def save(cls, network, phases=[], filename='', delim=' | ',
fill_nans=None, fill_infs=None):
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
phases : list, optional
A list containing OpenPNM Phase object(s) containing data to be
written
filename : string, optional
Filename to write data. If no name is given the file is named
after the network
delim : string
Specify which character is used to delimit the data names. The
default is ' | ' which creates a nice clean output in the Paraview
pipeline viewer (e.g. net | property | pore | diameter)
fill_nans : scalar
The value to use to replace NaNs with. The VTK file format does
not work with NaNs, so they must be dealt with. The default is
`None` which means property arrays with NaNs are not written to the
file. Other useful options might be 0 or -1, but the user must
be aware that these are not real values, only place holders.
fill_infs : scalar
The value to use to replace infs with. The default is ``None``
which means that property arrays containing ``None`` will *not*
be written to the file, and a warning will be issued. A useful
value is
"""
project, network, phases = cls._parse_args(network=network,
phases=phases)
# Check if any of the phases has time series
transient = GenericIO.is_transient(phases=phases)
if transient:
logger.warning('vtp format does not support transient data, ' +
'use xdmf instead')
if filename == '':
filename = project.name
filename = cls._parse_filename(filename=filename, ext='vtp')
am = Dict.to_dict(network=network, phases=phases, interleave=True,
categorize_by=['object', 'data'])
am = FlatDict(am, delimiter=delim)
key_list = list(sorted(am.keys()))
network = network[0]
points = network['pore.coords']
pairs = network['throat.conns']
num_points = np.shape(points)[0]
num_throats = np.shape(pairs)[0]
root = ET.fromstring(VTK._TEMPLATE)
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')
cell_data_node = piece_node.find('CellData')
for key in key_list:
array = am[key]
if array.dtype == 'O':
logger.warning(key + ' has dtype object,' +
' will not write to file')
else:
if array.dtype == np.bool:
array = array.astype(int)
if np.any(np.isnan(array)):
if fill_nans is None:
logger.warning(key + ' has nans,' +
' will not write to file')
continue
else:
array[np.isnan(array)] = fill_nans
if np.any(np.isinf(array)):
if fill_infs is None:
logger.warning(key + ' has infs,' +
' will not write to file')
continue
else:
array[np.isinf(array)] = fill_infs
element = VTK._array_to_element(key, array)
if (array.size == num_points):
point_data_node.append(element)
elif (array.size == num_throats):
cell_data_node.append(element)
tree = ET.ElementTree(root)
tree.write(filename)
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(cls, network, phases=[], filename=''):
r"""
Saves (transient/steady-state) data from the given objects into the
specified file.
Parameters
----------
network : OpenPNM Network Object
The network containing the desired data
phases : list of OpenPNM Phase Objects (optional, default is none)
A list of phase objects whose data are to be included
Notes
-----
This method only saves the data, not any of the pore-scale models or
other attributes. To save an actual OpenPNM Project use the
``Workspace`` object.
"""
project, network, phases = cls._parse_args(network=network,
phases=phases)
network = network[0]
# Check if any of the phases has time series
transient = GenericIO.is_transient(phases=phases)
if filename == '':
filename = project.name
path = cls._parse_filename(filename=filename, ext='xmf')
# Path is a pathlib object, so slice it up as needed
fname_xdf = path.name
d = Dict.to_dict(network, phases=phases, interleave=True,
flatten=False, categorize_by=['element', 'data'])
D = FlatDict(d, delimiter='/')
# Identify time steps
t_steps = []
if transient:
for key in D.keys():
if '@' in key:
t_steps.append(key.split('@')[1])
t_grid = create_grid(Name="TimeSeries", GridType="Collection",
CollectionType="Temporal")
# If steady-state, define '0' time step
if not transient:
t_steps.append('0')
# Setup xdmf file
root = create_root('Xdmf')
domain = create_domain()
# Iterate over time steps present
for t in range(len(t_steps)):
# Define the hdf file
if not transient:
fname_hdf = path.stem+".hdf"
else:
fname_hdf = path.stem+'@'+t_steps[t]+".hdf"
path_p = path.parent
f = h5py.File(path_p.joinpath(fname_hdf), "w")
# Add coordinate and connection information to top of HDF5 file
f["coordinates"] = network["pore.coords"]
f["connections"] = network["throat.conns"]
# geometry coordinates
row, col = f["coordinates"].shape
dims = ' '.join((str(row), str(col)))
hdf_loc = fname_hdf + ":coordinates"
geo_data = create_data_item(value=hdf_loc, Dimensions=dims,
Format='HDF', DataType="Float")
geo = create_geometry(GeometryType="XYZ")
geo.append(geo_data)
