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msm/ShoulderModel_rTSA/Visualisation_Original_Meshings/MESHING_check_mesh.m
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MESHING_check_mesh.m
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clc; clear all; close all;
% few lines to transform the stl file to the bone fixed frame
% one need to first run the first few parts of the code to have the
% rotation matrices and the bony landmarks neccessary for these
% transfromations.
% transform the points from Amira frame to the Matlab fram
Current_Folder = pwd;
load([Current_Folder, '/Visualisation_Original_Meshings/Ulna_Mesh_Try3']);
load([Current_Folder, '/Visualisation_Original_Meshings/Radius_Mesh_Try3']);
Ulna_Mesh_Try1.points = Ulna_Mesh_Try3.points;
Ulna_Mesh_Try1.tri = Ulna_Mesh_Try3.tri;
Radius_Mesh_Try1.points = Radius_Mesh_Try3.points;
Radius_Mesh_Try1.tri = Radius_Mesh_Try3.tri;
P_yasmine_correction = [9.37 -116.5 116.3]';
IJ = BLDATA.Amira_to_MATLAB.IJ - P_yasmine_correction; % origin of the Matlab frame, the Amira frame is the zero 10 -90 120
n_yas = [-0.98 0 -0.18]'; n_yas = n_yas/norm(n_yas);
theta_yas = 12.4;
R_yasmine_correction = [n_yas(1)*n_yas(1)*(1-cosd(theta_yas))+cosd(theta_yas) n_yas(1)*n_yas(2)*(1-cosd(theta_yas))-n_yas(3)*sind(theta_yas) n_yas(1)*n_yas(3)*(1-cosd(theta_yas))-n_yas(2)*sind(theta_yas);
n_yas(1)*n_yas(2)*(1-cosd(theta_yas))+n_yas(3)*sind(theta_yas) n_yas(2)*n_yas(2)*(1-cosd(theta_yas))+cosd(theta_yas) n_yas(2)*n_yas(3)*(1-cosd(theta_yas))-n_yas(1)*sind(theta_yas);
n_yas(1)*n_yas(3)*(1-cosd(theta_yas))-n_yas(2)*sind(theta_yas) n_yas(2)*n_yas(3)*(1-cosd(theta_yas))+n_yas(1)*sind(theta_yas) n_yas(3)*n_yas(3)*(1-cosd(theta_yas))+cosd(theta_yas)];
R_am = BLDATA.Amira_to_MATLAB.Rt*R_yasmine_correction'; % Rotation matrix from Amira to MATLAB
H_am = [[R_am, -R_am*IJ]; [0, 0, 0, 1]]; % Homogeneous transformation matrix from Amira to Matlab
for i = 1:1:size(Ulna_Mesh_Try1.points,1)
Transformed_point_ulna1(:,i) = H_am*[Ulna_Mesh_Try1.points(i,:), 1]';
Ulna_Mesh_Try2.points(i,:) = Transformed_point_ulna1(1:3,i)';
Ulna_Mesh_Try2.tri = Ulna_Mesh_Try1.tri;
end
hold on
trisurf(Ulna_Mesh_Try2.tri, Ulna_Mesh_Try2.points(:,1), Ulna_Mesh_Try2.points(:,2), Ulna_Mesh_Try2.points(:,3));
for j = 1:1:size(Radius_Mesh_Try1.points,1)
Transformed_point_radius1(:,j) = H_am*[Radius_Mesh_Try1.points(j,:), 1]';
Radius_Mesh_Try2.points(j,:) = Transformed_point_radius1(1:3,j)';
Radius_Mesh_Try2.tri = Radius_Mesh_Try1.tri;
end
trisurf(Radius_Mesh_Try2.tri, Radius_Mesh_Try2.points(:,1), Radius_Mesh_Try2.points(:,2), Radius_Mesh_Try2.points(:,3));
Ru = BLDATA.Original_Matrices_L2A.Ru';
HU = BLDATA.Original_Points.HU;
H_T2U = [[Ru, -Ru*HU]; [0, 0, 0, 1]]; % Homogeneous transformation matrix from absolute to local frame
Rr = BLDATA.Original_Matrices_L2A.Rr';
CP = BLDATA.Original_Points.CP;
H_T2R = [[Rr, -Rr*CP]; [0, 0, 0, 1]]; % Homogeneous transformation matrix from absolute to local frame
for i = 1:1:size(Ulna_Mesh_Try2.points,1)
Transformed_point_ulna2(:,i) = H_T2U*[Ulna_Mesh_Try2.points(i,:), 1]';
Ulna_Mesh_Try3.points(i,:) = Transformed_point_ulna2(1:3,i)';
Ulna_Mesh_Try3.tri = Ulna_Mesh_Try2.tri;
end
for j = 1:1:size(Radius_Mesh_Try2.points,1)
Transformed_point_radius2(:,j) = H_T2R*[Radius_Mesh_Try2.points(j,:), 1]';
Radius_Mesh_Try3.points(j,:) = Transformed_point_radius2(1:3,j)';
Radius_Mesh_Try3.tri = Radius_Mesh_Try2.tri;
end
Current_Folder = pwd;% pwd displays the MATLAB current folder.
