levelset2isosurface

Below is a demonstration of the features of the levelset2isosurface function

Contents

clear; close all; clc;

Syntax

[F,V]=levelset2isosurface(K,controlPar);

Description

This function computes the isosurface for an input levelset image at a desired intensity level.

The input consists of:

Examples

Import image data for this demo

defaultFolder = fileparts(fileparts(mfilename('fullpath'))); %Set main folder
pathNameImageData=fullfile(defaultFolder,'data','DICOM','0001_human_calf');
loadNameImageData=fullfile(pathNameImageData,'IMDAT','IMDAT.mat');
IMDAT_struct=load(loadNameImageData); %The image data structure
G = IMDAT_struct.G; %Geometric/spatial information
v=G.v; %The voxel size
M= IMDAT_struct.type_1; %The image data
contourName='imseg_calf_tibia';
pathName=fullfile(defaultFolder,'data','imseg'); %Folder name for contours

Compute levelset

loadName=fullfile(pathName,contourName);
load(loadName); %Load segmentation structure
Vcs=saveStruct.ContourSet; %Access the contour data

[K]=contour2levelset(M,v,Vcs,2);

Visualize levelset and contours together

%Visualize levelset
vizStruct.colormap=warmcold(250); %Set colormap for levelset visualization
vizStruct.clim=[-abs(min(K(:))) abs(min(K(:)))]; %Set color limits
[~,indMin]=min(K(:)); %assume centre of shape is at lowest value
[i,j,k]=ind2sub(size(M),indMin); %Convert index to subscript indices
vizStruct.sliceIndices=[i,j,k]; %Set indices as slices to plot

hf2=sv3(K,v,vizStruct); %Open slice viewer for levelset

%Visualize contours
optionStruct.Color='k';
plotContours({Vcs},optionStruct);  %Plot contours
drawnow;
pointSpacing=2;

controlPar.contourLevel=0;
controlPar.voxelSize=v;
controlPar.capOpt=1;
controlPar.nSub=ceil(pointSpacing./v);
[Fi,Vi]=levelset2isosurface(K,controlPar);

%Smoothen
numSmoothSteps=10;

Eb=patchBoundary(Fi,Vi);
controlPar_smooth.Method='HC';
controlPar_smooth.Alpha=0.1;
controlPar_smooth.Beta=0.5;
controlPar_smooth.n=numSmoothSteps;
controlPar_smooth.RigidConstraints=unique(Eb(:));
[Vi]=patchSmooth(Fi,Vi,[],controlPar_smooth);
sv3(M,v);
gpatch(Fi,Vi,'bw','none',0.5);
optionStruct.pathName=pathName;
optionStruct.Color='w';
plotContours(contourName,optionStruct);  %Plot contours
axisGeom;
% camlight headlight;
drawnow;
cFigure;
subplot(1,2,1); hold on;
gpatch(Fi,Vi,'bw','k',1);
axisGeom;
camlight headlight;

subplot(1,2,2); hold on;
gpatch(Fi,Vi,'bw','none',0.5);
optionStruct.pathName=pathName;
optionStruct.Color='g';
plotContours(contourName,optionStruct);  %Plot contours
axisGeom;
camlight headlight;

drawnow;
%
% <<gibbVerySmall.gif>>
%
% _*GIBBON*_
% <www.gibboncode.org>
%
% _Kevin Mattheus Moerman_, <gibbon.toolbox@gmail.com>

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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.

Copyright (C) 2019 Kevin Mattheus Moerman

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.

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