[vtkusers] Error using vtk.numpy_interface.algorithms - volume

[Cory Quammen]

Hi Richard,

It looks like you need to wrap your VTK data object, i.e.,

cell_volumes = algs.volume(dsa.WrapDataObject(ds))

This wraps the VTK object in an object that can be passed into the
functions in the numpy_interface.algorithms module.

It looks like you had this in the code, but commented it out. Did wrapping
the VTK object not work?

Thanks,
Cory


On Fri, Oct 16, 2015 at 8:42 PM, McDonald, Richard <rmcd at usgs.gov> wrote:

> Hello,
> I've got a short VTK python code that I'm using the test the
> vtk.numpy_interface.algorithms.  It follows from an example in a paper Cory
> Quammen wrote for 14th Python in Science Conference ("Scientific Data
> Analysis and Visualization with Python, VTK, and Paraview").  I've got a
> numerical simulation of flow in a river saved as a vtk file.  It's a 3D
> solution and I'd really like to get the volume of all the cells in the
> grid.  I've tried the following example using the
> vtk-6.2.0-cp27-none-win_amd64.whl distribution from the Christoph Gohlke
> website and I've also tried it using the VTK 6.3 standalone version of
> python.  The error is the same (AttributeError: VTKObject) that occurs in
> the internal_algorithms.py", line 90, in _cell_quality
>     ds.CopyStructure(dataset.VTKObject).  The code is below and the
> terminal output follows.
>
> Any help would be greatly appreciated.   Also, any other suggestions for
> calculating the volume of cells in an VTKStructuredGrid would also be
> appreciated.
>
> Thanks,
>
> Rich
>
> import vtk
> import vtk.numpy_interface.algorithms as algs
> from vtk.numpy_interface import dataset_adapter as dsa
> import numpy as np
> import vtk.util.numpy_support as nps
>
> file_name3Da = r'E:\RMCD_KOOTENAI_DRIVE_BACKUP\Arcrom\PartTrack\Result_VTK_3D_ASCII1.vtk'
> file_name2Da = r'E:\RMCD_KOOTENAI_DRIVE_BACKUP\Arcrom\PartTrack\Result_VTK_2D_ASCII1.vtk'
> vtkSGrid3D = vtk.vtkStructuredGrid()
> reader3D = vtk.vtkStructuredGridReader()
> reader3D.SetFileName(file_name3Da)
> reader3D.SetOutput(vtkSGrid3D)
> reader3D.Update() # Needed because of GetScalarRange
> output3D = reader3D.GetOutput()
>
> #use vtk.numpy interface
> #ds = dsa.WrapDataObject(reader3D.GetOutput())
>
> ds = reader3D.GetOutput()
> pd = ds.GetPointData()
> Velocity = pd.GetArray("Velocity (magnitude)")
> np_Velocity = nps.vtk_to_numpy(Velocity)
> min_v = np.min(np_Velocity)
> max_v = np.max(np_Velocity)
>
> print min_v, max_v
>
> cell_volumes = algs.volume(ds)
> print cell_volumes
>
> Terminal output:
>
> "C:\VTK 6.3.0\bin\python.exe" "C:/Python Projects/Arcrom/TestVTKNumpy.py"
> Traceback (most recent call last):
>   File "C:/Python Projects/Arcrom/TestVTKNumpy.py", line 29, in <module>
>     cell_volumes = algs.volume(ds)
> 0.0 1.64687
>   File "C:\Python27\Lib\site-packages\vtk\numpy_interface\algorithms.py",
> line 130, in new_dsfunc2
>     return dsfunc(ds)
>   File
> "C:\Python27\Lib\site-packages\vtk\numpy_interface\internal_algorithms.py",
> line 484, in volume
>     return _cell_quality(dataset, "volume")
>   File
> "C:\Python27\Lib\site-packages\vtk\numpy_interface\internal_algorithms.py",
> line 90, in _cell_quality
>     ds.CopyStructure(dataset.VTKObject)
> AttributeError: VTKObject
>
> --
> Richard McDonald
> Hydrologist
> U.S. Geological Survey
> Geomorphology and Sediment Transport Laboratory
> 4620 Technology Drive, Golden, CO 80403
> rmcd at usgs.gov
> 303-278-7952
>
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-- 
Cory Quammen
R&D Engineer
Kitware, Inc.
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