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msm/ShoulderModel_NoElbow/Visualisation_Original_Meshings/MAIN_INITIALISATION_build_data_bony_landmark_vis.m
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MAIN_INITIALISATION_build_data_bony_landmark_vis.m
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function BLDATA = MAIN_INITIALISATION_build_data_bony_landmark()
% Function to initialise the bony landmark dataset
%--------------------------------------------------------------------------
% Syntax :
% BLDATA = MAIN_INITIALISATION_build_data_bony_landmark()
%--------------------------------------------------------------------------
%
% EPFL - LA - LBO SHOULDER MODEL
% Created by : David Ingram
%
% File Description :
% This function generates the initial bony landmark data structure. There
% are three important sub parts of the data structure.
% 1) Original Data from the AMIRA data set. Raw from collection.
% 2) Initial Data, this can be changed by the initial configuration
% 3) Current Data, this is used when working with motion.
%
% Data Structure Format :
% Original Data from the CHUV dataset
% BLDATA.Original_Points.IJ
% BLDATA.Original_Points.PX
% BLDATA.Original_Points.T8
% BLDATA.Original_Points.C7
% BLDATA.Original_Points.SC
% BLDATA.Original_Points.AC
% BLDATA.Original_Points.AA
% BLDATA.Original_Points.TS
% BLDATA.Original_Points.AI
% BLDATA.Original_Points.GH
% BLDATA.Original_Points.HU
% BLDATA.Original_Points.EL
% BLDATA.Original_Points.EM
% BLDATA.Original_WFBones.Thorax
% BLDATA.Original_WFBones.Clavicula
% BLDATA.Original_WFBones.Scapula
% BLDATA.Original_WFBones.Humerus
% BLDATA.Original_Matrices_L2A.Rc
% BLDATA.Original_Matrices_L2A.Rs
% BLDATA.Original_Matrices_L2A.Rh
%
% The user can define a new initial configuration
% BLDATA.Initial_Points.IJ
% BLDATA.Initial_Points.PX
% BLDATA.Initial_Points.T8
% BLDATA.Initial_Points.C7
% BLDATA.Initial_Points.SC
% BLDATA.Initial_Points.AC
% BLDATA.Initial_Points.AA
% BLDATA.Initial_Points.TS
% BLDATA.Initial_Points.AI
% BLDATA.Initial_Points.GH
% BLDATA.Initial_Points.HU
% BLDATA.Initial_Points.EL
% BLDATA.Initial_Points.EM
% BLDATA.Initial_WFBones.Thorax
% BLDATA.Initial_WFBones.Clavicula
% BLDATA.Initial_WFBones.Scapula
% BLDATA.Initial_WFBones.Humerus
% BLDATA.Initial_Matrices_L2A.Rc
% BLDATA.Initial_Matrices_L2A.Rs
% BLDATA.Initial_Matrices_L2A.Rh
%
% AMIRA -> MATLAB transformation required to initialise the muscle data
% BLDATA.Amira_to_MATLAB.Rt
% BLDATA.Amira_to_MATLAB.IJ
%
% Current location of landmarks used visualise the motion
% BLDATA.Current_Points.IJ
% BLDATA.Current_Points.PX
% BLDATA.Current_Points.T8
% BLDATA.Current_Points.C7
% BLDATA.Current_Points.SC
% BLDATA.Current_Points.AC
% BLDATA.Current_Points.AA
% BLDATA.Current_Points.TS
% BLDATA.Current_Points.AI
% BLDATA.Current_Points.GH
% BLDATA.Current_Points.HU
% BLDATA.Current_Points.EL
% BLDATA.Current_Points.EM
% BLDATA.Current_WFBones.Thorax
% BLDATA.Current_WFBones.Clavicula
% BLDATA.Current_WFBones.Scapula
% BLDATA.Current_WFBones.Humerus
% BLDATA.Current_Matrices_L2A.Rc
% BLDATA.Current_Matrices_L2A.Rs
% BLDATA.Current_Matrices_L2A.Rh
%
% Garner & Pandy Scapular reference frame to compare moment arms and
% validate
% BLDATA.Original_GnP.Rs
% BLDATA.Initial_GnP.Rs
% BLDATA.Current_GnP.Rs
%--------------------------------------------------------------------------
% Initialiase the Output
BLDATA = [];
%--------------------------------------------------------------------------
% BONY LANDMARKS IN AMIRA REFERENCE FRAME
%--------------------------------------------------------------------------
IJ = [ 74.1129; -74.8060; 68.9446]; % Incisura Jugularis
PX = [ 82.5171; -133.1130; -76.9724]; % Processus Xiphoideus
T8 = [ 78.9481; -24.5985; -40.6273]; % Vertebra T8
C7 = [ 70.5729; -35.7244; 150.7640]; % Vertebra C7
SC = [ 56.6771; -69.2782; 72.7629]; % Sternoclaviuclar joint
