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@NataCalc
NataCalc authored Jun 2, 2022
1 parent cf2134d commit 574af4f
Showing 1 changed file with 96 additions and 27 deletions.
123 changes: 96 additions & 27 deletions mcode/C_BodyParts3D_isolate_LegOuterSkinSurface_LegMuscles_vs1.m
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Original file line number Diff line number Diff line change
Expand Up @@ -27,11 +27,12 @@

pointSpacing=4;
cutHeight=810;
cutHeight1=860;
saveOn=1;


Select_layer='outer_muscles_surface';%'outer_skin_surface';'outer_muscles_surface'
switch Select_layer
Select_layer='outer_skin_surface';%'outer_skin_surface';'outer_muscles_surface'
switch Select_layer
case 'outer_skin_surface'
%% Original
fileName_mat=fullfile(loadFolder,[fileName_FMA,'.mat']);
Expand All @@ -54,6 +55,7 @@
axisGeom;
camlight headlight;
drawnow;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Cut again preserving only right leg
optionStruct.outputType='label';
Expand All @@ -62,14 +64,14 @@
logicKeep=G==indMax;
Fs=Fs(logicKeep,:);
[Fs,Vs]=patchCleanUnused(Fs,Vs);

cFigure; hold on;
gpatch(Fs,Vs,'w','none',0.25);
axis off;
axisGeom;
camlight headlight;
drawnow;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Slice the surface of the right leg at cutHeight
%% to detect all edges to form the list of curves within the slice
Expand Down Expand Up @@ -100,12 +102,13 @@
VTc=Vc(indCurveNow,:);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Forming the 2D convex hull around the curve
[V_slice_curve]=convexhull_curve(VTc,200);
[VT0]=convexhull_curve(VTc,200);
[Fc,Vc]=patchCleanUnused(Fc(logicSide,:),Vc);

VT0(:,3)=VT0(:,3)+25;
cFigure; hold on;
gpatch(Fc,Vc,'w','none',0.25);
plotV(V_slice_curve,'k-','LineWidth',4);
plotV(VT0,'k-','LineWidth',4);
axis off;
axisGeom;
camlight headlight;
Expand All @@ -116,33 +119,99 @@
%Set-up orientation and location of cutting plane
snapTolerance=mean(patchEdgeLengths(Fc,Vc))/100; %Tolerance for surface slicing
n=vecnormalize([0 0 1]); %Normal direction to plane
Q1=euler2DCM([0.4*pi 0 0.8*pi]);

Q1=euler2DCM([0.38*pi 0 0.8*pi]);
n=n*Q1;
P_cut=[0 0 0]+n*306; %Point on plane
%Slicing surface
[Fd,Vd,Cd,logicSide,Ed]=triSurfSlice(Fc,Vc,[],P_cut,n);
%Compose isolated cut geometry and boundary curves
[Fe,Ve]=patchCleanUnused(Fd(logicSide==1,:),Vd);


Ebs=patchBoundary(Fe);
groupStruct.outputType='label';
[G,~,groupSize]=tesgroup(Ebs,groupStruct);

logicKeep=G==1;
Eb_keep=Ebs(logicKeep,:);
indCutLine=edgeListToCurve(Eb_keep);

%Smoothen line
logicRigid=true(size(Ve,1),1);
logicRigid(indCutLine)=0;

cPar.n=10;
cPar.Method='LAP';
cPar.RigidConstraints=find(logicRigid);
[Ve]=patchSmooth(Ebs,Ve,[],cPar);

%Smoothen mesh
logicTouch=any(ismember(Fe,indCutLine),2);
indTouch=unique(Fe(logicTouch,:));

for q=1:1:2
logicTouch=any(ismember(Fe,indTouch),2);
indTouch=unique(Fe(logicTouch,:));
end
%Smoothen line
logicRigid=true(size(Ve,1),1);
logicRigid(indTouch)=0;
logicRigid(indCutLine)=1;
%Smoothen mesh
clear cPar;
cPar.n=100;
cPar.Method='HC';
cPar.RigidConstraints=find(logicRigid);
[Ve]=patchSmooth(Fe,Ve,[],cPar);

VT=Ve(indCutLine,:);

