DEMO_MixedTetHexMeshing

Below is a demonstration of how to create a mixed mesh consisting of (linear) hexahedral and tetrahedral elements. The hexahedral mesh is regular while the tetrahedral mesh is derived using TetGen.

Contents

clear; close all; clc;

Plot settings for the examples below

fontSize=20;
faceAlpha1=1;
faceAlpha2=0.3;
plotColors=gjet(4);
searchRadius=6;

CONVERTING A TRIANGULATED SURFACE TO AN IMAGE WITH DESIRED SIZE, VOXEL SIZE AND ORIGIN

Defining an example triangulated surface model

[Fs,Vs]=stanford_bunny;

Setting control parameters

% Defining the full set of possible control parameters
voxelSize=6; % The output image voxel size.
imOrigin=min(Vs,[],1)-voxelSize;
imMax=max(Vs,[],1)+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)

% Using |triSurf2Im| function to convert patch data to image data
[M,~]=triSurf2Im(Fs,Vs,voxelSize,imOrigin,imSiz);

Plotting the results

hf1=cFigure;
subplot(1,2,1);
title('Closed triangulated surface','FontSize',fontSize);
xlabel('X','FontSize',fontSize);ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;
gpatch(Fs,Vs,'g','none');
axis equal; view(3); axis tight;  grid on;  set(gca,'FontSize',fontSize);
camlight('headlight'); lighting phong;
set(gca,'fontSize',fontSize);

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

gpatch(Fs,Vs,'g','none',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),:);
gpatch(Fm,Vm,Cm,'k');

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),:);
gpatch(Fm,Vm,Cm,'k');

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),:);
gpatch(Fm,Vm,Cm,'k');

colormap(gray(3)); caxis([0 2]);
hc=colorbar;
set(hc,'YTick',[1/3 1 5/3]);
set(hc,'YTickLabel',{'Exterior','Boundary','Intertior'});
set(hc,'fontSize',fontSize);
axis equal; view(3); axis tight;  grid on;  set(gca,'FontSize',fontSize);
set(gca,'fontSize',fontSize);
drawnow;

GET HEXAHEDRAL ELEMENT SET

L_model=(M==2); %Interior&Boundary choosen here

%Defining erosion/dilation kernel
k=3;
p=k-round(k./2);
hb=zeros(3,3);
hb(2,2,2)=1;
hb(2,2,1)=1;
hb(2,2,3)=1;
hb(1,2,2)=1;
hb(3,2,2)=1;
hb(2,3,2)=1;
hb(2,1,2)=1;

L_model_rep=zeros(size(L_model)+(2.*p));
L_model_rep(p+(1:size(L_model,1)),p+(1:size(L_model,2)),p+(1:size(L_model,3)))=L_model;
L_model_blur = convn(double(L_model_rep),hb,'valid');
L_model=L_model_blur>=(sum(hb(:)));

[E_hex,V_hex,C_hex]=ind2patch(L_model,M,'hu');

% Convert Coordinates
[V_hex(:,1),V_hex(:,2),V_hex(:,3)]=im2cart(V_hex(:,2),V_hex(:,1),V_hex(:,3),voxelSize*ones(1,3));
V_hex=V_hex+imOrigin(ones(size(V_hex,1),1),:);

% Use element2patch to get patch data to plot the model
[F_hex_cut1,C_hex_F]=element2patch(E_hex,C_hex);

%Pass through unique_patch to reduce "weight" of plot
[Fp,Vp,~,~,~,F_count]=unique_patch(F_hex_cut1,V_hex,[],5);
logicUni=F_count==1; %Logic for boundary faces

Fq=Fp(logicUni,:);
Vq=Vp;
[Fq,Vq,~]=patchCleanUnused(Fq,Vq);

[Ft,Vt]=quad2tri(Fq,Vq,'b');

Plotting the results

hf1=cFigure;
title('Visualizing internal voxels=hexahedral elements','FontSize',fontSize);
xlabel('X','FontSize',fontSize);ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;

gpatch(Fs,Vs,0.5*ones(1,3),'none',faceAlpha2);
gpatch(Fq,Vq,plotColors(2,:),'k');

camlight('headlight'); lighting flat;
axis equal; view(3); axis tight;  grid on;  set(gca,'FontSize',fontSize);
drawnow;
%Joining surface sets
F=[Fs;Ft+size(Vs,1)];
V=[Vs;Vt];
C_tet=[ones(size(Fs,1),1);2*ones(size(Ft,1),1)]; %Surface marker colors

