polySet2Im

Below is a demonstration of the features of the polySet2Im function

EXAMPLE 1: CONVERTING EDGES ON A PATCH TYPE SURFACE TO AN EDGE IMAGE WITH DESIRED SIZE, VOXEL SIZE, ORIGIN AND EDGE SUBDEVISIONS
EXAMPLE 2: CONVERTING A POLYGON TO AN IMAGE WITH DESIRED SIZE, VOXEL SIZE, ORIGIN AND LINE SUBDEVISIONS
EXAMPLE 3: THICKNENING OF THE RESULT AND CREATING SURFACE STRUCTURES

clear; close all; clc;

% Plot settings for the examples below
fontSize=10;
faceAlpha1=1;
faceAlpha2=0.3;

EXAMPLE 1: CONVERTING EDGES ON A PATCH TYPE SURFACE TO AN EDGE IMAGE WITH DESIRED SIZE, VOXEL SIZE, ORIGIN AND EDGE SUBDEVISIONS

Defining an example surface model, in this case a torus consisting of hexagonal faces mesh

% Defining a deformed and rotated torus shape
r=1; %Sphere radius
rc=2; %Central radius
nr=10;
nc=12;
ptype='honey';
[F,V]=patchTorus(r,nr,rc,nc,ptype);

Setting control parameters

% Defining the full set of possible control parameters
voxelSize=0.1; % The output image voxel size.
imOrigin=min(V,[],1)-3*voxelSize;
imMax=max(V,[],1)+3*voxelSize;
imSiz=round((imMax-imOrigin)/voxelSize);
imSiz=imSiz([2 1 3]); %Image size (x, y corresponds to j,i in image coordinates, hence the permutation)
n=50;

% Using |polySet2Im| function to convert patch data to image data

E=patchEdges(F,1);

[M,~]=polySet2Im(E,V,voxelSize,imOrigin,imSiz,n);

Plotting the results

hf1=cFigure;
subplot(1,2,1);
title('The polygon','FontSize',fontSize);
xlabel('X','FontSize',fontSize);ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;
patch('Faces',F,'Vertices',V,'FaceColor','g','EdgeColor','k','FaceAlpha',faceAlpha1);
camlight('headlight'); lighting flat;
axis equal; view(3); axis tight;  grid on;  set(gca,'FontSize',fontSize);

subplot(1,2,2);
title('Edge image','FontSize',fontSize);
xlabel('X','FontSize',fontSize);ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;

patch('Faces',F,'Vertices',V,'FaceColor','g','EdgeColor','none','FaceAlpha',faceAlpha2);

L_plot=false(size(M));
L_plot(:,:,round(size(M,3)/2))=1;
[Fm,Vm,Cm]=ind2patch(L_plot,double(M),'sk');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);
patch('Faces',Fm,'Vertices',Vm,'FaceColor','flat','CData',Cm,'EdgeColor','k','FaceAlpha',faceAlpha1);

L_plot=false(size(M));L_plot(round(size(M,1)/2),:,:)=1;
[Fm,Vm,Cm]=ind2patch(L_plot,M,'si');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);
patch('Faces',Fm,'Vertices',Vm,'FaceColor','flat','CData',Cm,'EdgeColor','k','FaceAlpha',faceAlpha1);

L_plot=false(size(M));L_plot(:,round(size(M,2)/2),:)=1;
[Fm,Vm,Cm]=ind2patch(L_plot,M,'sj');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);
patch('Faces',Fm,'Vertices',Vm,'FaceColor','flat','CData',Cm,'EdgeColor','k','FaceAlpha',faceAlpha1);

[Fm,Vm,Cm]=ind2patch(M>0,M,'v');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);
patch('Faces',Fm,'Vertices',Vm,'FaceColor','flat','CData',Cm,'EdgeColor','k','FaceAlpha',faceAlpha1);

colormap(gray(2)); caxis([0 1]); colorbar;
axis equal; view(3); axis tight;  grid on;  set(gca,'FontSize',fontSize);
drawnow;

EXAMPLE 2: CONVERTING A POLYGON TO AN IMAGE WITH DESIRED SIZE, VOXEL SIZE, ORIGIN AND LINE SUBDEVISIONS

% Creating example curve
ns=150;
t=linspace(0,-pi,ns);
r=10+7.*sin(8*t);
[x,y] = pol2cart(t,r);
z=7*cos(10.*t);
V=[x(:) y(:) z(:)];

ind1=1:size(V,1)-1;
ind2=2:size(V,1);
E=[ind1(:) ind2(:)];

% Defining the full set of possible control parameters
voxelSize=0.2; % The output image voxel size.
imOrigin=min(V,[],1)-3*voxelSize;
imMax=max(V,[],1)+3*voxelSize;
imSiz=round((imMax-imOrigin)/voxelSize);
imSiz=imSiz([2 1 3]); %Image size (x, y corresponds to j,i in image coordinates, hence the permutation)
n=50;

