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import numpy as np
from paraview.util.vtkAlgorithm import (
VTKPythonAlgorithmBase,
smdomain,
smhint,
smproperty,
smproxy,
)
from vtkmodules.numpy_interface import dataset_adapter as dsa
from vtkmodules.vtkCommonDataModel import vtkUnstructuredGrid
import meshio
paraview_plugin_version = meshio.__version__
vtk_to_meshio_type = meshio._vtk_common.vtk_to_meshio_type
meshio_to_vtk_type = meshio._vtk_common.meshio_to_vtk_type
meshio_input_filetypes = list(meshio._helpers.reader_map.keys())
meshio_extensions = [ext[1:] for ext in meshio.extension_to_filetypes.keys()]
meshio_input_filetypes = ["automatic"] + meshio_input_filetypes
@smproxy.reader(
name="meshio reader",
extensions=meshio_extensions,
file_description="meshio-supported files",
support_reload=False,
)
class MeshioReader(VTKPythonAlgorithmBase):
def __init__(self):
VTKPythonAlgorithmBase.__init__(
self, nInputPorts=0, nOutputPorts=1, outputType="vtkUnstructuredGrid"
)
self._filename = None
self._file_format = None
@smproperty.stringvector(name="FileName")
@smdomain.filelist()
@smhint.filechooser(
extensions=meshio_extensions, file_description="meshio-supported files"
)
def SetFileName(self, filename):
if self._filename != filename:
self._filename = filename
self.Modified()
@smproperty.stringvector(name="StringInfo", information_only="1")
def GetStrings(self):
return meshio_input_filetypes
@smproperty.stringvector(name="FileFormat", number_of_elements="1")
@smdomain.xml(
"""
<StringListDomain name="list">
<RequiredProperties>
<Property name="StringInfo" function="StringInfo"/>
</RequiredProperties>
</StringListDomain>
"""
)
def SetFileFormat(self, file_format):
# Automatically deduce input format
if file_format == "automatic":
file_format = None
if self._file_format != file_format:
self._file_format = file_format
self.Modified()
def RequestData(self, request, inInfoVec, outInfoVec):
output = dsa.WrapDataObject(vtkUnstructuredGrid.GetData(outInfoVec))
# Use meshio to read the mesh
mesh = meshio.read(self._filename, self._file_format)
points, cells = mesh.points, mesh.cells
# Points
if points.shape[1] == 2:
points = np.hstack([points, np.zeros((len(points), 1))])
output.SetPoints(points)
# CellBlock, adapted from test/legacy_writer.py
cell_types = np.array([], dtype=np.ubyte)
cell_offsets = np.array([], dtype=int)
cell_conn = np.array([], dtype=int)
for cellblock in cells:
meshio_type = cellblock.type
data = cellblock.data
vtk_type = meshio_to_vtk_type[meshio_type]
ncells, npoints = data.shape
cell_types = np.hstack(
[cell_types, np.full(ncells, vtk_type, dtype=np.ubyte)]
)
offsets = len(cell_conn) + (1 + npoints) * np.arange(ncells, dtype=int)
cell_offsets = np.hstack([cell_offsets, offsets])
conn = np.hstack(
[npoints * np.ones((ncells, 1), dtype=int), data]
).flatten()
cell_conn = np.hstack([cell_conn, conn])
output.SetCells(cell_types, cell_offsets, cell_conn)
# Point data
for name, array in mesh.point_data.items():
output.PointData.append(array, name)
# Cell data
for name, data in mesh.cell_data.items():
array = np.concatenate(data)
output.CellData.append(array, name)
# Field data
for name, array in mesh.field_data.items():
output.FieldData.append(array, name)
return 1
@smproxy.writer(
name="meshio Writer",
extensions=meshio_extensions,
file_description="meshio-supported files",
support_reload=False,
)
@smproperty.input(name="Input", port_index=0)
@smdomain.datatype(dataTypes=["vtkUnstructuredGrid"], composite_data_supported=False)
class MeshioWriter(VTKPythonAlgorithmBase):
def __init__(self):
VTKPythonAlgorithmBase.__init__(
self, nInputPorts=1, nOutputPorts=0, inputType="vtkUnstructuredGrid"
)
self._filename = None
@smproperty.stringvector(name="FileName", panel_visibility="never")
@smdomain.filelist()
def SetFileName(self, filename):
if self._filename != filename:
self._filename = filename
self.Modified()
def RequestData(self, request, inInfoVec, outInfoVec):
mesh = dsa.WrapDataObject(vtkUnstructuredGrid.GetData(inInfoVec[0]))
# Read points
points = np.asarray(mesh.GetPoints())
# Read cells
# Adapted from test/legacy_reader.py
cell_conn = mesh.GetCells()
cell_offsets = mesh.GetCellLocations()
cell_types = mesh.GetCellTypes()
cells_dict = {}
for vtk_cell_type in np.unique(cell_types):
offsets = cell_offsets[cell_types == vtk_cell_type]
ncells = len(offsets)
npoints = cell_conn[offsets[0]]
array = np.empty((ncells, npoints), dtype=int)
for i in range(npoints):
array[:, i] = cell_conn[offsets + i + 1]
cells_dict[vtk_to_meshio_type[vtk_cell_type]] = array
cells = [meshio.CellBlock(key, cells_dict[key]) for key in cells_dict]
# Read point and field data
# Adapted from test/legacy_reader.py
def _read_data(data):
out = {}
for i in range(data.VTKObject.GetNumberOfArrays()):
name = data.VTKObject.GetArrayName(i)
array = np.asarray(data.GetArray(i))
out[name] = array
return out
point_data = _read_data(mesh.GetPointData())
field_data = _read_data(mesh.GetFieldData())
# Read cell data
cell_data_flattened = _read_data(mesh.GetCellData())
cell_data = {}
for name, array in cell_data_flattened.items():
cell_data[name] = []
for cell_type in cells_dict:
vtk_cell_type = meshio_to_vtk_type[cell_type]
mask_cell_type = cell_types == vtk_cell_type
cell_data[name].append(array[mask_cell_type])
# Use meshio to write mesh
meshio.write_points_cells(
self._filename,
points,
cells,
point_data=point_data,
cell_data=cell_data,
field_data=field_data,
)
return 1
def Write(self):
self.Modified()
self.Update()
|
