3D image

Asked by Ali Abdallah on 2021-03-05

Hello,

I am trying to obtain a 3D image for my domain, as I know we can obtain a .vtu file which is a 3D surface and not a voxelated 3D image like the one obtained by x-ray (.raw or .tif). I need this 3D image for pore network extraction.

Is there any possible way to obtain a 3D image(.raw) or do you know any free tool that can convert from 3D surfaces to 3D images . For example there is AMIRA software that can do such a job but it is a commercial software.

Thank you

Question information

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For:
Yade Edit question
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Solved by:
Ali Abdallah
Solved:
2021-03-05
Last query:
2021-03-05
Last reply:
2021-03-05
Jan Stránský (honzik) said : #1

Hello,

please read [1] and provide more information, ideally also a MWE [1].

> I am trying to obtain a 3D image...

just image? or data?

> for my domain

what is "my domain"?

> a .vtu file which is a 3D surface

MAY be a 3D surface, but definitely not necessarily.
Also I doubt you get directly the surface for most of Yade scenarios..
E.g. for sphere, you get .vtu file, but only containing centers of spheres with radii in the data, so the surface can be constructed, but indirectly.

> Is there any possible way to obtain a 3D image(.raw) or do you know any free tool that can convert from 3D surfaces to 3D images

what is "3D surface"?
Anyway, vozelization does not seem like a very big task and a not-so-difficult script should do the job..

Most of the questions would be answered by a MWE [1]

cheers
Jan

[1] https://www.yade-dem.org/wiki/Howtoask

Ali Abdallah (ali96) said : #2

Thank you very much for your reply

I want to have a raw 3D voxel-based image (.raw or .tif) just as the one obtained in a micro-CT Xray image that can be later processed by a pore network extraction code.

By the domain I just meant any sample of particles either spheres or polyhedral that's why I didn't mention a MWE.

Yes you are right the .vtu is not a direct 3D surface but has data that can be converted into 3D surfaces using Paraview . Is there any free tool that can convert this .vtu file to a raw 3D voxel-based images (.raw or .tif).

I wrote a simple algorithm that can voxelize the domain(sample of particles) and I saved the data into a binary file (.npy) consisting of voxels with a value of either 1 or 0 which represent if the voxel is inside a particle or in a void space; Is it possible to convert this data (the position of each voxel and its type 0or 1) to a .raw file?

Thank you very helping me

Jan Stránský (honzik) said : #3

Hello,
thanks for more info

> By the domain I just meant any sample of particles either spheres or polyhedral that's why I didn't mention a MWE.

This is exactly the reason why you SHOULD provide a MWE :-)

> I wrote a simple algorithm

so you have the data, you just want to save them in a specific file format?

> Is it possible to convert this data (the position of each voxel and its type 0or 1) to a .raw file?

for sure it is possible :-)
How, it is another question :-D

cheers
Jan

Robert Caulk (rcaulk) said : #4

>Yes you are right the .vtu is not a direct 3D surface but has data that can be converted into 3D surfaces using Paraview . Is there any free tool that can convert this .vtu file to a raw 3D voxel-based images (.raw or .tif).

Paraview lets you take slices and export images accordingly. Then you have your "slices" folder which you could construct into a single .tif using imageJ. Same way you would get "slices" from tomography reconstruction.

Cheers,

Robert

Ali Abdallah (ali96) said : #5

Thank you very much Jan and Robert, that solved my question.