[vtkusers] No module named vtk when installing mayavi
KIM TRAN DONG
kimtran1208 at gmail.com
Mon Aug 24 03:03:32 EDT 2015
Dear Ben,
'sys.path' gives me this:
['', '/Library/Python/2.7/site-packages/pip-7.1.0-py2.7.egg',
'/Library/Python/2.7/site-packages/setuptools-18.1-py2.7.egg',
'/Library/Python/2.7/site-packages/cvu-0.5-py2.7.egg',
'/Library/Python/2.7/site-packages/traits-4.5.0-py2.7-macosx-10.9-intel.egg',
'/Library/Python/2.7/site-packages/traitsui-4.5.1-py2.7.egg',
'/Library/Python/2.7/site-packages/pyface-4.5.1-py2.7.egg',
'/Library/Python/2.7/site-packages/port-0.3.1-py2.7.egg',
'/Library/Python/2.7/site-packages/Whoosh-2.7.0-py2.7.egg',
'/Library/Python/2.7/site-packages/PyYAML-3.11-py2.7-macosx-10.9-intel.egg',
'/Library/Python/2.7/site-packages/py_gfm-0.1.1-py2.7.egg',
'/Library/Python/2.7/site-packages/Flask-0.10.1-py2.7.egg',
'/Library/Python/2.7/site-packages/click-4.1-py2.7.egg',
'/Library/Python/2.7/site-packages/unittest2-1.1.0-py2.7.egg',
'/Library/Python/2.7/site-packages/Markdown-2.6.2-py2.7.egg',
'/Library/Python/2.7/site-packages/itsdangerous-0.24-py2.7.egg',
'/Library/Python/2.7/site-packages/Jinja2-2.8-py2.7.egg',
'/Library/Python/2.7/site-packages/Werkzeug-0.10.4-py2.7.egg',
'/Library/Python/2.7/site-packages/traceback2-1.4.0-py2.7.egg',
'/Library/Python/2.7/site-packages/six-1.9.0-py2.7.egg',
'/Library/Python/2.7/site-packages/argparse-1.3.0-py2.7.egg',
'/Library/Python/2.7/site-packages/MarkupSafe-0.23-py2.7-macosx-10.9-intel.egg',
'/Library/Python/2.7/site-packages/linecache2-1.0.0-py2.7.egg',
'/usr/local/VTKBuild/Wrapping/Python/vtk',
'/usr/local/VTKBuild/Wrapping/Python', '/usr/local/VTKBuild/bin',
'/usr/local/vtkpython/bin/vtk', '/usr/local/VTKBuild/lib',
'/Users/kimtran/Downloads/mayavi-4.4.3',
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip',
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7',
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin',
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac',
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages',
'/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python',
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk',
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old',
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload',
'/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyObjC',
'/Library/Python/2.7/site-packages']
and for the 'set -x':
+ source /Users/kimtran/.bash_profile
++ 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
+++ '[' -z /Applications/freesurfer ']'
+++ '[' -z /Applications/freesurfer/subjects ']'
+++ '[' -z /Applications/freesurfer/sessions ']'
+++ source /Applications/freesurfer/FreeSurferEnv.sh
++++ VERSION='$Id: FreeSurferEnv.sh,v 1.50.2.2 2011/03/29 22:06:48 greve
Exp $'
++++ '[' 0 -gt 1 ']'
+++++ uname -s
++++ os=Darwin
++++ export OS=Darwin
++++ OS=Darwin
++++ '[' -n '' ']'
++++ output=1
++++ [[ -z kimtran ]]
++++ [[ -z \h:\W \u\$ ]]
++++ '[' -z /Applications/freesurfer ']'
++++ '[' '!' -d /Applications/freesurfer ']'
++++ [[ 1 == 1 ]]
++++ '[' -e /Applications/freesurfer/build-stamp.txt ']'
+++++ cat /Applications/freesurfer/build-stamp.txt
++++ echo '-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------'
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
++++ echo 'Setting up environment for FreeSurfer/FS-FAST (and FSL)'
Setting up environment for FreeSurfer/FS-FAST (and FSL)
++++ '[' 0 -gt 1 ']'
++++ '[' -z
/usr/fsl/bin:/usr/local/VTKBuild/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/usr/fsl/bin
']'
++++ '[' -z 0 ']'
++++ [[ -z /Applications/freesurfer/fsfast ]]
++++ [[ 0 != 0 ]]
++++ [[ -z /Applications/freesurfer/subjects ]]
++++ [[ 0 != 0 ]]
++++ [[ -z '' ]]
++++ [[ -z /Applications/freesurfer/mni/bin ]]
++++ [[ 0 != 0 ]]
++++ [[ -z '' ]]
++++ [[ -z /Applications/freesurfer/mni/lib ]]
++++ [[ 0 != 0 ]]
++++ [[ -z '' ]]
++++ [[ -z /Applications/freesurfer/mni/data ]]
++++ [[ 0 != 0 ]]
++++ [[ -z /usr/fsl ]]
++++ [[ 0 != 0 ]]
++++ export FREESURFER_HOME=/Applications/freesurfer
++++ FREESURFER_HOME=/Applications/freesurfer
++++ export LOCAL_DIR=/Applications/freesurfer/local
++++ LOCAL_DIR=/Applications/freesurfer/local
++++ for d in '"$FSFAST_HOME"' '"$SUBJECTS_DIR"'
++++ '[' '!' -d /Applications/freesurfer/fsfast ']'