Get hole point

[V_hole]=getInnerPoint(Ft,Vt,searchRadius,voxelSize/2,0);
plotV(V_hole,'r.','MarkerSize',25);

Get region point

L_in=(M==1);

[indInternal]=getInnerVoxel(double(L_in),searchRadius,0);

[I_in,J_in,K_in]=ind2sub(size(L_in),indInternal); %Convert to subscript coordinates
[X_in,Y_in,Z_in]=im2cart(I_in,J_in,K_in,voxelSize*ones(1,3));
V_in=[X_in Y_in Z_in];
V_in=V_in+imOrigin(ones(size(V_in,1),1),:);

plotV(V_in,'k.','MarkerSize',25);

DEFINE FACE BOUNDARY MARKERS

faceBoundaryMarker=C_tet;

Define region points

V_regions=[V_in];

Define hole points

V_holes=[V_hole];

Regional mesh parameters

[edgeLengths]=patchEdgeLengths(F,V);
edgeLengthsMean=mean(edgeLengths);
meanProposedVolume=edgeLengthsMean^3./(6*sqrt(2)); %For regular tetrahedron
regionA=meanProposedVolume;

CREATING THE SMESH STRUCTURE, meshing without the surface constraints imposed by the -Y this time.

stringOpt='-pq1.2AaY';

modelName='tetGenModel';

meshStruct.stringOpt=stringOpt;
meshStruct.Faces=F;
meshStruct.Nodes=V;
meshStruct.holePoints=V_holes;
meshStruct.faceBoundaryMarker=faceBoundaryMarker; %Face boundary markers
meshStruct.regionPoints=V_regions; %region points
meshStruct.regionA=regionA;
meshStruct.minRegionMarker=2; %Minimum region marker
meshStruct.modelName=modelName;

Mesh model using tetrahedral elements using tetGen (see: http://wias-berlin.de/software/tetgen/)

[meshOutput]=runTetGen(meshStruct); %Run tetGen
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 04-Jun-2019 12:10:34
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 04-Jun-2019 12:10:34
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 04-Jun-2019 12:10:34
--- Running TetGen to mesh input boundary--- 04-Jun-2019 12:10:34
Opening /mnt/data/MATLAB/GIBBON/data/temp/tetGenModel.smesh.
Delaunizing vertices...
Delaunay seconds:  0.035795
Creating surface mesh ...
Surface mesh seconds:  0.00535
Recovering boundaries...
Boundary recovery seconds:  0.023344
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.003808
Suppressing Steiner points ...
Steiner suppression seconds:  9e-06
Recovering Delaunayness...
Delaunay recovery seconds:  0.009362
Refining mesh...
Refinement seconds:  0.034344
Optimizing mesh...
Optimization seconds:  0.003459
Jettisoning redundant points.

Writing /mnt/data/MATLAB/GIBBON/data/temp/tetGenModel.1.node.
Writing /mnt/data/MATLAB/GIBBON/data/temp/tetGenModel.1.ele.
Writing /mnt/data/MATLAB/GIBBON/data/temp/tetGenModel.1.face.
Writing /mnt/data/MATLAB/GIBBON/data/temp/tetGenModel.1.edge.

Output seconds:  0.040193
Total running seconds:  0.155877

Statistics:

  Input points: 2729
  Input facets: 5460
  Input segments: 8185
  Input holes: 1
  Input regions: 1

  Mesh points: 3514
  Mesh tetrahedra: 13888
  Mesh faces: 30506
  Mesh faces on exterior boundary: 5460
  Mesh faces on input facets: 5460
  Mesh edges on input segments: 8185
  Steiner points inside domain: 785

--- Done --- 04-Jun-2019 12:10:34
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 04-Jun-2019 12:10:34
--- Done --- 04-Jun-2019 12:10:34

