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Alpha shapes

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Alpha shapes

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27 Sep 2010 (Updated )

Alpha shape of 2D/3D point set.

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Description

Computes the basic Alpha shape of a 2D/3D point set by Delaunay triangulation.

OUTPUT:
- Area/Volume
- Triangulation of Alpha shape
- Boundary of Alpha shape
- Plot

MATLAB release MATLAB 7.11 (R2010b)
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Comments and Ratings (28)
13 Oct 2014 John

Excellent. It is very easy to use and provides much better detail than using plot3 on a data-set.

03 Oct 2014 David  
01 Oct 2014 Murat Aykin  
16 Aug 2014 kamuran turksoy

Once you define the alpha shape based on n number or points 2D, how would you check if a new point is inside the shape or not? Thanks

16 Jun 2014 Violeta

Thank you very much for this useful code. I have a question, it would be great if you could help. Consider 3D data sampled from the same type of physical object whose shape/size varies from one sample to another, which means the radius as a parameter of triangulation varies across samples as well. What would then be the best criterion for the choice of radius? Any idea(s) would be very helpful. Many thanks in advance.

16 Jun 2014 Violeta  
30 Apr 2014 Yahui

What does the command "freeBoundary(TriRep(T,X))" mean? I didn't see any function about freeBoundary, but it works. So confused!

30 Apr 2014 Yahui

Thanks! very useful.

24 Oct 2013 Edwin  
02 Apr 2013 Adam

This code is awesome! Thnaks!

11 Feb 2013 Carsten Mørch  
16 Dec 2012 Maurizio De Pitta'

Hi Jonas,
I am not sure I understand your last edit to the code. Changing DELAUNAYN to DELAUNAY (line 66) fails alphavol to work on 3D data sets.

20 Aug 2012 Gustavo Oliveira Santos

Dear Jonas,

My name is Gustavo and I am PhD student in Ecology in Brazil. I am working in a R code to estimate home range of arboreal mammals. Because these species are arboreal, I am trying to estimate three-dimensional volume based on Kernel probability density functions. Unfortunately, these tetrahedrons are non-convex and I am having a lot of difficult to estimate these volumes. I got very excited when I saw your Matlab forum statements (http://www.mathworks.com/matlabcentral/fileexchange/28851-alpha-shape-volume). The R have a package alphashape3d to deal with these issues, but the functions are new and extremely unstable (the results are crazy, the R crash or no values are returned). The package geometry also is very useful, but it have functions to estimate only convex tetrahedrons.

I am ecologist, not math, and the I have a lot of difficulty with deal with this 3D geometry. Additionally, I have not intimacy with Matlab code. I would like to know if you could help me, or to indicate who can help me to solve this problem. I could send to you a dataset (dataframe com 3 columns [x,y,z] that describe the kernel surface of 95% probability of the opossum to you inspect the data.

If you or other people are interested in helping me. Please send a email to gu_tapirus@hotmail.com

Thank you in advance. Gustavo.

08 Aug 2012 Thomas Clark

Ahhh... thankyou! SO overdue as part of the triangulation toolset that we get.

08 Jun 2012 Yavor Kamer  
22 May 2012 Md Wahid

hi, just a quick note. 'delaunay()' requires at least 2 inputs (x,y as a vector, probably couldnt take matrix). i was trying with the 2d example that provided in the code. changed in the 65th line as 'delaunay(X(:,1),X(:,2))'. now it works, the graph looks nice. thanks for the code. i didnt look inside or try with the theory yet, could be wrong! just to let you know...

27 Apr 2012 Jonas Lundgren

Jorge Leandro, tilde represents an unused argument. This notation was introduced in MATLAB 2009b. You can safely replace tilde by a dummy variable.

26 Apr 2012 Jorge Leandro

As I try to run one of your examples, Matlab (7.8.0 R2009) complains with the following message: "??? Error: File: alphavol.m Line: 78 Column: 3
Expression or statement is incorrect--possibly unbalanced (, {, or [."

Examining the referred line, I see:
[~,rcc] = circumcenters(TriRep(T,X));

It seems that Matlab cannot understand the tilde as an output value. I tried to change it to [cc rcc] = circumcenters... and now Matlab complains about line 194, which reads:
[~,p,r] = dmperm(C);
Again, the tilde seems to be the problem.
By the way, as far I as know, tilde is used as a negation operator in Matlab. What is its use here? Any clue on how to solve this problem?

Regards.

27 Feb 2012 Jonas Lundgren

Borc, Yes I am aware of these artefacts in the 3D case. Thats why the code only delivers volume and not boundary faces. I will give this some thought.

24 Feb 2012 Borc

Thanks for this nice code!
One Question:
There are some artefacts inside the volume (like rectangles). How could I avoid them?
As an example run the "3D Example - Ring" with the plotsettings 'FaceColor','r' and 'FaceAlpha',0.5 to see the artefacts inside the volume.
A solution would be very helpfully for me.
Thanks in advance

24 Feb 2012 Borc  
30 Dec 2011 ping  
22 Dec 2011 Jonas Lundgren

Yuri, try the command "axis equal".

21 Dec 2011 Yuri K

It looks like the algorithm unequally connects point vertically and horizontally.
Try this data, for example:
n = 1000;
k = 10;
x = linspace(0,1,n)';
y(:,1) = k*x + randn(n,1) - k/2;
y(:,2) = -k*x + randn(n,1) + k/2;
xx = [x;x];
yy = y(:);
alphavol([xx yy], 0.5, 1);

21 Jun 2011 HARI KRISHNAN

thanks a lot

15 May 2011 Ajay

Works well and easy to use, thanks much.

30 Sep 2010 Jonas Lundgren

k Z, Thank you for the feedback. It seems to be a problem with DelaunayTri and nonunique data points. DelaunauyTri is also very slow for equally spaced data. I will switch to delaunayn and remove nonunique data points - when I have the time.

29 Sep 2010 k Z

Hi, nice code. Although the algorithm is useful when nonconvex data is used, I tested on convex data to check how robust it is. I try the sphere function. The volume of the sphere using alpha=Inf is not the same as the sphere volume, in this case the function convhulln computes more accurately the volume. It seems that summing the volume of all tetrahedron counts more that the overal volume, at least for this case. Check this please.

Updates
05 Oct 2010

DelaunayTri replaced by delaunayn. 3D plots added.

29 Sep 2011

New contact info

08 Mar 2012

More output added. DELAUNAYN replaced by DELAUNAY.

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