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Diffusion ShoulderDB_ImportSegmentMeasureAnalyze (Bashardoust_SystCoord) Browse

R8218/ShoulderCase/@Shoulder/Shoulder.m
b22704467228Bashardoust_SystCoord

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Shoulder.m
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classdef (Abstract) Shoulder < handle
properties
side % R or L
scapula
humerus
muscles
CTscan
comment
end
properties (Hidden = true)
SCase
end
methods (Abstract, Access = protected)
createScapula(obj);
end
methods
function obj = Shoulder(SCase)
obj.side = '';
obj.humerus = Humerus(obj);
obj.muscles = Muscles(obj);
obj.CTscan = '';
obj.comment = '';
obj.SCase = SCase;
obj.createScapula;
end
function output = plot(obj)
% Create a figure and plot inside:
% the scapula surface, coordSys, groove points and landmarks;
% the glenoid surface, sphere and centerLine;
% the humerus sphere and centerLine.
figure;
hold on;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Scapula
% Plot the segmented surface
if not(isempty(obj.scapula.surface))
points = obj.scapula.surface.points;
faces = obj.scapula.surface.faces;
x = points(:,1);
y = points(:,2);
z = points(:,3);
trisurf(faces,x,y,z,'Facecolor','yellow','FaceAlpha',0.5,'EdgeColor','none','FaceLighting','gouraud');
end
% Plot scapula groove
if not(isempty(obj.scapula.groove))
points = obj.scapula.groove;
x = points(:,1);
y = points(:,2);
z = points(:,3);
scatter3(x,y,z,100,'blue');
end
% Plot scapula markers
points = [...
obj.scapula.angulusInferior;
obj.scapula.trigonumSpinae;
obj.scapula.processusCoracoideus;
obj.scapula.acromioClavicular;
obj.scapula.angulusAcromialis;
obj.scapula.spinoGlenoidNotch...
];
x = points(:,1);
y = points(:,2);
z = points(:,3);
scatter3(x,y,z,100,'blue','LineWidth',2);
% Plot scapular plane
axisLength = 50;
pt0 = obj.scapula.coordSys.origin;
pt1 = pt0 + (obj.scapula.coordSys.ML + obj.scapula.coordSys.IS) * axisLength ;
pt2 = pt1 - obj.scapula.coordSys.IS * pdist([pt1 ; obj.scapula.angulusInferior]);
pt3 = pt2 - obj.scapula.coordSys.ML * pdist([pt1 ; obj.scapula.trigonumSpinae] );
pt4 = pt3 + obj.scapula.coordSys.IS * pdist([pt1 ; obj.scapula.angulusInferior]);
X = [pt1(1) pt2(1) pt3(1) pt4(1)];
Y = [pt1(2) pt2(2) pt3(2) pt4(2)];
Z = [pt1(3) pt2(3) pt3(3) pt4(3)];
patch(X,Y,Z,'black','FaceAlpha',0.3); % Transparent plane
% Plot scapular axis
pt1 = obj.scapula.coordSys.origin;
axisLength = 10 + pdist([pt1 ; obj.scapula.trigonumSpinae]);
pt2 = pt1 - obj.scapula.coordSys.ML * axisLength;
x = [pt1(1), pt2(1)];
y = [pt1(2), pt2(2)];
z = [pt1(3), pt2(3)];
plot3(x,y,z,'Color','blue','LineWidth', 5);
% Plot scapular coordinate system
axisLength = 50; % Length of the coord. sys. axes
pt0 = obj.scapula.coordSys.origin;
pt1 = pt0 + obj.scapula.coordSys.PA*axisLength; % X
pt2 = pt0 + obj.scapula.coordSys.IS*axisLength; % Y
pt3 = pt0 + obj.scapula.coordSys.ML*axisLength; % Z
x = [pt0(1), pt1(1)];
y = [pt0(2), pt1(2)];
z = [pt0(3), pt1(3)];
plot3(x,y,z,'Color','red','LineWidth', 5);
x = [pt0(1), pt2(1)];
y = [pt0(2), pt2(2)];
z = [pt0(3), pt2(3)];
plot3(x,y,z,'Color','green','LineWidth', 5);
x = [pt0(1), pt3(1)];
y = [pt0(2), pt3(2)];
z = [pt0(3), pt3(3)];
plot3(x,y,z,'Color','blue','LineWidth', 5);
% plot scapular axis on glenoid center
axisLength = 50;
pt1 = obj.scapula.glenoid.center;
pt2 = pt1 + obj.scapula.coordSys.ML*axisLength;
x = [pt1(1), pt2(1)];
y = [pt1(2), pt2(2)];
z = [pt1(3), pt2(3)];
plot3(x,y,z,'Color','magenta','LineWidth', 5);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Glenoid
% Plot the glenoid surface
% We might move them in the direction of th glenoid center
% instead of the ML axis
points = obj.scapula.glenoid.surface.points +...
