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msm/ShoulderModel/scapula_coordinate_system/MAIN_TOOL_geometry_functions.m
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MAIN_TOOL_geometry_functions.m
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function Output = MAIN_TOOL_geometry_functions(task, varargin)
% Function containing all geometry related tasks.
%{
--------------------------------------------------------------------------
Syntax :
Output = MAIN_TOOL_geometry_functions(task, varargin)
--------------------------------------------------------------------------
File Description :
This file contains all the routines related to geometry. These routines
affect the intial and current geometric configuration of the model.
This function can have multiple intputs depending on the task. However,
the first input is always the desired to task to be performed. The list
of tasks are as follows:
Task 1 : Build Rotation Matrices From Euler Angles
Task 2 : Get Euler Angles From Original Rotation Matrices
Task 3 : Get Euler Angles From Initial Rotation Matrices
Task 4 : Get Euler Angles From Current Rotation Matrices
Task 5 : Rotate Points From Local To Global Frame (Initial)
Task 6 : Rotate Points From Global To Local Frame (Initial)
Task 7 : Rotate Points From Local To Global Frame (Current)
Task 8 : Rotate Points From Global To Local Frame (Current)
Task 9 : Update Initial Bony Landmark Data from Joint Rotation Matrices
Task 10: Update Current Bony Landmark Data from Joint Rotation Matrices
--------------------------------------------------------------------------
%}
% Initialise the Output
Output = [];
%--------------------------------------------------------------------------
% TASK 1 : BUILD ROTATION MATRICES
% Inputs :
% 1) Task
% 2) Joint Euler angles
% Outputs :
% A single array containing three joint rotation matrices [Rc, Rs, Rh]
%--------------------------------------------------------------------------
if isequal(task, 'Build Rotation Matrices From Euler Angles')
% Get the Joint Angles
JEA = varargin{1,1};% varargin is a 1-by-N cell array, where N is the number of inputs that the function receives after the explicitly declared inputs
BLDATA = varargin{1,2}; % lately added to feed in the BLDATA for the rotation matrices of the ulna and radius regarding their proximal segments
% Clavicula Rotation Matrix
Rcx = [1.00, 0.0000, 0.0000;
0.00, cos(JEA(1)), -sin(JEA(1));
0.00, sin(JEA(1)), cos(JEA(1))];
Rcy = [cos(JEA(2)), 0.00, -sin(JEA(2));
0.0000, 1.00, 0.0000;
sin(JEA(2)), 0.00, cos(JEA(2))];
Rcz = [cos(JEA(3)), -sin(JEA(3)), 0.00;
sin(JEA(3)), cos(JEA(3)), 0.00;
0.0000, 0.0000, 1.00];
Rc = Rcz*Rcy'*Rcx;
% Scapula Rotation Matrix
Rsx = [1.00, 0.0000, 0.0000;
0.00, cos(JEA(4)), -sin(JEA(4));
0.00, sin(JEA(4)), cos(JEA(4))];
Rsy = [cos(JEA(5)), 0.00, -sin(JEA(5));
0.0000, 1.00, 0.0000;
sin(JEA(5)), 0.00, cos(JEA(5))];
Rsz = [cos(JEA(6)), -sin(JEA(6)), 0.00;
sin(JEA(6)), cos(JEA(6)), 0.00;
0.0000, 0.0000, 1.00];
Rs = Rsz*Rsy'*Rsx;
