def test_find_connected_sites_with_logic_flattened(self):
am = self.net.get_adjacency_matrix(fmt='coo')
a = topotools.find_connected_sites(bonds=[0, 2],
am=am,
logic='or',
flatten=True)
assert np.all(a == [0, 1, 3])
a = topotools.find_connected_sites(bonds=[0, 2],
am=am,
logic='and',
flatten=True)
assert np.all(a == [])
a = topotools.find_connected_sites(bonds=[0, 2],
am=am,
logic='xor',
flatten=True)
assert np.all(a == [0, 3])
a = topotools.find_connected_sites(bonds=[0, 2],
am=am,
logic='xnor',
flatten=True)
assert np.all(a == [1])
with pytest.raises(Exception):
topotools.find_neighbor_bonds(bonds=[0], am=am, logic='nor')
with pytest.raises(Exception):
topotools.find_neighbor_bonds(bonds=[0], am=am, logic='nand')
def test_find_neighbor_bonds_given_am(self):
am = self.net.create_adjacency_matrix(fmt='lil')
Ts = topotools.find_neighbor_bonds(sites=[0], am=am)
assert np.all(Ts == [0, 1])
with pytest.raises(Exception):
_ = topotools.find_neighbor_bonds(sites=[0],
am=am,
logic="unsupported_logic")
def test_find_neighbor_bonds_with_am_exceptions(self):
am = self.net.get_adjacency_matrix(fmt='coo')
with pytest.raises(Exception):
topotools.find_neighbor_bonds(sites=[1], am=am, flatten=True,
logic='intersection')
with pytest.raises(Exception):
topotools.find_neighbor_bonds(sites=[1], am=am, flatten=False,
logic='or')
def test_find_neighbr_bonds_unflattened(self):
im = self.net.create_incidence_matrix(fmt='lil')
Ts = topotools.find_neighbor_bonds(sites=[0, 1, 5],
logic="and",
im=im,
flatten=False)
assert np.allclose(Ts, [np.array([], dtype="int64")] * 3)
def test_find_neighbor_bonds_with_am_and_logic(self):
am = self.net.get_adjacency_matrix(fmt='coo')
im = self.net.get_incidence_matrix(fmt='coo')
Ts1 = topotools.find_neighbor_bonds(sites=[1],
am=am,
flatten=True,
logic='or')
Ts2 = topotools.find_neighbor_bonds(sites=[1],
im=im,
flatten=True,
logic='or')
assert np.all(Ts1 == Ts2)
Ts1 = topotools.find_neighbor_bonds(sites=[1],
am=am,
flatten=True,
logic='xor')
Ts2 = topotools.find_neighbor_bonds(sites=[1],
im=im,
flatten=True,
logic='xor')
assert np.all(Ts1 == Ts2)
Ts1 = topotools.find_neighbor_bonds(sites=[1],
am=am,
flatten=True,
logic='xnor')
Ts2 = topotools.find_neighbor_bonds(sites=[1],
im=im,
flatten=True,
logic='xnor')
assert np.all(Ts1 == Ts2)
def test_find_neighbor_bonds_with_logic(self):
im = self.net.get_incidence_matrix(fmt='lil')
a = topotools.find_neighbor_bonds(sites=[0, 2], im=im, logic='or')
assert np.all(a == [0, 1, 3])
a = topotools.find_neighbor_bonds(sites=[0, 2], im=im, logic='and')
assert np.all(a == [])
a = topotools.find_neighbor_bonds(sites=[0], im=im, logic='xor')
assert np.all(a == [0, 1])
a = topotools.find_neighbor_bonds(sites=[0], im=im, logic='xnor')
assert np.all(a == [])
with pytest.raises(Exception):
topotools.find_neighbor_bonds(sites=[0], im=im, logic='nor')
with pytest.raises(Exception):
topotools.find_neighbor_bonds(sites=[0], im=im, logic='nand')
def test_find_neighbor_bonds(self):
im = self.net.create_incidence_matrix(fmt='lil')
Ts = topotools.find_neighbor_bonds(sites=[0], im=im)
assert np.all(Ts == [0, 1])
Ts = topotools.find_neighbor_bonds(sites=[1], im=im)
assert np.all(Ts == [0, 2, 3, 5])
Ts = topotools.find_neighbor_bonds(sites=[2], im=im)
assert np.all(Ts == [3])
Ts = topotools.find_neighbor_bonds(sites=[3], im=im)
assert np.all(Ts == [1, 2, 4])
Ts = topotools.find_neighbor_bonds(sites=[4], im=im)
assert np.all(Ts == [4, 5, 6])
Ts = topotools.find_neighbor_bonds(sites=[5], im=im)
