSet = 'all';%{'BRA'};
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


% setting which muscles will be followed
muscleNames = ArrayStr;
if strcmp(aOsimMuscleNameSet,'all')
% getmuscles
muscles.getNames(muscleNames);
else
% assign given muscle names to the set to be analyzed
for n_mn = 1:length( aOsimMuscleNameSet )
muscleNames.append(aOsimMuscleNameSet{n_mn})
end
end

for n_mus = 0:muscleNames.getSize()-1

% current muscle
curr_muscle = muscles.get(muscleNames.getitem(n_mus));

% EXTRACTING THE WRAPPING POINTS
si = osimModel.initSystem();

% get the geometry path for the current state
PathpointArray = curr_muscle.getGeometryPath().getCurrentPath(si);

% normal pathpoints attached to bodies
ModelPathpoint = curr_muscle.getGeometryPath().getPathPointSet();

% check if there are wrapping points
NrOfWrappingPoints = PathpointArray.getSize()-ModelPathpoint.getSize();

% header
display(['Muscle ',char(curr_muscle.getName()), ' (',num2str(NrOfWrappingPoints),' wrapping points)']);

for n_p = 0:PathpointArray.getSize()-1

% get the coordinates of the current pathpoint
curr_point_loc_OS = Vec3(PathpointArray.getitem(n_p).getLocation);
curr_point_loc = [curr_point_loc_OS.get(0),curr_point_loc_OS.get(1),curr_point_loc_OS.get(2)];

% body where the body is attached to
display(['Point ',num2str(n_p+1), ' attached to body ',char(PathpointArray.getitem(n_p).getBodyName())]);
display([num2str(curr_point_loc_OS.get(0)),' ',num2str(curr_point_loc_OS.get(1)),' ',num2str(curr_point_loc_OS.get(2))])

end
display('-----------------------------------');
end
33 changes: 33 additions & 0 deletions matlab_tool_v4.0/getBodyorGround.m
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function Body = getBodyorGround(osimModel,BodyName)
%-------------------------------------------------------------------------%
% getBodyorGround gets a Body or Ground by name from an OpenSim model %
% (version 4.0 and up). %
% %
% INPUTS: %
% - osimModel: the OpenSim model object. %
% - BodyName: name pf body to get, a character string. %
% %
% OUTPUTS: %
% - Body: target PhysicalFrame object, either a Body or Ground. %
% %
% code edition log: %
% 18 Sep 2019: created for OpenSim 4.0 model Body/Ground format (KS). %
% ----------------------------------------------------------------------- %
% Author: Ke Song (Washington University in St. Louis) %
% E-mail: ksong23@wustl.edu %
% ----------------------------------------------------------------------- %

% load Library
import org.opensim.modeling.*;

% get name of Ground in model
osimGroundName = char(osimModel.getGround.getName());

% get Ground or Body based on name
if strcmp(BodyName,osimGroundName)
Body = osimModel.getGround(); %Ground
else
Body = osimModel.getBodySet.get(BodyName);
end

end
76 changes: 76 additions & 0 deletions matlab_tool_v4.0/getCurrentMusclePathAsMat.m
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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, 2017 %
% email: l.modenese@imperial.ac.uk %
% ----------------------------------------------------------------------- %
% Given a state, this script collects info about the path of a muscle.
% Bodies of muscle attachments and point coordinates are made available as
% a list and a matrix respectively.
%
% INPUTS:
% - osimMuscle: an OpenSim model (API object).
% - s: state, used to update the current muscle path and get
% active conditional viapoints.
%
% OUTPUTS:
% - mus_bodyset_list: matrix where each row is a muscle point and
% columns are its [X Y Z] coordinates in the reference system of
% the body they belong to (as in .osim file).
% - mus_pointset_mat: cell array of body names, same length as
% the PathPointSet, with the name of the Body for each point.
%
%
% last modified:
% 2017: created.
% 26 Jun 2018: comments (LM)
% 29 Nov 2018: renamed, recommented, modified, added to MFD Matlab version.
% 18 Sep 2019: using getCurrentPath to recognize wrap points (KS).
% ----------------------------------------------------------------------- %
function [mus_bodyset_list, mus_pointset_mat] = getCurrentMusclePathAsMat(osimMuscle, s)

% load libraries
import org.opensim.modeling.*;

% get geometry path point array (including wrap points) for current state
curr_PathPointSet = osimMuscle.getGeometryPath().getCurrentPath(s);

n_pp = 1;
for n_p = 0:curr_PathPointSet.getSize-1

% point under examination
curr_point = curr_PathPointSet.get(n_p);
attachBody = curr_point.getBodyName();

% if pathpoint is conditional, then check if it is active
if strcmp(char(curr_point.getConcreteClassName), 'ConditionalPathPoint')
cond_viapoint = ConditionalPathPoint.safeDownCast(curr_point);
% is it active?
if cond_viapoint.isActive(s)
% if yes add it to point set
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>
mus_bodyset_list(n_pp) = {char(attachBody)};
n_pp = n_pp+1;
else
continue
end
else
% if not conditional add it
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)];
mus_bodyset_list(n_pp) = {char(attachBody)};
n_pp = n_pp+1;
end
end

end
53 changes: 53 additions & 0 deletions matlab_tool_v4.0/getMatStructColumn.m
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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 %
% ----------------------------------------------------------------------- %
%
% Function that allows to retrieve the value of a specified variable whose
% name is specified in var_name.
%
% INPUTS
% struct: is a structure with fields 'colheaders', the headers, and 'data'
% that is a matrix of data.
% var_name: the name of the variable to extract.
%
% OUTPUTS
% var_value: the column of the matrix correspondent to the header specified
% in input as var_name.
%
%
% written: Luca Modenese, July 2014
% last modified:
% Header (February 2018, LM)
% 29 Nov 2018: renamed, recommented, added to MFD Matlab version (LM).
% ----------------------------------------------------------------------- %
function var_value = getMatStructColumn(struct, var_name)

% gets the index of the desired variable name in the colheaders of the
% structure from where it will be extracted
var_index = strncmp(struct.colheaders, var_name, length(var_name));

if sum(var_index) == 0
%error(['getValueColumnForHeader.m','. No header in structure is matching the name ''',var_name,'''.'])
display(['getValueColumnForHeader.m','. No header in structure is matching the name ''',var_name,''''])
var_value = [];
return
end

% uses the index to retrieve the column of values for that variable.
var_value = struct.data(:,var_index);

end
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