% Humerus Rotation Matrix
Rhz = [cos(JEA(7)), -sin(JEA(7)), 0.00;
sin(JEA(7)), cos(JEA(7)), 0.00;
0.0000, 0.0000, 1.00];
Rhy = [cos(JEA(8)), 0.00, -sin(JEA(8));
0.0000, 1.00, 0.0000;
sin(JEA(8)), 0.00, cos(JEA(8))];
Rhzz = [cos(JEA(9)), -sin(JEA(9)), 0.00;
sin(JEA(9)), cos(JEA(9)), 0.00;
0.0000, 0.0000, 1.00];
Rh = Rhzz*Rhy'*Rhz;
%Ulna Rotation Matrix
Rux = [1.00, 0.00, 0.00;
0.00, cos(JEA(10)), -sin(JEA(10));
0.00, sin(JEA(10)), cos(JEA(10))];% ulna to the proximal segment part 1
Ru_h = BLDATA.Original_Matrices_L2A.Rh'*BLDATA.Original_Matrices_L2A.Ru; % ulna to the proximal segment part 1
Ru = Rh*Ru_h*Rux; % ulna to the inertial frame (thorax)
%Radius Rotation Matrix
Rrz = [cos(JEA(11)), -sin(JEA(11)), 0.00;
sin(JEA(11)), cos(JEA(11)), 0.00;
0.00, 0.00, 1.00]; % radius to the proximal segment part 1
Rr_u = BLDATA.Original_Matrices_L2A.Ru'*BLDATA.Original_Matrices_L2A.Rr; % radius to the proximal segment part 2
Rr = Ru*Rr_u*Rrz; % radius to the inertial frame (thorax)
Output = [Rc, Rs, Rh, Ru, Rr];
%--------------------------------------------------------------------------
% TASK 2 : EXTRACT EULER ANGLES FROM ORIGINAL MATRICES
% Inputs :
% 1) Task
% 2) BLDATA : Bonylandmark data structure
% Outputs :
% A single array containing nine joint rotation angles
%--------------------------------------------------------------------------
elseif isequal(task, 'Get Euler Angles From Original Rotation Matrices')
% Get the Rotation Matrices
BLDATA = varargin{1,1};
Rc = BLDATA.Original_Matrices_L2A.Rc;
Rs = BLDATA.Original_Matrices_L2A.Rs;
Rh = BLDATA.Original_Matrices_L2A.Rh;
Ru = BLDATA.Original_Matrices_L2A.Ru;
Rr = BLDATA.Original_Matrices_L2A.Rr;
% Get Clavicula Euler Angles
THETAc = asin(-Rc(3,1)); % Elevation/Depression
PSIc = atan(Rc(3,2)/Rc(3,3)); % Axial Rotation
PHIc = atan(Rc(2,1)/Rc(1,1)); % Protraction/Retraction
% Get Scapula Euler Angles
THETAs = asin(-Rs(3,1)); % Elevation/Depression
PSIs = atan(Rs(3,2)/Rs(3,3)); % Spinal Tilt
PHIs = atan(Rs(2,1)/Rs(1,1)); % Protraction/Retraction
% Get Humerus Euler Angles
THETAh = acos(Rh(3,3)); % Abduction/Adduction
PSIh = atan2(Rh(3,2),-Rh(3,1)); % Axial Rotation
PHIh = atan2(Rh(2,3),Rh(1,3)); % Elevation Plane
% Get Ulna Euler Angles
Ru_h = BLDATA.Original_Matrices_L2A.Rh'*BLDATA.Original_Matrices_L2A.Ru;
Rux=Ru_h'*Rh'*Ru;
THETAu = atan2(Rux(3,2),Rux(2,2)); % Flexion/Extension
% Get Ulna Euler Angles
Rr_u = BLDATA.Original_Matrices_L2A.Ru'*BLDATA.Original_Matrices_L2A.Rr;
Rrz = Rr_u'*Ru'*Rr;
THETAr = atan2(Rrz(2,1),Rrz(1,1)); % Pronation/Supination
% Save The Euler Angles
Output = [PSIc, THETAc, PHIc, PSIs, THETAs, PHIs, PSIh, THETAh, PHIh, THETAu, THETAr];
%--------------------------------------------------------------------------
% TASK 3 : EXTRACT EULER ANGLES FROM INITIAL MATRICES
% Inputs :
% 1) Task
% 2) BLDATA : Bonylandmark data structure
% Outputs :
% A single array containing nine joint rotation angles
%--------------------------------------------------------------------------
