Add endpoints, conduit_lengths and pore.area from network models

[TomTranter]

No description provided.

[TomTranter]

@jgostick I added openpnm to the requirments of porespy and now this pr is failing on python 3.5. This was done to make use of the endpoints and conduit_lengths models in openpnm.

[TomTranter]

import porespy as ps
import numpy as np
import openpnm as op

im = ps.generators.blobs([500, 500, 1], porosity=0.8)
snow = ps.filters.snow_partitioning(im, return_all=True)
net = ps.network_extraction.regions_to_network(im=snow.im*snow.regions,
                                               dt=snow.dt,
                                               voxel_size=1)
pn = op.network.GenericNetwork()
pn.update(net)

geo = op.geometry.GenericGeometry(network=pn,
                                  pores=pn.pores(),
                                  throats=pn.throats())
air = op.phases.Air(network=pn)
phys = op.physics.Standard(network=pn, phase=air, geometry=geo)

import matplotlib.pyplot as plt
fig, (ax1, ax2) = plt.subplots(1, 2)
ax1.imshow(im.squeeze())
ax2.imshow(snow.im.squeeze()*snow.regions.squeeze())

def plot_circle(axis, cx, cy, radius):
    theta = np.linspace(0, 2*np.pi, 101)
    x = cx + radius*np.cos(theta)
    y = cy + radius*np.sin(theta)
    axis.plot(x, y, 'r')

for p, [cx, cy, cz] in enumerate(pn['pore.centroid']):
    plot_circle(ax2, cy, cx, pn['pore.inscribed_diameter'][p]/2)

for t in pn.throats():
    ax2.plot([pn['throat.endpoints.tail'][t][1],
              pn['throat.endpoints.head'][t][1]],
             [pn['throat.endpoints.tail'][t][0],
              pn['throat.endpoints.head'][t][0]], 'b')

[TomTranter]

[TomTranter]

As you can see the results aren't perfect but probably good enough for now. @szbrooks has an idea on how to get better results I believe

[codecov]

Codecov Report

Merging #99 into dev will decrease coverage by 0.13%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##              dev      #99      +/-   ##
==========================================
- Coverage   90.62%   90.49%   -0.14%     
==========================================
  Files          17       17              
  Lines        1654     1672      +18     
==========================================
+ Hits         1499     1513      +14     
- Misses        155      159       +4

[TomTranter]

@jgostick I took 3.5 out of travis - is there anywhere else it needs to be updated for the package?

[jgostick]

Shall I merge?

[TomTranter]

I'm sure there will be conflicts. I can do it

[TomTranter]

@jgostick that lat pr just went straight into master!

[TomTranter]

Screw it then, Just merge the other two into dev and sort out the mess in dev

[jgostick]

Oh crap! I didn't even check that, just assumed it was setup correctly. I'll try to fix.

[jgostick]

ok, I fixed the PR and undid the commits to master. I'll try to resolve the conflicts, since I created most of them.