%SC= [ 52.0511; -79.0859; 75.0302]; % Sternoclaviuclar joint
AC = [ -82.2127; -25.2576; 148.444]; % Sternoclaviuclar joint
%AC = [ -82.1051; -30.7575; 145.4510]; % Acromioclavicular joint
GH = [ -86.1456; -31.7209; 107.6860]; % Glenohumeral joint
HU = [ -103.7780; -33.3235; -205.8640]; % Humeroulnar joint
TS = [ -0.9241; 52.0670; 121.3280]; % Trigonum Spinae
AI = [ -6.7869; 50.3866; -4.7008]; % Angulus Inferior
AA = [ -104.3290; -1.0350; 133.7840]; % Angulus Acromialis
EL = [ -127.2850; -54.8861; -208.4960]; % Lateral epicondyle
EM = [ -80.2709; -11.7610; -203.2320]; % Medial epicondyle
%--------------------------------------------------------------------------
% BUILD AMIRA TO MATLAB HOMOGENEOUS TRANFORMATION & TRANSFORM ALL POINTS
%--------------------------------------------------------------------------
% AMIRA -> MATLAB Rotation Matrix
Zt = (C7 + IJ)/2 - (T8 + PX)/2;
Xt = cross(C7 - IJ, (T8 + PX)/2-IJ);
Yt = cross(Zt, Xt);
R_am = [Xt/norm(Xt), Yt/norm(Yt), Zt/norm(Zt)]';
% Homogeneous transformation Matrix
H_am = [[R_am, -R_am*IJ]; [0, 0, 0, 1]];
%--------------------------------------------------------------------------
% SAVE THE AMIRA TO MATLAB HOMEGENEOUS TRANSFORMATON
%--------------------------------------------------------------------------
BLDATA.Amira_to_MATLAB.Rt = R_am;
BLDATA.Amira_to_MATLAB.IJ = IJ;
% Transform all points to MATLAB reference frame
IJ = H_am*[IJ; 1]; IJ = IJ(1:3,1);
PX = H_am*[PX; 1]; PX = PX(1:3,1);
T8 = H_am*[T8; 1]; T8 = T8(1:3,1);
C7 = H_am*[C7; 1]; C7 = C7(1:3,1);
SC = H_am*[SC; 1]; SC = SC(1:3,1);
AC = H_am*[AC; 1]; AC = AC(1:3,1);
GH = H_am*[GH; 1]; GH = GH(1:3,1);
HU = H_am*[HU; 1]; HU = HU(1:3,1);
TS = H_am*[TS; 1]; TS = TS(1:3,1);
AI = H_am*[AI; 1]; AI = AI(1:3,1);
AA = H_am*[AA; 1]; AA = AA(1:3,1);
EL = H_am*[EL; 1]; EL = EL(1:3,1);
EM = H_am*[EM; 1]; EM = EM(1:3,1);
%--------------------------------------------------------------------------
% BUILD ORIGINAL BONE REFERENCE FRAME ROTATION MATRICES
%--------------------------------------------------------------------------
% Clavicula Rotation Matrix
Xc = AC - SC; Xc = Xc/norm(Xc);
Yc = cross([0; 0; 1], Xc); Yc = Yc/norm(Yc);
Zc = cross(Xc, Yc); Zc = Zc/norm(Zc);
Rc = [Xc, Yc, Zc]; % Local -> absolute
% Scapula Rotation Matrix
Xs = AA - TS; Xs = Xs/norm(Xs);
Ys = cross(Xs, AI - TS); Ys = Ys/norm(Ys);
Zs = cross(Xs, Ys); Zs = Zs/norm(Zs);
Rs = [Xs, Ys, Zs]; % Local -> absolute
% Humerus Rotation Matrix
Zh = GH - (EM + EL)/2; Zh = Zh/norm(Zh);
Yh = cross(GH - EL, EL - EM); Yh = Yh/norm(Yh);
Xh = cross(Yh, Zh); Xh = Xh/norm(Xh);
Rh = [Xh, Yh, Zh]; % Local -> absolute
%--------------------------------------------------------------------------
% BUILD ORIGINAL BONY LANDMARK DATA STRUCTURE
%--------------------------------------------------------------------------
% List of points in the original configuration
BLDATA.Original_Points.IJ = IJ;
BLDATA.Original_Points.PX = PX;
BLDATA.Original_Points.T8 = T8;
BLDATA.Original_Points.C7 = C7;
BLDATA.Original_Points.SC = SC;
BLDATA.Original_Points.AC = AC;
BLDATA.Original_Points.GH = GH;
BLDATA.Original_Points.HU = HU;
BLDATA.Original_Points.TS = TS;
BLDATA.Original_Points.AI = AI;
BLDATA.Original_Points.AA = AA;
BLDATA.Original_Points.EL = EL;
BLDATA.Original_Points.EM = EM;
% Build the original bone wire frames for plotting purposes
BLDATA.Original_WFBones.Thorax = [IJ, PX, T8, C7, IJ];
BLDATA.Original_WFBones.Clavicula = [SC, AC];
BLDATA.Original_WFBones.Scapula = [AC, AA, TS, AI, GH, AC];
BLDATA.Original_WFBones.Humerus = [GH, HU, EL, EM];
% Original Rotation Matrices
BLDATA.Original_Matrices_L2A.Rc = Rc;
BLDATA.Original_Matrices_L2A.Rs = Rs;
BLDATA.Original_Matrices_L2A.Rh = Rh;
%--------------------------------------------------------------------------
% BUILD INITIAL BONY LANDMARK DATA STRUCTURE
%--------------------------------------------------------------------------
% To start, both initial and current data is set to original.
