def test_label_faces_tol(self):
net = op.network.Cubic(shape=[3, 3, 3], spacing=1, connectivity=6)
net.clear(mode='labels')
net['pore.coords'] += np.array([5, 5, 5])
topotools.label_faces(network=net, tol=0.2)
assert net.num_pores('surface') == 26
assert net.num_pores('left') == 9
assert net.num_pores('right') == 9
assert net.num_pores('front') == 9
assert net.num_pores('back') == 9
assert net.num_pores('top') == 9
assert net.num_pores('bottom') == 9
def test_label_faces_tol(self):
net = op.network.Cubic(shape=[3, 3, 3], spacing=1, connectivity=6)
net.clear(mode='labels')
net['pore.coords'] += np.array([5, 5, 5])
topotools.label_faces(network=net, tol=0.2)
assert net.num_pores('surface') == 26
assert net.num_pores('left') == 9
assert net.num_pores('right') == 9
assert net.num_pores('front') == 9
assert net.num_pores('back') == 9
assert net.num_pores('top') == 9
assert net.num_pores('bottom') == 9
def test_label_faces(self):
net = op.network.Cubic(shape=[3, 3, 3], connectivity=6)
net.clear(mode='labels')
assert net.labels() == ['pore.all', 'throat.all']
topotools.label_faces(network=net)
assert net.num_pores('surface') == 26
assert net.num_pores('left') == 9
assert net.num_pores('right') == 9
assert net.num_pores('front') == 9
assert net.num_pores('back') == 9
assert net.num_pores('top') == 9
assert net.num_pores('bottom') == 9
def test_label_faces(self):
net = op.network.Cubic(shape=[3, 3, 3], connectivity=6)
net.clear(mode='labels')
assert net.labels() == ['pore.all', 'throat.all']
topotools.label_faces(network=net)
assert net.num_pores('surface') == 26
assert net.num_pores('left') == 9
assert net.num_pores('right') == 9
assert net.num_pores('front') == 9
assert net.num_pores('back') == 9
assert net.num_pores('top') == 9
assert net.num_pores('bottom') == 9
def __init__(self, shape, mode, spacing=1, **kwargs):
super().__init__(**kwargs)
shape = np.array(shape)
if np.any(shape < 2):
raise Exception('Bravais lattice networks must have at least 2 '
'pores in all directions')
if mode == 'bcc':
# Make a basic cubic for the coner pores
net1 = Cubic(shape=shape)
net1['pore.net1'] = True
# Create a smaller cubic for the body pores, and shift it
net2 = Cubic(shape=shape-1)
net2['pore.net2'] = True
net2['pore.coords'] += 0.5
# Stitch them together
topotools.stitch(net1, net2, net1.Ps, net2.Ps, len_max=0.99)
self.update(net1)
ws.close_project(net1.project)
# Deal with labels
Ps1 = self['pore.net2']
self.clear(mode='labels')
self['pore.corner_sites'] = ~Ps1
self['pore.body_sites'] = Ps1
Ts = self.find_neighbor_throats(pores=self.pores('body_sites'),
mode='exclusive_or')
self['throat.corner_to_body'] = False
self['throat.corner_to_body'][Ts] = True
Ts = self.find_neighbor_throats(pores=self.pores('corner_sites'),
mode='xnor')
self['throat.corner_to_corner'] = False
self['throat.corner_to_corner'][Ts] = True
Ts = self.find_neighbor_throats(pores=self.pores('body_sites'),
mode='xnor')
self['throat.body_to_body'] = False
self['throat.body_to_body'][Ts] = True
elif mode == 'fcc':
shape = np.array(shape)
# Create base cubic network of corner sites
net1 = Cubic(shape=shape)
# Create 3 networks to become face sites
net2 = Cubic(shape=shape - [1, 1, 0])
net3 = Cubic(shape=shape - [1, 0, 1])
net4 = Cubic(shape=shape - [0, 1, 1])
net2['pore.coords'] += np.array([0.5, 0.5, 0])
net3['pore.coords'] += np.array([0.5, 0, 0.5])
net4['pore.coords'] += np.array([0, 0.5, 0.5])
