Closed MrTzschr closed 7 months ago
Thanks for the report. I am already struggling to maintain the Python wrapping functional with the default external module options. I am using
cmake $SCRIPT_PATH/itk \
-DCMAKE_BUILD_TYPE=RelWithDebInfo \
-DBUILD_EXAMPLES=OFF \
-DBUILD_SHARED_LIBS=OFF \
-DBUILD_TESTING=OFF \
-DITK_WRAP_PYTHON=ON \
-DCMAKE_INSTALL_PREFIX=$INSTALL_PATH \
-DModule_RTK:BOOL=ON \
-DModule_RTK_GIT_TAG="" \
-DModule_CudaCommon:BOOL=ON \
-DModule_CudaCommon_GIT_TAG="" \
-DRTK_USE_CUDA:BOOL=ON \
-DRTK_BUILD_APPLICATIONS:BOOL=OFF \
-DPY_SITE_PACKAGES_PATH:STRING=${BINDINGS_PATH} \
-DITK_WRAP_unsigned_short:BOOL=ON \
-DITK_WRAP_double:BOOL=ON \
-DITK_WRAP_complex_double:BOOL=ON \
-DITK_WRAP_IMAGE_DIMS:STRING="2;3;4"
to mimick ITK (see here I think). That will be hard to manage all possible combinations of CMake options but the default options should be better managed, I'll try to fix it.
Can you check that #576 fixes the issue for your too?
Works. Thanks for the fast fix!
At first I tested this with seperate builds of ITK and RTK to apply the patch. Now, after the merge, I compiled RTK as module of ITK by setting the commit tag explicitly and end up with a lot of warnings on executing python code. The code itself works without issues but the warning appears on every code execution :/ Compilation went without errors.
Template itk::CudaImage<itk::Vector<float,5>,4>
already defined as <class 'itk.itkCudaImageRTKPython.itkCudaImageVF54'>
is redefined as <class 'itk.itkCudaImageRTKPython.itkCudaImageVF54'>
Warning: template already defined 'itk::CudaImage<itk::Vector<float,5>,4>'
Template itk::CudaImage<itk::CovariantVector<float,5>,4>
already defined as <class 'itk.itkCudaImageRTKPython.itkCudaImageCVF54'>
is redefined as <class 'itk.itkCudaImageRTKPython.itkCudaImageCVF54'>
Warning: template already defined 'itk::CudaImage<itk::CovariantVector<float,5>,4>'
Template itk::ImageSource<itk::CudaImage<float,2>>
already defined as <class 'itk.itkImageSourceCudaCommonPython.itkImageSourceCIF2'>
is redefined as <class 'itk.itkImageSourceRTKPython.itkImageSourceCIF2'>
Warning: template already defined 'itk::ImageSource<itk::CudaImage<float,2>>'
Template itk::ImageSource<itk::CudaImage<float,3>>
already defined as <class 'itk.itkImageSourceCudaCommonPython.itkImageSourceCIF3'>
is redefined as <class 'itk.itkImageSourceRTKPython.itkImageSourceCIF3'>
Warning: template already defined 'itk::ImageSource<itk::CudaImage<float,3>>'
Template itk::ImageSource<itk::CudaImage<float,4>>
already defined as <class 'itk.itkImageSourceRTKPython.itkImageSourceCIF4'>
is redefined as <class 'itk.itkImageSourceRTKPython.itkImageSourceCIF4'>
Warning: template already defined 'itk::ImageSource<itk::CudaImage<float,4>>'
Template itk::ImageSource<itk::CudaImage<itk::Vector<float,2>,2>>
already defined as <class 'itk.itkImageSourceCudaCommonPython.itkImageSourceCIVF22'>
is redefined as <class 'itk.itkImageSourceRTKPython.itkImageSourceCIVF22'>
Warning: template already defined 'itk::ImageSource<itk::CudaImage<itk::Vector<float,2>,2>>'
Template itk::ImageSource<itk::CudaImage<itk::Vector<float,2>,3>>
already defined as <class 'itk.itkImageSourceCudaCommonPython.itkImageSourceCIVF23'>
