def _save_structured_grid(file_name, vtkStructGrid, directory=""):
"""Saves a VTK structured grid file (vtk) for an already generated
:class:`pyvista.StructuredGrid` object.
Parameters
----------
file_name : str
path to the output vtk file or just its name if directory is specified
directory : str
directory where the UBC GIF file lives
"""
if not isinstance(vtkStructGrid, _vtk.vtkStructuredGrid):
raise RuntimeError(
"`_save_structured_grid` can only handle `vtkStructuredGrid` objects. `{}` is not supported.".format(
vtkStructGrid.__class__
)
)
# Check the extension of the file_name
fname = os.path.join(directory, file_name)
ext = os.path.splitext(fname)[1]
if ext == "":
fname = fname + ".vts"
elif ext not in ".vts":
raise IOError("{:s} is an incorrect extension, has to be .vts".format(ext))
# Make the writer
writer = _vtkStrucWriter()
if float(_vtk_version.split(".")[0]) >= 6:
writer.SetInputDataObject(vtkStructGrid)
else:
writer.SetInput(vtkStructGrid)
writer.SetFileName(fname)
# Write the file
writer.Update()
def _save_rectilinear_grid(filename, vtkRectGrid, directory=''):
"""Saves a VTK rectilinear file (vtr) ffor an already generated
:class:`pyvista.RectilinearGrid` object.
Parameters
----------
filename : str
path to the output vtk file or just its name if directory is specified
directory : str
directory where the UBC GIF file lives
"""
if not isinstance(vtkRectGrid, _vtk.vtkRectilinearGrid):
raise RuntimeError('`_save_rectilinear_grid` can only handle `vtkRectilinearGrid` objects. `{}` is not supported.'.format(vtkRectGrid.__class__))
# Check the extension of the filename
fname = os.path.join(directory, filename)
ext = os.path.splitext(fname)[1]
if ext is '':
fname = fname + '.vtr'
elif ext not in '.vtr':
raise IOError('{:s} is an incorrect extension, has to be .vtr'.format(ext))
# Write the file.
vtrWriteFilter = _vtkRectWriter()
if float(_vtk_version.split('.')[0]) >= 6:
vtrWriteFilter.SetInputDataObject(vtkRectGrid)
else:
vtuWriteFilter.SetInput(vtuObj)
vtrWriteFilter.SetFileName(fname)
vtrWriteFilter.Update()
def _save_unstructured_grid(filename, vtkUnstructGrid, directory=''):
"""Saves a VTK unstructured grid file (vtu) for an already generated
:class:`pyvista.UnstructuredGrid` object.
Parameters
----------
filename : str
path to the output vtk file or just its name if directory is specified
directory : str
directory where the UBC GIF file lives
"""
if not isinstance(vtkUnstructGrid, vtk.vtkUnstructuredGrid):
raise RuntimeError(
'`_save_unstructured_grid` can only handle `vtkUnstructuredGrid` objects. `%s` is not supported.'
% vtkUnstructGrid.__class__)
# Check the extension of the filename
fname = os.path.join(directory, filename)
ext = os.path.splitext(fname)[1]
if ext is '':
fname = fname + '.vtu'
elif ext not in '.vtu':
raise IOError(
'{:s} is an incorrect extension, has to be .vtu'.format(ext))
# Make the writer
vtuWriteFilter = vtkXMLUnstructuredGridWriter()
if float(VTK_VERSION.split('.')[0]) >= 6:
vtuWriteFilter.SetInputDataObject(vtkUnstructGrid)
else:
vtuWriteFilter.SetInput(vtkUnstructGrid)
vtuWriteFilter.SetFileName(fname)
# Write the file
vtuWriteFilter.Update()
def _saveStructuredGrid(fileName, vtkStructGrid, directory=''):
"""Saves a VTK structured grid file (vtk) for an already generated
``vtkStructuredGrid`` object.
Input:
:param str fileName: path to the output vtk file or just its name if directory is specified
:param str directory: directory where the UBC GIF file lives
"""
if not isinstance(vtkStructGrid, vtk.vtkStructuredGrid):
raise RuntimeError(
'`_saveStructuredGrid` can only handle `vtkStructuredGrid` objects. `{}` is not supported.'
.format(vtkStructGrid.__class__))
# Check the extension of the fileName
fname = os.path.join(directory, fileName)
ext = os.path.splitext(fname)[1]
if ext is '':
fname = fname + '.vts'
elif ext not in '.vts':
raise IOError(
'{:s} is an incorrect extension, has to be .vts'.format(ext))
# Make the writer
writer = vtkXMLStructuredGridWriter()
if float(VTK_VERSION.split('.')[0]) >= 6:
writer.SetInputDataObject(vtkStructGrid)
else:
writer.SetInput(vtkStructGrid)
writer.SetFileName(fname)
# Write the file
writer.Update()
def writeVTK(mesh, fileName, models=None):
"""
Makes and saves a VTK rectilinear file (vtr) for a simpeg Tensor mesh and model.
