def _get_writer(filetype, filename):
import vtk
if filetype in "vtk-ascii":
logging.warning("VTK ASCII files are only meant for debugging.")
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToASCII()
elif filetype == "vtk-binary":
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToBinary()
elif filetype == "vtu-ascii":
logging.warning("VTU ASCII files are only meant for debugging.")
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToAscii()
elif filetype == "vtu-binary":
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToBinary()
elif filetype == "xdmf2":
writer = vtk.vtkXdmfWriter()
elif filetype == "xdmf3":
writer = vtk.vtkXdmf3Writer()
else:
assert filetype == "exodus", "Unknown file type '{}'.".format(filename)
writer = vtk.vtkExodusIIWriter()
# if the mesh contains vtkmodeldata information, make use of it
# and write out all time steps.
writer.WriteAllTimeStepsOn()
return writer
def write(
filename,
vtk_mesh,
point_data = None,
cell_data = None,
field_data = None
):
'''Writes mesh together with data to a file.
:params filename: File to write to.
:type filename: str
:params point_data: Named additional point data to write to the file.
:type point_data: dict
'''
import os
extension = os.path.splitext(filename)[1]
# add point data
is_exodus_format = extension in [ '.ex2', '.exo', '.e' ]
if point_data:
for name, data in point_data.iteritems():
new_name = name
# There is a naming inconsistency in VTK when it comes to
# multivectors in Exodus files:
# If a vector 'v' has two components, they are called 'v_r',
# 'v_z' (note the underscore), if it has three, then they are
# called 'vx', 'vy', 'vz'.
# Make this consistent by appending an underscore if needed.
# Note that for VTK files, this problem does not occur since
# the label of a vector is always stored as a string.
is_3d_vector = len(data.shape) == 2 and data.shape[1] == 3
if is_exodus_format and is_3d_vector and name[-1] != '_':
new_name += '_'
vtk_mesh.GetPointData() \
.AddArray(_create_vtkarray(data, new_name))
# add cell data
if cell_data:
for key, value in cell_data.iteritems():
vtk_mesh.GetCellData() \
.AddArray(_create_vtkarray(value, key))
# add field data
if field_data:
for key, value in field_data.iteritems():
vtk_mesh.GetFieldData() \
.AddArray(_create_vtkarray(value, key))
import re
extension = os.path.splitext(filename)[1]
if extension == '.vtu': # VTK XML format
from vtk import vtkXMLUnstructuredGridWriter
writer = vtkXMLUnstructuredGridWriter()
elif extension == '.pvtu': # parallel VTK XML format
from vtk import vtkXMLPUnstructuredGridWriter
writer = vtkXMLPUnstructuredGridWriter()
elif extension == '.vtk': # classical VTK format
from vtk import vtkUnstructuredGridWriter
writer = vtkUnstructuredGridWriter()
writer.SetFileTypeToASCII()
elif extension == '.xmf': # XDMF format
from vtk import vtkXdmfWriter
writer = vtkXdmfWriter()
elif extension in [ '.ex2', '.exo', '.e' ]: # Exodus II format
from vtk import vtkExodusIIWriter
writer = vtkExodusIIWriter()
# If the mesh contains vtkModelData information, make use of it
# and write out all time steps.
writer.WriteAllTimeStepsOn()
elif re.match('[^\.]*\.e\.\d+\.\d+', filename):
# TODO handle parallel I/O with vtkPExodusIIWriter
from vtk import vtkExodusIIWriter
writer = vtkExodusIIWriter()
# If the mesh contains vtkModelData information, make use of it
# and write out all time steps.
writer.WriteAllTimeStepsOn()
else:
raise IOError( 'Unknown file type \'%s\'.' % filename )
writer.SetFileName( filename )
writer.SetInputData( vtk_mesh )
writer.Write()
return
def write(filetype,
filename,
points,
cells,
point_data=None,
cell_data=None,
field_data=None):
import vtk
from vtk.util import numpy_support
def _create_vtkarray(X, name):
array = vtk.util.numpy_support.numpy_to_vtk(X, deep=1)
array.SetName(name)
return array
if point_data is None:
point_data = {}
if cell_data is None:
cell_data = {}
if field_data is None:
field_data = {}
vtk_mesh = _generate_vtk_mesh(points, cells)
# add point data
pd = vtk_mesh.GetPointData()
for name, X in point_data.items():
