DEMO_febio_0052_breast_gap_close_01.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 breat model
Rotate model
Visualizing mesh using meshView, see also anim8
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 2.5
febio, FEBio
Surgery
Breast, soft tissue
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;
skinColor=[1 0.95 0.8];

r=40;
r1=r/2.5;
r2=r/7;
rm=mean([r1 r2]);
w=(r1-r2)/20;
h=r2;
dx=r/2;
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

%Material parameter set
c1_1=1e-3; %Shear-modulus-like parameter
m1_1=6; %Material parameter setting degree of non-linearity
k_factor=1e2; %Bulk modulus factor
k_1=c1_1*k_factor; %Bulk modulus

c1_2=5e-3; %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;

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 breat 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;

Rotate model

R=euler2DCM([pi -0.5*pi 0]);
V=V*R;

Visualize breast model

[C_skin_F]=vertexToFaceMeasure(F,C_skin);
C_skin_F=round(C_skin_F);
C_skin_F(C_hemiSphereLabel==2)=max(C_skin(:))+1;
C_skin_F_RGB=cmaperise(C_skin_F,bloodbone(250),[0 5]);

cFigure; hold on;
gpatch(F,V,C_skin_F_RGB,'none',1);

axisGeom; view([-140,16]);
camlight headlight;
drawnow;

cFigure; hold on;
gpatch(F,V,C_skin,'none',0.5);
% gpatch(Fs,Vs,'kw','none',1);
axisGeom; view([-140,16]);
camlight headlight;
drawnow;

% rCut=[10 20 23];
% nRefineCut=nRefine;
% [Fs,Vs]=geoSphere(nRefineCut,1);
% Fs=fliplr(Fs);
% R_cut=euler2DCM([0.5*pi -0.15*pi -0.25*pi]);
% Vs=Vs.*rCut(ones(size(Vs,1),1),:);
% Vs=Vs*R_cut;
% T_cut=[-25 25 -25];
% Vs=Vs+T_cut(ones(size(Vs,1),1),:);

rCut=[10 20 20];
nRefineCut=nRefine;
[Fs,Vs]=geoSphere(nRefineCut,1);
Fs=fliplr(Fs);
R_cut1=euler2DCM([0 0 0.*pi]);
R_cut2=euler2DCM([-0.5*pi -0.1*pi -0.2*pi]);
R_cut=R_cut1*R_cut2;
Vs=Vs.*rCut(ones(size(Vs,1),1),:);
Vs=Vs*R_cut;
T_cut=[-25 25 -25];
Vs=Vs+T_cut(ones(size(Vs,1),1),:);

cFigure; hold on;
gpatch(F,V,skinColor,'none',0.5);
gpatch(Fs,Vs,'gw','none',1);

axisGeom; view([-140,16]);
camlight headlight;
drawnow;

[regionLabel]=simplexImIntersect(Fs,Vs,[],V,pointSpacing/2);
logicCutVertices=~isnan(regionLabel);
logicCutFaces=any(logicCutVertices(F),2);
logicCutFaces=triSurfLogicSharpFix(F,logicCutFaces,3);
Eb=patchBoundary(F(logicCutFaces,:),V);
logicCutFaces=~logicCutFaces & ~any(ismember(F,Eb),2);
logicCutFaces=triSurfLogicSharpFix(F,logicCutFaces,3);

[regionLabel]=simplexImIntersect(F,V,[],Vs,pointSpacing/2);
logicCutVertices=(regionLabel==1);
logicCutFaces_s=any(logicCutVertices(Fs),2);
logicCutFaces_s=triSurfLogicSharpFix(Fs,logicCutFaces_s,3);

% Eb=patchBoundary(Fs(logicCutFaces_s,:),Vs);
% logicCutFaces_s=logicCutFaces_s & ~any(ismember(Fs,Eb),2);
% logicCutFaces_s=triSurfLogicSharpFix(Fs,logicCutFaces_s,3);

