[vtkusers] from vtk import * ImportError: (Python VTK 6.2 on ubuntu 14.04)
Dan Lipsa
dan.lipsa at kitware.com
Mon Aug 10 16:10:48 EDT 2015
Manjunath,
Can you try 6.3.0.rc1 rather than 6.2.0? As I said I tried your example on
my build of VTK (which was a recent version from the git repository) and I
did not get the error you are seeing.
Dan
On Mon, Aug 10, 2015 at 11:12 AM Manjunath K E <ke.manjunath at gmail.com>
wrote:
> Hi Dan Lipsa,
>>
>>
>> I checked out vtk 6.2 as per the instructions in
>> https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/download.md
>>
>> I rebuilt VTK and when I try to run the following code, the problem of
>> GetRange() still persists.
>>
>> >>> from vtk import *
>> >>> reader = vtkNetCDFCFReader()
>> >>> reader.SetFileName("3d.nc")
>> >>> reader.SphericalCoordinatesOff()
>> >>> reader.SetReplaceFillValueWithNan(1)
>> >>> reader.Update()
>> >>>
>> reader.GetOutput().GetPointData().SetScalars(reader.GetOutput().GetPointData().GetArray("SAL"))
>> 0
>> >>> reader.UpdateMetaData()
>> 1
>> >>> reader.Update()
>> >>> reader.UpdateInformation()
>> >>> reader.GetOutput().GetPointData().GetScalars().GetRange()
>> (nan, nan)
>>
>> Although the range is (28.04-36.88), but I get (nan, nan). Please help me.
>>
>> Thanks and Regards,
>> Manjunath K E
>>
>> ---------- Forwarded message ----------
>> From: Dan Lipsa <dan.lipsa at kitware.com>
>> Date: Wed, Aug 5, 2015 at 8:06 PM
>> Subject: Re: [vtkusers] from vtk import * ImportError: (Python VTK 6.2 on
>> ubuntu 14.04)
>> To: Manjunath K E <ke.manjunath at gmail.com>, VTK Users <vtkusers at vtk.org>
>>
>>
>> Manjunath,
>> I get a range rather than NaN when I run it on my machine with the latest
>> VTK from git master.
>>
>> Range of SAL: 28.04-36.88
>>
>> I do have error complaining about missing
>> sliceOn.jpg and sliceOff.jpg.
>>
>> Could you try your example on the latest VTK master (your have to build
>> it)
>>
>>
>> http://www.vtk.org/Wiki/VTK/Configure_and_Build
>>
>> or on VTK 6.3 rc1?
>> http://www.vtk.org/download/
>>
>> I am not sure what your other python error is, maybe related to
>>
>> http://stackoverflow.com/questions/15608236/eclipse-and-google-app-engine-importerror-no-module-named-sysconfigdata-nd-u
>>
>>
>> On Wed, Aug 5, 2015 at 9:41 AM, Manjunath K E <ke.manjunath at gmail.com>
>> wrote:
>>
>>> Hi Dan Lipsa,
>>>
>>> Please find the required file "3d.nc" and the python code is
>>> attached in "datareader.py1".
>>>
>>> The problem is that the *a,b = reader.GetOutput().*
>>> *GetPointData().GetScalars().**GetRange() *is returning NaN value.
>>>
>>> one more thing I found was, when I start *"vtkpython**"* by keeping *"*
>>> */usr/lib/python2.7**" *in *"PYTHONPATH**" *then following error will
>>> be obtained. If I remove *"**/usr/lib/python2.7" *from *"PYTHONPATH**"*,
>>> I wont get any error.