# Remove throats from net2 (trim doesn't work when removing ALL)
for n in [net2, net3, net4]:
n.clear(element='throat', mode='all')
n.update({'throat.all': np.array([], dtype=bool)})
n.update({'throat.conns': np.ndarray([0, 2], dtype=bool)})
# Join networks 2, 3 and 4 into one with all face sites
topotools.stitch(net2, net3, net2.Ps, net3.Ps,
len_min=0.70, len_max=0.75)
topotools.stitch(net2, net4, net2.Ps, net4.Ps,
len_min=0.70, len_max=0.75)
# Join face sites network with the corner sites network
topotools.stitch(net1, net2, net1.Ps, net2.Ps,
len_min=0.70, len_max=0.75)
self.update(net1)
ws.close_project(net1.project)
# Deal with labels
self.clear(mode='labels')
Ps = np.any(np.mod(self['pore.coords'], 1) == 0, axis=1)
self['pore.face_sites'] = Ps
self['pore.corner_sites'] = ~Ps
Ts = self.find_neighbor_throats(pores=self.pores('corner_sites'),
mode='xnor')
self['throat.corner_to_corner'] = False
self['throat.corner_to_corner'][Ts] = True
Ts = self.find_neighbor_throats(pores=self.pores('face_sites'))
self['throat.corner_to_face'] = False
self['throat.corner_to_face'][Ts] = True
elif mode == 'hcp':
raise NotImplementedError('hcp is not implemented yet')
elif mode == 'sc':
net = Cubic(shape=shape, spacing=1)
self.update(net)
ws.close_project(net.project)
self.clear(mode='labels')
self['pore.corner_sites'] = True
self['throat.corner_to_corner'] = True
else:
raise Exception('Unrecognized lattice type: ' + mode)
# Finally scale network to specified spacing
topotools.label_faces(self)
Ps = self.pores(['left', 'right', 'top', 'bottom', 'front', 'back'])
Ps = self.tomask(pores=Ps)
self['pore.surface'] = Ps
self['pore.internal'] = ~Ps
self['pore.coords'] *= np.array(spacing)
def __init__(self, shape, spacing=[1, 1, 1], connectivity=6,
name=None, project=None, **kwargs):
super().__init__(name=name, project=project, **kwargs)
# Take care of 1D/2D networks
shape = np.array(shape, ndmin=1)
shape = np.concatenate((shape, [1] * (3 - shape.size))).astype(int)
arr = np.atleast_3d(np.empty(shape))
# Store original network shape
self.settings['shape'] = np.shape(arr)
# Store network spacing
spacing = np.float64(spacing)
if spacing.size == 2:
spacing = np.concatenate((spacing, [1]))
spacing = np.ones(3, dtype=float) * np.array(spacing, ndmin=1)
self.settings['spacing'] = spacing.tolist()
z = np.tile(np.arange(shape[2]), shape[0] * shape[1])
y = np.tile(np.repeat(np.arange(shape[1]), shape[2]), shape[0])
x = np.repeat(np.arange(shape[0]), shape[1] * shape[2])
points = (np.vstack([x, y, z]).T).astype(float) + 0.5
idx = np.arange(arr.size).reshape(arr.shape)
face_joints = [(idx[:, :, :-1], idx[:, :, 1:]),
(idx[:, :-1], idx[:, 1:]),
(idx[:-1], idx[1:])]
corner_joints = [(idx[:-1, :-1, :-1], idx[1:, 1:, 1:]),
(idx[:-1, :-1, 1:], idx[1:, 1:, :-1]),
(idx[:-1, 1:, :-1], idx[1:, :-1, 1:]),
(idx[1:, :-1, :-1], idx[:-1, 1:, 1:])]
edge_joints = [(idx[:, :-1, :-1], idx[:, 1:, 1:]),
(idx[:, :-1, 1:], idx[:, 1:, :-1]),
(idx[:-1, :, :-1], idx[1:, :, 1:]),
(idx[1:, :, :-1], idx[:-1, :, 1:]),
(idx[1:, 1:, :], idx[:-1, :-1, :]),
(idx[1:, :-1, :], idx[:-1, 1:, :])]
if connectivity == 6:
joints = face_joints
elif connectivity == 6 + 8:
joints = face_joints + corner_joints
elif connectivity == 6 + 12:
joints = face_joints + edge_joints
elif connectivity == 12 + 8:
joints = edge_joints + corner_joints
elif connectivity == 6 + 8 + 12:
joints = face_joints + corner_joints + edge_joints
else:
raise Exception("Invalid connectivity. Must be 6, 14, 18, 20 or 26.")