Fs=Fs(logicCutFaces_s,:);
[Fs,Vs]=patchCleanUnused(Fs,Vs);
Eb=patchBoundary(Fs,Vs); %Get boundary edges
indBoundary=edgeListToCurve(Eb); %Convert boundary edges to a curve list
indBoundary=indBoundary(1:end-1); %Trim off last point since it is equal to first on a closed loop
angleThreshold=pi*(120/180); %threshold for self triangulation
[Fs,Vs,indBoundaryTop]=triSurfSelfTriangulateBoundary(Fs,Vs,indBoundary,angleThreshold,1);

F=F(logicCutFaces,:);
C_skin_F=C_skin_F(logicCutFaces,:);
[F,V]=patchCleanUnused(F,V);
Eb=patchBoundary(F,V);
ind1=edgeListToCurve(Eb);
ind1=ind1(1:end-1);

Eb=patchBoundary(Fs,Vs);
ind2=edgeListToCurve(Eb);
ind2=ind2(1:end-1);

% Fs=Fs(~logicCutFaces_s,:);

[Fn,Vn]=regionTriMesh3D({V(ind1,:),Vs(ind2,:)},pointSpacing,0,'linear');
Fn=fliplr(Fn);

cFigure; hold on;
gpatch(F,V,C_skin_F,'none',0.5);
gpatch(Fs,Vs,'rw','k',1);
gpatch(Fn,Vn,'bw','k',1);
axisGeom; view([-140,16]);
camlight headlight;
colormap gjet; icolorbar;
drawnow;

[FT,VT,CT]=joinElementSets({F,Fs,Fn},{V,Vs,Vn},{C_skin_F,(max(C_skin_F)+1)*ones(size(Fs,1),1),(max(C_skin_F)+2)*ones(size(Fn,1),1)});
[FT,VT]=mergeVertices(FT,VT);

indRim=unique(FT(CT==5,:));
logicFacesSmooth=any(ismember(FT,indRim),2);
indSmooth=FT(logicFacesSmooth,:);
indRigid=FT(~ismember(FT,indSmooth));

clear cParSmooth;
cParSmooth.n=25;
cParSmooth.Method='HC';
cParSmooth.RigidConstraints=indRigid;
[VT]=patchSmooth(FT,VT,[],cParSmooth);

cFigure; hold on;
gpatch(FT,VT,CT,'k',1);
axisGeom; view([-140,16]);
camlight headlight;
colormap gjet; icolorbar;
drawnow;

V_regions=getInnerPoint(FT,VT);

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

% 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 --- 13-Mar-2020 12:37:49
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Writing SMESH file --- 13-Mar-2020 12:37:49
----> Adding node field
----> Adding facet field
----> Adding holes specification
----> Adding region specification
--- Done --- 13-Mar-2020 12:37:49
--- Running TetGen to mesh input boundary--- 13-Mar-2020 12:37:49
Opening /mnt/data/MATLAB/GIBBON/data/temp/temp.smesh.
Delaunizing vertices...
Delaunay seconds:  0.016227
Creating surface mesh ...
Surface mesh seconds:  0.004969
Recovering boundaries...
Boundary recovery seconds:  0.00622
Removing exterior tetrahedra ...
Spreading region attributes.
Exterior tets removal seconds:  0.001858
Recovering Delaunayness...
Delaunay recovery seconds:  0.002516
Refining mesh...
Refinement seconds:  0.067685
Optimizing mesh...
Optimization seconds:  0.00487

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:  0.066552
Total running seconds:  0.171112

Statistics:

  Input points: 2091
  Input facets: 4178
  Input segments: 6267
  Input holes: 0
  Input regions: 1

  Mesh points: 5049
  Mesh tetrahedra: 25202
  Mesh faces: 52493
  Mesh faces on exterior boundary: 4178
  Mesh faces on input facets: 4178
  Mesh edges on input segments: 6267
  Steiner points inside domain: 2958