save([pwd, '/Visualisation_Original_Meshings/Ulna_Mesh_Try32'],'Ulna_Mesh_Try3');
save([pwd, '/Visualisation_Original_Meshings/Radius_Mesh_Try32'],'Radius_Mesh_Try3');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% the older part of the code for checking visualization stuffs
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
load Ulna_Mesh_Try1;%Clavicula_Mesh0
%Clavicula_Mesh0 = Clavicula_Mesh;
%Clavicula_Mesh0.points = [Clavicula_Mesh0.points(:,3), Clavicula_Mesh0.points(:,1), Clavicula_Mesh0.points(:,2)];
%subplot(1,2,1)
figure
trisurf(Ulna_Mesh_Try2.tri, Ulna_Mesh_Try2.points(:,1), Ulna_Mesh_Try2.points(:,2), Ulna_Mesh_Try2.points(:,3));
trisurf(Radius_Mesh0.tri, Radius_Mesh0.points(:,1), Radius_Mesh0.points(:,2), Radius_Mesh0.points(:,3));
axis equal;
hold on;
stop
% load Clavicula_Meshold;
%
% subplot(1,2,2)
% trisurf(Clavicula_Mesh0.tri, Clavicula_Mesh0.points(:,1), Clavicula_Mesh0.points(:,2), Clavicula_Mesh0.points(:,3));
% axis equal;
% hold on;
% R = [cos(pi/40), 0, -sin(pi/40);
% 0, 1, 0;
% sin(pi/40), 0, cos(pi/40)];
% Rz = [cos(2*pi/180), -sin(2*pi/180), 0;
% sin(2*pi/180), cos(2*pi/180), 0;
% 0, 0, 1];
% points = Rz'*Clavicula_Mesh0.points';
% points = points';
% trisurf(Clavicula_Mesh0.tri, points(:,1), points(:,2), points(:,3), 'facecolor', 'blue');
% axis equal;
BLDATA = MAIN_INITIALISATION_build_data_bony_landmark;
BLDATAOld = MAIN_INITIALISATION_build_data_bony_landmarkOld;
SC = BLDATA.Original_Points.SC;
SCold = BLDATAOld.Original_Points.SC;
dvec = SC-SCold;
dvec = BLDATA.Original_Matrices_L2A.Rc'*dvec;
dvec = dvec/1000;
points = Clavicula_Mesh0.points' - diag(dvec)*ones(3,size(Clavicula_Mesh0.points,1));
points = points';
trisurf(Clavicula_Mesh0.tri, points(:,1), points(:,2), points(:,3));
axis equal;
plot3(dvec(1), dvec(2), dvec(3), 'marker', 'o', 'color', 'red', 'markersize', 12, 'markerfacecolor', 'red');
%
% Clavicula_Mesh0.points = points;
% save Clavicula_Mesh0 Clavicula_Mesh0;
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