[vtkusers] No module named vtk when installing mayavi

KIM TRAN DONG kimtran1208 at gmail.com
Mon Aug 24 12:21:21 EDT 2015


Dear Ben,

Thank you for your reply, but I get always the same error message for
installing mayavi after setting PYTHONPATH as the sys.path:

  File "tvtk/code_gen.py", line 10, in <module>
    import vtk
ImportError: No module named vtk

For the error of the terminal, I noticed that if I save .bash _profile with
the terminal opened, the 'source ~/.bash_profile' will return the error "a
listing of the *current **directory* and it is being used as a command", do
you have any suggests about this?

Thank you very much,

Kim

2015-08-24 16:52 GMT+02:00 Ben Boeckel <ben.boeckel at kitware.com>:

> On Mon, Aug 24, 2015 at 09:03:32 +0200, KIM TRAN DONG wrote:
> > 'sys.path' gives me this:
> ...
> > '/usr/local/VTKBuild/Wrapping/Python/vtk',
> > '/usr/local/VTKBuild/Wrapping/Python', '/usr/local/VTKBuild/bin',
> > '/usr/local/vtkpython/bin/vtk', '/usr/local/VTKBuild/lib',
> ...
>
> These look to be the paths you need.
>
> > and for the 'set -x':
> > + source /Users/kimtran/.bash_profile
>
> This file seems to have the wrong commands (based on the '+' context
> used).
>
> > ++ set -x
> > ++ FSLDIR=/usr/fsl
> > ++ . /usr/fsl/etc/fslconf/fsl.sh
> > +++ FSLOUTPUTTYPE=NIFTI_GZ
> > +++ export FSLOUTPUTTYPE
> > +++ FSLMULTIFILEQUIT=TRUE
> > +++ export FSLMULTIFILEQUIT
> > +++ FSLTCLSH=/usr/fsl/bin/fsltclsh
> > +++ FSLWISH=/usr/fsl/bin/fslwish
> > +++ export FSLTCLSH FSLWISH
> > +++ FSLLOCKDIR=
> > +++ FSLMACHINELIST=
> > +++ FSLREMOTECALL=
> > +++ export FSLLOCKDIR FSLMACHINELIST FSLREMOTECALL
> > +++ FSLGECUDAQ=cuda.q
> > +++ export FSLGECUDAQ
> > +++ '[' -f /usr/local/etc/fslconf/fsl.sh ']'
> > +++ '[' -f /etc/fslconf/fsl.sh ']'
> > +++ '[' -f /Users/kimtran/.fslconf/fsl.sh ']'
> > ++
> PATH=/usr/fsl/bin:/usr/local/VTKBuild/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> > ++ export FSLDIR PATH
> > ++ export FREESURFER_HOME=/Applications/freesurfer
> > ++ FREESURFER_HOME=/Applications/freesurfer
> > ++ source /Applications/freesurfer/SetUpFreeSurfer.sh
> ...output from SetUpFreeSurfer.sh...
> > ++ Desktop Documents Downloads Library Movies Music OSX-10.8.iso
> Pictures Public Qt5.2.1 bootdisk.sh build.log license.txt matlab perl5
> stat.sh voxel_volume.txt
> > -bash: Desktop: command not found
>
> Here's one problem.
>
> > ++ PERL_MB_OPT='--install_base "/Users/kimtran/perl5"'
> > ++ export PERL_MB_OPT
> > ++ PERL_MM_OPT=INSTALL_BASE=/Users/kimtran/perl5
> > ++ export PERL_MM_OPT
> > ++ Desktop Documents Downloads Library Movies Music OSX-10.8.iso
> Pictures Public Qt5.2.1 bootdisk.sh build.log license.txt matlab perl5
> stat.sh voxel_volume.txt
> > -bash: Desktop: command not found
>
> A second.
>
> > ++ export
> >
> PATH=/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> > ++
> >
> PATH=/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> > ++ Desktop Documents Downloads Library Movies Music OSX-10.8.iso
> Pictures Public Qt5.2.1 bootdisk.sh build.log license.txt matlab perl5
> stat.sh voxel_volume.txt
> > -bash: Desktop: command not found
>
> Third.
>
> > ++ export
> PATH=/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> > ++
> PATH=/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> > ++ Desktop Documents Downloads Library Movies Music OSX-10.8.iso
> Pictures Public Qt5.2.1 bootdisk.sh build.log license.txt matlab perl5
> stat.sh voxel_volume.txt
> > -bash: Desktop: command not found
>
> Fourth.
>
> > ++ export
> LD_LIBRARY_PATH=/usr/local/VTKBuild/lib:/usr/lib/python2.7:/usr/local/VTKBuild/lib:/usr/lib/python2.7:/usr/local/VTKBuild/lib:/usr/lib/python2.7:
> > ++
> LD_LIBRARY_PATH=/usr/local/VTKBuild/lib:/usr/lib/python2.7:/usr/local/VTKBuild/lib:/usr/lib/python2.7:/usr/local/VTKBuild/lib:/usr/lib/python2.7:
> > ++ export
> DYLD_LIBRARY_PATH=/usr/local/VTKBuild/lib:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/lib:
> > ++
> DYLD_LIBRARY_PATH=/usr/local/VTKBuild/lib:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/lib:
> > ++ export
> PYTHONPATH=/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:
> > ++
> PYTHONPATH=/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:/usr/local/VTKBuild/Wrapping/Python/vtk:/usr/local/VTKBuild/Wrapping/Python:/usr/local/VTKBuild/bin:/usr/local/vtkpython/bin/vtk:/usr/local/VTKBuild/lib:
> > ++ export
> PATH=/usr/local/VTKBuild/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> > ++
> PATH=/usr/local/VTKBuild/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
> > ++ Desktop Documents Downloads Library Movies Music OSX-10.8.iso
> Pictures Public Qt5.2.1 bootdisk.sh build.log license.txt matlab perl5
> stat.sh voxel_volume.txt
> > -bash: Desktop: command not found
>
> Fifth.
>
> > ++ update_terminal_cwd
> > ++ local 'SEARCH= '
> > ++ local REPLACE=%20
> > ++ local PWD_URL=file://Kims-Mac-2.local/Users/kimtran
> > ++ printf '\e]7;%s\a' file://Kims-Mac-2.local/Users/kimtran
>
> It appears that some variable may contain a listing of your home
> directory and is being used as a command? I'd check what's around the
> SetUpFreeSurfer.sh line to see what variables are being used and see if
> the logs mention it being set or overridden inside that
> SetUpFreeSurfer.sh output section.
>
> --Ben
>
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