--- Done --- 13-Mar-2020 12:37:49
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- Importing TetGen files --- 13-Mar-2020 12:37:49
--- Done --- 13-Mar-2020 12:37:49

cFigure; hold on;
hp=gpatch(Fb,V,Cb,'none',0.5);
axisGeom; view([-140,16]);
camlight headlight;
icolorbar;
drawnow;

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

% meshView(meshOutput);

Eb=patchBoundary(Fb(Cb==4,:),V);
indRim=edgeListToCurve(Eb);
indRim=indRim(1:end-1);

nContract=18;
V_rim_resample=evenlySampleCurve(V(indRim,:),nContract,'linear',1);
[~,indMin]=minDist(V_rim_resample,V(indRim,:));
indPresribeStitch=indRim(indMin)';
V_stitch=V(indPresribeStitch,:);

cFigure; hold on;
gpatch(Fb,V,Cb,'k',1);
plotV(V(indRim,:),'b-','LineWidth',3);
plotV(V_stitch,'y.','MarkerSize',25);
axisGeom; view([-140,16]);
camlight headlight;
colormap gjet; icolorbar;
drawnow;

V_stitch_temp=V_stitch-T_cut(ones(size(V_stitch,1),1),:);
V_stitch_temp=V_stitch_temp*R_cut';
[~,indStart]=min((V_stitch_temp(:,2)));
if indStart>1
    V_stitch=[V_stitch(indStart:end,:); V_stitch(1:indStart-1,:)];
    indPresribeStitch=[indPresribeStitch(indStart:end); indPresribeStitch(1:indStart-1)];
end

indStitchOrigin=(1:round(nContract/2))';
indStitchEnd=nContract-(indStitchOrigin-1);
indStitchPair=[indStitchOrigin indStitchEnd];

V_stitchGoal=patchCentre(indStitchPair,V_stitch);

u1=V_stitchGoal-V_stitch(indStitchOrigin,:);
u2=V_stitchGoal-V_stitch(indStitchEnd,:);

cFigure; hold on;
gpatch(Fb,V,skinColor,'none',1);
% plotV(V(indRim,:),'b-','LineWidth',3);
% plotV(V_stitch,'y.-','MarkerSize',25,'LineWidth',3);
plotV(V_stitchGoal,'r+','MarkerSize',25);
gpatch(indStitchPair,V_stitch,'none','k',1,3);
axisGeom; view([-140,16]);
camlight headlight;
drawnow;

Define boundary conditions

%Supported nodes
logicRigid=Cb==3;
Fr=Fb(logicRigid,:);
bcSupportList=unique(Fr(:));

bcPrescribeList1=indPresribeStitch(indStitchOrigin);
bcPrescribeList2=indPresribeStitch(indStitchEnd);

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);

hl2(1)=plotV(V(bcSupportList,:),'k.','MarkerSize',markerSize);
hl2(2)=plotV(V(bcPrescribeList1,:),'r.','MarkerSize',markerSize);
hl2(3)=plotV(V(bcPrescribeList2,:),'g.','MarkerSize',markerSize);

legend(hl2,{'BC support','BC Prescribe 1','BC Prescribe 2'});

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

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='2.5';

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

%Control section
febio_spec.Control.analysis.ATTR.type='static';
febio_spec.Control.time_steps=numTimeSteps;
febio_spec.Control.step_size=1/numTimeSteps;
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;
febio_spec.Control.max_refs=max_refs;
febio_spec.Control.max_ups=max_ups;
febio_spec.Control.symmetric_stiffness=symmetric_stiffness;
febio_spec.Control.min_residual=min_residual;

%Material section
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;

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

% -> Elements
febio_spec.Geometry.Elements{1}.ATTR.type='tet4'; %Element type of this set
febio_spec.Geometry.Elements{1}.ATTR.mat=1; %material index for this set
febio_spec.Geometry.Elements{1}.ATTR.name='breastNormal'; %Name of the element set
febio_spec.Geometry.Elements{1}.elem.ATTR.id=(1:1:size(E,1))'; %Element id's
febio_spec.Geometry.Elements{1}.elem.VAL=E;