>>>
>>> export
>>> PYTHONPATH=/usr/lib/python2.7:/usr/local/lib/python2.7/site-packages:$PYTHONPATH
>>>
>>> manju at iiitb-gvcl-Z800:~/manju/academics/iiitb/project/codes/incois__laptp/src_vtk6$
>>> vtkpython
>>> vtk version 6.2.0
>>> Traceback (most recent call last):
>>> File "/usr/lib/python2.7/site.py", line 563, in <module>
>>> main()
>>> File "/usr/lib/python2.7/site.py", line 545, in main
>>> known_paths = addusersitepackages(known_paths)
>>> File "/usr/lib/python2.7/site.py", line 272, in addusersitepackages
>>> user_site = getusersitepackages()
>>> File "/usr/lib/python2.7/site.py", line 247, in getusersitepackages
>>> user_base = getuserbase() # this will also set USER_BASE
>>> File "/usr/lib/python2.7/site.py", line 237, in getuserbase
>>> USER_BASE = get_config_var('userbase')
>>> File "/usr/lib/python2.7/sysconfig.py", line 578, in get_config_var
>>> return get_config_vars().get(name)
>>> File "/usr/lib/python2.7/sysconfig.py", line 524, in get_config_vars
>>> _init_posix(_CONFIG_VARS)
>>> File "/usr/lib/python2.7/sysconfig.py", line 408, in _init_posix
>>> from _sysconfigdata import build_time_vars
>>> File "/usr/lib/python2.7/_sysconfigdata.py", line 6, in <module>
>>> from _sysconfigdata_nd import *
>>> ImportError: No module named _sysconfigdata_nd
>>>
>>>
>>> Thanks and Regards,
>>>
>>> Manjunath K E
>>> Help Ever Hurt Never
>>>
>>>
>>> On Tue, Aug 4, 2015 at 10:15 PM, Dan Lipsa <dan.lipsa at kitware.com>
>>> wrote:
>>>
>>>> It would be great if you could share your data as well so that I can
>>>> check it with my installation. Thanks,
>>>> Dan
>>>>
>>>>
>>>> On Tue, Aug 4, 2015 at 11:31 AM Manjunath K E <ke.manjunath at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Dan Lipsa,
>>>>>
>>>>> Thanks for the reply. The error is occurring during runtime. There was
>>>>> no error, when i ran it in interpreter. All the lines in the script
>>>>> executed smoothly.
>>>>> I have tested the same code using vtk 6.0.0 there was no error.
>>>>>
>>>>> Also, the output that i get is not proper. There is problem in the
>>>>> color map of the output produced. The scale bar is not displayed properly.
>>>>> ==========================================
>>>>> #!/usr/bin/env python
>>>>> from vtk import *
>>>>>
>>>>> reader = vtkNetCDFCFReader()
>>>>> reader.SetFileName("3d.nc")
>>>>> reader.SphericalCoordinatesOff()
>>>>> reader.SetOutputType(6)
>>>>> reader.SetReplaceFillValueWithNan(1)
>>>>> reader.Update()
>>>>> #Copy SAL Array to scalar value field of point data ..this makes point
>>>>> data to point to SAL array
>>>>>
>>>>> reader.GetOutput().GetPointData().SetScalars(reader.GetOutput().GetPointData().GetArray("SAL"))
>>>>> reader.UpdateMetaData()
>>>>> reader.Update()
>>>>> reader.UpdateInformation()
>>>>> output = reader.GetOutput()
>>>>>
>>>>> a,b = reader.GetOutput().GetPointData().GetScalars().GetRange()
>>>>> lut = vtk.vtkColorTransferFunction()
>>>>> lut.AddRGBPoint(a, 0.0, 0.0, 0.8)
>>>>> lut.AddRGBPoint(a+(b-a)/4, 0.0, 0.5, 0.5)
>>>>> lut.AddRGBPoint(a+(b-a)/2, 0.0, 1.0, 0.0)
>>>>> lut.AddRGBPoint(b-(b-a)/4, 0.5, 0.5, 0.0)
>>>>> lut.AddRGBPoint(b, 1.0, 0.0, 0.0)
>>>>> lut.SetNanColor(0,0,1)
>>>>>
>>>>> # the mapper that will use the lookup table
>>>>> mapper = vtkDataSetMapper()
>>>>> mapper.SetInputData(reader.GetOutput())
>>>>> mapper.SetScalarModeToUsePointData()
>>>>> mapper.SetLookupTable(lut)
>>>>> mapper.SetScalarRange(a,b)
>>>>> # the actor
>>>>> gridActor = vtkActor()
>>>>> gridActor.SetMapper( mapper )
>>>>> scaleBarActor = vtkScalarBarActor()
>>>>> scaleBarActor.SetLookupTable( mapper.GetLookupTable() )
>>>>> scaleBarActor.SetTitle("Color Map for Point Data")
>>>>> scaleBarActor.SetOrientationToHorizontal()
>>>>> scaleBarActor.GetLabelTextProperty().SetColor(0,0,1)
