BUG: Define GetOutput() for Python wrapping

[thewtex]

Explicitly define GetOutput() for Python wrapping without the index and
with the ResultImageType as a return type.

[romangrothausmann]

Changes look good, but so far I had no luck with getting this to work when used in an object-oriented python script, neither with a self-compiled debug version (https://gitlab.com/romangrothausmann/elastix_scripts/pipelines/127160739) nor with pip install (https://gitlab.com/romangrothausmann/elastix_scripts/pipelines/127159377).

The self-compiled debug version fails on cmake of ITKElastix with

CMake Error at /ITK/Wrapping/Generators/Python/CMakeLists.txt:3 (include_directories):
  include_directories given empty-string as include directory.

although things used to work here before #40 and use of ITK-5.1rc01.
The pip install version fails on execution with

    selx = itk.ElastixRegistrationMethod[rType, rType].New() # https://itkpythonpackage.readthedocs.io/en/latest/Quick_start_guide.html#instantiate-an-itk-object
  File "/usr/local/lib/python3.6/dist-packages/itkLazy.py", line 52, in __getattribute__
    itkBase.LoadModule(module, namespace)
  File "/usr/local/lib/python3.6/dist-packages/itkBase.py", line 93, in LoadModule
    module = loader.load(swigModuleName)
  File "/usr/local/lib/python3.6/dist-packages/itkBase.py", line 211, in load
    return importlib.import_module(name)
  File "/usr/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 994, in _gcd_import
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/usr/local/lib/python3.6/dist-packages/itk/Configuration/../ElastixPython.py", line 114, in <module>
    from itkElastixRegistrationMethodPython import *
  File "/usr/local/lib/python3.6/dist-packages/itk/Configuration/../itkElastixRegistrationMethodPython.py", line 1661, in <module>
    @itkHelpers.accept_numpy_array_like
AttributeError: module 'itkHelpers' has no attribute 'accept_numpy_array_like'

[thewtex]

CMake Error at /ITK/Wrapping/Generators/Python/CMakeLists.txt:3 (include_directories):
include_directories given empty-string as include directory.

This is an issue in ITK 5.1 RC 2, and we will need ITK 5.1 RC 3 to continue.

[romangrothausmann]

Many thanks @thewtex for that info, I was expecting that it was an incomplete/false configuration in the DF. Looking forward to rc3 then;-)

While searching for a solution I stumbled over this:
weidai11/cryptopp#199

[romangrothausmann]

In the meanwhile, @thewtex do you have an idea concerning the pip install failure? Is that related or a different issue for which I should open an issue for tracking?

[thewtex]

pip install error are related current limitations of the pip dependency resolver -- it will no longer an issue once 5.1.0 is out.

[romangrothausmann]

Many thanks @thewtex for the update. I gave it a try with ITK-5.1rc03 and self-compiling ITKElastix but it seems elastix is not compatible with it:
https://gitlab.com/romangrothausmann/elastix_scripts/-/jobs/520141463

[ 28%] Building CXX object _deps/elastix_fetch-build/Components/Metrics/SumSquaredTissueVolumeDifferenceMetric/CMakeFiles/SumSquaredTissueVolumeDifferenceMetric.dir/elxSumSquaredTissueVolumeDifferenceMetric.cxx.o
17126 In file included from /ITKElastix_build/_deps/elastix_fetch-src/Core/ComponentBaseClasses/elxTransformBase.h:384:0,
17127                  from /ITKElastix_build/_deps/elastix_fetch-src/Core/Kernel/elxElastixTemplate.h:39,
17128                  from /ITKElastix_build/_deps/elastix_fetch-src/Core/Install/elxIncludes.h:39,
17129                  from /ITKElastix_build/_deps/elastix_fetch-src/Components/Interpolators/LinearInterpolator/elxLinearInterpolator.h:21,
17130                  from /ITKElastix_build/_deps/elastix_fetch-src/Components/Interpolators/LinearInterpolator/elxLinearInterpolator.cxx:19:
17131 /ITKElastix_build/_deps/elastix_fetch-src/Core/ComponentBaseClasses/elxTransformBase.hxx: In member function 'void itk::PixelTypeChangeCommand<T>::Execute(itk::Object*, const itk::EventObject&)':
17132 /ITKElastix_build/_deps/elastix_fetch-src/Core/ComponentBaseClasses/elxTransformBase.hxx:75:68: error: 'VECTOR' is not a member of 'itk::ImageIOBase'
17133      castcaller->GetModifiableImageIO()->SetPixelType( ImageIOBase::VECTOR );
17134                                                                     ^~~~~~
17135 /ITKElastix_build/_deps/elastix_fetch-src/Core/ComponentBaseClasses/elxTransformBase.hxx: In member function 'void itk::PixelTypeChangeCommand<T>::Execute(const itk::Object*, const itk::EventObject&)':
17136 /ITKElastix_build/_deps/elastix_fetch-src/Core/ComponentBaseClasses/elxTransformBase.hxx:83:68: error: 'VECTOR' is not a member of 'itk::ImageIOBase'
17137      castcaller->GetModifiableImageIO()->SetPixelType( ImageIOBase::VECTOR );
17138                                                                     ^~~~~~

Is that a known problem or should I open a new issue for that?

[hjmjohnson]

@romangrothausmann Are you building with ITK_LEGACY_REMOVE:BOOL=ON?

ImageIOBase::VECTOR is deprecated, and should be undefined if ITK_LEGACY_REMOVE:BOOL=ON.

see line 113 in itkImageIOBase.h for the defintion.

NOTE: Many duplicate enum values were consolidated and converted to class enum in Core/Common for ITK 5.1.

[romangrothausmann]

Many thanks @hjmjohnson for your feedback. So far I did not have ITK_LEGACY_REMOVE:BOOL=ON, testing this now:
https://gitlab.com/romangrothausmann/elastix_scripts/-/jobs/522029016

[hjmjohnson]

That’s weird.

ITK_LEGACY_REMOVE:BOOL=ON should break the build, not fixit.

ITK_LEGACY_REMOVE:BOOL=OFF should expose the old enumerations.

Hans

[dzenanz]

I guess we forgot to expose some of the deprecated enums under legacy flag.

[thewtex]

I'll update to fix the enum's, and we will have nice-to-install packages after ITK 5.1.0 is out.