def save(network, filename='', phases=[]):
r"""
Save network and phase data to a single vtp file for visualizing in
Paraview
Parameters
----------
network : OpenPNM Network Object
The Network containing the data to be written
filename : string, optional
Filename to write data. If no name is given the file is named after
ther network
phases : list, optional
A list contain OpenPNM Phase object(s) containing data to be written
Examples
--------
>>> import OpenPNM
>>> pn = OpenPNM.Network.Cubic(shape=[3,3,3])
>>> geo = OpenPNM.Geometry.Stick_and_Ball(network=pn,
... pores=pn.pores(),
... throats=pn.throats())
>>> air = OpenPNM.Phases.Air(network=pn)
>>> phys = OpenPNM.Physics.Standard(network=pn, phase=air,
... pores=pn.pores(), throats=pn.throats())
>>> import OpenPNM.Utilities.IO as io
>>> io.VTK.save(pn,'test_pn.vtp',[air])
>>> # Delete the new file
>>> import os
>>> os.remove('test_pn.vtp')
"""
if filename == '':
filename = network.name
filename = filename.split('.')[0] + '.vtp'
root = _ET.fromstring(VTK._TEMPLATE)
objs = []
if type(phases) != list:
phases = [phases]
for phase in phases:
objs.append(phase)
objs.append(network)
am = misc.amalgamate_data(objs=objs)
key_list = list(sorted(am.keys()))
points = network['pore.coords']
pairs = network['throat.conns']
num_points = len(points)
num_throats = len(pairs)
piece_node = root.find('PolyData').find('Piece')
piece_node.set("NumberOfPoints", str(num_points))
piece_node.set("NumberOfLines", str(num_throats))
points_node = piece_node.find('Points')
coords = VTK._array_to_element("coords", points.T.ravel('F'), n=3)
points_node.append(coords)
lines_node = piece_node.find('Lines')
connectivity = VTK._array_to_element("connectivity", pairs)
lines_node.append(connectivity)
offsets = VTK._array_to_element("offsets", 2*_np.arange(len(pairs))+2)
lines_node.append(offsets)
point_data_node = piece_node.find('PointData')
for key in key_list:
array = am[key]
if array.dtype == _np.bool:
array = array.astype(int)
if array.size != num_points:
continue
element = VTK._array_to_element(key, array)
point_data_node.append(element)
cell_data_node = piece_node.find('CellData')
for key in key_list:
array = am[key]
if array.dtype == _np.bool:
array = array.astype(int)
if array.size != num_throats:
continue
element = VTK._array_to_element(key, array)
cell_data_node.append(element)
tree = _ET.ElementTree(root)
tree.write(filename)
# Make pretty
with open(filename, 'r+') as f:
string = f.read()
string = string.replace('</DataArray>', '</DataArray>\n\t\t\t')
f.seek(0)
# consider adding header: '<?xml version="1.0"?>\n'+
f.write(string)
def save(network, filename='', phases=[]):
r'''
Save network and phase data to a single vtp file for visualizing in
Paraview
Parameters
----------
network : OpenPNM Network Object
The Network containing the data to be written
filename : string, optional
Filename to write data. If no name is given the file is named after
ther network
phases : list, optional
A list contain OpenPNM Phase object(s) containing data to be written
Examples
--------
>>> import OpenPNM
>>> pn = OpenPNM.Network.Cubic(shape=[3,3,3])
>>> geo = OpenPNM.Geometry.Stick_and_Ball(network=pn,pores=pn.pores(),throats=pn.throats())
>>> air = OpenPNM.Phases.Air(network=pn)