[M,~]=polySet2Im(E,V,voxelSize,imOrigin,imSiz,n);

Plotting the results

hf1=cFigure;
subplot(1,2,1);
title('The patch model','FontSize',fontSize);
xlabel('X','FontSize',fontSize);ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;
patch('Faces',E,'Vertices',V,'FaceColor','g','EdgeColor','k','FaceAlpha',faceAlpha1);
camlight('headlight'); lighting flat;
axis equal; view(3); axis tight;  grid on;  set(gca,'FontSize',fontSize);

subplot(1,2,2);
title('Edge image','FontSize',fontSize);
xlabel('X','FontSize',fontSize);ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;

patch('Faces',E,'Vertices',V,'FaceColor','g','EdgeColor','none','FaceAlpha',faceAlpha2);

L_plot=false(size(M));
L_plot(:,:,round(size(M,3)/2))=1;
[Fm,Vm,Cm]=ind2patch(L_plot,double(M),'sk');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);
patch('Faces',Fm,'Vertices',Vm,'FaceColor','flat','CData',Cm,'EdgeColor','k','FaceAlpha',faceAlpha1);

L_plot=false(size(M));L_plot(round(size(M,1)/2),:,:)=1;
[Fm,Vm,Cm]=ind2patch(L_plot,M,'si');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);
patch('Faces',Fm,'Vertices',Vm,'FaceColor','flat','CData',Cm,'EdgeColor','k','FaceAlpha',faceAlpha1);

L_plot=false(size(M));L_plot(:,round(size(M,2)/2),:)=1;
[Fm,Vm,Cm]=ind2patch(L_plot,M,'sj');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);
patch('Faces',Fm,'Vertices',Vm,'FaceColor','flat','CData',Cm,'EdgeColor','k','FaceAlpha',faceAlpha1);

[Fm,Vm,Cm]=ind2patch(M>0,M,'v');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);
patch('Faces',Fm,'Vertices',Vm,'FaceColor','flat','CData',Cm,'EdgeColor','k','FaceAlpha',faceAlpha1);

colormap(gray(2)); caxis([0 1]); colorbar;
axis equal; view(3); axis tight;  grid on;  set(gca,'FontSize',fontSize);
drawnow;

EXAMPLE 3: THICKNENING OF THE RESULT AND CREATING SURFACE STRUCTURES

%Create grow kernel
k=ones(3,3,3);
k=k./sum(k(:));
M = convn(M,k,'same');
M=M./max(M(:));

%Build iso-surface

[I,J,K]=ndgrid(1:1:size(M,1),1:1:size(M,2),1:1:size(M,3));
[X,Y,Z]=im2cart(I,J,K,voxelSize*ones(1,3));
X=X+imOrigin(1);
Y=Y+imOrigin(2);
Z=Z+imOrigin(3);

isoLevel=0.25;
[Fi,Vi] = isosurface(X,Y,Z,M,isoLevel); %main isosurface
Fi=fliplr(Fi); %Flip so normal faces outward
[Fc,Vc] = isocaps(X,Y,Z,M,isoLevel); %Caps to close the shape
Fc=fliplr(Fc); %Flip so normal faces outward

%Join model segments
Vs=[Vi;Vc];
Fs=[Fi;Fc+size(Vi,1)];

%Merge nodes
[Fs,Vs]=mergeVertices(Fs,Vs);

cPar.Method='HC';
cPar.n=25;
[Vs]=patchSmooth(Fs,Vs,[],cPar);

Plotting the results

hf2=cFigure;
title('iso-surface of thickened structure','FontSize',fontSize);
xlabel('X','FontSize',fontSize);ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;

patch('Faces',Fs,'Vertices',Vs,'FaceColor','b','EdgeColor','none','FaceAlpha',faceAlpha1);

camlight('headlight'); lighting phong;
axis equal; view(3); axis tight;  grid on;  set(gca,'FontSize',fontSize);
drawnow;

GIBBON www.gibboncode.org

Kevin Mattheus Moerman, [email protected]

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License: https://github.com/gibbonCode/GIBBON/blob/master/LICENSE

GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for image segmentation, image-based modeling, meshing, and finite element analysis.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

polySet2Im

Contents

EXAMPLE 1: CONVERTING EDGES ON A PATCH TYPE SURFACE TO AN EDGE IMAGE WITH DESIRED SIZE, VOXEL SIZE, ORIGIN AND EDGE SUBDEVISIONS

EXAMPLE 2: CONVERTING A POLYGON TO AN IMAGE WITH DESIRED SIZE, VOXEL SIZE, ORIGIN AND LINE SUBDEVISIONS

EXAMPLE 3: THICKNENING OF THE RESULT AND CREATING SURFACE STRUCTURES