Example_deform_distal_tibia_gait2392.m

%-------------------------------------------------------------------------%
%    Copyright (c) 2021 Modenese L.                                       %
%    Author:   Luca Modenese,  2021                                       %
%    email:    l.modenese@imperial.ac.uk                                  %
% ----------------------------------------------------------------------- %
clear;clc
addpath('./tool_funcs')
% import libraries
import org.opensim.modeling.*

%---------------  MAIN SETTINGS -----------
% Model to deform
modelFileName = './examples/gait2392_simbody.osim';

% where the bone geometries are stored
OpenSim_Geometry_folder = 'C:\OpenSim 4.2\Geometry';

% body to deform
bone_to_deform = 'tibia_l';

% axis of deformatio
torsionAxis = 'y';

% define the rotational profile at the joint centres of the bone of
% interest: TorsionProfilePointsDeg = [ proximalTorsion DistalTorsion ];
TorsionProfilePointsDeg = [ 0  -30 ];

% decide if you want to apply torsion to joint as well as other objects.
% E.g. choose no for investigating the effect of femoral anteversion in a
% leg with straight alignment.
% Choose yes for modelling a CP child with deformation of bone resulting in
% joint rotation, meaning the kinematic model is altered.
apply_torsion_to_joints = 'yes';

% where the deformed models will be saved
altered_models_folder = './examples';
%----------------------------------------------

% import model
osimModel = Model(modelFileName);

% compute bone length
[Pprox, Pdist, total_L, V] = getJointCentresForBone(osimModel, bone_to_deform);

% define length corresponding to torsion points
LengthProfilePoints = [ Pprox; Pdist];

% compute torsion profile
[torsion_angle_func_rad, torsion_doc_string]= createTorsionProfile(LengthProfilePoints, TorsionProfilePointsDeg, torsionAxis);

% suffix used for saving geometries
bone_short = bone_to_deform([1:3,end-1:end]);
deformed_model_suffix = ['_Tors',upper(bone_short(1)),bone_short(2:end),'_',torsion_doc_string];

% if you want you can apply torsion to joints
if strcmp(apply_torsion_to_joints, 'yes')
    osimModel = applyTorsionToJoints(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad);
end

% get wrapping objects
bone_body = osimModel.getBodySet.get(bone_to_deform);
if getOpenSimVersion()<4.0
    % get wrapset
    wrap_set  = bone_body.get_WrapObjectSet();
    % get nr of wrapping objects
    N_wrap = wrap_set.getSize();
    % loop through wrapping surf
    for nw = 0:N_wrap-1
        cur_obj = wos.get(nw);

        % compute new orientation
        orientation = obj.get_xyz_body_rotation();
        XYZ_orient_vec = [orientation.get(0), orientation.get(1), orientation.get(2)];
        jointRotMat = orientation2MatRot(XYZ_orient_vec);
        newJointRotMat =  jointRotMat * torsion_RotMat;
        new_Orientation  = computeXYZAngleSeq(newJointRotMat);
        newOrientation = Vec3(new_Orientation(1), new_Orientation(2), new_Orientation(3));
    end
end

% deforming muscle attachments
osimModel = applyTorsionToMuscleAttachments(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad);

% if there are markers rotate them
osimModel = applyTorsionToMarkers(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad);

% deform the bone geometries of the generic model
osimModel = applyTorsionToVTPBoneGeom(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad, torsion_doc_string, OpenSim_Geometry_folder);

% save output model
if ~isfolder(altered_models_folder); mkdir(altered_models_folder); end
[~, name,ext] = fileparts(modelFileName);
deformed_model_name = [name, deformed_model_suffix,ext];
output_model_path = fullfile(altered_models_folder, deformed_model_name);
osimModel.setName([char(osimModel.getName()),deformed_model_suffix]);

% save model
saveDeformedModel(osimModel, output_model_path);