>>> phys = OpenPNM.Physics.Standard(network=pn,phase=air,pores=pn.pores(),throats=pn.throats())
>>> import OpenPNM.Utilities.IO as io
>>> io.VTK.save(pn,'test_pn.vtp',[air])
>>> # Delete the new file
>>> import os
>>> os.remove('test_pn.vtp')
'''
if filename == '':
filename = network.name
filename = filename.split('.')[0] + '.vtp'
root = _ET.fromstring(VTK._TEMPLATE)
objs = []
if type(phases) != list:
phases = [phases]
for phase in phases:
objs.append(phase)
objs.append(network)
am = misc.amalgamate_data(objs=objs)
key_list = list(sorted(am.keys()))
points = network['pore.coords']
pairs = network['throat.conns']
num_points = len(points)
num_throats = len(pairs)
piece_node = root.find('PolyData').find('Piece')
piece_node.set("NumberOfPoints", str(num_points))
piece_node.set("NumberOfLines", str(num_throats))
points_node = piece_node.find('Points')
coords = VTK._array_to_element("coords", points.T.ravel('F'), n=3)
points_node.append(coords)
lines_node = piece_node.find('Lines')
connectivity = VTK._array_to_element("connectivity", pairs)
lines_node.append(connectivity)
offsets = VTK._array_to_element("offsets",
2 * _np.arange(len(pairs)) + 2)
lines_node.append(offsets)
point_data_node = piece_node.find('PointData')
for key in key_list:
array = am[key]
if array.dtype == _np.bool: array = array.astype(int)
if array.size != num_points: continue
element = VTK._array_to_element(key, array)
point_data_node.append(element)
cell_data_node = piece_node.find('CellData')
for key in key_list:
array = am[key]
if array.dtype == _np.bool: array = array.astype(int)
if array.size != num_throats: continue
element = VTK._array_to_element(key, array)
cell_data_node.append(element)
tree = _ET.ElementTree(root)
tree.write(filename)
#Make pretty
with open(filename, "r+") as f:
string = f.read()
string = string.replace("</DataArray>", "</DataArray>\n\t\t\t")
f.seek(0)
# consider adding header: '<?xml version="1.0"?>\n'+
f.write(string)
def test_amalgamate_data(self):
dict_ = misc.amalgamate_data(objs=[self.net, self.air])
assert 'pore.'+self.air.name+'_molecular_weight' in dict_.keys()
dict_ = misc.amalgamate_data(objs=[self.net, self.air], delimiter='|')
assert 'pore.'+self.air.name+'|molecular_weight' in dict_.keys()
def test_amalgamate_data(self):
dict_ = misc.amalgamate_data(objs=[self.net, self.air])
assert 'pore.'+self.air.name+'_molecular_weight' in dict_.keys()
dict_ = misc.amalgamate_data(objs=[self.net, self.air], delimiter='|')
assert 'pore.'+self.air.name+'|molecular_weight' in dict_.keys()
def save(network, filename='', phases=[], legacy=True):
r"""
Save network and phase data to a single vtp file for visualizing in
Paraview
Parameters
----------
network : OpenPNM Network Object
The Network containing the data to be written
filename : string, optional
Filename to write data. If no name is given the file is named
after ther network
phases : list, optional
A list contain OpenPNM Phase object(s) containing data to be
written
legacy : boolean
If True (default) the property names will be of the format
\'pore.Cubic_asd43_diameter'\, while if False they will be
\'pore.diameter|Cubic_asd43\'. The latter style is consistent
with all of the other IO methods, while the former is compatible
with existing code, such as Paraview State files. Eventually,
this option will be derprecated and removed.