# topolgy connections
row, col = f["connections"].shape # col first then row
dims = ' '.join((str(row), str(col)))
hdf_loc = fname_hdf + ":connections"
topo_data = create_data_item(value=hdf_loc, Dimensions=dims,
Format="HDF", NumberType="Int")
topo = create_topology(TopologyType="Polyline",
NodesPerElement=str(2),
NumberOfElements=str(row))
topo.append(topo_data)
# Make HDF5 file with all datasets, and no groups
for item in D.keys():
if D[item].dtype == 'O':
logger.warning(item + ' has dtype object,' +
' will not write to file')
del D[item]
elif 'U' in str(D[item][0].dtype):
pass
elif ('@' in item and t_steps[t] == item.split('@')[1]):
f.create_dataset(name='/'+item.split('@')[0]+'@t',
shape=D[item].shape,
dtype=D[item].dtype,
data=D[item])
elif ('@' not in item and t == 0):
f.create_dataset(name='/'+item, shape=D[item].shape,
dtype=D[item].dtype, data=D[item])
# Create a grid
grid = create_grid(Name=t_steps[t], GridType="Uniform")
time = create_time(type='Single', Value=t_steps[t])
grid.append(time)
# Add pore and throat properties
for item in D.keys():
if item not in ['coordinates', 'connections']:
if (('@' in item and t_steps[t] == item.split('@')[1]) or
('@' not in item)):
attr_type = 'Scalar'
shape = D[item].shape
dims = (''.join([str(i) +
' ' for i in list(shape)[::-1]]))
if '@' in item:
item = item.split('@')[0]+'@t'
hdf_loc = fname_hdf + ":" + item
elif ('@' not in item and t == 0):
hdf_loc = fname_hdf + ":" + item
elif ('@' not in item and t > 0):
hdf_loc = (path.stem+'@'+t_steps[0]+".hdf" +
":" + item)
attr = create_data_item(value=hdf_loc,
Dimensions=dims,
Format='HDF',
Precision='8',
DataType='Float')
name = item.replace('/', ' | ')
if 'throat' in item:
Center = "Cell"
else:
Center = "Node"
el_attr = create_attribute(Name=name, Center=Center,
AttributeType=attr_type)
el_attr.append(attr)
grid.append(el_attr)
else:
pass
grid.append(topo)
grid.append(geo)
t_grid.append(grid)
# CLose the HDF5 file
f.close()
domain.append(t_grid)
root.append(domain)
with open(path_p.joinpath(fname_xdf), 'w') as file:
file.write(cls._header)
file.write(ET.tostring(root).decode("utf-8"))
def save(cls,
network,
phases=[],
filename='',
delim=' | ',
fill_nans=None,
fill_infs=None):
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
phases : list, optional
A list containing OpenPNM Phase object(s) containing data to be
written
filename : string, optional
Filename to write data. If no name is given the file is named
after the network
delim : string
Specify which character is used to delimit the data names. The
default is ' | ' which creates a nice clean output in the Paraview
pipeline viewer (e.g. net | property | pore | diameter)
fill_nans : scalar
The value to use to replace NaNs with. The VTK file format does
not work with NaNs, so they must be dealt with. The default is
`None` which means property arrays with NaNs are not written to the
file. Other useful options might be 0 or -1, but the user must
be aware that these are not real values, only place holders.
fill_infs : scalar
The value to use to replace infs with. The default is ``None``
which means that property arrays containing ``None`` will *not*
be written to the file, and a warning will be issued. A useful
value is
"""
project, network, phases = cls._parse_args(network=network,
phases=phases)
# Check if any of the phases has time series
transient = GenericIO.is_transient(phases=phases)
if transient:
logger.warning('vtp format does not support transient data, ' +
'use xdmf instead')
if filename == '':
filename = project.name
filename = cls._parse_filename(filename=filename, ext='vtp')
am = Dict.to_dict(network=network,
phases=phases,
interleave=True,
categorize_by=['object', 'data'])
am = FlatDict(am, delimiter=delim)
key_list = list(sorted(am.keys()))
network = network[0]
points = network['pore.coords']
pairs = network['throat.conns']
num_points = np.shape(points)[0]
num_throats = np.shape(pairs)[0]
root = ET.fromstring(VTK._TEMPLATE)
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')
cell_data_node = piece_node.find('CellData')
for key in key_list:
array = am[key]
if array.dtype == 'O':
logger.warning(key + ' has dtype object,' +
' will not write to file')
else:
if array.dtype == np.bool:
array = array.astype(int)
if np.any(np.isnan(array)):
if fill_nans is None:
logger.warning(key + ' has nans,' +
' will not write to file')
continue
else:
array[np.isnan(array)] = fill_nans
if np.any(np.isinf(array)):
if fill_infs is None:
logger.warning(key + ' has infs,' +
' will not write to file')
continue
else:
array[np.isinf(array)] = fill_infs
element = VTK._array_to_element(key, array)
if (array.size == num_points):
point_data_node.append(element)
elif (array.size == num_throats):
cell_data_node.append(element)
tree = ET.ElementTree(root)
tree.write(filename)
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)