How to extract pores from an image and export it to paraview

[UnaisAshraf]

Hello Professor Jeff,

I hope this email finds you well. I started learning openpnm recently. I am trying to extract the pores from an image in openpnm and export it to paraview to see it in 3D but its not working. I tried different codes but its not working. Please help.

This is my code:

import numpy as np
from skimage import io, filters, morphology
import openpnm as op
import os
current_directory = os.getcwd()
from skimage import color

im = io.imread('C:/Users/unais/Downloads/poresys_2d.png')

im_gray = color.rgb2gray(im)
im_binary = im_gray > filters.threshold_otsu(im_gray)

im_binary_clean = morphology.binary_closing(im_binary)

pn = op.network.Cubic(shape=im_binary_clean.shape, spacing=1, connectivity=20)
pn['pore.all'] = True
pn['pore.coords'] = np.argwhere(im_binary_clean)

pn.add_model_collection(op.models.collections.geometry.spheres_and_cylinders)

path_to_file = current_directory
op.io._vtk.project_to_vtk(pn.project, filename=path_to_file+'/Paraview1_net')

I am trying to extract the pores from this picture below:

when i export it to paraview. It shows this " Cannot read points array from Points in piece 0. The data array in the element may be too short." Can you please tell me what the problem is?

I would really appreciate your help.

[jgostick]

I'm not totally sure what you're trying to do, but I don't think that assigning the result of np.where to the pore.coords is what you want. We have a number of tutorials on the porespy website that explain how pore network extraction works, so I suggest you start there.

[UnaisAshraf]

Ok sir. Thanks for your reply.