DEMO_febio_0061_breast_gravity.m

Below is a demonstration for:

Building geometry for a slab with hexahedral elements, and a triangulated sphere.
Defining the boundary conditions
Coding the febio structure
Running the model
Importing and visualizing the displacement results

Keywords
Plot settings
Control parameters
Create hemi-sphere
Change shape of hemi-sphere to create basic breast model
Create inclusion
Rotate model
Visualizing mesh using meshView, see also anim8
Split element sets
Define boundary conditions
Defining the FEBio input structure
Quick viewing of the FEBio input file structure
Exporting the FEBio input file
Running the FEBio analysis
Import FEBio results

Keywords

febio_spec version 3.0
febio, FEBio
indentation
contact, sliding, sticky, friction
rigid body constraints
tetrahedral elements, tet4
triangular elements, tri3
slab, block, rectangular
sphere
static, solid
hyperelastic, Ogden
displacement logfile
stress logfile

clear; close all; clc;

Plot settings

fontSize=15;
faceAlpha1=0.8;
faceAlpha2=0.3;
markerSize=40;
lineWidth=3;

r=60; %Breast radius
r1=r/2.5;
r2=r/7;
rm=mean([r1 r2]);
w=(r1-r2)/20;
h=r2;
dx=r/4; %Gravity direction shape alteration factor
nRefine=3; %Number of refine steps for hemi-sphere
volumeFactor=3;

Control parameters

% Path names
defaultFolder = fileparts(fileparts(mfilename('fullpath')));
savePath=fullfile(defaultFolder,'data','temp');

% Defining file names
febioFebFileNamePart='tempModel';
febioFebFileName=fullfile(savePath,[febioFebFileNamePart,'.feb']); %FEB file name
febioLogFileName=fullfile(savePath,[febioFebFileNamePart,'.txt']); %FEBio log file name
febioLogFileName_disp=[febioFebFileNamePart,'_disp_out.txt']; %Log file name for exporting displacement
febioLogFileName_force=[febioFebFileNamePart,'_force_out.txt']; %Log file name for exporting force
febioLogFileName_strainEnergy=[febioFebFileNamePart,'_energy_out.txt']; %Log file name for exporting strain energy density

%Material parameter set
c1_1=0.2*1e-3; %Shear-modulus-like parameter
m1_1=2; %Material parameter setting degree of non-linearity
k_factor=1e2; %Bulk modulus factor
k_1=c1_1*k_factor; %Bulk modulus

c1_2=c1_1; %Shear-modulus-like parameter
m1_2=2; %Material parameter setting degree of non-linearity
k_factor=1e2; %Bulk modulus factor
k_2=c1_2*k_factor; %Bulk modulus

% FEA control settings
numTimeSteps=10; %Number of time steps desired
max_refs=25; %Max reforms
max_ups=0; %Set to zero to use full-Newton iterations
opt_iter=10; %Optimum number of iterations
max_retries=5; %Maximum number of retires
dtmin=(1/numTimeSteps)/100; %Minimum time step size
dtmax=1/numTimeSteps; %Maximum time step size
symmetric_stiffness=1;
min_residual=1e-20;
runMode='external';

tissueDensity=1e-9; %ton/mm^3
gravityConstant=9.81.*1e-3; %mm/s^2

Create hemi-sphere

[F,V,C_hemiSphereLabel]=hemiSphereMesh(nRefine,r,1); %Construct hemi-shere mesh
pointSpacing=mean(patchEdgeLengths(F,V)); % Get point spacing from mesh

Change shape of hemi-sphere to create basic breast model

indExclude=unique(F(C_hemiSphereLabel==2,:));
logicExclude=false(size(V,1),1);
logicExclude(indExclude)=1;

dt=sqrt(sum(V(:,[1 2]).^2,2));
logicHigh1=dt<r1 & ~logicExclude;
logicHigh2=dt<r2 & ~logicExclude;

C_skin=double(logicHigh1);
C_skin(logicHigh2)=2;

t=linspace(0,2*pi,500);
x=rm*sin(t);
y=rm*cos(t);
vc=[x(:) y(:)];