elseif isequal(task, 'Get Euler Angles From Initial Rotation Matrices')
% Get the Rotation Matrices
BLDATA = varargin{1,1};
Rc = BLDATA.Initial_Matrices_L2A.Rc;
Rs = BLDATA.Initial_Matrices_L2A.Rs;
Rh = BLDATA.Initial_Matrices_L2A.Rh;
Ru = BLDATA.Initial_Matrices_L2A.Ru;
Rr = BLDATA.Initial_Matrices_L2A.Rr;
% Get Clavicula Euler Angles
THETAc = asin(-Rc(3,1)); % Elevation/Depression
PSIc = atan(Rc(3,2)/Rc(3,3)); % Axial Rotation
PHIc = atan(Rc(2,1)/Rc(1,1)); % Protraction/Retraction
% Get Scapula Euler Angles
THETAs = asin(-Rs(3,1)); % Elevation/Depression
PSIs = atan(Rs(3,2)/Rs(3,3)); % Spinal Tilt
PHIs = atan(Rs(2,1)/Rs(1,1)); % Protraction/Retraction
% Get Humerus Euler Angles
THETAh = acos(Rh(3,3)); % Abduction/Adduction
PSIh = atan2(Rh(3,2),-Rh(3,1)); % Axial Rotation
PHIh = atan2(Rh(2,3),Rh(1,3)); % Elevation Plane
% Get Ulna Euler Angles
Ru_h = BLDATA.Original_Matrices_L2A.Rh'*BLDATA.Original_Matrices_L2A.Ru;
Rux=Ru_h'*Rh'*Ru;
%Rux=Rh'*Ru;
THETAu = atan2(Rux(3,2),Rux(2,2)); % Flexion/Extension
% Get Radius Euler Angles
Rr_u = BLDATA.Original_Matrices_L2A.Ru'*BLDATA.Original_Matrices_L2A.Rr;
Rrz = Rr_u'*Ru'*Rr;
%Rrz=Ru'*Rr;
THETAr = atan2(Rrz(2,1),Rrz(1,1)); % Pronation/Supination
% Save The Euler Angles
Output = [PSIc, THETAc, PHIc, PSIs, THETAs, PHIs, PSIh, THETAh, PHIh, THETAu, THETAr];
%--------------------------------------------------------------------------
% TASK 4: EXTRACT EULER ANGLES FROM CURRENT MATRICES
% Inputs :
% 1) Task
% 2) BLDATA : Bonylandmark data structure
% Outputs :
% A single array containing nine joint rotation angles
%--------------------------------------------------------------------------
elseif isequal(task, 'Get Euler Angles From Current Rotation Matrices')
% Get the Rotation Matrices
BLDATA = varargin{1,1};
Rc = BLDATA.Current_Matrices_L2A.Rc;
Rs = BLDATA.Current_Matrices_L2A.Rs;
Rh = BLDATA.Current_Matrices_L2A.Rh;
Ru = BLDATA.Current_Matrices_L2A.Ru;
Rr = BLDATA.Current_Matrices_L2A.Rr;
% Get Clavicula Euler Angles
THETAc = asin(-Rc(3,1)); % Elevation/Depression
PSIc = atan(Rc(3,2)/Rc(3,3)); % Axial Rotation
PHIc = atan(Rc(2,1)/Rc(1,1)); % Protraction/Retraction
% Get Scapula Euler Angles
THETAs = asin(-Rs(3,1)); % Elevation/Depression
PSIs = atan(Rs(3,2)/Rs(3,3)); % Spinal Tilt
PHIs = atan(Rs(2,1)/Rs(1,1)); % Protraction/Retraction
% Get Humerus Euler Angles
THETAh = acos(Rh(3,3)); % Abduction/Adduction
PSIh = atan2(Rh(3,2),-Rh(3,1)); % Axial Rotation
PHIh = atan2(Rh(2,3),Rh(1,3)); % Elevation Plane
% Get Ulna Euler Angles
Ru_h = BLDATA.Original_Matrices_L2A.Rh'*BLDATA.Original_Matrices_L2A.Ru;
Rux=Ru_h'*Rh'*Ru;
%Rux=Rh'*Ru;
THETAu = atan2(Rux(3,2),Rux(2,2)); % Flexion/Extension
% Get Ulna Euler Angles
Rr_u = BLDATA.Original_Matrices_L2A.Ru'*BLDATA.Original_Matrices_L2A.Rr;
Rrz = Rr_u'*Ru'*Rr;
%Rrz=Ru'*Rr;
THETAr = atan2d(Rrz(2,1),Rrz(1,1)); % Pronation/Supination
% Save The Euler Angles
Output = [PSIc, THETAc, PHIc, PSIs, THETAs, PHIs, PSIh, THETAh, PHIh, THETAu, THETAr];
%--------------------------------------------------------------------------