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

febio_spec.Geometry.NodeSet{2}.ATTR.name='bcPrescribeList1';
febio_spec.Geometry.NodeSet{2}.node.ATTR.id=bcPrescribeList1(:);

febio_spec.Geometry.NodeSet{3}.ATTR.name='bcPrescribeList2';
febio_spec.Geometry.NodeSet{3}.node.ATTR.id=bcPrescribeList2(:);

%Boundary condition section
% -> Fix boundary conditions
febio_spec.Boundary.fix{1}.ATTR.bc='x';
febio_spec.Boundary.fix{1}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Boundary.fix{2}.ATTR.bc='y';
febio_spec.Boundary.fix{2}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;
febio_spec.Boundary.fix{3}.ATTR.bc='z';
febio_spec.Boundary.fix{3}.ATTR.node_set=febio_spec.Geometry.NodeSet{1}.ATTR.name;

% -> Prescribed boundary conditions
%Define mesh data and prescribed displacements
bcNames={'x','y','z'};
nodeSetNames={febio_spec.Geometry.NodeSet{2}.ATTR.name,febio_spec.Geometry.NodeSet{3}.ATTR.name};
febio_spec.MeshData.NodeData=[];%Initialize so we can use end+1 indexing
cc=0;
for q=1:1:numel(nodeSetNames)
    switch q
        case 1
            bcPrescribeMagnitudesStep=u1;
            bcPrescribeList=bcPrescribeList1;
        case 2
            bcPrescribeMagnitudesStep=u2;
            bcPrescribeList=bcPrescribeList2;
    end
    nodeSetName=nodeSetNames{q};

    for q_dir=1:1:3 %Loop over coordinates dimensions

        %Define mesh data for displacement increments
        c=numel(febio_spec.MeshData.NodeData)+1; %Current step index
        febio_spec.MeshData.NodeData{c}.ATTR.name=['displacement_',bcNames{q_dir},'_step_',num2str(q)];
        febio_spec.MeshData.NodeData{c}.ATTR.node_set=nodeSetName;
        febio_spec.MeshData.NodeData{c}.node.ATTR.lid=(1:1:numel(bcPrescribeList))';
        febio_spec.MeshData.NodeData{c}.node.VAL=bcPrescribeMagnitudesStep(:,q_dir);

        %Define prescribed displacements
        febio_spec.Boundary.prescribe{cc+q_dir}.ATTR.bc=bcNames{q_dir};
        febio_spec.Boundary.prescribe{cc+q_dir}.ATTR.relative=1;
        febio_spec.Boundary.prescribe{cc+q_dir}.ATTR.node_set=nodeSetName;
        febio_spec.Boundary.prescribe{cc+q_dir}.scale.ATTR.lc=1;
        febio_spec.Boundary.prescribe{cc+q_dir}.scale.VAL=1;
        febio_spec.Boundary.prescribe{cc+q_dir}.relative=1;
        febio_spec.Boundary.prescribe{cc+q_dir}.value.ATTR.node_data=febio_spec.MeshData.NodeData{c}.ATTR.name;
    end
    cc=numel(febio_spec.Boundary.prescribe);
end

%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.node_data{2}.ATTR.file=febioLogFileName_force;
febio_spec.Output.logfile.node_data{2}.ATTR.data='Rx;Ry;Rz';
febio_spec.Output.logfile.node_data{2}.ATTR.delim=',';
febio_spec.Output.logfile.node_data{2}.VAL=1:size(V,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='internal';%'internal';
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!!!!!!!!

