levelset2isosurface

Below is a demonstration of the features of the levelset2isosurface function

Syntax
Description
Examples
Import image data for this demo
Compute levelset

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:

A 3D levelset image K
A structure with control parameters controlPar with the fields: contourLevel (the level for the isosurface), voxelSize (specifying the voxel size), capOpt (specifying how to cap the surface if needed), and nSub (specifying if the surface should be drawn at the native resolution nSub=[1 1 1] or if it should be courser, e.g. by skippin every 2nd voxels if nSub=[2 2 2]).

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_, <[email protected]>

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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.

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