contourRegularise

Below is a demonstration of the features of the contourRegularise function

Syntax
Description
Examples
Regularising a contour set
Compute levelset
Visualize the results as a mesh

clear; close all; clc;

Syntax

[X,Y,Z]=contourRegularise(Vcs,n,interpMethod);

Description

This function converts the contour data in Vcs (cell containing 3D polygons e.g. as derived from segmentation with imx) to a grid format whereby the 3D coordinates are resampled in the form of a set of 3 nxm matrices (where m is the number of contours, and n is the number of desired points). The input n defines the number of points to resample each contour with, and interpMethod defines the interpolation method. The interpolation method can be any MATLAB supported polygon interpolation method (such as linear and pchip). If interMethod is set as a scalar between 0 and 1, then a cubic smoothing spline with this scalar smoothing parameter is used.

Examples

Regularising a contour set

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

Resample contours

n=25;
interPar='pchip';
[X,Y,Z]=contourRegularise(Vcs,n,interPar);

size(X)

ans =

    56    25

Visualize the results as a mesh

[F,V]=grid2patch(X,Y,Z,[],[0 1]); %Convert grid to patch mesh
[F,V]=quad2tri(F,V,'a'); %Convert quads to triangles (not required)

Visualize logic image and contours together

%Visualize logic image
sv3(M,v); %Open slice viewer for levelset

%Visualize contours
optionStruct.Color='r';
optionStruct.LineWidth=2;
plotContours({Vcs},optionStruct);  %Plot contours

gpatch(F,V,'gw');

gdrawnow;

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.

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.

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