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--- STARTING FEBIO JOB --- 13-Mar-2020 12:37:54
===========================================================================
         ________    _________   _________     __     _________            
        |        |\ |        |\ |        |\   |  |\  /         \\          
        |    ____|| |    ____|| |    __  ||   |__|| |    ___    ||         
        |   |\___\| |   |\___\| |   |\_| ||    \_\| |   //  \   ||         
        |   ||      |   ||      |   || | ||    __   |  ||    |  ||         
        |   ||__    |   ||__    |   ||_| ||   |  |\ |  ||    |  ||         
        |       |\  |       |\  |         \\  |  || |  ||    |  ||         
        |    ___||  |    ___||  |    ___   || |  || |  ||    |  ||         
        |   |\__\|  |   |\__\|  |   |\__|  || |  || |  ||    |  ||         
        |   ||      |   ||      |   ||  |  || |  || |  ||    |  ||         
        |   ||      |   ||___   |   ||__|  || |  || |   \\__/   ||         
        |   ||      |        |\ |          || |  || |           ||         
        |___||      |________|| |__________|| |__||  \_________//          
                                                                           
      F I N I T E   E L E M E N T S   F O R   B I O M E C H A N I C S      
                                                                           
                 --- v e r s i o n - 2 . 9 . 1 ---                 
                                                                           
                                                                           
  http://febio.org                                                         
  FEBio is a registered trademark.                                         
  copyright (c) 2006-2019 - All rights reserved                            
                                                                           
===========================================================================


Reading file /mnt/data/MATLAB/GIBBON/data/temp/tempModel.feb ...SUCCESS!
 ]0;(0%) tempModel.feb - FEBio 2.9.1.0  
===== beginning time step 1 : 0.1 =====
Reforming stiffness matrix: reformation #1

===== reforming stiffness matrix:
	Nr of equations ........................... : 13215
	Nr of nonzeroes in stiffness matrix ....... : 279510

 1
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.928680e-01    8.672460e-04    0.000000e+00 
	   energy              1.359467e+00    3.738028e-03    1.359467e-02 
	   displacement        1.090775e+02    1.090775e+02    1.090775e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.928680e-01    4.402008e-08    0.000000e+00 
	   energy              1.359467e+00    4.928199e-06    1.359467e-02 
	   displacement        1.090775e+02    1.002608e-01    1.111701e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.928680e-01    1.911750e-13    0.000000e+00 
	   energy              1.359467e+00    2.174501e-11    1.359467e-02 
	   displacement        1.090775e+02    1.580928e-04    1.111788e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.1
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.928680e-01    6.909171e-26    0.000000e+00 
	   energy              1.359467e+00    6.756908e-20    1.359467e-02 
	   displacement        1.090775e+02    5.131556e-11    1.111788e-04 

------- converged at time : 0.1

 ]0;(10%) tempModel.feb - FEBio 2.9.1.0  
===== beginning time step 2 : 0.2 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.910760e-01    8.301203e-04    0.000000e+00 
	   energy              1.343481e+00    1.142225e-03    1.343481e-02 
	   displacement        1.141560e+02    1.141560e+02    1.141560e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.910760e-01    7.192927e-08    0.000000e+00 
	   energy              1.343481e+00    1.990115e-07    1.343481e-02 
	   displacement        1.141560e+02    2.079463e-01    1.175995e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.910760e-01    4.622291e-13    0.000000e+00 
	   energy              1.343481e+00    3.696269e-10    1.343481e-02 
	   displacement        1.141560e+02    3.492711e-04    1.176572e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.2
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.910760e-01    2.954653e-24    0.000000e+00 
	   energy              1.343481e+00    3.709407e-18    1.343481e-02 
	   displacement        1.141560e+02    4.142761e-10    1.176573e-04 

