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
Contents
- 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]
GIBBON footer text
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) 2006-2022 Kevin Mattheus Moerman and the GIBBON contributors
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/.