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msm/ShoulderModel_rTSA/TOOLBOX_Moment_Arms/MOMENT_ARM_TOOL_compute_all.m
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MOMENT_ARM_TOOL_compute_all.m
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function MADATA = MOMENT_ARM_TOOL_compute_all(MWDATA, BLDATA, KEDATA, WBHandle, SSDATA)
%{
Computes all the muscle moment-arms using both methods
--------------------------------------------------------------------------
Syntax :
MDATA = MOMENT_ARM_TOOL_compute_all(MWDATA, BLDATA, KEDATA, WBHandle)
--------------------------------------------------------------------------
Function Description :
This function computes the moment arms of all the muscle segments using
both the geometric method and the tendon excursion method. Note that the
moment arm calculated here includes only the matrix C of page 86 of the
thesis. In other world, it's not the generalized moment arm matrix (W*C).
The muscle lengths, and the moment arms computed in the scapular plane are
included in the function's outputs. The scapular plane means the body-fixed
frame attached to the scapula. The scapular plane is defined according
to both the Garner's definition and the ISB convention (Rs). The function
also gives a matrix consisting of the unit vectors of the forces acting on
different bodies. It's a 15xnumber of segments matrix. Its 7-8th rows
includes the direction of the forces acting on the humerus.
The Output Data Structure is defined as follows
MADATA{MuscleId,1}.MomentArms
MADATA{MuscleId,1}.FDirection
MADATA{MuscleId,1}.ScapularPlane_GnP
MADATA{MuscleId,1}.ScapularPlane
--------------------------------------------------------------------------
%}
% Initialise the MADATA structure
MADATA = cell(42, 1);
% Each element in the cell will contain an N x 15 matrix
for MuscleId = 1:42
MADATA{MuscleId, 1}.MomentArms = cell(1,20);
MADATA{MuscleId, 1}.MomentArmsNum = cell(1,20);
MADATA{MuscleId, 1}.FDirection = cell(1,20);
MADATA{MuscleId, 1}.ScapularPlane_GnP = cell(1,20);
MADATA{MuscleId, 1}.ScapularPlane = cell(1,20);
for SegmentId = 1:20
MADATA{MuscleId, 1}.MomentArms{1,SegmentId} = zeros(size(KEDATA.Joint_Angle_Evolution,2),15);
MADATA{MuscleId, 1}.MomentArmsNum{1,SegmentId} = zeros(size(KEDATA.Joint_Angle_Evolution,2),15);
MADATA{MuscleId, 1}.FDirection{1,SegmentId} = zeros(size(KEDATA.Joint_Angle_Evolution,2),15);
MADATA{MuscleId, 1}.MuscleLength(:,SegmentId) = zeros(size(KEDATA.Joint_Angle_Evolution,2),1);
MADATA{MuscleId, 1}.ScapularPlane_GnP{1,SegmentId} = zeros(size(KEDATA.Joint_Angle_Evolution,2),15);
MADATA{MuscleId, 1}.ScapularPlane {1,SegmentId} = zeros(size(KEDATA.Joint_Angle_Evolution,2),15);
end
end
%--------------------------------------------------------------------------
% Define Angles, Velocities, & Accelerations
%--------------------------------------------------------------------------
% first chose among the two available options for the kinematics
if isfield(SSDATA, 'Joint_Angle_Reconstruction')
% Create the Time
% t = linspace(0,ESTDATA.Tmax,size(KEDATA.Joint_Angle_Evolution,2));
% Pre-Define the Joint Angles, Velocities, and Accelerations
JEA = SSDATA.Joint_Angle_Reconstruction;
% dJEAdt = [];
% d2JEAdt2 = [];
% for TimeId = 1:size(t,2)-1
% % Velocity
% dJEAdt = [dJEAdt, (JEA(:,TimeId+1) - JEA(:,TimeId))/(t(TimeId+1) - t(TimeId))];
%
% if TimeId < size(t,2)-1
% % Acceleration
% d2JEAdt2 = [d2JEAdt2, (JEA(:,TimeId+2) - 2*JEA(:,TimeId+1) + JEA(:,TimeId))/((t(TimeId+2) - t(TimeId+1))*(t(TimeId+1) - t(TimeId)))];
% end
% end
else
% option 1: use the joint angles acieved directly from the IK
JEA = KEDATA.Joint_Angle_Evolution;
% t = linspace(0,ESTDATA.Tmax,length(SSDATA.Joint_Angle_Reconstruction));
% dJEAdt = [];
% d2JEAdt2 = [];
% for TimeId = 1:length(t)-1
% dJEAdt = [dJEAdt, (JEA(:,TimeId+1) - JEA(:,TimeId))/(t(TimeId+1) - t(TimeId))];
% if TimeId < length(t)-1