Input:
:param str, path to the output vtk file
:param mesh, SimPEG TensorMesh object - mesh to be transfer to VTK
:param models, dictionary of numpy.array - Name('s) and array('s). Match number of cells
"""
# Import
from vtk import vtkRectilinearGrid as rectGrid, vtkXMLRectilinearGridWriter as rectWriter, VTK_VERSION
from vtk.util.numpy_support import numpy_to_vtk
# Deal with dimensionalities
if mesh.dim >= 1:
vX = mesh.vectorNx
xD = mesh.nNx
yD,zD = 1,1
vY, vZ = np.array([0,0])
if mesh.dim >= 2:
vY = mesh.vectorNy
yD = mesh.nNy
if mesh.dim == 3:
vZ = mesh.vectorNz
zD = mesh.nNz
# Use rectilinear VTK grid.
# Assign the spatial information.
vtkObj = rectGrid()
vtkObj.SetDimensions(xD,yD,zD)
vtkObj.SetXCoordinates(numpy_to_vtk(vX,deep=1))
vtkObj.SetYCoordinates(numpy_to_vtk(vY,deep=1))
vtkObj.SetZCoordinates(numpy_to_vtk(vZ,deep=1))
# Assign the model('s) to the object
if models is not None:
for item in models.iteritems():
# Convert numpy array
vtkDoubleArr = numpy_to_vtk(item[1],deep=1)
vtkDoubleArr.SetName(item[0])
vtkObj.GetCellData().AddArray(vtkDoubleArr)
# Set the active scalar
vtkObj.GetCellData().SetActiveScalars(models.keys()[0])
# vtkObj.Update()
# Check the extension of the fileName
ext = os.path.splitext(fileName)[1]
if ext is '':
fileName = fileName + '.vtr'
elif ext not in '.vtr':
raise IOError('{:s} is an incorrect extension, has to be .vtr')
# Write the file.
vtrWriteFilter = rectWriter()
if float(VTK_VERSION.split('.')[0]) >=6:
vtrWriteFilter.SetInputData(vtkObj)
else:
vtuWriteFilter.SetInput(vtuObj)
vtrWriteFilter.SetFileName(fileName)
vtrWriteFilter.Update()
def writeVTK(mesh, fileName, models=None):
"""
Makes and saves a VTK rectilinear file (vtr) for a simpeg Tensor mesh and model.
Input:
:param str, path to the output vtk file
:param mesh, SimPEG TensorMesh object - mesh to be transfer to VTK
:param models, dictionary of numpy.array - Name('s) and array('s). Match number of cells
"""
# Import
from vtk import vtkRectilinearGrid as rectGrid, vtkXMLRectilinearGridWriter as rectWriter, VTK_VERSION
from vtk.util.numpy_support import numpy_to_vtk
# Deal with dimensionalities
if mesh.dim >= 1:
vX = mesh.vectorNx
xD = mesh.nNx
yD, zD = 1, 1
vY, vZ = np.array([0, 0])
if mesh.dim >= 2:
vY = mesh.vectorNy
yD = mesh.nNy
if mesh.dim == 3:
vZ = mesh.vectorNz
zD = mesh.nNz
# Use rectilinear VTK grid.
# Assign the spatial information.
vtkObj = rectGrid()
vtkObj.SetDimensions(xD, yD, zD)
vtkObj.SetXCoordinates(numpy_to_vtk(vX, deep=1))
vtkObj.SetYCoordinates(numpy_to_vtk(vY, deep=1))
vtkObj.SetZCoordinates(numpy_to_vtk(vZ, deep=1))
# Assign the model('s) to the object
if models is not None:
for item in models.iteritems():
# Convert numpy array
vtkDoubleArr = numpy_to_vtk(item[1], deep=1)
vtkDoubleArr.SetName(item[0])
vtkObj.GetCellData().AddArray(vtkDoubleArr)
# Set the active scalar
vtkObj.GetCellData().SetActiveScalars(models.keys()[0])
# vtkObj.Update()
# Check the extension of the fileName
ext = os.path.splitext(fileName)[1]
if ext is '':
fileName = fileName + '.vtr'
elif ext not in '.vtr':
raise IOError('{:s} is an incorrect extension, has to be .vtr')
# Write the file.
vtrWriteFilter = rectWriter()
if float(VTK_VERSION.split('.')[0]) >= 6:
vtrWriteFilter.SetInputData(vtkObj)
else:
vtuWriteFilter.SetInput(vtuObj)
vtrWriteFilter.SetFileName(fileName)
vtrWriteFilter.Update()
def writeVTK(mesh, fileName, models=None):
"""
Function to write a VTU file from a SimPEG TreeMesh and model.
"""
import vtk
from vtk import vtkXMLUnstructuredGridWriter as Writer, VTK_VERSION
from vtk.util.numpy_support import numpy_to_vtk, numpy_to_vtkIdTypeArray
if str(type(mesh)).split()[-1][1:-2] not in 'SimPEG.Mesh.TreeMesh.TreeMesh':
raise IOError('mesh is not a SimPEG TreeMesh.')