is redefined as <class 'itk.itkImageSourceRTKPython.itkImageSourceCIVF23'>
Warning: template already defined 'itk::ImageSource<itk::CudaImage<itk::Vector<float,2>,3>>'
Template itk::ImageSource<itk::CudaImage<itk::Vector<float,3>,2>>
already defined as <class 'itk.itkImageSourceCudaCommonPython.itkImageSourceCIVF32'>
is redefined as <class 'itk.itkImageSourceRTKPython.itkImageSourceCIVF32'>
Warning: template already defined 'itk::ImageSource<itk::CudaImage<itk::Vector<float,3>,2>>'
Template itk::ImageSource<itk::CudaImage<itk::Vector<float,3>,3>>
already defined as <class 'itk.itkImageSourceCudaCommonPython.itkImageSourceCIVF33'>
is redefined as <class 'itk.itkImageSourceRTKPython.itkImageSourceCIVF33'>
Warning: template already defined 'itk::ImageSource<itk::CudaImage<itk::Vector<float,3>,3>>'
Template itk::ImageSource<itk::CudaImage<itk::Vector<float,4>,2>>
already defined as <class 'itk.itkImageSourceCudaCommonPython.itkImageSourceCIVF42'>
is redefined as <class 'itk.itkImageSourceRTKPython.itkImageSourceCIVF42'>
Warning: template already defined 'itk::ImageSource<itk::CudaImage<itk::Vector<float,4>,2>>'
Template itk::ImageSource<itk::CudaImage<itk::Vector<float,4>,3>>
already defined as <class 'itk.itkImageSourceCudaCommonPython.itkImageSourceCIVF43'>
is redefined as <class 'itk.itkImageSourceRTKPython.itkImageSourceCIVF43'>
Warning: template already defined 'itk::ImageSource<itk::CudaImage<itk::Vector<float,4>,3>>'
Template itk::CudaImageDataManager<itk::CudaImage<itk::Vector<float,5>,4>>
already defined as <class 'itk.itkCudaImageDataManagerRTKPython.itkCudaImageDataManagerCIVF54'>
is redefined as <class 'itk.itkCudaImageDataManagerRTKPython.itkCudaImageDataManagerCIVF54'>
Warning: template already defined 'itk::CudaImageDataManager<itk::CudaImage<itk::Vector<float,5>,4>>'
Template itk::CudaImageDataManager<itk::CudaImage<itk::CovariantVector<float,5>,4>>
already defined as <class 'itk.itkCudaImageDataManagerRTKPython.itkCudaImageDataManagerCICVF54'>
is redefined as <class 'itk.itkCudaImageDataManagerRTKPython.itkCudaImageDataManagerCICVF54'>
Warning: template already defined 'itk::CudaImageDataManager<itk::CudaImage<itk::CovariantVector<float,5>,4>>'
EDIT: I repeated the ninja test and must have done something different in the first test. The same wall of warnings appears here. Sorry for the confusion. Maybe one of your compiler flags removes the warnings?
Sorry about that... Should be addressed by #577 which requires RTKConsortium/ITKCudaCommon#31, i.e. -DModule_CudaCommon_GIT_TAG:STRING=9d3fe9bdedbac76abc38ea61beff4158de65109f"
.
CI-compiled packages (CudaCommon + RTK) work fine, I'm closing the issue but reopen if I missed something (again).
I am afraid it is still not working as intended. I noticed f5aab1f68e53061264f4f6f3af5e0d49c5f7481d bumps the ITK modules to the required versions but I still end up with the warnings.
Perhaps my description was too imprecise. The warnings appear when running python code, not during compilation, e.g. when calling:
import itk
from itk import RTK as rtk
rtk.Image
So you are using ITK master and you have removed -DModule_CudaCommon_GIT_TAG:STRING=v1.0.1
from your cmake command?