% TASK 5: ROTATE A SET OF POINTS INTO THE GLOBAL FRAME (INITIAL CONFIG)
% Inputs :
% 1) Task
% 2) Q : The list of points (3 x n)
% 3) BLDATA : Bonylandmark data structure
% 4) frameId : local frame in which the points are defined
% Outputs :
% A single (3 x n) array containing the transformed points
%--------------------------------------------------------------------------
elseif isequal(task, 'Rotate Points From Local To Global Frame (Initial)')
% Get the List of points
Q = varargin{1,1};
% Get the BLDATA structure
BLDATA = varargin{1,2};
% Get the Frame Identification
frameId = varargin{1,3};
% Initialise the output
Output = Q;
% Get the Current Rotation Matrices (Local -> Absolute)
Rc = BLDATA.Initial_Matrices_L2A.Rc;
Rs = BLDATA.Initial_Matrices_L2A.Rs;
Rh = BLDATA.Initial_Matrices_L2A.Rh;
Ru = BLDATA.Initial_Matrices_L2A.Ru;
Rr = BLDATA.Initial_Matrices_L2A.Rr;
% Get the necessary bony landmarks
SC = BLDATA.Initial_Points.SC;
AA = BLDATA.Initial_Points.AA;
GH = BLDATA.Initial_Points.GH;
HU = BLDATA.Initial_Points.HU;
CP = BLDATA.Initial_Points.CP;
% Rotate the set of points
for i = 1:size(Q,2)
% Transform point
if frameId == 0
Output(:,i) = P(:,i);
elseif frameId == 1
Output(:,i) = Rc*Q(:,i) + SC;
elseif frameId == 2
Output(:,i) = Rs*Q(:,i) + AA;
elseif frameId == 3
Output(:,i) = Rh*Q(:,i) + GH;
elseif frameId == 4
Output(:,i) = Ru*Q(:,i) + HU;
elseif frameId == 5
Output(:,i) = Rr*Q(:,i) + CP;
else
% The wrong frame was provided
end
end
%--------------------------------------------------------------------------
% TASK 6: ROTATE A SET OF POINTS INTO A LOCAL FRAME (INITIAL CONFIG)
% Inputs :
% 1) Task
% 2) Q : The list of points (3 x n)
% 3) BLDATA : Bonylandmark data structure
% 4) frameId : local frame in which the points are to be transformed
% Outputs :
% A single (3 x n) array containing the transformed points
%--------------------------------------------------------------------------
elseif isequal(task, 'Rotate Points From Global To Local Frame (Initial)')
% Get the List of points
Q = varargin{1,1};
% Get the BLDATA structure
BLDATA = varargin{1,2};
% Get the Frame Identification
frameId = varargin{1,3};
% Initialise the output
Output = Q;
% Get the Current Rotation Matrices (Local -> Absolute)
Rc = BLDATA.Initial_Matrices_L2A.Rc;
Rs = BLDATA.Initial_Matrices_L2A.Rs;
Rh = BLDATA.Initial_Matrices_L2A.Rh;
Ru = BLDATA.Initial_Matrices_L2A.Ru;
Rr = BLDATA.Initial_Matrices_L2A.Rr;
% Get the necessary bony landmarks
SC = BLDATA.Initial_Points.SC;
AA = BLDATA.Initial_Points.AA;
GH = BLDATA.Initial_Points.GH;
HU = BLDATA.Initial_Points.HU;
CP = BLDATA.Initial_Points.CP;
% Rotate the set of points
for i = 1:size(Q,2)
% Transform point
if frameId == 0
Output(:,i) = Q(:,i);
elseif frameId == 1
Output(:,i) = Rc'*(Q(:,i) - SC);
elseif frameId == 2
Output(:,i) = Rs'*(Q(:,i) - AA);
elseif frameId == 3
Output(:,i) = Rh'*(Q(:,i) - GH);
elseif frameId == 4
Output(:,i) = Ru'*(Q(:,i) - HU);
elseif frameId == 5