# There is a naming inconsistency in VTK when it comes to multivectors
# in Exodus files:
# If a vector 'v' has two components, they are called 'v_x', 'v_y'
# (note the underscore), if it has three, then they are called 'vx',
# 'vy', 'vz'. See bug <http://www.vtk.org/Bug/view.php?id=15894>.
# For VT{K,U} files, no underscore is ever added.
pd.AddArray(_create_vtkarray(X, name))
# Add cell data.
# The cell_data is structured like
#
# cell_type ->
# key -> array
# key -> array
# [...]
# cell_type ->
# key -> array
# key -> array
# [...]
# [...]
#
# VTK expects one array for each `key`, so assemble the keys across all
# mesh_types. This requires each key to be present for each mesh_type, of
# course.
all_keys = []
for cell_type in cell_data:
all_keys += cell_data[cell_type].keys()
# create unified cell data
for key in all_keys:
for cell_type in cell_data:
assert key in cell_data[cell_type]
unified_cell_data = {
key: numpy.concatenate(
[cell_data[cell_type][key] for cell_type in cell_data])
for key in all_keys
}
# add the array data to the mesh
cd = vtk_mesh.GetCellData()
for name, array in unified_cell_data.items():
cd.AddArray(_create_vtkarray(array, name))
# add field data
fd = vtk_mesh.GetFieldData()
for key, value in field_data.items():
fd.AddArray(_create_vtkarray(value, key))
if filetype in 'vtk-ascii':
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToASCII()
elif filetype == 'vtk-binary':
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToBinary()
elif filetype == 'vtu': # vtk xml format
writer = vtk.vtkXMLUnstructuredGridWriter()
elif filetype == 'xdmf':
writer = vtk.vtkXdmfWriter()
elif filetype == 'exodus': # exodus ii format
writer = vtk.vtkExodusIIWriter()
# if the mesh contains vtkmodeldata information, make use of it
# and write out all time steps.
writer.WriteAllTimeStepsOn()
else:
raise RuntimeError('unknown file type \'%s\'.' % filetype)
writer.SetFileName(filename)
try:
writer.SetInput(vtk_mesh)
except AttributeError:
writer.SetInputData(vtk_mesh)
writer.Write()
return
def write(filetype,
filename,
points,
cells,
point_data=None,
cell_data=None,
field_data=None
):
import vtk
from vtk.util import numpy_support
def _create_vtkarray(X, name):
array = vtk.util.numpy_support.numpy_to_vtk(X, deep=1)
array.SetName(name)
return array
if point_data is None:
point_data = {}
if cell_data is None:
cell_data = {}
if field_data is None:
field_data = {}
vtk_mesh = _generate_vtk_mesh(points, cells)
# add point data
pd = vtk_mesh.GetPointData()
for name, X in point_data.iteritems():
# There is a naming inconsistency in VTK when it comes to multivectors
# in Exodus files:
# If a vector 'v' has two components, they are called 'v_x', 'v_y'
# (note the underscore), if it has three, then they are called 'vx',
# 'vy', 'vz'. See bug <http://www.vtk.org/Bug/view.php?id=15894>.
# For VT{K,U} files, no underscore is ever added.
pd.AddArray(_create_vtkarray(X, name))
# add cell data
cd = vtk_mesh.GetCellData()
for key, value in cell_data.iteritems():
cd.AddArray(_create_vtkarray(value, key))
# add field data
fd = vtk_mesh.GetFieldData()
for key, value in field_data.iteritems():
fd.AddArray(_create_vtkarray(value, key))
if filetype in 'vtk-ascii':
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToASCII()
elif filetype == 'vtk-binary':
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToBinary()
elif filetype == 'vtu': # vtk xml format
writer = vtk.vtkXMLUnstructuredGridWriter()
elif filetype == 'xdmf':
writer = vtk.vtkXdmfWriter()
elif filetype == 'exodus': # exodus ii format
writer = vtk.vtkExodusIIWriter()
# if the mesh contains vtkmodeldata information, make use of it
# and write out all time steps.
writer.WriteAllTimeStepsOn()
else:
raise RuntimeError('unknown file type \'%s\'.' % filetype)
writer.SetFileName(filename)
try:
writer.SetInput(vtk_mesh)
except AttributeError:
writer.SetInputData(vtk_mesh)
writer.Write()
return
def write(filetype,
filename,
points,
cells,
point_data=None,
cell_data=None,
field_data=None):
# pylint: disable=import-error
import vtk
def _create_vtkarray(X, name):
array = vtk.util.numpy_support.numpy_to_vtk(X, deep=1)
array.SetName(name)
return array
point_data = {} if point_data is None else point_data
cell_data = {} if cell_data is None else cell_data
field_data = {} if field_data is None else field_data
# assert data integrity
for key in point_data:
assert len(point_data[key]) == len(points), \
'Point data mismatch.'
for key in cell_data:
assert key in cells, 'Cell data without cell'
for key2 in cell_data[key]:
assert len(cell_data[key][key2]) == len(cells[key]), \
'Cell data mismatch.'
