label_phases

Version 2 of PoreSpy included the ability to perform network extractions on images that contain multiple phases, as outlined by Khan et al. The regions_to_network function includes the ability to label each pore with the phase to which it belongs, but does nothing else. The label_phases function then analyzes the network output by regions_to_network to create the labels that can be used within OpenPNM.

import porespy as ps
import openpnm as op
import matplotlib.pyplot as plt
import numpy as np
from edt import edt
import scipy.ndimage as spim

/opt/hostedtoolcache/Python/3.8.16/x64/lib/python3.8/site-packages/openpnm/algorithms/_invasion_percolation.py:358: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  def _find_trapped_pores(inv_seq, indices, indptr, outlets):  # pragma: no cover

np.random.seed(13)
im = ps.generators.overlapping_spheres([100, 100], r=7, porosity=0.7)
snow = ps.filters.snow_partitioning_n(im=im.astype(int) + 1)
ps.imshow(snow.regions, origin='lower', interpolation='none');

network

The dictionary returned from the regions_to_network function must be supplied:

net = ps.networks.regions_to_network(regions=snow.regions, phases=snow.im)

net = ps.networks.label_phases(network=net)

for item in net.keys():
    print(item)

throat.conns
pore.coords
pore.all
throat.all
pore.region_label
pore.phase
throat.phases
pore.region_volume
pore.equivalent_diameter
pore.local_peak
pore.global_peak
pore.geometric_centroid
throat.global_peak
pore.inscribed_diameter
pore.extended_diameter
throat.inscribed_diameter
throat.total_length
throat.direct_length
throat.perimeter
pore.volume
pore.surface_area
throat.cross_sectional_area
throat.equivalent_diameter
pore.void
throat.void_void
throat.void_solid
pore.solid
throat.solid_void
throat.solid_solid

In the above print-out we can see that several labels have been added to the list, such as 'throat.void_void' which is True for all throats which connect a void pore to another void pore, and so forth.

alias

We can override the default names of 'solid' and 'void' by providing a dict which maps the phase number to our desired name as follows:

net = ps.networks.regions_to_network(regions=snow.regions, phases=snow.im)
net = ps.networks.label_phases(network=net, alias={1: 'void', 2: 'grain'})
for item in net.keys():
    print(item)

throat.conns
pore.coords
pore.all
throat.all
pore.region_label
pore.phase
throat.phases
pore.region_volume
pore.equivalent_diameter
pore.local_peak
pore.global_peak
pore.geometric_centroid
throat.global_peak
pore.inscribed_diameter
pore.extended_diameter
throat.inscribed_diameter
throat.total_length
throat.direct_length
throat.perimeter
pore.volume
pore.surface_area
throat.cross_sectional_area
throat.equivalent_diameter
pore.void
throat.void_void
throat.void_grain
pore.grain
throat.grain_void
throat.grain_grain

Now we can see that 'solid' and 'void' have been replaced by 'void' and 'grain'.