Output(:,i) = Rr'*(Q(:,i) - CP);
else
% The wrong frame was provided
end
end
%--------------------------------------------------------------------------
% TASK 7: ROTATE A SET OF POINTS INTO THE GLOBAL FRAME (CURRENT CONFIG)
% Inputs :
% 1) Task
% 2) Q : The list of points (3 x n)
% 3) BLDATA : Bonylandmark data structure
% 4) frameId : local frame in which the points are defined
% Outputs :
% A single (3 x n) array containing the transformed points
%--------------------------------------------------------------------------
elseif isequal(task, 'Rotate Points From Local To Global Frame (Current)')
% Get the List of points
Q = varargin{1,1};
% Get the BLDATA structure
BLDATA = varargin{1,2};
% Get the Frame Identification
frameId = varargin{1,3};
% Initialise the output
Output = Q;
% Get the Current Rotation Matrices (Local -> Absolute)
Rc = BLDATA.Current_Matrices_L2A.Rc;
Rs = BLDATA.Current_Matrices_L2A.Rs;
Rh = BLDATA.Current_Matrices_L2A.Rh;
Ru = BLDATA.Current_Matrices_L2A.Ru;
Rr = BLDATA.Current_Matrices_L2A.Rr;
% Get the necessary bony landmarks
SC = BLDATA.Current_Points.SC;
AA = BLDATA.Current_Points.AA;
GH = BLDATA.Current_Points.GH;
HU = BLDATA.Current_Points.HU;
CP = BLDATA.Current_Points.CP;
% Rotate the set of points
for i = 1:size(Q,2)
% Transform point
if frameId == 0
Output(:,i) = Q(:,i);
elseif frameId == 1
Output(:,i) = Rc*Q(:,i) + SC;
elseif frameId == 2
Output(:,i) = Rs*Q(:,i) + AA;
elseif frameId == 3
Output(:,i) = Rh*Q(:,i) + GH;
elseif frameId == 4
Output(:,i) = Ru*Q(:,i) + HU;
elseif frameId == 5
Output(:,i) = Rr*Q(:,i) + CP;
else
% The wrong frame was provided
end
end
%--------------------------------------------------------------------------
% TASK 8: ROTATE A SET OF POINTS INTO A LOCAL FRAME (Current CONFIG)
% Inputs :
% 1) Task
% 2) Q : The list of points (3 x n)
% 3) BLDATA : Bonylandmark data structure
% 4) frameId : local frame in which the points are to be transformed
% Outputs :
% A single (3 x n) array containing the transformed points
%--------------------------------------------------------------------------
elseif isequal(task, 'Rotate Points From Global To Local Frame (Current)')
% Get the List of points
Q = varargin{1,1};
% Get the BLDATA structure
BLDATA = varargin{1,2};
% Get the Frame Identification
frameId = varargin{1,3};
% Initialise the output
Output = Q;
% Get the Current Rotation Matrices (Local -> Absolute)
Rc = BLDATA.Current_Matrices_L2A.Rc;
Rs = BLDATA.Current_Matrices_L2A.Rs;
Rh = BLDATA.Current_Matrices_L2A.Rh;
Ru = BLDATA.Current_Matrices_L2A.Ru;
Rr = BLDATA.Current_Matrices_L2A.Rr;
% Get the necessary bony landmarks
SC = BLDATA.Current_Points.SC;
AA = BLDATA.Current_Points.AA;
GH = BLDATA.Current_Points.GH;
HU = BLDATA.Current_Points.HU;
CP = BLDATA.Current_Points.CP;
% Rotate the set of points
for i = 1:size(Q,2)
% Transform point
if frameId == 0
Output(:,i) = Q(:,i);
elseif frameId == 1
Output(:,i) = Rc'*(Q(:,i) - SC);
elseif frameId == 2
Output(:,i) = Rs'*(Q(:,i) - AA);% why this point is AA?