% % Acceleration
% d2JEAdt2 = [d2JEAdt2, (JEA(:,TimeId+2) - 2*JEA(:,TimeId+1) + JEA(:,TimeId))/((t(TimeId+2) - t(TimeId+1))*(t(TimeId+1) - t(TimeId)))];
% end
% end
%
% % the clavicle axial rotation is always noisy
% dJEAdt(1,:) = polyval(SSDATA.Joint_Velocity_Coefficients(1, :), t(1, 1:end-1));
% d2JEAdt2(1,:) = polyval(SSDATA.Joint_Acceleration_Coefficients(1, :), t(1, 1:end-2));
% option 2: use the smoothened joint angles from IK
% t = linspace(0,ESTDATA.Tmax,100);
% for ja_id = 1:11
% JEA(ja_id,:) = polyval(SSDATA.Joint_Angle_Coefficients(ja_id,:),t);
% dJEAdt(ja_id,:) = polyval(SSDATA.Joint_Velocity_Coefficients(ja_id,:),t);
% d2JEAdt2(ja_id,:) = polyval(SSDATA.Joint_Acceleration_Coefficients(ja_id,:),t);
% end
% SSDATA.Smoothened_Joint_Angle_Reconstruction = JEA;
end
%--------------------------------------------------------------------------
% Run through all the motion
%--------------------------------------------------------------------------
for TimeId = 1:size(JEA,2)
waitbar(TimeId/size(JEA,2), WBHandle);
% Display
disp(['Computing All Moment-Arms, Time Stamp : ', num2str(TimeId), '/', num2str(size(JEA,2))]);
% Get the Current Rotation Matrices
Rmat = MAIN_TOOL_geometry_functions('Build Rotation Matrices From Euler Angles', JEA(:,TimeId), BLDATA);
% Update the current configuration
BLDATA = MAIN_TOOL_geometry_functions(...
'Update Current Bony Landmark Data from Joint Rotation Matrices', Rmat(:,1:3), Rmat(:,4:6), Rmat(:,7:9), Rmat(:,10:12), Rmat(:,13:15), BLDATA);
% Pre-define data matrices
Wmat = []; % moment arm using geometrical method
Wmatnum = []; % moment arm using tendon excursion
Dmat = []; % used to be the direction of the forces acting on the humerus. But, it's now a 15xnumber of segments force direction matrix.
Lmat = []; % muscle length
% Run through all the muscles and their segments
for MuscleId = 1:42
for SegmentId = 1:MWDATA{MuscleId, 1}.MSCInfo.NbSegments
%----------------------------------------------------------------------
% MOMENT ARMS: GEOMETRIC METHOD FOR EACH MUSCLE
%----------------------------------------------------------------------
% Construct a One-Time Muscle Structure for a single segment
Muscle_Seg.Origin = MWDATA{MuscleId,1}.Origin{1,SegmentId};
Muscle_Seg.ViaA = MWDATA{MuscleId,1}.ViaA{1,SegmentId};
Muscle_Seg.ViaB = MWDATA{MuscleId,1}.ViaB{1,SegmentId};
Muscle_Seg.Insertion = MWDATA{MuscleId,1}.Insertion{1,SegmentId};
Muscle_Seg.OriginRef = MWDATA{MuscleId,1}.MSCInfo.OriginRef;
Muscle_Seg.ViaARef = MWDATA{MuscleId,1}.MSCInfo.ViaARef;
Muscle_Seg.ViaBRef = MWDATA{MuscleId,1}.MSCInfo.ViaBRef;
Muscle_Seg.InsertionRef = MWDATA{MuscleId,1}.MSCInfo.InsertionRef;
Muscle_Seg.ObjectCentre = MWDATA{MuscleId,1}.MSCInfo.ObjectCentre;
Muscle_Seg.ObjectType = MWDATA{MuscleId,1}.MSCInfo.ObjectType;
Muscle_Seg.ObjectZaxis = MWDATA{MuscleId,1}.MSCInfo.ObjectZaxis;
Muscle_Seg.ObjectRef = MWDATA{MuscleId,1}.MSCInfo.ObjectRef;
Muscle_Seg.ObjectRadii = MWDATA{MuscleId,1}.MSCInfo.ObjectRadiiscale*MWDATA{MuscleId,1}.MSCInfo.ObjectRadii;
Muscle_Seg.NbPlot = MWDATA{MuscleId,1}.MSCInfo.NbPlotPoints;
% Compute the Wrapping
WRDATA = MUSCLE_TOOL_compute_wrapping(BLDATA, Muscle_Seg);
% Compute the moment arms using the geometric method
[MAi, DVi] = MOMENT_ARM_TOOL_compute_moment_arms(WRDATA.PathPoints, WRDATA.PathRefList, BLDATA);
% Fill The matrix
Wmat = [Wmat, MAi];
%----------------------------------------------------------------------
% MUSCLE LENGTH & GH JOINT FORCE DIRECTIONS
%----------------------------------------------------------------------
% Fill The Length
Lmat = [Lmat, 1.e-3*WRDATA.PathLength];
%{
This part here is not useful anymore. Because, we did some
modifications in the MOMENT_ARM_TOOL_compute_moment_arms that
results in a 15x1 unit direction vector for the forces. The
forces acting on the humerus have been already stored in rows
(7-9) of this vector.