------- converged at time : 0.2

 ]0;(20%) tempModel.feb - FEBio 2.9.1.0  
===== beginning time step 3 : 0.3 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.3
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.968533e-01    8.541018e-04    0.000000e+00 
	   energy              1.333299e+00    2.007871e-03    1.333299e-02 
	   displacement        1.212335e+02    1.212335e+02    1.212335e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.3
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.968533e-01    7.203372e-08    0.000000e+00 
	   energy              1.333299e+00    3.311818e-06    1.333299e-02 
	   displacement        1.212335e+02    1.486994e-01    1.241897e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.3
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.968533e-01    1.135125e-13    0.000000e+00 
	   energy              1.333299e+00    6.001232e-11    1.333299e-02 
	   displacement        1.212335e+02    2.145444e-04    1.242340e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.3
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            2.968533e-01    9.882961e-26    0.000000e+00 
	   energy              1.333299e+00    1.855383e-19    1.333299e-02 
	   displacement        1.212335e+02    6.948955e-11    1.242340e-04 

------- converged at time : 0.3

 ]0;(30%) tempModel.feb - FEBio 2.9.1.0  
===== beginning time step 4 : 0.4 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.4
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.101338e-01    9.674151e-04    0.000000e+00 
	   energy              1.328828e+00    5.040657e-03    1.328828e-02 
	   displacement        1.270455e+02    1.270455e+02    1.270455e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.4
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.101338e-01    2.151820e-07    0.000000e+00 
	   energy              1.328828e+00    8.974935e-07    1.328828e-02 
	   displacement        1.270455e+02    1.547186e-01    1.291886e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.4
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.101338e-01    3.273958e-13    0.000000e+00 
	   energy              1.328828e+00    4.863657e-10    1.328828e-02 
	   displacement        1.270455e+02    2.300121e-04    1.292531e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.4
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.101338e-01    9.129925e-25    0.000000e+00 
	   energy              1.328828e+00    1.364861e-18    1.328828e-02 
	   displacement        1.270455e+02    1.338680e-10    1.292531e-04 

------- converged at time : 0.4

 ]0;(40%) tempModel.feb - FEBio 2.9.1.0  
===== beginning time step 5 : 0.5 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.5
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.323036e-01    1.307451e-03    0.000000e+00 
	   energy              1.329367e+00    8.589758e-03    1.329367e-02 
	   displacement        1.314389e+02    1.314389e+02    1.314389e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.5
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.323036e-01    7.330027e-07    0.000000e+00 
	   energy              1.329367e+00    1.334072e-05    1.329367e-02 
	   displacement        1.314389e+02    2.958931e-01    1.334114e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.5
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.323036e-01    1.326607e-11    0.000000e+00 
	   energy              1.329367e+00    6.190166e-09    1.329367e-02 
	   displacement        1.314389e+02    1.123378e-03    1.335649e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.5
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.323036e-01    1.329518e-20    0.000000e+00 
	   energy              1.329367e+00    1.011324e-15    1.329367e-02 
	   displacement        1.314389e+02    7.552354e-09    1.335648e-04 

------- converged at time : 0.5

 ]0;(50%) tempModel.feb - FEBio 2.9.1.0  
===== beginning time step 6 : 0.6 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.6
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.634011e-01    2.080044e-03    0.000000e+00 
	   energy              1.331153e+00    1.444125e-02    1.331153e-02 
	   displacement        1.361844e+02    1.361844e+02    1.361844e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.6
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.634011e-01    4.229441e-07    0.000000e+00 
	   energy              1.331153e+00    1.147076e-05    1.331153e-02 
	   displacement        1.361844e+02    4.035992e-01    1.389889e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.6
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.634011e-01    5.251526e-10    0.000000e+00 
	   energy              1.331153e+00    1.812969e-08    1.331153e-02 
	   displacement        1.361844e+02    2.465817e-03    1.392521e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.6
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            3.634011e-01    2.381372e-19    0.000000e+00 
	   energy              1.331153e+00    3.014775e-14    1.331153e-02 
	   displacement        1.361844e+02    2.697202e-08    1.392520e-04 