"""
if filename == '':
filename = network.name
if ~filename.endswith('.vtp'):
filename = filename + '.vtp'
root = _ET.fromstring(VTK._TEMPLATE)
objs = []
if type(phases) != list:
phases = [phases]
for phase in phases:
objs.append(phase)
objs.append(network)
if legacy:
am = _misc.amalgamate_data(objs=objs)
else:
am = {
i: network[i]
for i in network.props(mode=['all', 'deep']) +
network.labels()
}
for phase in phases:
dict_ = {
i + '|' + phase.name: phase[i]
for i in phase.props(mode=['all', 'deep']) +
phase.labels()
}
am.update(dict_)
key_list = list(sorted(am.keys()))
points = network['pore.coords']
pairs = network['throat.conns']
num_points = _sp.shape(points)[0]
num_throats = _sp.shape(pairs)[0]
piece_node = root.find('PolyData').find('Piece')
piece_node.set("NumberOfPoints", str(num_points))
piece_node.set("NumberOfLines", str(num_throats))
points_node = piece_node.find('Points')
coords = VTK._array_to_element("coords", points.T.ravel('F'), n=3)
points_node.append(coords)
lines_node = piece_node.find('Lines')
connectivity = VTK._array_to_element("connectivity", pairs)
lines_node.append(connectivity)
offsets = VTK._array_to_element("offsets",
2 * _np.arange(len(pairs)) + 2)
lines_node.append(offsets)
point_data_node = piece_node.find('PointData')
for key in key_list:
array = am[key]
if array.dtype == _np.bool:
array = array.astype(int)
if array.size != num_points:
continue
element = VTK._array_to_element(key, array)
point_data_node.append(element)
cell_data_node = piece_node.find('CellData')
for key in key_list:
array = am[key]
if array.dtype == _np.bool:
array = array.astype(int)
if array.size != num_throats:
continue
element = VTK._array_to_element(key, array)
cell_data_node.append(element)
tree = _ET.ElementTree(root)
tree.write(filename)
# Make pretty
with open(filename, 'r+') as f:
string = f.read()
string = string.replace('</DataArray>', '</DataArray>\n\t\t\t')
f.seek(0)
# consider adding header: '<?xml version="1.0"?>\n'+
f.write(string)
def save(network, filename='', phases=[], legacy=True):
r"""
Save network and phase data to a single vtp file for visualizing in
Paraview
Parameters
----------
network : OpenPNM Network Object
The Network containing the data to be written
filename : string, optional
Filename to write data. If no name is given the file is named
after ther network
phases : list, optional
A list contain OpenPNM Phase object(s) containing data to be
written
legacy : boolean
If True (default) the property names will be of the format
\'pore.Cubic_asd43_diameter'\, while if False they will be
\'pore.diameter|Cubic_asd43\'. The latter style is consistent
with all of the other IO methods, while the former is compatible
with existing code, such as Paraview State files. Eventually,
this option will be derprecated and removed.
"""
if filename == '':
filename = network.name
if ~filename.endswith('.vtp'):
filename = filename+'.vtp'
root = _ET.fromstring(VTK._TEMPLATE)
objs = []
if type(phases) != list:
phases = [phases]
for phase in phases:
objs.append(phase)
objs.append(network)
if legacy:
am = _misc.amalgamate_data(objs=objs)
else:
am = {i: network[i] for i in
network.props(mode=['all', 'deep']) + network.labels()}
for phase in phases:
dict_ = {i+'|'+phase.name: phase[i] for i in
phase.props(mode=['all', 'deep']) + phase.labels()}
am.update(dict_)
key_list = list(sorted(am.keys()))
points = network['pore.coords']
pairs = network['throat.conns']
num_points = _sp.shape(points)[0]
num_throats = _sp.shape(pairs)[0]
piece_node = root.find('PolyData').find('Piece')
piece_node.set("NumberOfPoints", str(num_points))
piece_node.set("NumberOfLines", str(num_throats))
points_node = piece_node.find('Points')
coords = VTK._array_to_element("coords", points.T.ravel('F'), n=3)
points_node.append(coords)
lines_node = piece_node.find('Lines')
connectivity = VTK._array_to_element("connectivity", pairs)
lines_node.append(connectivity)
offsets = VTK._array_to_element("offsets", 2*_np.arange(len(pairs))+2)
lines_node.append(offsets)
point_data_node = piece_node.find('PointData')
for key in key_list:
array = am[key]
if array.dtype == _np.bool:
array = array.astype(int)
if array.size != num_points:
continue
element = VTK._array_to_element(key, array)
point_data_node.append(element)
cell_data_node = piece_node.find('CellData')
for key in key_list:
array = am[key]
if array.dtype == _np.bool:
array = array.astype(int)
if array.size != num_throats:
continue
element = VTK._array_to_element(key, array)
cell_data_node.append(element)
tree = _ET.ElementTree(root)
tree.write(filename)
# Make pretty
with open(filename, 'r+') as f:
string = f.read()
string = string.replace('</DataArray>', '</DataArray>\n\t\t\t')
f.seek(0)
# consider adding header: '<?xml version="1.0"?>\n'+
f.write(string)