Module pymskt.mesh.io

Functions

def read_vtk(filepath)

Function to read surface mesh using into vtk.vtkPolydata.

Parameters

filepath : str

String of filepath to read.

Returns

vtk.PolyData

The surface mesh at filepath.

Expand source code

def read_vtk(filepath):
    """
    Function to read surface mesh using into `vtk.vtkPolydata`.

    Parameters
    ----------
    filepath : str
        String of filepath to read. 

    Returns
    -------
    vtk.PolyData
        The surface mesh at `filepath`.
    """    
    reader = vtk.vtkPolyDataReader()
    reader.SetFileName(filepath)
    reader.Update()
    return reader.GetOutput()

def write_vtk(mesh, filepath, scalar_name=None, points_dtype=builtins.float, write_binary=False)

Save vtk polydata to disk.

Parameters

mesh : vtk.vtkPolyData

PolyData of surface mesh to be saved to disk.

filepath : str

Location & filename to save mesh to.

scalar_name : str, optional

A name to assign to the active scalars of the surface mesh before saving it, by default None meaning that no name will be applied.

points_dtype : type, optional

Specifies the datatype that the points should be. If they are the wrong datatype then they are changed to the requisite type before savinge (writing) the file.

write_binary : bool, optional

Specify if the save file should be binary (True) or ASCII (False). Default is False (so it will save in Binary).

Notes

Fileversion is the old legacy version because new tools (Slicer, Paraview) dont support vtk version 5.1 which shipped with VTK 9. https://discourse.vtk.org/t/legacy-polydata-file-compatibility/5354 https://discourse.vtk.org/t/can-we-write-out-the-old-vtk-4-2-file-format-with-vtk-9/5066/17 https://gitlab.kitware.com/vtk/vtk/-/merge_requests/7652/diffs?commit_id=7f76b9e97b1a05cfe4fcd5f9af58f0d7a385b639#528e66f324b988666af9696641f935da71b6f670

Expand source code

def write_vtk(
    mesh, 
    filepath, 
    scalar_name=None, 
    points_dtype=float,
    write_binary=False
):
    """
    Save vtk polydata to disk. 

    Parameters
    ----------
    mesh : vtk.vtkPolyData
        PolyData of surface mesh to be saved to disk. 
    filepath : str
        Location & filename to save mesh to. 
    scalar_name : str, optional
        A name to assign to the active scalars of the surface mesh before saving it, by default None
        meaning that no name will be applied.
    points_dtype : type, optional
        Specifies the datatype that the points should be. 
        If they are the wrong datatype then they are changed to the requisite
        type before savinge (writing) the file. 
    write_binary : bool, optional
        Specify if the save file should be binary (True) or ASCII (False). Default is False (so it will save in Binary).  

    
    Notes
    ----------
    Fileversion is the old legacy version because new tools (Slicer, Paraview) dont support vtk
    version 5.1 which shipped with VTK 9. 
    https://discourse.vtk.org/t/legacy-polydata-file-compatibility/5354
    https://discourse.vtk.org/t/can-we-write-out-the-old-vtk-4-2-file-format-with-vtk-9/5066/17
    https://gitlab.kitware.com/vtk/vtk/-/merge_requests/7652/diffs?commit_id=7f76b9e97b1a05cfe4fcd5f9af58f0d7a385b639#528e66f324b988666af9696641f935da71b6f670
    """

    _, extension = os.path.splitext(filepath)

    points = mesh.GetPoints()
    if vtk_to_numpy(points.GetData()).dtype != points_dtype:
        points.SetData(numpy_to_vtk(vtk_to_numpy(points.GetData()).astype(float)))

    if extension == '.vtk':
        writer = vtk.vtkPolyDataWriter()
    elif extension == '.stl':
        writer = vtk.vtkSTLWriter()
    writer.SetFileName(filepath)
    writer.SetInputData(mesh)
    if scalar_name is not None:
        writer.SetScalarsName(scalar_name)
    
    if write_binary is True:
        writer.SetFileTypeToBinary()
    elif write is False:
        writer.SetFileTypeToASCII()
    writer.Write()