How to get the histogram of coordination number？

[Devin-one]

Hello, professor. What codes can I use to get thes histogram of coordination number? Is it necessary to add coordination number in the geometry model？Thank you in advance for your reply.

[jgostick]

You can find the number of neighbors to a given pore using pn.num_neighbors(pores=1), and you can also get the result for ALL pores as z = pn.num_neighbors(pores=pn.Ps). The default format for the returned result is a list of the number of pores neighboring each of the given inputs. So you can then just to plt.hist(z).

[jgostick]

I should add that in V3 we started including a model on the network for pore.coordination_number which is not run, but you can run it using pn.regenerate_models(), then you'll have pn['pore.coordination_number'] on your network which you can then use as plt.hist(pn['pore.coordination_number']).

[budidharmala]

Hallo profesor,
I have input in the form of an image sequence from a rock sample. How can I calculate the 3D coordination number using OpenPNM? Also, how can I visualize it?

[jgostick]

I just wrote a long-overdue FAQ on network extraction in PoreSpy and analysis in OpenPNM. Please give this a read and see if that gets you started.

[budidharmala]

oke, thank you professor, i will start it.

[budidharmala]

Hello Professor,

First of all, I would like to thank you very much for your help.

I have succeeded in creating binary images in .tiff

in this form here i see the format of images in .npz.

path = Path(os.getcwd(), '../../tests/fixtures/berea_100_to_300.npz') data = np.load(path.resolve()) im = data['im']

Should I convert from .tiff to .npz?

and to calculate 3D coordination numbers, which format should I use?

Regards,
Bd

[jgostick]

npz is just a file format for storing a numpy array in a compressed form, which is preferred for our online examples. Whether using tiff -> numpy array or npz -> numpy array doesn't matter.

BTW, these questions are starting to fall under the category of "you need to learn more about Python before you ask the devs of the packages you're using for help". Try google or chatgpt first. I don't mind answering questions about openpnm and porespy, but my time is limited.