%Compute the force directions applied to the humerus
if WRDATA.PathRefList(1,end) == 3
% Augment the force direction vector
Dmat = [Dmat, DVi];
else
Dmat = [Dmat, zeros(3,1)];
end
%}
Dmat = [Dmat, DVi]; % a 15xnumber of segments force direction matrix
%----------------------------------------------------------------------
% MOMENT ARMS : NUMERIC METHOD
%----------------------------------------------------------------------
% To find the moment arm matrix using the tendon excursion
% method one needs to first find the dl/dq that is the
% variation of the length with respect to the variation of the
% generalized coordinates. Then having defined dW/ddq
% (projection matrix), the moment arm (C) can be found by solving
% dW/ddq * C = dl/dq. Therefore, C = (dW/ddq) \ (dl/dq).
% Initialise
MAit = zeros(11,1); % dl/dq
% Joint Angle Variations Vector.
JEA_Variation = zeros(11,1);
% List of small angle changes
dJEA = [1.e-6, -1.e-6, 1.e-6, 1.e-6, -1.e-6, 1.e-6, 1.e-6, -1.e-6, 1.e-6, -1.e-6, 1.e-6];
for AngleId = 1:11
JEA_Variation(AngleId,1) = dJEA(AngleId);
% Get the Current Rotation Matrices with small variation
Rmat = MAIN_TOOL_geometry_functions('Build Rotation Matrices From Euler Angles', [JEA(:,TimeId)+JEA_Variation], BLDATA);
% Update the current configuration
BLDATA = MAIN_TOOL_geometry_functions(...
'Update Current Bony Landmark Data from Joint Rotation Matrices', Rmat(:,1:3), Rmat(:,4:6), Rmat(:,7:9), Rmat(:,10:12), Rmat(:,13:15), BLDATA);
% Compute the Wrapping with updated bony landmark positions
WRDATAi = MUSCLE_TOOL_compute_wrapping(BLDATA, Muscle_Seg);
% Compute the length derivative
MAit(AngleId,1) = -1.e-3*(WRDATAi.PathLength - WRDATA.PathLength)/dJEA(AngleId);
% Reset BLDATA to the actual current values (without small variation)
Rmat = MAIN_TOOL_geometry_functions('Build Rotation Matrices From Euler Angles', JEA(:,TimeId), BLDATA);
BLDATA = MAIN_TOOL_geometry_functions(...
'Update Current Bony Landmark Data from Joint Rotation Matrices', Rmat(:,1:3), Rmat(:,4:6), Rmat(:,7:9), Rmat(:,10:12), Rmat(:,13:15), BLDATA);
% Reset the variation to zero
JEA_Variation(AngleId,1) = 0;
end
% Compute the projection matrices
TPmat = MOMENT_ARM_TOOL_projection_matrices(JEA(:,TimeId)'); % 11 x 15
% Fill the matrix
Wmatnum = [Wmatnum, TPmat\MAit]; % 15 x 1
end
end
Rss = [cos(pi/6), -sin(pi/6), 0;
sin(pi/6), cos(pi/6), 0;
0, 0, 1];
%----------------------------------------------------------------------
% SAVE DATA FOR ITH TIME STEP
%----------------------------------------------------------------------
valueId = 1;
for MuscleId = 1:42
for SegmentId = 1:MWDATA{MuscleId, 1}.MSCInfo.NbSegments
MADATA{MuscleId, 1}.MomentArms{1,SegmentId}(TimeId, :) = Wmat(:,valueId)';
MADATA{MuscleId, 1}.MomentArmsNum{1,SegmentId}(TimeId, :) = Wmatnum(:,valueId)';
MADATA{MuscleId, 1}.FDirection{1,SegmentId}(TimeId, :) = Dmat(:,valueId)';
MADATA{MuscleId, 1}.MuscleLength(TimeId,SegmentId) = Lmat(1, valueId);
MADATA{MuscleId, 1}.ScapularPlane_GnP{1,SegmentId}(TimeId, :) = [Wmat(1:6,valueId); BLDATA.Current_GnP.Rs'*Wmat(7:9,valueId); Wmat(10:15,valueId)]';
MADATA{MuscleId, 1}.ScapularPlane{1,SegmentId}(TimeId, :) = [Wmat(1:6,valueId); BLDATA.Current_Matrices_L2A.Rs'*Wmat(7:9,valueId); Wmat(10:15,valueId)]';
valueId = valueId + 1;
end
end
end
return;
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