obj.scapula.coordSys.ML * 0.2;
faces = obj.scapula.glenoid.surface.faces;
x = points(:,1);
y = points(:,2);
z = points(:,3);
trisurf(faces,x,y,z,'Facecolor','none','FaceAlpha',1,'EdgeColor','magenta','FaceLighting','none');
% plot glenoid centerline
pt1 = obj.scapula.glenoid.center;
pt2 = pt1 + obj.scapula.glenoid.centerLine;
x = [pt1(1), pt2(1)];
y = [pt1(2), pt2(2)];
z = [pt1(3), pt2(3)];
plot3(x,y,z,'Color','magenta','LineWidth', 5);
% We might add spherical cap
% plot glenoid sphere
n = 20; % number of lines
[X,Y,Z] = sphere(n);
X = X*obj.scapula.glenoid.radius;
Y = Y*obj.scapula.glenoid.radius;
Z = Z*obj.scapula.glenoid.radius;
Xc = pt2(1);
Yc = pt2(2);
Zc = pt2(3);
mesh(X+Xc,Y+Yc,Z+Zc,'LineStyle','none','FaceColor','magenta','FaceAlpha',0.3,'FaceLighting','gouraud');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Humerus
% plot humeral head sphere
n = 20; % number of lines
[X,Y,Z] = sphere(n);
X = X*obj.humerus.radius;
Y = Y*obj.humerus.radius;
Z = Z*obj.humerus.radius;
Xc = obj.humerus.center(1);
Yc = obj.humerus.center(2);
Zc = obj.humerus.center(3);
mesh(X+Xc,Y+Yc,Z+Zc,'LineStyle','none','FaceColor','magenta','FaceAlpha',0.3,'FaceLighting','gouraud');
% plot humeral head centerline
pt1 = obj.scapula.glenoid.center;
pt2 = obj.humerus.center;
x = [pt1(1), pt2(1)];
y = [pt1(2), pt2(2)];
z = [pt1(3), pt2(3)];
plot3(x,y,z,'Color','magenta','LineWidth', 5);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Graph properties
axis off; % remove axis
lightPosition = obj.scapula.glenoid.center + ...
(...
obj.scapula.coordSys.ML + ...
obj.scapula.coordSys.IS + ...
obj.scapula.coordSys.PA ...
) * 100;
light('Position',lightPosition,'Style','local');
grid on;
xlabel('X (CT)');
ylabel('Y (CT)');
zlabel('Z (CT)');
axis square;
axis vis3d; % fixed limits and scaling
viewPoint = obj.scapula.coordSys.ML + ...
obj.scapula.coordSys.IS + ...
obj.scapula.coordSys.PA;
viewPoint = obj.scapula.coordSys.PA;
view(viewPoint); % view from lateral side
% Align IS axis with window vertical axis
camup(obj.scapula.coordSys.IS);
figureHandle = gca;
figureHandle.DataAspectRatio = [1 1 1]; % Same relative length of data units along each axis
figureHandle.Box = 'On';
set(gcf,'color','w'); % Set background color to white
output = 1;
end
end
end
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