[d]=minDist(V(C_skin==1,[1 2]),vc);
dtt=d.^3;
dtt=dtt-min(dtt);
dtt=dtt./max(dtt);
dtt=abs(dtt-1)*w;
V(C_skin==1,3)=V(C_skin==1,3)+dtt;

f=V(:,3);
f=f-min(f(:));
f=f./max(f(:));
V(:,1)=V(:,1)+dx.*f;

dtt=dt(C_skin==2).^3;
dtt=dtt-min(dtt);
dtt=dtt./max(dtt);
dtt=abs(dtt-1)*h;
V(C_skin==2,3)=V(C_skin==2,3)+dtt;

Create inclusion

[Fs,Vs]=geoSphere(2,r/6);
Vs(:,3)=Vs(:,3)+r/2;
Vs(:,2)=Vs(:,2)+r/4;
Vs(:,1)=Vs(:,1)+r/2;

Rotate model

rotCase=2;
switch rotCase
    case 1 %Supine
        R=euler2DCM([0 0 pi]);
    case 2 %Standing
        R=euler2DCM([pi -0.5*pi 0]);
    case 3 %Prone
        R=euler2DCM([pi 0 pi]);
    case 4 %Side-45
        R=euler2DCM([0.25*pi 0 pi]);
end

V=V*R;
Vs=Vs*R;

Visualize breast model

cFigure; hold on;
gpatch(F,V,'w','none',0.5);
gpatch(Fs,Vs,'rw','none',1);
axisGeom; camlight headlight;
gdrawnow;

[surfaceVolume]=triSurfVolume(F,V);

tissueMass=tissueDensity.*surfaceVolume;
tissueMass_kg=tissueMass.*1000;
bodyForceMagnitude=tissueMass.*gravityConstant;

Get interior points

[V_in1]=getInnerPoint({F,Fs},{V,Vs});
[V_in2]=getInnerPoint(Fs,Vs);

C=[C_hemiSphereLabel;(max(C_hemiSphereLabel(:))+1)*ones(size(Fs,1),1)];
F=[F;Fs+size(V,1)];
V=[V;Vs];

cFigure; hold on;
gpatch(F,V,C,'none',0.5);
axisGeom;
camlight headlight;
colormap gjet; icolorbar;
gdrawnow;

V_regions=[V_in1; V_in2];

cFigure; hold on;
gpatch(F,V,C,'none',0.5);
% gpatch(Fs,Vs,'kw','none',1);
plotV(V_regions,'k.','markerSize',50);
axisGeom;
camlight headlight;
gdrawnow;

faceBoundaryMarker=C;

[regionA]=tetVolMeanEst(F,V); %Volume for regular tets
inputStruct.stringOpt='-pq1.2AaY';
inputStruct.Faces=fliplr(F);
inputStruct.Nodes=V;
inputStruct.holePoints=[];
inputStruct.faceBoundaryMarker=faceBoundaryMarker; %Face boundary markers
inputStruct.regionPoints=V_regions; %region points
inputStruct.regionA=regionA*ones(size(V_regions,1),1)*volumeFactor;
inputStruct.minRegionMarker=2; %Minimum region marker

% Mesh model using tetrahedral elements using tetGen
[meshOutput]=runTetGen(inputStruct); %Run tetGen

% Access model element and patch data
Fb=meshOutput.facesBoundary;
Cb=meshOutput.boundaryMarker;
V=meshOutput.nodes;
CE=meshOutput.elementMaterialID;
E=meshOutput.elements;

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- TETGEN Tetrahedral meshing --- 25-Feb-2022 15:42:29
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 25-Feb-2022 15:42:29
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 25-Feb-2022 15:42:29
--- Running TetGen to mesh input boundary--- 25-Feb-2022 15:42:29
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.031094
Creating surface mesh ...
Surface mesh seconds:  0.004145
Recovering boundaries...
Boundary recovery seconds:  0.00832
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.001795
Recovering Delaunayness...
Delaunay recovery seconds:  0.008417
Refining mesh...
  2731 insertions, added 2718 points, 82554 tetrahedra in queue.
Refinement seconds:  0.093463
Smoothing vertices...
Mesh smoothing seconds:  0.18905
Improving mesh...
Mesh improvement seconds:  0.006706