% List of Points in the current configuration
BLDATA.Initial_Points.IJ = IJ;
BLDATA.Initial_Points.PX = PX;
BLDATA.Initial_Points.T8 = T8;
BLDATA.Initial_Points.C7 = C7;
BLDATA.Initial_Points.SC = SC;
BLDATA.Initial_Points.AC = AC;
BLDATA.Initial_Points.GH = GH;
BLDATA.Initial_Points.HU = HU;
BLDATA.Initial_Points.TS = TS;
BLDATA.Initial_Points.AI = AI;
BLDATA.Initial_Points.AA = AA;
BLDATA.Initial_Points.EL = EL;
BLDATA.Initial_Points.EM = EM;
% Build the bone wire frames for plotting purposes
BLDATA.Initial_WFBones.Thorax = [IJ, PX, T8, C7, IJ];
BLDATA.Initial_WFBones.Clavicula = [SC, AC];
BLDATA.Initial_WFBones.Scapula = [AC, AA, TS, AI, GH, AC];
BLDATA.Initial_WFBones.Humerus = [GH, HU, EL, EM];
% Initial Rotation Matrices
BLDATA.Initial_Matrices_L2A.Rc = Rc;
BLDATA.Initial_Matrices_L2A.Rs = Rs;
BLDATA.Initial_Matrices_L2A.Rh = Rh;
%--------------------------------------------------------------------------
% BUILD CURRENT BONY LANDMARK DATA STRUCTURE
%--------------------------------------------------------------------------
% List of Points in the current configuration
BLDATA.Current_Points.IJ = IJ;
BLDATA.Current_Points.PX = PX;
BLDATA.Current_Points.T8 = T8;
BLDATA.Current_Points.C7 = C7;
BLDATA.Current_Points.SC = SC;
BLDATA.Current_Points.AC = AC;
BLDATA.Current_Points.GH = GH;
BLDATA.Current_Points.HU = HU;
BLDATA.Current_Points.TS = TS;
BLDATA.Current_Points.AI = AI;
BLDATA.Current_Points.AA = AA;
BLDATA.Current_Points.EL = EL;
BLDATA.Current_Points.EM = EM;
% Build the bone wire frames for plotting purposes
BLDATA.Current_WFBones.Thorax = [IJ, PX, T8, C7, IJ];
BLDATA.Current_WFBones.Clavicula = [SC, AC];
BLDATA.Current_WFBones.Scapula = [AC, AA, TS, AI, GH, AC];
BLDATA.Current_WFBones.Humerus = [GH, HU, EL, EM];
% Current Rotation Matrices
BLDATA.Current_Matrices_L2A.Rc = Rc;
BLDATA.Current_Matrices_L2A.Rs = Rs;
BLDATA.Current_Matrices_L2A.Rh = Rh;
%--------------------------------------------------------------------------
% BUILD THE GARNER & PANDY SCAPULAR ROTATION MATRIX
%--------------------------------------------------------------------------
% Define the Garner & Pandy Scapular Reference frame
Zaxis = AC - GH; Zaxis = Zaxis/norm(Zaxis);
Yaxis = cross(Zaxis, AC - TS); Yaxis = Yaxis/norm(Yaxis);
Xaxis = cross(Yaxis, Zaxis); Xaxis = Xaxis/norm(Xaxis);
Rgnp = [Xaxis, Yaxis, Zaxis];
BLDATA.Original_GnP.Rs = Rgnp;
BLDATA.Initial_GnP.Rs = Rgnp;
BLDATA.Current_GnP.Rs = Rgnp;
return;
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