tails, heads = np.array([], dtype=int), np.array([], dtype=int)
for T, H in joints:
tails = np.concatenate((tails, T.flatten()))
heads = np.concatenate((heads, H.flatten()))
pairs = np.vstack([tails, heads]).T
self["pore.all"] = np.ones([points.shape[0], ], dtype=bool)
self["throat.all"] = np.ones([pairs.shape[0], ], dtype=bool)
self["pore.coords"] = points
self["throat.conns"] = pairs
self["pore.internal"] = True
self["throat.internal"] = True
self._label_surface_pores()
topotools.label_faces(network=self)
Ps = self["pore.surface"]
self["throat.surface"] = np.all(Ps[self["throat.conns"]], axis=1)
# Scale network to requested spacing
self["pore.coords"] *= spacing
def __init__(self, shape, mode='sc', spacing=1, **kwargs):
super().__init__(**kwargs)
shape = np.array(shape)
if np.any(shape < 2):
raise Exception('Bravais lattice networks must have at least 2 '
'pores in all directions')
if mode == 'bcc':
# Make a basic cubic for the coner pores
net1 = Cubic(shape=shape)
net1['pore.net1'] = True
# Create a smaller cubic for the body pores, and shift it
net2 = Cubic(shape=shape - 1)
net2['pore.net2'] = True
net2['pore.coords'] += 0.5
# Stitch them together
topotools.stitch(net1, net2, net1.Ps, net2.Ps, len_max=0.99)
self.update(net1)
ws.close_project(net1.project)
# Deal with labels
Ps1 = self['pore.net2']
self.clear(mode='labels')
self['pore.corner_sites'] = ~Ps1
self['pore.body_sites'] = Ps1
Ts = self.find_neighbor_throats(pores=self.pores('body_sites'),
mode='exclusive_or')
self['throat.corner_to_body'] = False
self['throat.corner_to_body'][Ts] = True
Ts = self.find_neighbor_throats(pores=self.pores('corner_sites'),
mode='xnor')
self['throat.corner_to_corner'] = False
self['throat.corner_to_corner'][Ts] = True
Ts = self.find_neighbor_throats(pores=self.pores('body_sites'),
mode='xnor')
self['throat.body_to_body'] = False
self['throat.body_to_body'][Ts] = True
elif mode == 'fcc':
shape = np.array(shape)
# Create base cubic network of corner sites
net1 = Cubic(shape=shape)
# Create 3 networks to become face sites
net2 = Cubic(shape=shape - [1, 1, 0])
net3 = Cubic(shape=shape - [1, 0, 1])
net4 = Cubic(shape=shape - [0, 1, 1])
net2['pore.coords'] += np.array([0.5, 0.5, 0])
net3['pore.coords'] += np.array([0.5, 0, 0.5])
net4['pore.coords'] += np.array([0, 0.5, 0.5])
# Remove throats from net2 (trim doesn't work when removing ALL)
for n in [net2, net3, net4]:
n.clear(element='throat', mode='all')
n.update({'throat.all': np.array([], dtype=bool)})
n.update({'throat.conns': np.ndarray([0, 2], dtype=bool)})
# Join networks 2, 3 and 4 into one with all face sites
topotools.stitch(net2,
net3,
net2.Ps,
net3.Ps,
method='radius',
len_max=0.75)
topotools.stitch(net2,
net4,
net2.Ps,
net4.Ps,
method='radius',
len_max=0.75)
# Join face sites network with the corner sites network
topotools.stitch(net1,
net2,
net1.Ps,
net2.Ps,
method='radius',
len_max=0.75)
self.update(net1)
ws.close_project(net1.project)
# Deal with labels
self.clear(mode='labels')
Ps = np.any(np.mod(self['pore.coords'], 1) == 0, axis=1)
self['pore.face_sites'] = Ps
self['pore.corner_sites'] = ~Ps
Ts = self.find_neighbor_throats(pores=self.pores('corner_sites'),
