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

[McDonald, Richard]

Thanks Cory,
My fault - I skimmed your article too quickly and didn't understand that
the wrapping provided access to the numpy_interface.algorithms module.  I
appreciate the response. The following works:

#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



On Mon, Oct 19, 2015 at 8:38 AM, Cory Quammen <cory.quammen at kitware.com>
wrote:

> 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.
>



-- 
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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