------- converged at time : 0.6

 ]0;(60%) tempModel.feb - FEBio 2.9.1.0  
===== beginning time step 7 : 0.7 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.7
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.009898e-01    3.054057e-03    0.000000e+00 
	   energy              1.326274e+00    2.008057e-02    1.326274e-02 
	   displacement        1.430077e+02    1.430077e+02    1.430077e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.7
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.009898e-01    9.187322e-07    0.000000e+00 
	   energy              1.326274e+00    4.986567e-05    1.326274e-02 
	   displacement        1.430077e+02    4.005897e-01    1.471064e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.7
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.009898e-01    3.937853e-10    0.000000e+00 
	   energy              1.326274e+00    2.295298e-08    1.326274e-02 
	   displacement        1.430077e+02    1.219457e-03    1.472262e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.7
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.009898e-01    7.071632e-19    0.000000e+00 
	   energy              1.326274e+00    4.299665e-14    1.326274e-02 
	   displacement        1.430077e+02    4.113513e-08    1.472255e-04 

------- converged at time : 0.7

 ]0;(70%) tempModel.feb - FEBio 2.9.1.0  
===== beginning time step 8 : 0.8 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.8
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.454941e-01    3.603611e-03    0.000000e+00 
	   energy              1.313593e+00    2.100314e-02    1.313593e-02 
	   displacement        1.519769e+02    1.519769e+02    1.519769e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.8
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.454941e-01    3.519672e-06    0.000000e+00 
	   energy              1.313593e+00    7.542689e-05    1.313593e-02 
	   displacement        1.519769e+02    2.909318e-01    1.568800e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.8
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.454941e-01    2.654208e-11    0.000000e+00 
	   energy              1.313593e+00    8.409875e-09    1.313593e-02 
	   displacement        1.519769e+02    1.484091e-03    1.567447e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.8
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.454941e-01    3.831961e-21    0.000000e+00 
	   energy              1.313593e+00    3.528000e-16    1.313593e-02 
	   displacement        1.519769e+02    3.381865e-09    1.567450e-04 

------- converged at time : 0.8

 ]0;(80%) tempModel.feb - FEBio 2.9.1.0  
===== beginning time step 9 : 0.9 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 0.9
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.959079e-01    3.259118e-03    0.000000e+00 
	   energy              1.296495e+00    1.837207e-02    1.296495e-02 
	   displacement        1.616369e+02    1.616369e+02    1.616369e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 0.9
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.959079e-01    3.441999e-06    0.000000e+00 
	   energy              1.296495e+00    5.539485e-05    1.296495e-02 
	   displacement        1.616369e+02    1.974437e-01    1.664536e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 0.9
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.959079e-01    2.066884e-11    0.000000e+00 
	   energy              1.296495e+00    3.095502e-09    1.296495e-02 
	   displacement        1.616369e+02    1.339703e-03    1.662608e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 0.9
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            4.959079e-01    1.789842e-20    0.000000e+00 
	   energy              1.296495e+00    6.306556e-16    1.296495e-02 
	   displacement        1.616369e+02    1.434586e-08    1.662615e-04 

------- converged at time : 0.9

 ]0;(90%) tempModel.feb - FEBio 2.9.1.0  
===== beginning time step 10 : 1 =====
Reforming stiffness matrix: reformation #1

 1
 Nonlinear solution status: time= 1
	stiffness updates             = 0
	right hand side evaluations   = 2
	stiffness matrix reformations = 1
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.431244e-01    2.676530e-03    0.000000e+00 
	   energy              1.275596e+00    1.540717e-02    1.275596e-02 
	   displacement        1.709856e+02    1.709856e+02    1.709856e-04 
Reforming stiffness matrix: reformation #2

 2
 Nonlinear solution status: time= 1
	stiffness updates             = 0
	right hand side evaluations   = 3
	stiffness matrix reformations = 2
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.431244e-01    1.762891e-06    0.000000e+00 
	   energy              1.275596e+00    4.057138e-05    1.275596e-02 
	   displacement        1.709856e+02    1.546607e-01    1.757462e-04 
Reforming stiffness matrix: reformation #3