assert np.all(Ts == [6])
Ts = topotools.find_neighbor_bonds(sites=[], im=im)
assert Ts == []
def test_find_neighbor_bonds_fmt_not_lil(self):
# Make sure results are correct even if converting to lil internally
im = self.net.create_incidence_matrix(fmt='coo')
Ts = topotools.find_neighbor_bonds(sites=[0], im=im)
assert np.all(Ts == [0, 1])
Ts = topotools.find_neighbor_bonds(sites=[1], im=im)
assert np.all(Ts == [0, 2, 3, 5])
Ts = topotools.find_neighbor_bonds(sites=[2], im=im)
assert np.all(Ts == [3])
Ts = topotools.find_neighbor_bonds(sites=[3], im=im)
assert np.all(Ts == [1, 2, 4])
Ts = topotools.find_neighbor_bonds(sites=[4], im=im)
assert np.all(Ts == [4, 5, 6])
Ts = topotools.find_neighbor_bonds(sites=[5], im=im)
assert np.all(Ts == [6])
def find_neighbor_throats(self, pores, mode='union', flatten=True):
r"""
Returns a list of throats neighboring the given pore(s)
Parameters
----------
pores : array_like
Indices of pores whose neighbors are sought
flatten : boolean, optional
If ``True`` (default) a 1D array of unique throat indices is
returned. If ``False`` the returned array contains arrays of
neighboring throat indices for each input pore, in the order
they were sent.
mode : string
Specifies logic to filter the resulting list. Options are:
**'or'** : (default) All neighbors of the input pores. This is
also known as the 'union' in set theory or 'any' in boolean logic.
Both keywords are accepted and treated as 'or'.
**'xor'** : Only neighbors of one and only one input pore. This
is useful for finding the thraots that are not shared by any of the
input pores.
**'xnor'** : Neighbors that are shared by two or more input pores.
This is equivalent to finding all neighbors with 'or', minus those
found with 'xor', and is useful for finding neighbors that the
inputs have in common.
**'and'** : Only neighbors shared by all input pores. This is also
known as 'intersection' in set theory and (somtimes) as 'all' in
boolean logic. Both keywords are accepted and treated as 'and'.
Returns
-------
If ``flatten`` is ``True``, returns a 1D array of throat indices
filtered according to the specified mode. If ``flatten`` is ``False``,
returns a list of lists, where each list contains the neighbors of the
corresponding input pores.
Notes
-----
The ``logic`` options are applied to neighboring bonds only, thus it
is not possible to obtain bonds that are part of the global set but
not neighbors. This is because (a) the list of global bonds might be
very large, and (b) it is not possible to return a list of neighbors
for each input site if global sites are considered.
Examples
--------
>>> import openpnm as op
>>> pn = op.network.Cubic(shape=[5, 5, 5])
>>> Ts = pn.find_neighbor_throats(pores=[0, 1])
>>> print(Ts)
[ 0 1 100 101 200 201]
>>> Ts = pn.find_neighbor_throats(pores=[0, 1], flatten=False)
>>> print(Ts)
[array([ 0, 100, 200]), array([ 0, 1, 101, 201])]
"""
pores = self._parse_indices(pores)
if sp.size(pores) == 0:
return sp.array([], ndmin=1, dtype=int)
if 'lil' not in self._im.keys():
self.get_incidence_matrix(fmt='lil')
neighbors = topotools.find_neighbor_bonds(sites=pores,
logic=mode,
im=self._im['lil'],
flatten=flatten)
return neighbors
def test_find_neighbor_bonds_single(self):
im = self.net.create_incidence_matrix(fmt='lil')
Ts = topotools.find_neighbor_bonds(sites=0, im=im)
assert np.all(Ts == [0, 1])
def test_find_neighbor_bonds_missing_both_am_and_im(self):
with pytest.raises(Exception):
_ = topotools.find_neighbor_bonds(sites=[0])
