[vtkusers] from vtk import * ImportError: (Python VTK 6.2 on ubuntu 14.04)
Dan Lipsa
dan.lipsa at kitware.com
Mon Aug 10 16:25:18 EDT 2015
Indeed, I have tried 6.2.0 and I get NaNs as well. Unfortunately it seems
to be something wrong with the binary version for
VTK-6.3.0-RC1-Linux-64bit. For that I get:
Traceback (most recent call last):
File "dataReader.py1", line 3, in <module>
from vtk import *
File
"/home/danlipsa/Downloads/VTK-6.3.0-RC1-Linux-64bit/lib/python2.7/site-packages/vtk/__init__.py",
line 98, in <module>
from vtkRenderingOpenGL import *
File
"/home/danlipsa/Downloads/VTK-6.3.0-RC1-Linux-64bit/lib/python2.7/site-packages/vtk/vtkRenderingOpenGL.py",
line 1, in <module>
from vtkRenderingOpenGLPython import *
ImportError: libvtkRenderingOpenGLPython27D-6.3.so.1: cannot open shared
object file: No such file or directory
We'll look into it. So you'll either build VTK from sources or wait until
6.3.0.rc2
Dan
On Mon, Aug 10, 2015 at 4:10 PM Dan Lipsa <dan.lipsa at kitware.com> wrote:
> 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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