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

Output seconds:  0.079761
Total running seconds:  0.422998

Statistics:

  Input points: 2049
  Input facets: 4090
  Input segments: 6135
  Input holes: 0
  Input regions: 2

  Mesh points: 5450
  Mesh tetrahedra: 27625
  Mesh faces: 57135
  Mesh faces on exterior boundary: 3770
  Mesh faces on input facets: 4090
  Mesh edges on input segments: 6135
  Steiner points inside domain: 3401

--- Done --- 25-Feb-2022 15:42:30
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 25-Feb-2022 15:42:30
--- Done --- 25-Feb-2022 15:42:30

cFigure; hold on;
hp=gpatch(Fb,V,Cb,'none',0.5);
axisGeom;
camlight headlight;
icolorbar;
gdrawnow;

Visualizing mesh using `meshView`, see also `anim8`

meshView(meshOutput);

Split element sets

E1=E(meshOutput.elementMaterialID==-2,:);
E2=E(meshOutput.elementMaterialID==-3,:);

Define boundary conditions

%Supported nodes
logicRigid=Cb==2;
bcSupportList=unique(Fb(logicRigid,:));

E_rigid=Fb(Cb==2,:);

Visualize BC's

hf=cFigure;
title('Boundary conditions model','FontSize',fontSize);
xlabel('X','FontSize',fontSize); ylabel('Y','FontSize',fontSize); zlabel('Z','FontSize',fontSize);
hold on;

gpatch(Fb,V,'kw','none',faceAlpha2);

gpatch(E_rigid,V,'gw','g',1);

hl2(1)=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize);

legend(hl2,{'BC support'});

axisGeom(gca,fontSize);
camlight headlight;
gdrawnow;

Defining the FEBio input structure

See also febioStructTemplate and febioStruct2xml and the FEBio user manual.

%Get a template with default settings
[febio_spec]=febioStructTemplate;

%febio_spec version
febio_spec.ATTR.version='3.0';

%Module section
febio_spec.Module.ATTR.type='solid';

%Control section
febio_spec.Control.analysis='STATIC';
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=1/numTimeSteps;
febio_spec.Control.solver.max_refs=max_refs;
febio_spec.Control.solver.max_ups=max_ups;
febio_spec.Control.solver.symmetric_stiffness=symmetric_stiffness;
febio_spec.Control.solver.min_residual=min_residual;
febio_spec.Control.time_stepper.dtmin=dtmin;
febio_spec.Control.time_stepper.dtmax=dtmax;
febio_spec.Control.time_stepper.max_retries=max_retries;
febio_spec.Control.time_stepper.opt_iter=opt_iter;

%Material section
materialName1='Material1';
febio_spec.Material.material{1}.ATTR.name=materialName1;
febio_spec.Material.material{1}.ATTR.type='Ogden';
febio_spec.Material.material{1}.ATTR.id=1;
febio_spec.Material.material{1}.c1=c1_1;
febio_spec.Material.material{1}.m1=m1_1;
febio_spec.Material.material{1}.c2=c1_1;
febio_spec.Material.material{1}.m2=-m1_1;
febio_spec.Material.material{1}.k=k_1;

materialName2='Material2';
febio_spec.Material.material{2}.ATTR.name=materialName2;
febio_spec.Material.material{2}.ATTR.type='Ogden';
febio_spec.Material.material{2}.ATTR.id=2;
febio_spec.Material.material{2}.c1=c1_2;
febio_spec.Material.material{2}.m1=m1_2;
febio_spec.Material.material{2}.c2=c1_2;
febio_spec.Material.material{2}.m2=-m1_2;
febio_spec.Material.material{2}.k=k_2;

% Mesh section
% -> Nodes
febio_spec.Mesh.Nodes{1}.ATTR.name='All'; %The node set name
febio_spec.Mesh.Nodes{1}.node.ATTR.id=(1:size(V,1))'; %The node id's
febio_spec.Mesh.Nodes{1}.node.VAL=V; %The nodel coordinates