 3
 Nonlinear solution status: time= 1
	stiffness updates             = 0
	right hand side evaluations   = 4
	stiffness matrix reformations = 3
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.431244e-01    3.387260e-12    0.000000e+00 
	   energy              1.275596e+00    1.167939e-09    1.275596e-02 
	   displacement        1.709856e+02    4.730198e-04    1.756567e-04 
Reforming stiffness matrix: reformation #4

 4
 Nonlinear solution status: time= 1
	stiffness updates             = 0
	right hand side evaluations   = 5
	stiffness matrix reformations = 4
	step from line search         = 1.000000
	convergence norms :     INITIAL         CURRENT         REQUIRED
	   residual            5.431244e-01    1.308478e-22    0.000000e+00 
	   energy              1.275596e+00    1.159304e-18    1.275596e-02 
	   displacement        1.709856e+02    1.809344e-09    1.756569e-04 

------- converged at time : 1

 ]0;(100%) tempModel.feb - FEBio 2.9.1.0  

N O N L I N E A R   I T E R A T I O N   I N F O R M A T I O N

	Number of time steps completed .................... : 10

	Total number of equilibrium iterations ............ : 40

	Average number of equilibrium iterations .......... : 4

	Total number of right hand evaluations ............ : 50

	Total number of stiffness reformations ............ : 40

	Time in linear solver: 0:00:07


 Elapsed time : 0:00:10


 N O R M A L   T E R M I N A T I O N

Waiting for log file...
Proceeding to check log file...13-Mar-2020 12:38:04
------- converged at time : 0.1
------- converged at time : 0.2
------- converged at time : 0.3
------- converged at time : 0.4
------- converged at time : 0.5
------- converged at time : 0.6
------- converged at time : 0.7
------- converged at time : 0.8
------- converged at time : 0.9
------- converged at time : 1
--- Done --- 13-Mar-2020 12:38:04

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=N_disp_mat(:,:,end);
    DN_magnitude=sqrt(sum(DN(:,3).^2,2));
    V_def=V+DN;
    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,:);
%     [CF]=vertexToFaceMeasure(Fb,DN_magnitude);

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',1); %Add graphics object to animate
    hp1.FaceColor='Interp';

%     gpatch(Fb,V,0.5*ones(1,3),'none',0.25); %A static graphics object

    axisGeom(gca,fontSize); view([-140,16]);
    colormap(gjet(250)); colorbar;
    caxis([0 max(DN_magnitude)]);
    axis([min(X_DEF(:)) max(X_DEF(:)) min(Y_DEF(:)) max(Y_DEF(:)) min(Z_DEF(:)) max(Z_DEF(:))]);
    camlight headlight;
    view([-112,12]);

    % 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=N_disp_mat(:,:,qt); %Current displacement
        DN_magnitude=sqrt(sum(DN.^2,2)); %Current displacement magnitude
        V_def=V+DN; %Current nodal coordinates
%         [CF]=vertexToFaceMeasure(Fb,DN_magnitude); %Current color data to use

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

%     [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;
%
% L_plot=false(size(M));
% L_plot(:,:,round(size(M,3)/2)-7)=1;
% L_plot(round(size(M,1)/2)-10,:,:)=1;
% L_plot(:,round(size(M,2)/2),:)=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),:);
%
% cFigure;
% subplot(1,2,1); hold on;
% title('Closed patch surface','FontSize',fontSize);
%
% gpatch(Fb,V_def,CF,'k',0.5);
% axisGeom(gca,fontSize);
% camlight('headlight');
% colormap(gca,gjet(250)); colorbar;
%
% subplot(1,2,2); hold on;
% title('Patch data derived image data (3 slices)','FontSize',fontSize);
%
% gpatch(Fb,V_def,'kw','none',0.25);
% gpatch(Fm,Vm,Cm,'k',faceAlpha1);
%
% colormap(gca,gray(250)); colorbar; caxis([0 1]);
% axisGeom(gca,fontSize);
% camlight('headlight');
% drawnow;

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.

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/.