>>>>> scaleBarActor.GetTitleTextProperty().SetColor(0,0,1)
>>>>>
>>>>> # position it in window
>>>>> coord = scaleBarActor.GetPositionCoordinate()
>>>>> coord.SetCoordinateSystemToNormalizedViewport()
>>>>> coord.SetValue(0.1,0.05)
>>>>> scaleBarActor.SetWidth(.5)
>>>>> scaleBarActor.SetHeight(.1)
>>>>>
>>>>> # renderer and render window
>>>>> renderer = vtkRenderer()
>>>>> renderer.SetBackground(1, 1, 1)
>>>>> renderer.SetGradientBackground(1) # Set background to white
>>>>> renWindow = vtk.vtkRenderWindow()
>>>>> renWindow.SetSize(512, 512)
>>>>> renWindow.AddRenderer( renderer )
>>>>>
>>>>> # render window interactor
>>>>> renWinInteractor = vtkRenderWindowInteractor()
>>>>> renWinInteractor.SetRenderWindow( renWindow )
>>>>> # add the actors to the renderer
>>>>> renderer.AddActor( gridActor )
>>>>> renderer.AddActor( scaleBarActor )
>>>>>
>>>>> #show axes
>>>>> axesActor = vtkAxesActor()
>>>>> widget = vtkOrientationMarkerWidget()
>>>>> widget.SetOrientationMarker( axesActor )
>>>>> widget.SetInteractor( renWinInteractor )
>>>>> widget.SetViewport( 0.0, 0.0, 0.4, 0.4 )
>>>>> widget.SetEnabled( 1 )
>>>>> widget.InteractiveOff()
>>>>>
>>>>> # render
>>>>> renderer.ResetCamera();
>>>>> renWindow.Render()
>>>>> # initialize and start the interactor
>>>>> renWinInteractor.Initialize()
>>>>> renWinInteractor.Start()
>>>>> ==================================================
>>>>>
>>>>>
>>>>> Thanks and Regards,
>>>>>
>>>>> Manjunath K E
>>>>> Help Ever Hurt Never
>>>>>
>>>>>
>>>>> On Tue, Aug 4, 2015 at 12:31 AM, Dan Lipsa <dan.lipsa at kitware.com>
>>>>> wrote:
>>>>>
>>>>>> Manjunath,
>>>>>> Can you share the script you are trying to run? This seems like a
>>>>>> problem with the script rather than an installation issue.
>>>>>>
>>>>>> On Mon, Aug 3, 2015 at 2:16 PM Manjunath K E <ke.manjunath at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Shawn,
>>>>>>>
>>>>>>> I followed your instructions, now the vtk importing problem is
>>>>>>> solved.
>>>>>>> But, following error is obtained
>>>>>>>
>>>>>>> ERROR: In
>>>>>>> /home/kitware/Desktop/vtkbuild/build/vtk/src/vtk/Rendering/OpenGL/vtkOpenGLTexture.cxx,
>>>>>>> line 200
>>>>>>> vtkOpenGLTexture (0x2f2ac90): No scalar values found for texture
>>>>>>> input!
>>>>>>>
>>>>>>> The error is seen for every frame
>>>>>>>
>>>>>>> Thanks and Regards,
>>>>>>>
>>>>>>> Manjunath K E
>>>>>>> Help Ever Hurt Never
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Aug 3, 2015 at 11:36 PM, Shawn Waldon <
>>>>>>> shawn.waldon at kitware.com> wrote:
>>>>>>>
>>>>>>>> Hi Manjunath,
>>>>>>>>
>>>>>>>> Please keep discussions on the list so that others can benefit
>>>>>>>> later.
>>>>>>>>
>>>>>>>> I haven't used an install tree on Linux for a while but according
>>>>>>>> to my notes you should need the following assuming it is installed to
>>>>>>>> /usr/local:
>>>>>>>>
>>>>>>>> export
>>>>>>>> LD_LIBRARY_PATH=/usr/local/lib:/usr/local/lib/python2.7/site-packages/vtk:$LD_LIBRARY_PATH
>>>>>>>>
>>>>>>>> export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH
>>>>>>>>
>>>>>>>> HTH,
>>>>>>>> Shawn
>>>>>>>>
>>>>>>>> On Mon, Aug 3, 2015 at 1:59 PM, Manjunath K E <
>>>>>>>> ke.manjunath at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Shawn
>>>>>>>>>
>>>>>>>>> Thanks for the reply.
>>>>>>>>> My python script is set up to use the system's python not
>>>>>>>>> vtkpython.
>>>>>>>>>
>>>>>>>>> I have set export
>>>>>>>>> PYTHONPATH="/usr/local/lib/python2.7/site-packages/vtk/:$PYTHONPATH".
>>>>>>>>> export LD_LIBRARY_PATH=/usr/local/lib/:$LD_LIBRARY_PATH
>>>>>>>>>
>>>>>>>>> I have installed vtk-6.2 to /usr/local.
>>>>>>>>>
>>>>>>>>> Is the should i change the values of PYTHONPATH and
>>>>>>>>> LD_LIBRARY_PATH to something else.
