Surface capper / boundary extractor

[Yumnah Mohamied]

Hi All, 

I'm having problems running any script that identifies boundaries/holes on the .tec input surface file (obtained from an in-house code). 

Using vmtksurfacecapper as an example, and a basic test case of a cylindrical pipe, the script will run and give an output with no error messages, however, in the renderer, rather than identifying the two boundary holes of the pipe, hundreds of apparent hole ids are given throughout the surface (see attached file 'surface capper.png'). 

I've attached the input file for this test case also: 'surface.tec'. I was originally having this problem on a full aorta model. 

Any help would be greatly appreciated. I am running an old binary package (version 1.0.1) on mac OS X 10.8.5. 

Cheers, 

Yumnah

[Luca Antiga]

Hello Yumnah,

apparently the reader cannot guess the triangles are connected, I suppose all triangle vertices are duplicated instead of being shared among triangles.

Try running the surface through vmtksurfacetriangle, which will merge and stitch everything back together, this way 

vmtksurfacetriangle -ifile surface.tec --pipe vmtksurfacecapper -ofile surface_capped.vtp

Luca

— 

Luca Antiga, PhD 

Co-founder and Principal Scientist, Orobix Srl

via G. Camozzi 144, Bergamo, Italy

http://www.orobix.com 

http://lantiga.github.io 

github: https://github.com/lantiga 

twitter: @lantiga 

mobile: +39.347.43.16.596

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<surface capper.png><surface.tec>

[Yumnah Mohamied]

Hi Luca, 

Brilliant thanks very much. It solved the problem with the pipe test case. However, on my actual geometry of interest, although it improves the situation, there still remains some apparent holes. Close up view of one of these shows a small gap between the elements. Is there any way around this? 

Cheers, 

Yumnah

[Luca Antiga]

Apparently you need to merge vertices using a tolerance.

VTK has that, however vmtk doesn’t expose this functionality at the script level.

Try loading the surface in Paraview and select the Clean filter. You’ll then be able to specify a tolerance that controls how close two vertices have to be in order to be considered coinciding and be merged in the output dataset.

Hope this helps.

Luca

— 

Luca Antiga, PhD 

Co-founder and Principal Scientist, Orobix Srl

via G. Camozzi 144, Bergamo, Italy

http://www.orobix.com 

http://lantiga.github.io 

github: https://github.com/lantiga 

twitter: @lantiga 

mobile: +39.347.43.16.596

<Screen Shot 2014-11-07 at 18.47.55.png>

[Yumnah Mohamied]

That did the trick! Was trying and failing to do that myself in matlab - didn't know of that functionality in paraview. Thanks very much!

Cheers,

Yumnah