def test_clone_pores_mode_isolated(self):
net = op.network.Cubic(shape=[5, 5, 5])
topotools.clone_pores(network=net,
pores=net.pores('left'),
mode='isolated')
assert net.Np == 150
assert net.Nt == 300
def test_clone_pores_with_labels(self):
net = op.network.Cubic(shape=[5, 5, 5])
topotools.clone_pores(network=net,
pores=net.pores('left'),
labels=['test1', 'test2'])
assert net.num_pores('test1') == 25
assert net.num_pores('test2') == 25
def add_boundary_pores(
self,
labels=["top", "bottom", "front", "back", "left", "right"],
spacing=None):
r"""
Add pores to the faces of the network for use as boundary pores.
Pores are offset from the faces by 1/2 a lattice spacing such that
they lie directly on the boundaries.
Parameters
----------
labels : string or list of strings
The labels indicating the pores defining each face where boundary
pores are to be added (e.g. 'left' or ['left', 'right'])
spacing : scalar or array_like
The spacing of the network (e.g. [1, 1, 1]). This should be given
since it can be quite difficult to infer from the network, for
instance if boundary pores have already added to other faces.
"""
if isinstance(labels, str):
labels = [labels]
x, y, z = self["pore.coords"].T
if spacing is None:
spacing = self._get_spacing()
else:
spacing = np.array(spacing)
if spacing.size == 1:
spacing = np.ones(3) * spacing
Lcx, Lcy, Lcz = spacing
offset = {}
shape = self.settings['shape']
offset["front"] = offset["left"] = offset["bottom"] = [0, 0, 0]
offset["right"] = [Lcx * shape[0], 0, 0]
offset["back"] = [0, Lcy * shape[1], 0]
offset["top"] = [0, 0, Lcz * shape[2]]
scale = {}
scale["left"] = scale["right"] = [0, 1, 1]
scale["front"] = scale["back"] = [1, 0, 1]
scale["bottom"] = scale["top"] = [1, 1, 0]
for label in labels:
try:
Ps = self.pores(label)
topotools.clone_pores(network=self,
pores=Ps,
labels=label + "_boundary",
mode='parents')
# Translate cloned pores
ind = self.pores(label + "_boundary")
coords = self["pore.coords"][ind]
coords = coords * scale[label] + offset[label]
self["pore.coords"][ind] = coords
except KeyError:
logger.warning("No pores labelled " + label +
" were found, skipping boundary addition")
def test_clone_pores_mode_sibings(self):
net = op.network.Cubic(shape=[5, 5, 5])
topotools.clone_pores(network=net,
pores=net.pores('left'),
mode='siblings')
assert net.Np == 150
assert net.Nt == 340
def add_boundary_pores(self, labels=['top', 'bottom', 'front', 'back',
'left', 'right'], spacing=None):
r"""
Add pores to the faces of the network for use as boundary pores.
Pores are offset from the faces by 1/2 a lattice spacing such that
they lie directly on the boundaries.
Parameters
----------
labels : string or list of strings
The labels indicating the pores defining each face where boundary
pores are to be added (e.g. 'left' or ['left', 'right'])
spacing : scalar or array_like
The spacing of the network (e.g. [1, 1, 1]). This should be given
since it can be quite difficult to infer from the network, for
instance if boundary pores have already added to other faces.
"""
if type(labels) == str:
labels = [labels]
x, y, z = self['pore.coords'].T
if spacing is None:
spacing = self._get_spacing()
else:
spacing = sp.array(spacing)
if spacing.size == 1:
spacing = sp.ones(3)*spacing
Lcx, Lcy, Lcz = spacing
offset = {}
offset['front'] = offset['left'] = offset['bottom'] = [0, 0, 0]
offset['back'] = [Lcx*self._shape[0], 0, 0]
offset['right'] = [0, Lcy*self._shape[1], 0]
offset['top'] = [0, 0, Lcz*self._shape[2]]
scale = {}
scale['front'] = scale['back'] = [0, 1, 1]
scale['left'] = scale['right'] = [1, 0, 1]
scale['bottom'] = scale['top'] = [1, 1, 0]
for label in labels:
try:
Ps = self.pores(label)
topotools.clone_pores(network=self, pores=Ps,
labels=label+'_boundary')
# Translate cloned pores
ind = self.pores(label+'_boundary')
coords = self['pore.coords'][ind]
coords = coords*scale[label] + offset[label]
self['pore.coords'][ind] = coords
except KeyError:
logger.warning('No pores labelled ' + label + ' were found, ' +
'skipping boundary addition')
def test_clone_pores_mode_parents(self):
net = op.network.Cubic(shape=[5, 5, 5])
topotools.clone_pores(network=net, pores=net.pores('left'))
assert net.Np == 150
assert net.Nt == 325
def test_clone_pores_mode_isolated(self):
net = op.network.Cubic(shape=[5, 5, 5])
topotools.clone_pores(network=net, pores=net.pores('left'),
mode='isolated')
assert net.Np == 150
assert net.Nt == 300
def test_clone_pores_mode_sibings(self):
net = op.network.Cubic(shape=[5, 5, 5])
topotools.clone_pores(network=net, pores=net.pores('left'),
mode='siblings')
assert net.Np == 150
assert net.Nt == 340
def test_clone_pores_mode_parents(self):
net = op.network.Cubic(shape=[5, 5, 5])
topotools.clone_pores(network=net, pores=net.pores('left'))
assert net.Np == 150
assert net.Nt == 325
