Visualizing extracted network and tiff image together in Paraview

[nuritg]

Hello,
I got the 3D network but when I'm trying to save it by:

ps.io.to_vtk(np.array(m3d, dtype=int)[:, :, :], '3d-test')

I'm getting the error:

OSError: [Errno 22] Invalid argument: '3d-test.vti'

(this line: prj.export_data(filename= '3d-try', filetype='vtk'), seems to work fine).

Thanks!

[nuritg]

I think my question was not clear, so I will try to make it better.
after running the code below:

snow_output = ps.networks.snow2(
    m3d[:,:,:],
    voxel_size=1,
)
net = ps.networks.regions_to_network(snow_output.regions, voxel_size=1)
pn = op.network.GenericNetwork()
pn.update(net)

I get only vtp file in the Paraview, and working on it gives me that result:

Is there something that I should do differently?
Thanks a lot!

[jgostick]

Judging by your colorbar you have pore sizes spaning 6 orders of magnitude, so maybe they are present but not visible. You can try to remove scaling and just put them all as a constant size? You can also try to overlay the tiff image which you did the extraction on. Note that you may have to rotate/flip your tiff image so it lines up. There is a function (porespy.tools.align_image_with_openpnm) which can do this for you.

[nuritg]

Thanks! It seems to show all pores without scaling.

How can I overlay the image?

[jgostick]

Just do "file/open/" and navigate to your tiff image. YOu have to do a few things though...like rotate it before opening, and scale it in the properties pane once it's in paraview.

[nuritg]

After opening the image (file- open-AVS UCD Reader), the image doesn't appear. My images are bmp files, is the reader correct? Should I choose something else or open it in a different way?

[jgostick]

Try saving it as a TIFF file, using imageio in python, or imagej. This should open directly.

[nuritg]

It works! However, not all pores appear to be displayed in the pore network.. any idea what can be the reason for that?
Thank you so much for the fast answer each time!

[jgostick]

I don't think it's working yet. The image and the glyphs should line-up much nicer than what is showing. Maybe a few more flips? That might also solve the issue of the missing glyphs too.

[nuritg]

Is it possible to do several flips using the code itself? if so, how? or where? and do you know how many flips should I make?
I still didn't find a way to rotate it in Paraview...

[jgostick]

I know it's a pain, sorry. You should do:

1. Extract network from original image using snow2
2. THEN use porespy.tools.align_image_to_openpnm on the oringal binary image
3. Save the rotated image to a new tiff file using imageio.volsave(...)
4. Save the network using OpenPNM
5. Then open the network and the rotated image in paraview

If this is already what you're doing, then it must mean that the align_image_to_openpnm function is not doing what it's supposed to. You could try to do the rotations and flips yourself, by trial and error. You'd use some combination of np.flipud, np.fliplr, & np.swapaxes.

[nuritg]

I tried a bit, and it doesn't look good...
but I'll keep trying, and let you know when it works.