% -> Elements
partName1='Part1_breast_normal';
febio_spec.Mesh.Elements{1}.ATTR.name=partName1; %Name of this part
febio_spec.Mesh.Elements{1}.ATTR.type='tet4'; %Element type
febio_spec.Mesh.Elements{1}.elem.ATTR.id=(1:1:size(E1,1))'; %Element id's
febio_spec.Mesh.Elements{1}.elem.VAL=E1; %The element matrix

partName2='Part2_tumor';
febio_spec.Mesh.Elements{2}.ATTR.name=partName2; %Name of this part
febio_spec.Mesh.Elements{2}.ATTR.type='tet4'; %Element type
febio_spec.Mesh.Elements{2}.elem.ATTR.id=size(E1,1)+(1:1:size(E2,1))'; %Element id's
febio_spec.Mesh.Elements{2}.elem.VAL=E2; %The element matrix

%MeshDomains section
febio_spec.MeshDomains.SolidDomain{1}.ATTR.name=partName1;
febio_spec.MeshDomains.SolidDomain{1}.ATTR.mat=materialName1;

febio_spec.MeshDomains.SolidDomain{2}.ATTR.name=partName2;
febio_spec.MeshDomains.SolidDomain{2}.ATTR.mat=materialName2;

% -> NodeSets
nodeSetName1='bcSupportList';
febio_spec.Mesh.NodeSet{1}.ATTR.name=nodeSetName1;
febio_spec.Mesh.NodeSet{1}.node.ATTR.id=bcSupportList(:);

%Define loads
febio_spec.Loads.body_load.ATTR.type='const';
febio_spec.Loads.body_load.z.ATTR.lc=1;
febio_spec.Loads.body_load.z.VAL=bodyForceMagnitude;

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.bc{1}.ATTR.type='fix';
febio_spec.Boundary.bc{1}.ATTR.node_set=nodeSetName1;
febio_spec.Boundary.bc{1}.dofs='x,y,z';

%LoadData section
% -> load_controller
febio_spec.LoadData.load_controller{1}.ATTR.id=1;
febio_spec.LoadData.load_controller{1}.ATTR.type='loadcurve';
febio_spec.LoadData.load_controller{1}.interpolate='LINEAR';
febio_spec.LoadData.load_controller{1}.points.point.VAL=[0 0; 1 1];

%Output section
% -> log file
febio_spec.Output.logfile.ATTR.file=febioLogFileName;
febio_spec.Output.logfile.node_data{1}.ATTR.file=febioLogFileName_disp;
febio_spec.Output.logfile.node_data{1}.ATTR.data='ux;uy;uz';
febio_spec.Output.logfile.node_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.node_data{1}.VAL=1:size(V,1);

febio_spec.Output.logfile.element_data{1}.ATTR.file=febioLogFileName_strainEnergy;
febio_spec.Output.logfile.element_data{1}.ATTR.data='sed';
febio_spec.Output.logfile.element_data{1}.ATTR.delim=',';
febio_spec.Output.logfile.element_data{1}.VAL=1:(size(E1,1)+size(E2,1));

Quick viewing of the FEBio input file structure

The febView function can be used to view the xml structure in a MATLAB figure window.

febView(febio_spec); %Viewing the febio file

Exporting the FEBio input file

Exporting the febio_spec structure to an FEBio input file is done using the febioStruct2xml function.

febioStruct2xml(febio_spec,febioFebFileName); %Exporting to file and domNode

Running the FEBio analysis

To run the analysis defined by the created FEBio input file the runMonitorFEBio function is used. The input for this function is a structure defining job settings e.g. the FEBio input file name. The optional output runFlag informs the user if the analysis was run succesfully.

febioAnalysis.run_filename=febioFebFileName; %The input file name
febioAnalysis.run_logname=febioLogFileName; %The name for the log file
febioAnalysis.disp_on=1; %Display information on the command window
febioAnalysis.disp_log_on=1; %Display convergence information in the command window
febioAnalysis.runMode=runMode;
febioAnalysis.t_check=0.25; %Time for checking log file (dont set too small)
febioAnalysis.maxtpi=1e99; %Max analysis time
febioAnalysis.maxLogCheckTime=10; %Max log file checking time

[runFlag]=runMonitorFEBio(febioAnalysis);%START FEBio NOW!!!!!!!!