elseif frameId == 3
Output(:,i) = Rh'*(Q(:,i) - GH);
elseif frameId == 4
Output(:,i) = Ru'*(Q(:,i) - HU);
elseif frameId == 5
Output(:,i) = Rr'*(Q(:,i) - CP);
else
% The wrong frame was provided
end
end
%--------------------------------------------------------------------------
% TASK 9: UPDATE BONY LANDMARK DATA FROM JOINT ROTATION MATRICES
% Inputs :
% 1) Task
% 2) Rc : SC rotation matrix
% 3) Rs : AC rotation matrix
% 4) Rh : GH rotation matrix
% 5) Ru : HU rotation matrix
% 6) Rr : RU rotation matrix
% 7) BLDATA : bonylandmark data
% Outputs :
% BLDATA : the bony landmark data with updated initial configuration
%--------------------------------------------------------------------------
elseif isequal(task, 'Update Initial Bony Landmark Data from Joint Rotation Matrices')
% Get the SC joint rotation matrix
Rc = varargin{1,1};
% Get the AC joint rotation matrix
Rs = varargin{1,2};
% Get the GH joint rotation matrix
Rh = varargin{1,3};
% Get the HU joint rotation matrix
Ru = varargin{1,4};
% Get the RU joint rotation matrix
Rr = varargin{1,5};
% Get the BLDATA input
BLDATA = varargin{1,6};
% Get Initial Rotation Matrices
Rci = BLDATA.Original_Matrices_L2A.Rc;
Rsi = BLDATA.Original_Matrices_L2A.Rs;
Rhi = BLDATA.Original_Matrices_L2A.Rh;
Rui = BLDATA.Original_Matrices_L2A.Ru;
Rri = BLDATA.Original_Matrices_L2A.Rr;
% Ge all the points (these points are in the thorax frame i.e. matlab frame)
IJ = BLDATA.Original_Points.IJ;
PX = BLDATA.Original_Points.PX;
T8 = BLDATA.Original_Points.T8;
C7 = BLDATA.Original_Points.C7;
SC = BLDATA.Original_Points.SC;
AC = BLDATA.Original_Points.AC;
AA = BLDATA.Original_Points.AA;
TS = BLDATA.Original_Points.TS;
AI = BLDATA.Original_Points.AI;
GH = BLDATA.Original_Points.GH;
HU = BLDATA.Original_Points.HU;
EL = BLDATA.Original_Points.EL;
EM = BLDATA.Original_Points.EM;
CP = BLDATA.Original_Points.CP;
US = BLDATA.Original_Points.US;
RS = BLDATA.Original_Points.RS;
% Set the Points
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 = Rc*Rci'*(AC - SC) + BLDATA.Initial_Points.SC;% Rci'*(AC - SC) is AC in Clavicle coordinate, so with the rotation matrix Rc we can define its new position in the inertial frame as such.
BLDATA.Initial_Points.AA = Rs*Rsi'*(AA - AC) + BLDATA.Initial_Points.AC;
BLDATA.Initial_Points.TS = Rs*Rsi'*(TS - AC) + BLDATA.Initial_Points.AC;
BLDATA.Initial_Points.AI = Rs*Rsi'*(AI - AC) + BLDATA.Initial_Points.AC;
BLDATA.Initial_Points.GH = Rs*Rsi'*(GH - AC) + BLDATA.Initial_Points.AC;
BLDATA.Initial_Points.HU = Rh*Rhi'*(HU - GH) + BLDATA.Initial_Points.GH;
BLDATA.Initial_Points.EL = Rh*Rhi'*(EL - GH) + BLDATA.Initial_Points.GH;
BLDATA.Initial_Points.EM = Rh*Rhi'*(EM - GH) + BLDATA.Initial_Points.GH;
BLDATA.Initial_Points.US = Ru*Rui'*(US - HU) + BLDATA.Initial_Points.HU;
BLDATA.Initial_Points.CP = Rh*Rhi'*(CP - GH) + BLDATA.Initial_Points.GH;
BLDATA.Initial_Points.RS = Rr*Rri'*(RS - CP) + BLDATA.Initial_Points.CP;
% Set the Rotation Matrices
BLDATA.Initial_Matrices_L2A.Rc = Rc;
BLDATA.Initial_Matrices_L2A.Rs = Rs;
BLDATA.Initial_Matrices_L2A.Rh = Rh;
BLDATA.Initial_Matrices_L2A.Ru = Ru;
BLDATA.Initial_Matrices_L2A.Rr = Rr;
% Set the wire frame bones
BLDATA.Initial_WFBones.Thorax = [IJ, PX, T8, C7, IJ];
BLDATA.Initial_WFBones.Clavicula = ...
[BLDATA.Initial_Points.SC,...
BLDATA.Initial_Points.AC];
BLDATA.Initial_WFBones.Scapula = ...
[BLDATA.Initial_Points.AC,...