>>>>>>>>>
>>>>>>>>> Thanks and Regards,
>>>>>>>>>
>>>>>>>>> Manjunath K E
>>>>>>>>> Help Ever Hurt Never
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Aug 3, 2015 at 11:17 PM, Shawn Waldon <
>>>>>>>>> shawn.waldon at kitware.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Manjunath,
>>>>>>>>>>
>>>>>>>>>> Is your python script set up to use vtkpython as the
>>>>>>>>>> interpreter? Or is it using the system's python? If you are trying to
>>>>>>>>>> import vtk from system python you have to set your LD_LIBRARY_PATH and
>>>>>>>>>> PYTHONPATH environment variables. If you want to change the script to use
>>>>>>>>>> vtkpython then change the first like to #!/path/to/vtkpython
>>>>>>>>>>
>>>>>>>>>> HTH,
>>>>>>>>>> Shawn
>>>>>>>>>>
>>>>>>>>>> On Mon, Aug 3, 2015 at 1:43 PM, Manjunath K E <
>>>>>>>>>> ke.manjunath at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi all
>>>>>>>>>>>
>>>>>>>>>>> I have installed VTK 6.2 along with vtk 6.2 python interface on
>>>>>>>>>>> ubuntu 14.04 manually.
>>>>>>>>>>>
>>>>>>>>>>> When I run vtkpython in interpreter mode, the import of vtk is
>>>>>>>>>>> successful.
>>>>>>>>>>> It doesn't have any problem and the same is shown below.
>>>>>>>>>>>
>>>>>>>>>>> ===========================================================
>>>>>>>>>>> manju at iiitb-gvcl-Z800:~/manju/academics/iiitb/project/codes/incois__laptp/src_vtk6$
>>>>>>>>>>> vtkpython
>>>>>>>>>>> vtk version 6.2.0
>>>>>>>>>>> Python 2.7.2 (default, Feb 12 2015, 18:30:44)
>>>>>>>>>>> [GCC 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)] on linux2
>>>>>>>>>>> Type "help", "copyright", "credits" or "license" for more
>>>>>>>>>>> information.
>>>>>>>>>>> >>> from vtk import *
>>>>>>>>>>> >>> print vtk
>>>>>>>>>>> <module 'vtk' from
>>>>>>>>>>> '/usr/local/lib/python2.7/site-packages/vtk/__init__.pyc'>
>>>>>>>>>>> >>>
>>>>>>>>>>> ===========================================================
>>>>>>>>>>>
>>>>>>>>>>> But, If i run a python script then an error is obtained for this
>>>>>>>>>>> line "from vtk import *". The error is as shown below.
>>>>>>>>>>> ===========================================================
>>>>>>>>>>> manju at iiitb-gvcl-Z800:~/manju/academics/iiitb/project/codes/incois__laptp/src_vtk6$
>>>>>>>>>>> ./demo1.py
>>>>>>>>>>> Traceback (most recent call last):
>>>>>>>>>>> File "./demo1.py", line 6, in <module>
>>>>>>>>>>> from vtk import *
>>>>>>>>>>> ImportError: No module named vtk
>>>>>>>>>>> ===========================================================
>>>>>>>>>>>
>>>>>>>>>>> Please help me in solving this issue. I appreciate your time and
>>>>>>>>>>> help.
>>>>>>>>>>>
>>>>>>>>>>> Thanks and Regards,
>>>>>>>>>>>
>>>>>>>>>>> Manjunath K E
>>>>>>>>>>> Help Ever Hurt Never
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Powered by www.kitware.com
>>>>>>>>>>>
>>>>>>>>>>> Visit other Kitware open-source projects at
>>>>>>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>>>>>>
>>>>>>>>>>> Please keep messages on-topic and check the VTK FAQ at:
>>>>>>>>>>> http://www.vtk.org/Wiki/VTK_FAQ
>>>>>>>>>>>
>>>>>>>>>>> Search the list archives at:
>>>>>>>>>>> http://markmail.org/search/?q=vtkusers
>>>>>>>>>>>
>>>>>>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>>>>>>> http://public.kitware.com/mailman/listinfo/vtkusers
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Powered by www.kitware.com
>>>>>>>
>>>>>>> Visit other Kitware open-source projects at
>>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>>
>>>>>>> Please keep messages on-topic and check the VTK FAQ at:
>>>>>>> http://www.vtk.org/Wiki/VTK_FAQ
>>>>>>>
>>>>>>> Search the list archives at: http://markmail.org/search/?q=vtkusers
>>>>>>>
>>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>>> http://public.kitware.com/mailman/listinfo/vtkusers
>>>>>>>
>>>>>>
>>>>>
>>>
>>
>>
>
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