++++ for d in '"$FSFAST_HOME"' '"$SUBJECTS_DIR"'
++++ '[' '!' -d /Applications/freesurfer/subjects ']'
++++ [[ -z nii.gz ]]
++++ [[ 0 != 0 ]]
++++ [[ 1 == 1 ]]
++++ echo 'FREESURFER_HOME /Applications/freesurfer'
FREESURFER_HOME /Applications/freesurfer
++++ echo 'FSFAST_HOME /Applications/freesurfer/fsfast'
FSFAST_HOME /Applications/freesurfer/fsfast
++++ echo 'FSF_OUTPUT_FORMAT nii.gz'
FSF_OUTPUT_FORMAT nii.gz
++++ echo 'SUBJECTS_DIR /Applications/freesurfer/subjects'
SUBJECTS_DIR /Applications/freesurfer/subjects
++++ [[ -z '' ]]
++++ export FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast
++++ FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast
++++ SUF=/Users/kimtran/matlab/startup.m
++++ '[' '!' -e /Users/kimtran/matlab/startup.m ']'
+++++ grep FSFAST_HOME /Users/kimtran/matlab/startup.m
+++++ wc -l
++++ tmp1=' 1'
+++++ grep FMRI_ANALYSIS_DIR /Users/kimtran/matlab/startup.m
+++++ wc -l
++++ tmp2=' 0'
+++++ grep FREESURFER_HOME /Users/kimtran/matlab/startup.m
+++++ wc -l
++++ tmp3=' 1'
++++ [[ 1 == 0 ]]
++++ [[ 1 == 1 ]]
++++ [[ -n /Applications/freesurfer/mni ]]
++++ echo 'MNI_DIR /Applications/freesurfer/mni'
MNI_DIR /Applications/freesurfer/mni
++++ '[' -z '' ']'
++++ '[' -n /Applications/freesurfer/mni/bin ']'
++++ '[' '!' -d /Applications/freesurfer/mni/bin ']'
++++ '[' -n /Applications/freesurfer/mni/lib ']'
++++ '[' '!' -d /Applications/freesurfer/mni/lib ']'
++++ '[' -z /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0
']'
++++ '[' -z /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0
']'
++++ '[' /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0
'!=' /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0 ']'
++++ '[' -z '' ']'
++++ '[' -n /Applications/freesurfer/mni/bin ']'
++++
PATH=/Applications/freesurfer/mni/bin:/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
++++ '[' -d /Applications/freesurfer/lib/misc/bin ']'
++++ '[' -d /Applications/freesurfer/lib/misc/lib ']'
++++ [[ 1 == 1 ]]
++++ [[ -n '' ]]
++++ '[' -d /Applications/freesurfer/bin/freeview.app ']'
++++ '[' -n '' ']'
++++ [[ 1 == 1 ]]
++++ [[ -n '' ]]
++++ '[' -n /usr/fsl ']'
++++ export FSLDIR=/usr/fsl
++++ FSLDIR=/usr/fsl
++++ export FSL_BIN=/usr/fsl/bin
++++ FSL_BIN=/usr/fsl/bin
++++ '[' '!' -d /usr/fsl/bin ']'
++++ '[' -e /usr/fsl/etc/fslconf/fsl.sh ']'
++++ source /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 ']'
++++ export FSLOUTPUTTYPE=NIFTI_GZ
++++ FSLOUTPUTTYPE=NIFTI_GZ
++++ '[' -e /usr/bin/display ']'
++++ '[' -e /usr/bin/convert ']'
++++ '[' -n /usr/fsl/bin ']'
++++
PATH=/usr/fsl/bin:/Applications/freesurfer/mni/bin:/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
++++ [[ 1 == 1 ]]
++++ [[ -n /usr/fsl ]]
++++ echo 'FSL_DIR /usr/fsl'
FSL_DIR /usr/fsl
++++ '[' -d /Applications/freesurfer/tktools ']'
++++
PATH=/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/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
PATH=/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/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
++++
PATH=/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/fsl/bin:/Applications/freesurfer/mni/bin:/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 FIX_VERTEX_AREA=
++++ FIX_VERTEX_AREA=
++++ return 0
++ 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
++ 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
++ 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
++ 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
++ 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
++ 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
I'm sorry for this 'mess', could you please check this for me? Thank you
very much,
Kim
2015-08-21 18:39 GMT+02:00 Ben Boeckel <ben.boeckel at kitware.com>:
> [ Please keep the list CC'd. ]
>
> On Fri, Aug 21, 2015 at 18:29:19 +0200, KIM TRAN DONG wrote:
> > Thank you for your reply, but how can I inspect sys.path from vtkpython?
> I
> > tried changing the pythonpath into:
>
> import sys
> sys.path
>
> > I searched in .bash_profile, but didn't find space letter in the path.
> When
> > I called `bash -x`, the terminal returned just `bash-3.2$ `. Could you
> give
> > me any suggests?
>
> You could try putting `set -x` at the top of .bash_profile then.
>
> --Ben
>
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