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-------->    RUNNING/MONITORING FEBIO JOB    <-------- 25-Feb-2022 15:42:37
FEBio path: /home/kevin/FEBioStudio/bin/febio3
# Attempt removal of existing log files                25-Feb-2022 15:42:37
 * Removal succesful                                   25-Feb-2022 15:42:37
# Attempt removal of existing .xplt files              25-Feb-2022 15:42:37
 * Removal succesful                                   25-Feb-2022 15:42:37
# Starting FEBio...                                    25-Feb-2022 15:42:37
  Max. total analysis time is: 1e+99 s
 * Waiting for log file creation                       25-Feb-2022 15:42:37
   Max. wait time: 10 s
 * Log file found.                                     25-Feb-2022 15:42:37
# Parsing log file...                                  25-Feb-2022 15:42:37
    number of iterations   : 3                         25-Feb-2022 15:42:39
    number of reformations : 3                         25-Feb-2022 15:42:39
------- converged at time : 0.1                        25-Feb-2022 15:42:39
    number of iterations   : 3                         25-Feb-2022 15:42:40
    number of reformations : 3                         25-Feb-2022 15:42:40
------- converged at time : 0.2                        25-Feb-2022 15:42:40
    number of iterations   : 3                         25-Feb-2022 15:42:42
    number of reformations : 3                         25-Feb-2022 15:42:42
------- converged at time : 0.                         25-Feb-2022 15:42:42
    number of iterations   : 3                         25-Feb-2022 15:42:43
    number of reformations : 3                         25-Feb-2022 15:42:43
------- converged at time : 0.4                        25-Feb-2022 15:42:43
    number of iterations   : 3                         25-Feb-2022 15:42:45
    number of reformations : 3                         25-Feb-2022 15:42:45
------- converged at time : 0.5                        25-Feb-2022 15:42:45
    number of iterations   : 3                         25-Feb-2022 15:42:46
    number of reformations : 3                         25-Feb-2022 15:42:46
------- converged at time : 0.6                        25-Feb-2022 15:42:46
    number of iterations   : 3                         25-Feb-2022 15:42:47
    number of reformations : 3                         25-Feb-2022 15:42:47
------- converged at time : 0.7                        25-Feb-2022 15:42:47
    number of iterations   : 3                         25-Feb-2022 15:42:48
    number of reformations : 3                         25-Feb-2022 15:42:48
------- converged at time : 0.8                        25-Feb-2022 15:42:48
    number of iterations   : 4                         25-Feb-2022 15:42:50
    number of reformations : 4                         25-Feb-2022 15:42:50
------- converged at time : 0.9                        25-Feb-2022 15:42:50
    number of iterations   : 4                         25-Feb-2022 15:42:52
    number of reformations : 4                         25-Feb-2022 15:42:52
------- converged at time : 1                          25-Feb-2022 15:42:52
 Elapsed time : 0:00:15                                25-Feb-2022 15:42:52
 N O R M A L   T E R M I N A T I O N
# Done                                                 25-Feb-2022 15:42:52
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Import FEBio results

if runFlag==1 %i.e. a succesful run

    % Importing nodal displacements from a log file
    [time_mat, N_disp_mat,~]=importFEBio_logfile(fullfile(savePath,febioLogFileName_disp)); %Nodal displacements
    time_mat=[0; time_mat(:)]; %Time

    N_disp_mat=N_disp_mat(:,2:end,:);
    sizImport=size(N_disp_mat);
    sizImport(3)=sizImport(3)+1;
    N_disp_mat_n=zeros(sizImport);
    N_disp_mat_n(:,:,2:end)=N_disp_mat;
    N_disp_mat=N_disp_mat_n;
    DN_magnitude_all=sqrt(sum(N_disp_mat.^2,2));
    DN_magnitude=DN_magnitude_all(:,end);
    V_def=V+N_disp_mat(:,:,end);
    V_DEF=N_disp_mat+repmat(V,[1 1 size(N_disp_mat,3)]);
    X_DEF=V_DEF(:,1,:);
    Y_DEF=V_DEF(:,2,:);
    Z_DEF=V_DEF(:,3,:);