BLDATA.Initial_Points.AA,...
BLDATA.Initial_Points.TS,...
BLDATA.Initial_Points.AI,...
BLDATA.Initial_Points.GH,...
BLDATA.Initial_Points.AC];
BLDATA.Initial_WFBones.Humerus =...
[BLDATA.Initial_Points.GH,...
BLDATA.Initial_Points.HU,...
BLDATA.Initial_Points.EL,...
BLDATA.Initial_Points.EM];
BLDATA.Initial_WFBones.Ulna =...
[BLDATA.Initial_Points.CP,...
BLDATA.Initial_Points.HU,...
BLDATA.Initial_Points.EM,...
BLDATA.Initial_Points.US];
BLDATA.Initial_WFBones.Radius =...
[BLDATA.Initial_Points.CP,...
BLDATA.Initial_Points.RS];
% Set the Garner and Pandy Scapular Rotation Matrix
Zaxis = BLDATA.Initial_Points.AC - BLDATA.Initial_Points.GH; Zaxis = Zaxis/norm(Zaxis);
Yaxis = cross(Zaxis, BLDATA.Initial_Points.AC - BLDATA.Initial_Points.TS); Yaxis = Yaxis/norm(Yaxis);
Xaxis = cross(Yaxis, Zaxis); Xaxis = Xaxis/norm(Xaxis);
% Set the rotation matrix
BLDATA.Initial_GnP.Rs = [Xaxis, Yaxis, Zaxis];
% Set the output
Output = BLDATA;
%--------------------------------------------------------------------------
% TASK 10: UPDATE BONY LANDMARK DATA FROM JOINT ROTATION MATRICES
% Inputs :
% 1) Task
% 2) Rc : SC rotation matrix
% 3) Rs : AC rotation matrix
% 4) Rh : GH rotation matrix
% 5) Ru : HU rotation matrix
% 6) Rr : RU rotation matrix
% 7) BLDATA : bonylandmark data
% Outputs :
% BLDATA : the bony landmark data with updated current configuration
%--------------------------------------------------------------------------
elseif isequal(task, 'Update Current Bony Landmark Data from Joint Rotation Matrices')
% Get the SC joint rotation matrix
Rc = varargin{1,1};
% Get the AC joint rotation matrix
Rs = varargin{1,2};
% Get the GH joint rotation matrix
Rh = varargin{1,3};
% Get the HU joint rotation matrix
Ru = varargin{1,4};
% Get the RU joint rotation matrix
Rr = varargin{1,5};
% Get the BLDATA input
BLDATA = varargin{1,6};
% Get Initial Rotation Matrices
Rci = BLDATA.Initial_Matrices_L2A.Rc;
Rsi = BLDATA.Initial_Matrices_L2A.Rs;
Rhi = BLDATA.Initial_Matrices_L2A.Rh;
Rui = BLDATA.Initial_Matrices_L2A.Ru;
Rri = BLDATA.Initial_Matrices_L2A.Rr;
% Ge all the points
IJ = BLDATA.Initial_Points.IJ;
PX = BLDATA.Initial_Points.PX;
T8 = BLDATA.Initial_Points.T8;
C7 = BLDATA.Initial_Points.C7;
SC = BLDATA.Initial_Points.SC;
AC = BLDATA.Initial_Points.AC;
AA = BLDATA.Initial_Points.AA;
TS = BLDATA.Initial_Points.TS;
AI = BLDATA.Initial_Points.AI;
GH = BLDATA.Initial_Points.GH;
HU = BLDATA.Initial_Points.HU;
EL = BLDATA.Initial_Points.EL;
EM = BLDATA.Initial_Points.EM;
CP = BLDATA.Initial_Points.CP;
US = BLDATA.Initial_Points.US;
RS = BLDATA.Initial_Points.RS;
% Rotate all points
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 = Rc*Rci'*(AC - SC) + SC;
BLDATA.Current_Points.AA = Rs*Rsi'*(AA - AC) + BLDATA.Current_Points.AC;
BLDATA.Current_Points.TS = Rs*Rsi'*(TS - AC) + BLDATA.Current_Points.AC;
BLDATA.Current_Points.AI = Rs*Rsi'*(AI - AC) + BLDATA.Current_Points.AC;
BLDATA.Current_Points.GH = Rs*Rsi'*(GH - AC) + BLDATA.Current_Points.AC;