vtk_mesh = _generate_vtk_mesh(points, cells)
# add point data
pd = vtk_mesh.GetPointData()
for name, X in point_data.items():
# There is a naming inconsistency in VTK when it comes to multivectors
# in Exodus files:
# If a vector 'v' has two components, they are called 'v_x', 'v_y'
# (note the underscore), if it has three, then they are called 'vx',
# 'vy', 'vz'. See bug <http://www.vtk.org/Bug/view.php?id=15894>.
# For VT{K,U} files, no underscore is ever added.
pd.AddArray(_create_vtkarray(X, name))
# Add cell data.
# The cell_data is structured like
#
# cell_type ->
# key -> array
# key -> array
# [...]
# cell_type ->
# key -> array
# key -> array
# [...]
# [...]
#
# VTK expects one array for each `key`, so assemble the keys across all
# mesh_types. This requires each key to be present for each mesh_type, of
# course.
all_keys = []
for cell_type in cell_data:
all_keys += cell_data[cell_type].keys()
# create unified cell data
for key in all_keys:
for cell_type in cell_data:
assert key in cell_data[cell_type]
unified_cell_data = {
key: numpy.concatenate([
cell_data[cell_type][key]
for cell_type in cell_data
])
for key in all_keys
}
# add the array data to the mesh
cd = vtk_mesh.GetCellData()
for name, array in unified_cell_data.items():
cd.AddArray(_create_vtkarray(array, name))
# add field data
fd = vtk_mesh.GetFieldData()
for key, value in field_data.items():
fd.AddArray(_create_vtkarray(value, key))
if filetype in 'vtk-ascii':
logging.warning('VTK ASCII files are only meant for debugging.')
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToASCII()
elif filetype == 'vtk-binary':
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToBinary()
elif filetype == 'vtu-ascii':
logging.warning('VTU ASCII files are only meant for debugging.')
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToAscii()
elif filetype == 'vtu-binary':
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToBinary()
elif filetype == 'xdmf2':
writer = vtk.vtkXdmfWriter()
elif filetype == 'xdmf3':
writer = vtk.vtkXdmf3Writer()
else:
assert filetype == 'exodus', \
'Unknown file type \'{}\'.'.format(filename)
writer = vtk.vtkExodusIIWriter()
# if the mesh contains vtkmodeldata information, make use of it
# and write out all time steps.
writer.WriteAllTimeStepsOn()
writer.SetFileName(filename)
try:
writer.SetInput(vtk_mesh)
except AttributeError:
writer.SetInputData(vtk_mesh)
writer.Write()
return
def write(filetype,
filename,
points,
cells,
point_data=None,
cell_data=None,
field_data=None):
import vtk
from vtk.util import numpy_support
def _create_vtkarray(X, name):
array = vtk.util.numpy_support.numpy_to_vtk(X, deep=1)
array.SetName(name)
return array
if point_data is None:
point_data = {}
if cell_data is None:
cell_data = {}
if field_data is None:
field_data = {}
vtk_mesh = _generate_vtk_mesh(points, cells)
# add point data
pd = vtk_mesh.GetPointData()
for name, X in point_data.iteritems():
# There is a naming inconsistency in VTK when it comes to multivectors
# in Exodus files:
# If a vector 'v' has two components, they are called 'v_x', 'v_y'
# (note the underscore), if it has three, then they are called 'vx',
# 'vy', 'vz'. See bug <http://www.vtk.org/Bug/view.php?id=15894>.
# For VT{K,U} files, no underscore is ever added.
pd.AddArray(_create_vtkarray(X, name))
# add cell data
cd = vtk_mesh.GetCellData()
for key, value in cell_data.iteritems():
cd.AddArray(_create_vtkarray(value, key))
# add field data
fd = vtk_mesh.GetFieldData()
for key, value in field_data.iteritems():
fd.AddArray(_create_vtkarray(value, key))
if filetype in 'vtk-ascii':
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToASCII()
elif filetype == 'vtk-binary':
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToBinary()
elif filetype == 'vtu': # vtk xml format
writer = vtk.vtkXMLUnstructuredGridWriter()
elif filetype == 'xdmf':
writer = vtk.vtkXdmfWriter()
elif filetype == 'exodus': # exodus ii format
writer = vtk.vtkExodusIIWriter()
# if the mesh contains vtkmodeldata information, make use of it
# and write out all time steps.
writer.WriteAllTimeStepsOn()
else:
raise RuntimeError('unknown file type \'%s\'.' % filetype)
writer.SetFileName(filename)
try:
writer.SetInput(vtk_mesh)
except AttributeError:
writer.SetInputData(vtk_mesh)
writer.Write()
return