Plotting the simulated results using anim8 to visualize and animate deformations

    % Create basic view and store graphics handle to initiate animation
    hf=cFigure; %Open figure
    gtitle([febioFebFileNamePart,': Press play to animate']);
    hp1=gpatch(Fb,V_def,DN_magnitude,'none',0.5); %Add graphics object to animate
    hp1.FaceColor='Interp';
    hp2=gpatch(Fb(Cb==3,:),V_def,'kw','none',1); %Add graphics object to animate

    axisGeom(gca,fontSize);
    colormap(gjet(250)); colorbar;
    caxis([0 max(DN_magnitude_all(:))]);
    axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]);
    camlight headlight;

    % Set up animation features
    animStruct.Time=time_mat; %The time vector
    for qt=1:1:size(N_disp_mat,3) %Loop over time increments
        DN_magnitude=DN_magnitude_all(:,qt); %Current displacement magnitude
        V_def=V+N_disp_mat(:,:,qt); %Current nodal coordinates

        %Set entries in animation structure
        animStruct.Handles{qt}=[hp1 hp1 hp2]; %Handles of objects to animate
        animStruct.Props{qt}={'Vertices','CData','Vertices'}; %Properties of objects to animate
        animStruct.Set{qt}={V_def,DN_magnitude,V_def}; %Property values for to set in order to animate
    end
    anim8(hf,animStruct); %Initiate animation feature
    gdrawnow;

   [M,G,bwLabels]=patch2Im(Fb,V_def,Cb,1);
   M(M==1)=0.25;
   M(M==3)=1;
   M(M==0)=0.1;
   M=M+0.25*rand(size(M));
   voxelSize=G.voxelSize;
   imOrigin=G.origin;
   Vp=mean(V_def(Fb(Cb==3,:),:),1)-imOrigin;
   [i,j,k]=cart2im(Vp(:,1),Vp(:,2),Vp(:,3),voxelSize*ones(1,3));
   L_plot=false(size(M));
   L_plot(round(i),:,:)=1;
   L_plot(:,round(j),:)=1;
   L_plot(:,:,round(k))=1;
   L_plot=L_plot & ~isnan(M);
   [Fm,Vm,Cm]=ind2patch(L_plot,double(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),:);

   hf=cFigure;

   hp1=gpatch(Fb,V_def,'bw','none',0.35);
   hp2=gpatch(Fm,Vm,Cm,'none',1);

   colormap(gca,gray(250)); colorbar; caxis([0 1]);
   axisGeom(gca,fontSize);
   axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]);
   camlight('headlight');
   gdrawnow;

   % Set up animation features
   animStruct.Time=time_mat; %The time vector
   for qt=1:1:size(N_disp_mat,3) %Loop over time increments

       V_def=V+N_disp_mat(:,:,qt); %Current nodal coordinates

       [M,G,bwLabels]=patch2Im(Fb,V_def,Cb,1);
       M(M==1)=0.25;
       M(M==3)=1;
       M(M==0)=0.1;
%         M(isnan(M))=0;
       M=M+0.1*rand(size(M));

       voxelSize=G.voxelSize;
       imOrigin=G.origin;
       Vp=mean(V_def(Fb(Cb==3,:),:),1)-imOrigin;
       [i,j,k]=cart2im(Vp(:,1),Vp(:,2),Vp(:,3),voxelSize*ones(1,3));
       L_plot=false(size(M));
       L_plot(round(i),:,:)=1;
       L_plot(:,round(j),:)=1;
       L_plot(:,:,round(k))=1;
       L_plot=L_plot & ~isnan(M);
       [Fm,Vm,Cm]=ind2patch(L_plot,double(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),:);

       %Set entries in animation structure
       animStruct.Handles{qt}=[hp1 hp2 hp2 hp2]; %Handles of objects to animate
       animStruct.Props{qt}={'Vertices','Faces','Vertices','CData'}; %Properties of objects to animate
       animStruct.Set{qt}={V_def,Fm,Vm,Cm}; %Property values for to set in order to animate
   end
   anim8(hf,animStruct); %Initiate animation feature
   gdrawnow;

end

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/.