Using Neighborhood Queries

The OpenPNM GenericNetwork objects (e.g. Cubic, Voronoi, etc) have methods that let you query the connected pores and throats. This tutorial will explain how these work and illustrate why they are useful.



In [1]:

    
import openpnm as op
import numpy as np
np.random.seed(10)
%matplotlib inline
ws = op.Workspace()
ws.settings["loglevel"] = 40



In [2]:

    
pn = op.network.Cubic(shape=[4, 4, 1])

The following examples are relatively trivial, but their intention is to illustrate the different functions and options. More realistic use cases will be presented further down.

Start by finding all pores on the 'left' and 'front'



In [3]:

    
P_left = pn.pores('left')
P_bottom = pn.pores('front')

Find Neighoring Pores

We now have two sets of pores that actually overlap each other, as illustrated below:



In [4]:

    
#NBVAL_IGNORE_OUTPUT
fig = op.topotools.plot_coordinates(pn, pn.Ps, c='lightgrey')
fig = op.topotools.plot_coordinates(pn, P_left, c='red', marker='*', fig=fig)
fig = op.topotools.plot_coordinates(pn, P_bottom, c='blue', marker='.', fig=fig)

We'll merge these pores into a single set, and explore the different ways to find neighbors to this set. Note that the pore at [x,y] = [1.5, 1.5] has two neighbors (one 'bottom' and one 'left').

Find All Neighbors: OR

Finds all pores with one or more connections to the input pores

Given a set of pores, find the pores that are neighbors to one or more of the inputs. This is called OR since it gives the neighbors of either the bottom pores or the left pores, or both.



In [5]:

    
#NBVAL_IGNORE_OUTPUT
fig = op.topotools.plot_coordinates(pn, pn.Ps, c='lightgrey')
fig = op.topotools.plot_coordinates(pn, P_left, c='red', marker='*', fig=fig)
fig = op.topotools.plot_coordinates(pn, P_bottom, c='blue', marker='.', fig=fig)



In [6]:

    
Ps = pn.pores(['left', 'front'])
print(Ps)
Ps = pn.find_neighbor_pores(pores=Ps, mode='or')
print(Ps)









    



[ 0  1  2  3  4  8 12]
[ 5  6  7  9 13]



In [7]:

    
#NBVAL_IGNORE_OUTPUT
fig = op.topotools.plot_coordinates(pn, Ps, c='green', marker='s', fig=fig)

Find Non-Shared Neighbors: XOR

Finds all pores with exactly one connection to the input pores

Given a set of pores find the pores that are neighbors of one and only one of the input pores. This is called XOR, or 'exclusve_or' because it finds the pores that are neigbhors to the 'bottom' or the 'left', but not both.



In [8]:

    
#NBVAL_IGNORE_OUTPUT
fig = op.topotools.plot_coordinates(pn, pn.Ps, c='lightgrey')
fig = op.topotools.plot_coordinates(pn, P_left, c='red', marker='*', fig=fig)
fig = op.topotools.plot_coordinates(pn, P_bottom, c='blue', marker='.', fig=fig)



In [9]:

    
Ps = pn.pores(['left', 'front'])
print(Ps)
Ps = pn.find_neighbor_pores (pores=Ps, mode='xor')
print(Ps)









    



[ 0  1  2  3  4  8 12]
[ 6  7  9 13]



In [10]:

    
#NBVAL_IGNORE_OUTPUT
fig = op.topotools.plot_coordinates(pn, Ps, c='green', marker='s', fig=fig)

Find Common Neighbors of Two Sets: XNOR

Finds all the pores with 2 or more connections to the input pores

This finds pores that are common to both 'left' and 'bottom' pores. It is called XNOR since it is the opposite of XOR , incidated by the N for not . Note that XNOR and NXOR are interchangable.



In [11]:

    
#NBVAL_IGNORE_OUTPUT
fig = op.topotools.plot_coordinates(pn, pn.Ps, c='lightgrey')
fig = op.topotools.plot_coordinates(pn, P_left, c='red', marker='*', fig=fig)
fig = op.topotools.plot_coordinates(pn, P_bottom, c='blue', marker='.', fig=fig)



In [12]:

    
Ps = pn.pores(['left', 'front'])
print(Ps)
Ps = pn.find_neighbor_pores(pores=Ps, mode='xnor')
print(Ps)









    



[ 0  1  2  3  4  8 12]
[5]



In [13]:

    
#NBVAL_IGNORE_OUTPUT
fig = op.topotools.plot_coordinates(pn, Ps, c='green', marker='s', fig=fig)

Find Neighboring Throats

Neighbor throat queries follow essentially the same logic as the neighboring queries outlined above.

Find All Neighboring Throats: OR

Finds all throats connected to any of the input pores



In [14]:

    
##NBVAL_IGNORE_OUTPUT
Ps = pn.pores(['left', 'front'])
Ts = pn.find_neighbor_throats(pores=Ps, mode='or')
fig = op.topotools.plot_connections(pn, Ts)
fig = op.topotools.plot_coordinates(pn, pn.Ps, c='lightgrey', fig=fig)
fig = op.topotools.plot_coordinates(pn, P_left, c='red', marker='*', fig=fig)
fig = op.topotools.plot_coordinates(pn, P_bottom, c='blue', marker='.', fig=fig)
ax = fig.gca()
ax.set_xlim(0.25, 3.75)
ax.set_ylim(0.25, 3.75)









    Out[14]:





(0.25, 3.75)

Find Common Neighbors: XNOR

Finds throats shared by input pores only



In [15]:

    
##NBVAL_IGNORE_OUTPUT
Ps = pn.pores(['left', 'front'])
Ts = pn.find_neighbor_throats(pores=Ps, mode='xnor')
fig = op.topotools.plot_connections(pn, Ts)

fig = op.topotools.plot_coordinates(pn, pn.Ps, c='lightgrey', fig=fig)
fig = op.topotools.plot_coordinates(pn, P_left, c='red', marker='*', fig=fig)
fig = op.topotools.plot_coordinates(pn, P_bottom, c='blue', marker='.', fig=fig)
ax = fig.gca()
ax.set_xlim(0.25, 3.75)
ax.set_ylim(0.25, 3.75)









    Out[15]:





(0.25, 3.75)

Find Non-Shared Neighbors: XOR

Finds throats that are only connected to one input pore



In [16]:

    
##NBVAL_IGNORE_OUTPUT
Ps = pn.pores(['left', 'front'])
Ts = pn.find_neighbor_throats(pores=Ps, mode='xor')
fig = op.topotools.plot_connections(pn, Ts)

fig = op.topotools.plot_coordinates(pn, pn.Ps, c='lightgrey', fig=fig)
fig = op.topotools.plot_coordinates(pn, P_left, c='red', marker='*', fig=fig)
fig = op.topotools.plot_coordinates(pn, P_bottom, c='blue', marker='.', fig=fig)
ax = fig.gca()
ax.set_xlim(0.25, 3.75)
ax.set_ylim(0.25, 3.75)









    Out[16]:





(0.25, 3.75)