VT0=evenlySampleCurve(VT0,size(VT,1),'pchip',1);
VT0=VT0(1:end-1,:);
indCurve_S=(linspace(1,size(VT0,1),size(VT0,1)));
indCurve_S=indCurve_S(1:end-1);
indCurve_L=indCurve_S;
%% Reorder curves
[~,indMin]=minDist(VT(indCurve_L(1),:),VT0(indCurve_S,:));

if indMin>1
indCurve_S=[indCurve_S(indMin:end) indCurve_S(1:indMin-1)];
end

D1=sum(sqrt(sum((VT(indCurve_L,:)-VT0(indCurve_S,:)).^2,2)));
D2=sum(sqrt(sum((VT(indCurve_L,:)-VT0(flip(indCurve_S),:)).^2,2)));

if D2<D1
indCurve_S=flip(indCurve_S);
end

cPar.closeLoopOpt=1;
cPar.patchType='tri_slash';
[Fn1,Vn1]=polyLoftLinear(VT(indCurve_L,:),VT0(indCurve_S,:),cPar);

%Smoothen mesh
clear cPar;
cPar.n=100;
cPar.Method='HC';
[Vn1]=patchSmooth(Fn1,Vn1,[],cPar);

[Fk,Vk]=regionTriMesh3D({VT0(indCurve_S,:)},pointSpacing,0,'natural');

cFigure; hold on;
gpatch(F,V,'w','none',0.25);
gpatch(Fe,Ve,'rw','none',1);
plotV(V_slice_curve,'k-','LineWidth',4);

plotV(VT,'g.-','MarkerSize',25,'LineWidth',3);
plotV(VT0,'g.-','MarkerSize',25,'LineWidth',3);
gpatch(Fe,Ve,'gw','none',1);
gpatch(Fn1,Vn1,'w','none',1);
gpatch(Fk,Vk,'w','none',1);
axis off;
axisGeom;
camlight headlight;
drawnow;

%% Forming the point cloud out of the processed cut right leg a
%% and the edge of the skin (curve) formed at cutHeight
Ve=[Ve;V_slice_curve;];
%% Construct alpha shape
% This deteriorates surface quality (bridges concave regions) but is a
% termporary "quick-and-dirty" work-around to obtain outer skin surface
% only.
shp = alphaShape(Ve,max(patchEdgeLengths(Fe,Ve)),'HoleThreshold',500,'RegionThreshold',100);


V_total=[Ve;Vn1;Vk];
shp = alphaShape(V_total,max(patchEdgeLengths(Fe,Ve)));%,'HoleThreshold',500,'RegionThreshold',100);
[Fa,Va] = boundaryFacets(shp); %Get boundary faces of alpha shape
[Fa,Va] = patchCleanUnused(Fa,Va); %Remove unused vertices

Expand All @@ -154,26 +223,26 @@
%% Visualisation
cFigure;
hAxis(1)=subplot(1,2,1); hold on;
%gpatch(Fs,Vs,'w','none',0.25);
gpatch(Fe,Ve,'w','none',1);
plotV(V_slice_curve,'k-','LineWidth',4);
gpatch(Fs,Vs,'w','none',0.25);
%gpatch(Fe,Ve,'w','none',1);
%plotV(VT0,'k-','LineWidth',4);

text(min(V(:,1))+50,min(V(:,2))+99,'A','FontSize',fontSize);
%text(min(V(:,1))+50,min(V(:,2))+99,'A','FontSize',fontSize);
axis off;
axisGeom;
camlight headlight;

hAxis(2)=subplot(1,2,2); hold on;
gpatch(Fn,Vn,'w','k',1,lineWidth);
text(min(V(:,1))+40,min(V(:,2))+110,'B','FontSize',fontSize);
%text(min(V(:,1))+40,min(V(:,2))+110,'B','FontSize',fontSize);
axis off;
axisGeom;
pos = get( hAxis(2), 'Position' );
pos(1)=pos(1)-0.3;
set( hAxis(2), 'Position', pos ) ;
camlight headlight;
gdrawnow;

%% Store model in structure
modelNew.source=fileName_FMA;
modelNew.faces=Fn;
Expand Down

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