Since r23915, VTK module can be imported and example can be simplified. It is not needed to explicitly updated the PYTHONPATH.

For reference:

//--------------
ENH: Allow vtk module to be imported from Slicer python

This commit update launcher settings associated with VTKv6 project so that
"import vtk" can be successfully executed from the python interpreter
executed in the Slicer environment.

./Slicer --launch python -c 'import vtk'
//--------------

Here is the solution:

(1) Apply the last commit associated with this branch: https://github.com/jcfr/Slicer/tree/3923-allow-registration-of-itk-factory-from-python

(2) Update your snipped to set ITK_AUTOLOAD_PATH and register the factory using ctypes

Updated example:

SLICERSUPER=/software/Slicer4/superbuild
${SLICERSUPER}/Slicer-build/Slicer --launcher-no-splash --launch ${SLICERSUPER}/CTK-build/CTK-build/bin/ctkSimplePythonShell
export ITK_AUTOLOAD_PATH="${SLICERSUPER}/Slicer-build/lib/Slicer-4.4/ITKFactories"

.. and the code to copy in the CTK python shell:

8<----8<----8<----8<----8<----8<----8<----8<----8<----8<----8<----8<----
library_path = './bin/libITKFactoryRegistration.so'
import ctypes
library = ctypes.cdll.LoadLibrary(library_path)
library.register_itk_factory()

modules = ('os', 'sys', 'vtk', 'slicer', 'vtkSlicerVolumesModuleLogic')

for m in modules:
exec('import %s' % m)
print('imported %s' % m)

mrmlScene = slicer.vtkMRMLScene()
volumesLogic = vtkSlicerVolumesModuleLogic.vtkSlicerVolumesLogic()
volumesLogic.SetMRMLScene(mrmlScene)

volumesLogic.AddArchetypeScalarVolume('./share/Slicer-4.4/qt-loadable-modules/EMSegment/Testing/TestData/MRI-Human-Brain/small_atlas_t1_stripped.nrrd', 'Image', 0, None)
8<----8<----8<----8<----8<----8<----8<----8<----8<----8<----8<----8<----

@Kilian: Let me know if the solution discuss in http://www.na-mic.org/Bug/view.php?id=3923#c13353 works for you. Thanks

I think it worked - I am just not sure if the following warning messgae is ok or not :

cannot import name _qSlicerCoreApplicationInstance

Here is what I dud :
1) I downloaded your branch and did a fresh compile
2) I went to CTK-build ; ccmake . ; set CTK_APP_ctkSimplePythonShell ON; regenerated cmake files; and ran make
3) SLICERSUPER=/software/Slicer4/superbuild
export ITK_AUTOLOAD_PATH="${SLICERSUPER}/Slicer-build/lib/Slicer-4.4/ITKFactories"
cd ${SLICERSUPER}/Slicer-build/
./Slicer --launcher-no-splash --launch ${SLICERSUPER}/CTK-build/CTK-build/bin/ctkSimplePythonShell
4) Ran the following in the shell

library_path = './bin/libITKFactoryRegistration.so'
import ctypes
library = ctypes.cdll.LoadLibrary(library_path)

library.register_itk_factory()
0
modules = ('os', 'sys', 'vtk', 'slicer', 'vtkSlicerVolumesModuleLogic')
for m in modules:
... exec('import %s' % m)
... print('imported %s' % m)
...
imported os
imported sys
imported vtk
cannot import name _qSlicerCoreApplicationInstance
cannot import name _qSlicerCoreApplicationInstance
cannot import name _qSlicerCoreApplicationInstance
cannot import name _qSlicerCoreApplicationInstance
imported slicer
imported vtkSlicerVolumesModuleLogic
mrmlScene = slicer.vtkMRMLScene()
volumesLogic = vtkSlicerVolumesModuleLogic.vtkSlicerVolumesLogic()
volumesLogic.SetMRMLScene(mrmlScene)

volumesLogic.AddArchetypeScalarVolume('./share/Slicer-4.4/qt-loadable-modules/EMSegment/Testing/TestData/MRI-Human-Brain/small_atlas_t1_stripped.nrrd', 'Image', 0, None)
(vtkMRMLScalarVolumeNode)0x7f421c043f50

The message is expected for now. It should be possible to tweak Slicer to avoid it.

Many things have changed since the problem was reported, but this works fine now:

Slicer.exe --no-main-window --show-python-interactor

volumesLogic = slicer.modules.volumes.logic()
volumesLogic.AddArchetypeScalarVolume("./share/Slicer-4.7/qt-loadable-modules/EMSegment/Tasks/MRI-Human-Brain/atlas_t2.nrrd", 'Image', 0, None)