[vmtk-users] Coordinates of a centerline

[Vikram Mehta]

Dear VMTK users,

I have a surface reconstruction of a catheter within a coronary artery and have also generated the centerlines for it.
However, for further processing, I need the coordinates of the catheter centerline and was wondering if you all had any idea to do this ?
I tried using vmtkcenterlinegeometry but I might be doing something wrong,

vmtksurfacereader -ifile /home/vm308/catheter.vtp --pipe vmtkcenterlines -seedselector openprofiles --pipe  vmtkcenterlinegeometry -ofile catheter_clg.vtp

Ideally I would like a .txt file (basically a point cloud) - is this achievable ?

Please advise.

Looking forward to your replies

Thanks in advance,
Vikram.

[Arjan Geers]

Hi Vikram, 

You could try this:

vmtksurfacereader -ifile /home/vm308/catheter.vtp --pipe vmtkcenterlines -seedselector openprofiles -ofile catheter_cl.dat

It should give you the coordinates of the centerline points in a human-readable format. 

Good luck with it, 

Arjan

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[Vikram Mehta]

Hi Arjan,

Thanks alot for your response. I seem to have got all the data I needed.


On a separate note,

Does anyone know how to save your surface file as an ASCII STL and not a binary one.

Thanks alot !

Vikram.

[Richard Downe]

Personally, I write my stl files myself, because I build my surfaces in another program.  Attached is a perl script I've used for converting .off files to .stl -- should be trivial to adapt it to python/iterate over a vtkPolyData instead of .off input.
-rd

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[Luca Antiga]

Hi everyone,

 about the STL thing, the vtk writer used in vmtk supports ASCII files out of the box, only 

I haven't exposed that option at the script level until today.

I just pushed a commit on the source code repository to allow this:

... --pipe vmtksurfacewriter -ofile foo.stl -mode ascii

It works for stl, vtu, vtk, vtp, ply.

If you're in a rush, get these two files

https://raw.github.com/vmtk/vmtk/master/vmtkScripts/vmtksurfacewriter.py

https://raw.github.com/vmtk/vmtk/master/vmtkScripts/vmtkmeshwriter.py

and copy them over to your {installpath}/lib/vmtk/vmtk folder, replacing the old ones.

Note, it's the lib folder, not the bin folder (you'll find two files called vmtksurfacewriter 

and vmtkmeshwriter, without the py extension: they're not the right ones to replace).

Luca

PS: Richard, thanks a lot for sharing the script, very much appreciated.

<stlBuilder.pl>------------------------------------------------------------------------------

[Teiv]

Hello Luca,

Could you please show me a way to output the result of the vmtkcenterlines command in the Ascii format so as it can be read by Gmesh.

I have used the following commands but it has not been successful:

$ vmtkcenterlines -ifile aorta.vtk --pipe vmtkmeshwriter -ofile foo.vtk -mode ascii

I really appreciate any help you can provide.

Best, Teiv.

[Simone Manini]

Dear Teiv,

try to use vmtksurfacewriter instead of vmtkmeshwriter.

The output of vmtkcenterlines is a polydata object.

Best Regards

Simone

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[Teiv]

Dear Simone,

I am now able to output the result of the vmtkcenterlines command in the Ascii format by the following commands:

$ vmtkcenterlines -ifile aorta.vtk -ofile ctl-bin.vtk

$ vmtksurfacewriter -ifile ctl-bin.vtk -ofile ctl-ascii.vtk -mode ascii

Thank you very much,

Best, Teiv.