BLDATA.Current_Points.HU = Rh*Rhi'*(HU - GH) + BLDATA.Current_Points.GH;
BLDATA.Current_Points.EL = Rh*Rhi'*(EL - GH) + BLDATA.Current_Points.GH;
BLDATA.Current_Points.EM = Rh*Rhi'*(EM - GH) + BLDATA.Current_Points.GH;
BLDATA.Current_Points.US = Ru*Rui'*(US - HU) + BLDATA.Current_Points.HU;
BLDATA.Current_Points.CP = Rh*Rhi'*(CP - GH) + BLDATA.Current_Points.GH;
BLDATA.Current_Points.RS = Rr*Rri'*(RS - CP) + BLDATA.Current_Points.CP;
% Set the Current rotation matrices
BLDATA.Current_Matrices_L2A.Rc = Rc;
BLDATA.Current_Matrices_L2A.Rs = Rs;
BLDATA.Current_Matrices_L2A.Rh = Rh;
BLDATA.Current_Matrices_L2A.Ru = Ru;
BLDATA.Current_Matrices_L2A.Rr = Rr;
% Set the current wire frames
BLDATA.Current_WFBones.Thorax = [IJ, PX, T8, C7, IJ];
BLDATA.Current_WFBones.Clavicula =...
[BLDATA.Current_Points.SC,...
BLDATA.Current_Points.AC];
BLDATA.Current_WFBones.Scapula =...
[BLDATA.Current_Points.AC,...
BLDATA.Current_Points.AA,...
BLDATA.Current_Points.TS,...
BLDATA.Current_Points.AI,...
BLDATA.Current_Points.GH,...
BLDATA.Current_Points.AC];
BLDATA.Current_WFBones.Humerus =...
[BLDATA.Current_Points.GH,...
BLDATA.Current_Points.HU,...
BLDATA.Current_Points.EL,...
BLDATA.Current_Points.EM];
BLDATA.Current_WFBones.Ulna =...
[BLDATA.Current_Points.CP,...
BLDATA.Current_Points.HU,...
BLDATA.Current_Points.EM,...
BLDATA.Current_Points.US];
BLDATA.Current_WFBones.Radius =...
[BLDATA.Current_Points.CP,...
BLDATA.Current_Points.RS];
% Set the Garner and Pandy Scapular Rotation Matrix
Zaxis = BLDATA.Current_Points.AC - BLDATA.Current_Points.GH; Zaxis = Zaxis/norm(Zaxis);
Yaxis = cross(Zaxis, BLDATA.Current_Points.AC - BLDATA.Current_Points.TS); Yaxis = Yaxis/norm(Yaxis);
Xaxis = cross(Yaxis, Zaxis); Xaxis = Xaxis/norm(Xaxis);
% Set the rotation matrix
BLDATA.Current_GnP.Rs = [Xaxis, Yaxis, Zaxis];
% Set the Output
Output = BLDATA;
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
% LIST OF TASKS ENDS HERE!!
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
else
% If the wrong task is given, MATLAB throws an error
ErrorMsg = [...
'The user supplied task is not valid.',...
'MAIN_TOOL_geometry_functions requires a valid task as first input.\n',...
'Try the Followings : \n',...
'Task 1 : Build Rotation Matrices From Euler Angles,\n',...
'Task 2 : Get Euler Angles From Original Rotation Matrices,\n',...
'Task 3 : Get Euler Angles From Initial Rotation Matrices,\n',...
'Task 4 : Get Euler Angles From Current Rotation Matrices,\n',...
'Task 5 : Rotate Points From Local To Global Frame (Initial),\n',...
'Task 6 : Rotate Points From Global To Local Frame (Initial),\n',...
'Task 7 : Rotate Points From Local To Global Frame (Current),\n',...
'Task 8 : Rotate Points From Global To Local Frame (Current),\n',...
'Task 9 : Update Initial Bony Landmark Data from Joint Rotation Matrices,\n',...
'Task 10: Update Current Bony Landmark Data from Joint Rotation Matrices.'];
% Throw the Error
error('MainApp:GomertricTaskCheck', ErrorMsg);
end
return;
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