Extract 3D Coordinates from VTK Output File

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1

Hello everybody,

How do you extract de 3D coordinates from a VTK output file? This VTK output file is created using the Model-to-Model Distance module. It does not matter if the coordinates are in the LPS or RAS system, as I need to compare different coordinates. I need to export these coordinates to Excel.

Any suggestions would be really helpful, thankyou in advance.

Kind regards,
Judith

2

You can use arrayFromModelPoints

3

@pieper thanks for providing the link. Iā€™m wondering if we should always use latest tag (https://slicer.readthedocs.io/en/latestā€¦) instead of a specific version (https://slicer.readthedocs.io/en/v4.11) in forum posts, because these posts may be read in several months or even years later and by that time specific tags may be outdated. We could also add a ā€œstableā€ tag to readthedocs.

4

Yes, thatā€™s always a tradeoff. Thereā€™s a risk that things will get reformatted and we end up with a dead link. On the wiki we would have a header that was added to pages when new versions were created; can we easily do the same on readthedocs?

Thereā€™s a similar tradeoff with github links to line numbers in branches which can get out of date compared to a link to the commit+line number.

5

There is no automatic redirect. Maybe after structure of documentation is stabilized we can establish a policy of never deleting documentation page but add links to pages where content is moved to.

1 Like
6

Hi Pieper,

I too need to extract the x,y,z coordinates from a VTK file that I imported to Slicer. I was hoping you could be a little more explicit about how to use arrayFromModelPoints? I have imported the VTK and can see the mesh in the viewer, now what? Sorry if this is a trivial question, Iā€™m relatively new to Slicer.

Hereā€™s what Iā€™m looking at:

Screen Shot 2022-07-24 at 6.05.39 PM
Screen Shot 2022-07-24 at 6.05.39 PM1920Ɨ919 69.4 KB

If you can see at the bottom, I attempted to run ā€˜slicer.util.arrayFromModelPoints(mesh)ā€™ since my ā€œNodeā€ is named mesh as far as I can tell. Dead end and I got the error ā€œNameError: name ā€˜meshā€™ is not definedā€

7

You need to use something like:

meshModelNode = slicer.util.getNode("mesh")
points = slicer.util. arrayFromModelPoints(meshModelNode)

(you can leave out slicer.util when typing at the console).

To get used to slicer python programming you can have a look at the FAQ and some of the tutorials.

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