[Neuroimaging] Problem with from dipy.viz.fvtk
Samuel St-Jean
stjeansam at gmail.com
Mon Jun 13 13:47:35 EDT 2016
Well, for anyone reading this afterward, the packaging from upstream vtk
seems to be the cause, and arch is still looking at how to fix it
properly. Good to know the workaround with the vtk-qt4 pkgbuild, here is
the bug report for people interested until it gets properly fixed
https://bugs.archlinux.org/task/49233?project=5&string=vtk&type%5B0%5D=&sev%5B0%5D=&pri%5B0%5D=&due%5B0%5D=&cat%5B0%5D=&status%5B0%5D=open&percent%5B0%5D=&reported%5B0%5D=
Le 2016-06-13 à 13:39, Vassia Katsageorgiou a écrit :
> Hi Samuel,
>
> thank you for the reply!
> Finally there is solution for arch linux (also manjaro)!
> So, in case someone has the same problem, he needs to install*vtk-qt4
> 7.0.0-2 *(here: https://aur.archlinux.org/packages/vtk-qt4/)
> and it works!
>
> Cheers,
> Vassia
>
> On 12 June 2016 at 20:13, Samuel St-Jean <stjeansam at gmail.com
> <mailto:stjeansam at gmail.com>> wrote:
>
> I am currently on arch (manjaro uses the same repo for the most
> part), and I just realized it is indeed plain broken, I'll flag a
> bug report for that. The repos also have vtk6, which get installed
> to a non standard path, and is also broken unfortunately.
>
>
> If you don't need it right now, they usually fix and rebuild stuff
> pretty fast, so might be worth to wait a few days before compiling
> everything in cmake if it's not urgent.
>
>
> Le 2016-06-12 à 19:25, Vassia Katsageorgiou a écrit :
>> Hi Ariel,
>>
>> Thank you very much for the reply!
>> So, this is what happens if you import vtk in python:
>>
>> ---------------------------------------------------------------------------
>> ImportError Traceback (most recent
>> call last)
>> <ipython-input-1-b7e11aadda62> in <module>()
>> ----> 1 import vtk
>>
>> /usr/lib/python2.7/site-packages/vtk/__init__.py in <module>()
>> 88 from .vtkParallelCore import *
>> 89 from .vtkFiltersAMR import *
>> ---> 90 from .vtkIOAMR import *
>> 91 from .vtkRenderingVolumeOpenGL2 import *
>> 92 from .vtkFiltersFlowPaths import *
>>
>> /usr/lib/python2.7/site-packages/vtk/vtkIOAMR.py in <module>()
>> 7 # during build and testing, the modules will be
>> elsewhere,
>> 8 # e.g. in lib directory or Release/Debug config
>> directories
>> ----> 9 from vtkIOAMRPython import *
>>
>> ImportError: No module named vtkIOAMRPython
>>
>> I found this link, which I think will work:
>> http://ghoshbishakh.github.io/blog/blogpost/2016/03/05/buid-vtk.html
>>
>> Though, after "cmake ." I get another error:
>>
>> CMake Error at CMake/vtkCompilerExtras.cmake:47 (if):
>> if given arguments:
>>
>> "cc: error: ARGS: No such file or directory
>>
>> cc (GCC) 6.1.1 20160501
>>
>> Copyright (C) 2016 Free Software Foundation, Inc.
>>
>> This is free software" " see the source for copying
>> conditions. There is
>> NO
>>
>> warranty" " not even for MERCHANTABILITY or FITNESS FOR A
>> PARTICULAR
>> PURPOSE.
>>
>>
>>
>> " "VERSION_GREATER" "4.2.0" "AND" "BUILD_SHARED_LIBS" "AND"
>> "HAVE_GCC_VISIBILITY" "AND" "VTK_USE_GCC_VISIBILITY" "AND"
>> "NOT" "MINGW"
>> "AND" "NOT" "CYGWIN"
>>
>> Unknown arguments specified
>> Call Stack (most recent call first):
>> CMakeLists.txt:286 (include)
>>
>>
>> -- Configuring incomplete, errors occurred!
>>
>> Which I think is due to gcc's compilation.. I am trying to fix
>> this.. If I manage to, I will report it!
>>
>> But of course, if you had to suggest something different, it
>> would be welcomed! :)
>>
>> Thanks again,
>> Vassia
>>
>>
>> On 12 June 2016 at 18:58, Ariel Rokem <arokem at gmail.com
>> <mailto:arokem at gmail.com>> wrote:
>>
>> Hi Vassia,
>>
>> Thanks for your email. Let's see if I can be helpful.
>> On Sun, Jun 12, 2016 at 6:46 AM, Vassia Katsageorgiou
>> <kats.vassia at gmail.com <mailto:kats.vassia at gmail.com>> wrote:
>>
>> Hello,
>>
>> I recently installed dipy and all the required additional
>> packages, including vtk, but when I try to use fvtk for
>> visualization (for example "r=fvtk.ren()", or
>> "fvtk.line()") I get the error "no module ren, line..".
>> I searched this error and I found these posts:
>>
>> https://github.com/nipy/dipy/issues/1016
>> https://neurostars.org/p/3724/
>>
>> saying that vtk needs to be installed (which in my case
>> is installed). I am using python2 under manjaro linux
>> distribution and I have installed vtk-7, I tried also
>> with vtk-6, but the same happens. I also tried to add in
>> the python path the path to vtk's installation and the
>> problem remains.
>> Did anyone using linux have the same problem? Any suggestion?
>>
>>
>> But first let me just make sure that I understand what is
>> going on. What happens when you `import vtk` in Python?
>>
>> Cheers,
>>
>> Ariel
>>
>> Thank you.
>> Vassia
>>
>> --
>> *Vasiliki-Maria Katsageorgiou*, M.Eng.
>>
>> Fellow-PhD, Pattern Analysis and Computer Vision
>> Istituto Italiano di Tecnologia
>> Genova, Italy
>>
>> Phone number: +39 3899171853 <tel:%2B39%203899171853>
>> E-mail: kats.vassia at gmail.com <mailto:kats.vassia at gmail.com>
>>
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>>
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>>
>>
>>
>> --
>> *Vasiliki-Maria Katsageorgiou*, M.Eng.
>>
>> Fellow-PhD, Pattern Analysis and Computer Vision
>> Istituto Italiano di Tecnologia
>> Genova, Italy
>>
>> Phone number: +39 3899171853 <tel:%2B39%203899171853>
>> E-mail: kats.vassia at gmail.com <mailto:kats.vassia at gmail.com>
>>
>>
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>
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>
>
>
> --
> *Vasiliki-Maria Katsageorgiou*, M.Eng.
>
> Fellow-PhD, Pattern Analysis and Computer Vision
> Istituto Italiano di Tecnologia
> Genova, Italy
>
> Phone number: +39 3899171853
> E-mail: kats.vassia at gmail.com <mailto:kats.vassia at gmail.com>
>
>
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