`vedo.file_io.write` throws a DeprecationWarning

[IgorTatarnikov]

Seems GetData and SetCells is deprecated as of vtk 9.6.0. See the traceback below:

  brainglobe_atlasapi/atlas_generation/mesh_utils.py:237: in create_region_mesh
      extract_mesh_from_mask(
  brainglobe_atlasapi/atlas_generation/mesh_utils.py:151: in extract_mesh_from_mask
      write(mesh, str(obj_filepath))
  .tox/py311/lib/python3.11/site-packages/vedo/file_io.py:1354: in write
      for i, f in enumerate(objct.cells):
                            ^^^^^^^^^^^
  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
  
  cls = <vedo.mesh.Mesh object at 0x7f55b19e6790>
  
      @property
      def cells(cls):
          """
          Get the cells connectivity ids as a numpy array.
      
          The output format is: `[[id0 ... idn], [id0 ... idm],  etc]`.
          """
          try:
              # valid for unstructured grid
              arr1d = utils.vtk2numpy(cls.dataset.GetCells().GetData())
          except AttributeError:
              try:
                  # valid for polydata
  >               arr1d = utils.vtk2numpy(cls.dataset.GetPolys().GetData())
                                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  E               DeprecationWarning: Call to deprecated method GetData. (Use ExportLegacyFormat, or GetOffsetsArray/GetConnectivityArray instead.) -- Deprecated since version 9.6.0.

[marcomusy]

Hi, I just committed a fix, can you test if it's ok?
I'm planning to make a release soon..

[IgorTatarnikov]

Thanks for addressing this so quickly! The changes in main address the GetData deprecation warning, it seems there are still some remaining for SetCells.

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
brainglobe_atlasapi/atlas_generation/mesh_utils.py:138: in extract_mesh_from_mask
    mesh = Mesh((vertices, triangles))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
../../miniforge3/envs/atlas-test/lib/python3.13/site-packages/vedo/mesh.py:80: in __init__
    self.dataset = buildPolyData(inputobj[0], inputobj[1])
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

vertices = array([[23.99768684, 24.        , 25.        ],
       [24.        , 23.99768684, 25.        ],
       [24.        , 2...  ],
       [74.00231316, 74.        , 25.        ],
       [74.00231316, 74.        , 73.        ]], shape=(15630, 3))
faces = array([[    2,     1,     0],
       [    1,     3,     0],
       [    6,     5,     4],
       ...,
       [15628, 13219, 13122],
       [15629, 13215, 13220],
       [15629, 13220, 13218]], shape=(31256, 3), dtype=uint64)
lines = None, strips = None, index_offset = 0

    def buildPolyData(vertices, faces=None, lines=None, strips=None, index_offset=0) -> vtki.vtkPolyData:
        """
        Build a `vtkPolyData` object from a list of vertices
        where faces represents the connectivity of the polygonal mesh.
        Lines and triangle strips can also be specified.

        E.g. :
            - `vertices=[[x1,y1,z1],[x2,y2,z2], ...]`
            - `faces=[[0,1,2], [1,2,3], ...]`
            - `lines=[[0,1], [1,2,3,4], ...]`
            - `strips=[[0,1,2,3,4,5], [2,3,9,7,4], ...]`

        A flat list of faces can be passed as `faces=[3, 0,1,2, 4, 1,2,3,4, ...]`.
        For lines use `lines=[2, 0,1, 4, 1,2,3,4, ...]`.

        Use `index_offset=1` if face numbering starts from 1 instead of 0.
        """
        if is_sequence(faces) and len(faces) == 0:
            faces=None
        if is_sequence(lines) and len(lines) == 0:
            lines=None
        if is_sequence(strips) and len(strips) == 0:
            strips=None

        poly = vtki.vtkPolyData()

        if len(vertices) == 0:
            return poly

        vertices = make3d(vertices)
        source_points = vtki.vtkPoints()
        if vedo.settings.force_single_precision_points:
            source_points.SetData(numpy2vtk(vertices, dtype=np.float32))
        else:
            source_points.SetData(numpy2vtk(vertices))
        poly.SetPoints(source_points)

        if lines is not None:
            # Create a cell array to store the lines in and add the lines to it
            linesarr = vtki.vtkCellArray()
            if is_sequence(lines[0]):  # assume format [(id0,id1),..]
                for iline in lines:
                    for i in range(0, len(iline) - 1):
                        i1, i2 = iline[i], iline[i + 1]
                        if i1 != i2:
                            vline = vtki.vtkLine()
                            vline.GetPointIds().SetId(0, i1)
                            vline.GetPointIds().SetId(1, i2)
                            linesarr.InsertNextCell(vline)
            else:  # assume format [id0,id1,...]
                # print("buildPolyData: assuming lines format [id0,id1,...]", lines)
                # TODO CORRECT THIS CASE, MUST BE [2, id0,id1,...]
                for i in range(0, len(lines) - 1):
                    vline = vtki.vtkLine()
                    vline.GetPointIds().SetId(0, lines[i])
                    vline.GetPointIds().SetId(1, lines[i + 1])
                    linesarr.InsertNextCell(vline)
            poly.SetLines(linesarr)

        if faces is not None:

            source_polygons = vtki.vtkCellArray()

            if isinstance(faces, np.ndarray) or not is_ragged(faces):
                ##### all faces are composed of equal nr of vtxs, FAST
                faces = np.asarray(faces)
                if vtki.vtkIdTypeArray().GetDataTypeSize() != 4:
                    ast = np.int64
                else:
                    ast = np.int32

                if faces.ndim > 1:
                    nf, nc = faces.shape
                    hs = np.hstack((np.zeros(nf)[:, None] + nc, faces))
                else:
                    nf = faces.shape[0]
                    hs = faces
                arr = numpy_to_vtkIdTypeArray(hs.astype(ast).ravel(), deep=True)
>               source_polygons.SetCells(nf, arr)
E               DeprecationWarning: Call to deprecated method SetCells. (Use ImportLegacyFormat or SetData instead.) -- Deprecated since version 9.6.0.

../../miniforge3/envs/atlas-test/lib/python3.13/site-packages/vedo/utils.py:1373: DeprecationWarning

[marcomusy]

Hi Igor, I'm currently restructuring the modules, hopefully without breaking anything... Would you give it a try with this branch:

  1. clone repository
     git clone https://github.com/marcomusy/vedo.git
     cd vedo

  2. fetch all branches
     git fetch --all --prune

  3. switch to target branch
     git switch experiment/remove-pointcloud-proxy
     # if branch is not local yet:
     # git switch -c experiment/remove-pointcloud-proxy --track origin/experiment/remove-pointcloud-proxy

  4. install package in editable mode
     python3 -m pip install -e .

[IgorTatarnikov]

Hi Marco, I can confirm all issues seem to be resolved by running with vedo installed from the experiment/remove-pointcloud-proxy branch.

Thanks!

[marcomusy]

Awesome, thanks for the feedback. I'll proceed with a new release soon.