Access model element and patch data

F_tet_cut1=meshOutput.faces;
V_tet=meshOutput.nodes;
C_tet=meshOutput.faceMaterialID;
E_tet=meshOutput.elements;

indBoundary=meshOutput.facesBoundary(meshOutput.boundaryMarker==1,:);
indBoundary=unique(indBoundary(:));

MERGING NODE SETS

V=[V_tet;V_hex];
E_hex=E_hex+size(V_tet,1);

[~,V,ind1,ind2]=mergeVertices(F_tet_cut1,V);

E_tet=ind2(E_tet);
E_hex=ind2(E_hex);
indBoundary=ind2(indBoundary);

E={E_tet, E_hex};

Visualizing mesh

cFigure;
title('Mixed TET/HEX mesh','FontSize',fontSize);

%Selecting half of the model to see interior
X=V(:,2); XE=mean(X(E{1}),2);
L=XE>mean(X);
[F_tet_cut1,~]=element2patch(E{1}(L,:),C_tet(L));

%Selecting half of the model to see interior
X=V(:,2); XE=mean(X(E{2}),2);
L=XE>mean(X);
[F_hex_cut1,~]=element2patch(E{2}(L,:),C_hex(L));

gpatch(F_tet_cut1,V,plotColors(1,:),'k');
gpatch(F_hex_cut1,V,plotColors(2,:),'k');
gpatch(Fs,Vs,0.5*ones(1,3),'none',faceAlpha2);

axisGeom(gca,fontSize);
camlight headlight;
set(gca,'FontSize',fontSize);
drawnow;

Smoothing meshes

cPar.Method='LAP';
cPar.n=25;
cPar.RigidConstraints=indBoundary;

[F1,~]=element2patch(E{1},[]);
[F1,~,~]=uniqueIntegerRow(F1);
[F2,~]=element2patch(E{2},[]);
[F2,~,~]=uniqueIntegerRow(F2);
[~,IND_V1,~]=tesIND(F1,V,0);
[~,IND_V2,~]=tesIND(F2,V,0);
IND_V=[IND_V1 IND_V2];

[VS]=tesSmooth([],V,IND_V,cPar);

Visualizing mesh

hf=cFigure;
title('Mixed TET/HEX mesh','FontSize',fontSize);

%Selecting half of the model to see interior
X=V(:,2); XE=mean(X(E{1}),2);
L=XE>mean(X);
[F_tet_cut1,~]=element2patch(E{1}(L,:),C_tet(L));

%Selecting half of the model to see interior
X=V(:,2); XE=mean(X(E{2}),2);
L=XE>mean(X);
[F_hex_cut1,~]=element2patch(E{2}(L,:),C_hex(L));

hp1=gpatch(F_tet_cut1,VS,plotColors(1,:),'k');
hp2=gpatch(F_hex_cut1,VS,plotColors(2,:),'k');
gpatch(Fs,Vs,0.5*ones(1,3),'none',faceAlpha2);

axisGeom(gca,fontSize);
camlight headlight;
set(gca,'FontSize',fontSize);
drawnow;

Set up animation

nSteps=25; %Number of animation steps
X=V(:,2);
XE1=mean(X(E{1}),2);
XE2=mean(X(E{2}),2);

animStruct.Time=linspace(0,1,nSteps); %Time vector
cutLevel=linspace(min(X(:)),max(X(:)),nSteps); %Property to set

for q=1:1:nSteps %Step through time
    cutLevelNow=cutLevel(q); %The current cut level

    L1=XE1>cutLevelNow;
    [F_tet_cut1,~]=element2patch(E{1}(L1,:));

    L2=XE2>cutLevelNow;
    [F_hex_cut1,~]=element2patch(E{2}(L2,:));

    %Set entries in animation structure
    animStruct.Handles{q}=[hp1 hp2]; %Handles of objects to animate
    animStruct.Props{q}={'Faces','Faces'}; %Properties of objects to animate
    animStruct.Set{q}={F_tet_cut1,F_hex_cut1}; %Property values for to set in order to animate
end

%Add animation layer
anim8(hf,animStruct);

GIBBON

Kevin M. 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.

Copyright (C) 2019 Kevin Mattheus Moerman

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.

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