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Iso-Surface

Asked by bahar cham on 27 Dec 2011
HI ALL,
MY Goal is:The iso-surface contains some small fragments which do not belong to the coronary arteries. In order to remove these fragments, a size filter is applied to all connected regions in the isosurface output. I run isosurface
>>[f,v] = isosurface(X,Y,Z,MASK,.3);
How can I apply morphological filter on isosurface output? when f,v are not 3D matrix.
Thanks

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2 Answers

Answer by Kevin Moerman on 7 Feb 2012

Use this function and have a look at the example to group the patch objects defined by the faces and vertices. I will also post this code soon on my page. The uses stepwise grouping so could be slow for large data sets.
function G=tesgroup(F)
% function G=tesgroup(F) % ------------------------------------------------------------------------ % % This function finds groups in the tesselation defined by F. F may % represent patch type faces or for instances node indices for % tetrehedrons, hexahedrons. Row entries in F (e.g. tetrahedron vertex % indices) which are "connected" (sharing vertex indices with other row % entries in F) are grouped together. The output G is a logic matrix of % size(F,1) rows and "number of groups" columns. Each column represents a % group and ones appear in the column for each face belonging to the group. % % % %EXAMPLE: % clear all; close all; clc; % % % %% Simulating some isosurface data % [X,Y,Z]=meshgrid(linspace(-5,5,35)); % phi=(1+sqrt(5))/2; % M=2 - (cos(X + phi*Y) + cos(X - phi*Y) + cos(Y + phi*Z) + cos(Y - phi*Z) + cos(Z - phi*X) + cos(Z + phi*X)); % M=M./max(M(:)); % [F,V] = isosurface(X,Y,Z,M,0.1); % % %% Normal isosurface plot showing seperate patch objects % figure; % h=patch('faces',F,'vertices',V); % set(h,'FaceColor','b','EdgeColor','none','FaceAlpha',0.5); % view(3);light; grid on; axis vis3d; % % %% Iso surface plots showing grouped patch objects % % G=tesgroup(F); %Logic array for patch groups % pcolors=jet(size(G,2)); % figure; % for i=1:1:size(G,2); % hg=patch('faces',F(G(:,i),:),'vertices',V); %Plotting individual group % set(hg,'FaceColor',pcolors(i,:),'EdgeColor','none','FaceAlpha',0.8); % end % view(3);light; grid on; axis vis3d; % colormap(pcolors); colorbar; caxis([0 size(G,2)]); % % Kevin Mattheus Moerman % kevinmoerman@hotmail.com % 15/07/2010 %------------------------------------------------------------------------
IND_F=(1:1:size(F,1))'; IND_F_search=IND_F;
G=false(size(F,1),1); v_search=[ ]; L=ones(size(IND_F)); done=0; num_v_search=[ ]; group_found=1; group_n=0; while done==0; if group_found==1; L=find(IND_F_search>0,1); %next un-grouped triangle v_new=F(L,:); v_new=v_new(:); v_search=[v_search; v_new]; v_search=unique(v_search(:)); %Growing number of search vertices
group_found=0;
else
L = any(ismember(F,v_search), 2);
IND_F_search=IND_F_search.*(L==0); %Setting found to zero
v_new=F(L,:); v_new=v_new(:);
v_search=[v_search; v_new]; v_search=unique(v_search(:)); %Growing number of search vertices
end
if numel(v_search)==num_v_search; %If the group has not grown
group_found=1;
group_n=group_n+1;
G(:,group_n)=L;
v_search=[ ];
end
num_v_search=numel(v_search);
if all(IND_F_search==0);
done=1;
group_found=1;
group_n=group_n+1;
if any(G)==0
G(:,group_n)=L;
end
v_search=[ ];
end
end

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Answer by Kevin Moerman on 7 Feb 2012

Now properly formatted.
function G=tesgroup(F)
% function G=tesgroup(F)
% ------------------------------------------------------------------------
%
% This function finds groups in the tesselation defined by F. F may
% represent patch type faces or for instances node indices for
% tetrehedrons, hexahedrons. Row entries in F (e.g. tetrahedron vertex
% indices) which are "connected" (sharing vertex indices with other row
% entries in F) are grouped together. The output G is a logic matrix of
% size(F,1) rows and "number of groups" columns. Each column represents a
% group and ones appear in the column for each face belonging to the group.
%
% % %EXAMPLE:
% clear all; close all; clc;
%
%
% %%Simulating some isosurface data
% [X,Y,Z]=meshgrid(linspace(-5,5,35));
% phi=(1+sqrt(5))/2;
% M=2 - (cos(X + phi*Y) + cos(X - phi*Y) + cos(Y + phi*Z) + cos(Y - phi*Z) + cos(Z - phi*X) + cos(Z + phi*X));
% M=M./max(M(:));
% [F,V] = isosurface(X,Y,Z,M,0.1);
%
% %%Normal isosurface plot showing seperate patch objects
% figure;
% h=patch('faces',F,'vertices',V);
% set(h,'FaceColor','b','EdgeColor','none','FaceAlpha',0.5);
% view(3);light; grid on; axis vis3d;
%
% %%Iso surface plots showing grouped patch objects
%
% G=tesgroup(F); %Logic array for patch groups
% pcolors=jet(size(G,2));
% figure;
% for i=1:1:size(G,2);
% hg=patch('faces',F(G(:,i),:),'vertices',V); %Plotting individual group
% set(hg,'FaceColor',pcolors(i,:),'EdgeColor','none','FaceAlpha',0.8);
% end
% view(3);light; grid on; axis vis3d;
% colormap(pcolors); colorbar; caxis([0 size(G,2)]);
%
% Kevin Mattheus Moerman
% kevinmoerman@hotmail.com
% 15/07/2010
%------------------------------------------------------------------------
IND_F=(1:1:size(F,1))';
IND_F_search=IND_F;
G=false(size(F,1),1);
v_search=[ ];
L=ones(size(IND_F));
done=0;
num_v_search=[ ];
group_found=1;
group_n=0;
while done==0;
if group_found==1;
L=find(IND_F_search>0,1); %next un-grouped triangle
v_new=F(L,:); v_new=v_new(:);
v_search=[v_search; v_new]; v_search=unique(v_search(:)); %Growing number of search vertices
group_found=0;
else
L = any(ismember(F,v_search), 2);
IND_F_search=IND_F_search.*(L==0); %Setting found to zero
v_new=F(L,:); v_new=v_new(:);
v_search=[v_search; v_new]; v_search=unique(v_search(:)); %Growing number of search vertices
end
if numel(v_search)==num_v_search; %If the group has not grown
group_found=1;
group_n=group_n+1;
G(:,group_n)=L;
v_search=[ ];
end
num_v_search=numel(v_search);
if all(IND_F_search==0);
done=1;
group_found=1;
group_n=group_n+1;
if any(G)==0
G(:,group_n)=L;
end
v_search=[ ];
end
end

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