mode='xnor')
self['throat.corner_to_corner'] = False
self['throat.corner_to_corner'][Ts] = True
Ts = self.find_neighbor_throats(pores=self.pores('face_sites'))
self['throat.corner_to_face'] = False
self['throat.corner_to_face'][Ts] = True
elif mode == 'hcp':
raise NotImplementedError('hcp is not implemented yet')
elif mode == 'sc':
net = Cubic(shape=shape, spacing=1)
self.update(net)
ws.close_project(net.project)
self.clear(mode='labels')
self['pore.corner_sites'] = True
self['throat.corner_to_corner'] = True
else:
raise Exception('Unrecognized lattice type: ' + mode)
# Finally scale network to specified spacing
topotools.label_faces(self)
Ps = self.pores(['left', 'right', 'top', 'bottom', 'front', 'back'])
Ps = self.to_mask(pores=Ps)
self['pore.surface'] = Ps
self['pore.coords'] *= np.array(spacing)
def __init__(self, shape, spacing=[1, 1, 1], connectivity=6, name=None,
project=None):
# Take care of 1D/2D networks
shape = sp.array(shape, ndmin=1)
shape = np.concatenate((shape, [1]*(3-shape.size))).astype(int)
arr = np.atleast_3d(np.empty(shape))
# Store original network shape
self._shape = sp.shape(arr)
# Store network spacing
spacing = sp.float64(spacing)
if spacing.size == 2:
spacing = sp.concatenate((spacing, [1]))
self._spacing = sp.ones(3, dtype=float)*sp.array(spacing, ndmin=1)
z = np.tile(np.arange(shape[2]), shape[0]*shape[1])
y = np.tile(np.repeat(np.arange(shape[1]), shape[2]), shape[0])
x = np.repeat(np.arange(shape[0]), shape[1]*shape[2])
points = (np.vstack([x, y, z]).T).astype(float) + 0.5
I = np.arange(arr.size).reshape(arr.shape)
face_joints = [(I[:, :, :-1], I[:, :, 1:]),
(I[:, :-1], I[:, 1:]),
(I[:-1], I[1:])]
corner_joints = [(I[:-1, :-1, :-1], I[1:, 1:, 1:]),
(I[:-1, :-1, 1:], I[1:, 1:, :-1]),
(I[:-1, 1:, :-1], I[1:, :-1, 1:]),
(I[1:, :-1, :-1], I[:-1, 1:, 1:])]
edge_joints = [(I[:, :-1, :-1], I[:, 1:, 1:]),
(I[:, :-1, 1:], I[:, 1:, :-1]),
(I[:-1, :, :-1], I[1:, :, 1:]),
(I[1:, :, :-1], I[:-1, :, 1:]),
(I[1:, 1:, :], I[:-1, :-1, :]),
(I[1:, :-1, :], I[:-1, 1:, :])]
if connectivity == 6:
joints = face_joints
elif connectivity == 8:
joints = corner_joints
elif connectivity == 12:
joints = edge_joints
elif connectivity == 14:
joints = face_joints + corner_joints
elif connectivity == 18:
joints = face_joints + edge_joints
elif connectivity == 20:
joints = edge_joints + corner_joints
elif connectivity == 26:
joints = face_joints + corner_joints + edge_joints
else:
raise Exception('Invalid connectivity receieved. Must be 6, 8, '
'12, 14, 18, 20 or 26')
tails, heads = np.array([], dtype=int), np.array([], dtype=int)
for T, H in joints:
tails = np.concatenate((tails, T.flatten()))
heads = np.concatenate((heads, H.flatten()))
pairs = np.vstack([tails, heads]).T
super().__init__(Np=points.shape[0], Nt=pairs.shape[0], name=name,
project=project)
self['pore.coords'] = points
self['throat.conns'] = pairs
self['pore.internal'] = True
self['throat.internal'] = True
self._label_surface_pores()
topotools.label_faces(network=self)
Ps = self['pore.surface']
self['throat.surface'] = sp.all(Ps[self['throat.conns']], axis=1)
# Scale network to requested spacing
self['pore.coords'] *= spacing