# Make the data parts for the vtu object
# Points
mesh.number()
ptsMat = mesh._gridN + mesh.x0
vtkPts = vtk.vtkPoints()
vtkPts.SetData(numpy_to_vtk(ptsMat,deep=True))
# Cells
cellConn = np.array([c.nodes for c in mesh],dtype=np.int64)
cellsMat = np.concatenate((np.ones((cellConn.shape[0],1),dtype=np.int64)*cellConn.shape[1],cellConn),axis=1).ravel()
cellsArr = vtk.vtkCellArray()
cellsArr.SetNumberOfCells(cellConn.shape[0])
cellsArr.SetCells(cellConn.shape[0],numpy_to_vtkIdTypeArray(cellsMat,deep=True))
# Make the object
vtuObj = vtk.vtkUnstructuredGrid()
vtuObj.SetPoints(vtkPts)
vtuObj.SetCells(vtk.VTK_VOXEL,cellsArr)
# Add the level of refinement as a cell array
cellSides = np.array([np.array(vtuObj.GetCell(i).GetBounds()).reshape((3,2)).dot(np.array([-1, 1])) for i in np.arange(vtuObj.GetNumberOfCells())])
uniqueLevel, indLevel = np.unique(np.prod(cellSides,axis=1),return_inverse=True)
refineLevelArr = numpy_to_vtk(indLevel.max() - indLevel,deep=1)
refineLevelArr.SetName('octreeLevel')
vtuObj.GetCellData().AddArray(refineLevelArr)
# Assign the model('s) to the object
if models is not None:
for item in models.iteritems():
# Convert numpy array
vtkDoubleArr = numpy_to_vtk(item[1],deep=1)
vtkDoubleArr.SetName(item[0])
vtuObj.GetCellData().AddArray(vtkDoubleArr)
# Make the writer
vtuWriteFilter = Writer()
if float(VTK_VERSION.split('.')[0]) >=6:
vtuWriteFilter.SetInputData(vtuObj)
else:
vtuWriteFilter.SetInput(vtuObj)
vtuWriteFilter.SetFileName(fileName)
# Write the file
vtuWriteFilter.Update()
def writeVTK(mesh, fileName, models=None):
"""
Function to write a VTU file from a SimPEG TreeMesh and model.
"""
import vtk
from vtk import vtkXMLUnstructuredGridWriter as Writer, VTK_VERSION
from vtk.util.numpy_support import numpy_to_vtk, numpy_to_vtkIdTypeArray
if str(type(mesh)).split()[-1][1:-2] not in 'SimPEG.Mesh.TreeMesh.TreeMesh':
raise IOError('mesh is not a SimPEG TreeMesh.')
# Make the data parts for the vtu object
# Points
mesh.number()
ptsMat = mesh._gridN + mesh.x0
vtkPts = vtk.vtkPoints()
vtkPts.SetData(numpy_to_vtk(ptsMat,deep=True))
# Cells
cellConn = np.array([c.nodes for c in mesh],dtype=np.int64)
cellsMat = np.concatenate((np.ones((cellConn.shape[0],1),dtype=np.int64)*cellConn.shape[1],cellConn),axis=1).ravel()
cellsArr = vtk.vtkCellArray()
cellsArr.SetNumberOfCells(cellConn.shape[0])
cellsArr.SetCells(cellConn.shape[0],numpy_to_vtkIdTypeArray(cellsMat,deep=True))
# Make the object
vtuObj = vtk.vtkUnstructuredGrid()
vtuObj.SetPoints(vtkPts)
vtuObj.SetCells(vtk.VTK_VOXEL,cellsArr)
# Add the level of refinement as a cell array
cellSides = np.array([np.array(vtuObj.GetCell(i).GetBounds()).reshape((3,2)).dot(np.array([-1, 1])) for i in np.arange(vtuObj.GetNumberOfCells())])
uniqueLevel, indLevel = np.unique(np.prod(cellSides,axis=1),return_inverse=True)
refineLevelArr = numpy_to_vtk(indLevel.max() - indLevel,deep=1)
refineLevelArr.SetName('octreeLevel')
vtuObj.GetCellData().AddArray(refineLevelArr)
# Assign the model('s) to the object
if models is not None:
for item in six.iteritems(models):
# Convert numpy array
vtkDoubleArr = numpy_to_vtk(item[1],deep=1)
vtkDoubleArr.SetName(item[0])
vtuObj.GetCellData().AddArray(vtkDoubleArr)
# Make the writer
vtuWriteFilter = Writer()
if float(VTK_VERSION.split('.')[0]) >=6:
vtuWriteFilter.SetInputData(vtuObj)
else:
vtuWriteFilter.SetInput(vtuObj)
vtuWriteFilter.SetFileName(fileName)
# Write the file
vtuWriteFilter.Update()