Yes, for the most recent test. For completeness I used this:
cmake -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_TESTING:BOOL=OFF -DITK_WRAP_PYTHON:BOOL=ON -DModule_RTK:BOOL=ON -DRTK_USE_CUDA:BOOL=ON -DRTK_BUILD_APPLICATIONS:BOOL=OFF -GNinja ../src
Ok, I don't know what happened, I probably did not test the right version because I can reproduce the issue... Re-opening. Thanks for your patience.
Hopefully #578 will do
Is there an easy way to test this fix as part of the RTK module in ITK? I tried replacing RTK.remote.cmake with
GIT_REPOSITORY https://github.com/SimonRit/RTK.git
GIT_TAG DefaultWrapping
but ended up with
-- NOTE: Using override 'Module_RTK_GIT_TAG=e9caad5b4409ded681bc1f39d76a1bdc7985f782'
instead of value 'GIT_TAG=DefaultWrapping'
specified in file C:/ITK/v5.4rc02/src/Modules/Remote/RTK.remote.cmake'
From https://github.com/SimonRit/RTK
* branch HEAD -> FETCH_HEAD
fatal: reference is not a tree: e9caad5b4409ded681bc1f39d76a1bdc7985f782
CMake Error at CMake/ITKModuleRemote.cmake:111 (message):
Failed to checkout tag: 'e9caad5b4409ded681bc1f39d76a1bdc7985f782'
Call Stack (most recent call first):
CMake/ITKModuleRemote.cmake:145 (_git_update)
CMake/ITKModuleRemote.cmake:274 (_fetch_with_git)
Modules/Remote/RTK.remote.cmake:40 (itk_fetch_module)
Modules/Remote/CMakeLists.txt:21 (include)
during configuring.
The second attempt was to build ITK and RTK separately by:
cmake -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_TESTING:BOOL=OFF -DModule_CudaCommon:BOOL=ON -DITK_WRAP_PYTHON:BOOL=ON -GNinja ../src-test
and
cmake -DRTK_USE_CUDA:BOOL=ON -DRTK_BUILD_APPLICATIONS:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=OF -DCMAKE_BUILD_TYPE:STRING=Release -DBUILD_TESTING:BOOL=OFF -DITK_DIR:STRING="C://ITK/bin-test" -GNinja ../rtk-src
but during runtime from python I encountered:
ImportError: DLL load failed while importing _RTKPython
I tried fixing this by adding os.add_dll_directory('C:/ITK/rtk-bin/bin')
to the FirstCudaReconstruction example but then ended with
RuntimeError: C:\ITK\src-test\Modules\Filtering\FFT\include\itkRealToHalfHermitianForwardFFTImageFilter.h:85:
ITK ERROR: Object factory failed to instantiate class itk::RealToHalfHermitianForwardFFTImageFilter<class itk::Image<float,3>,class itk::Image<class std::complex<float>,3> >
Is there something I missed for the seperate builds?
If you change RTK.remote.cmake
(which is a good idea), you should remove -DModule_RTK_GIT_TAG
from the command line (which you haven't since there is the message Using override 'Module_RTK_GIT_TAG=e9caad5b4409ded681bc1f39d76a1bdc7985f782'
).
I don't get the python load error but I don't compile it separately usually.
Oh boy, cached CMake variable. With a fresh build it works. Thanks a lot for the help and fixes!
Fixed by #578 578
Hi,
I am building RTK with the following settings:
This results in the following error during compilation:
This is just one example and happens for a lot of classes. I tried a similar build in WSL running Ubuntu, but with python 3.10.12, and the same errors appear, so it seems platform independent.
A possible solution seems to request the (missing?) 4th dimension by setting
-DITK_WRAP_IMAGE_DIMS:String="2;3;4"
but I assume the idea of https://github.com/RTKConsortium/RTK/blob/65f0b66f4ec6fb9a5754977ddb9c8df99267b3e9/wrapping/itkImageSourceRTK.wrap#L44-L46 was to generate the missing parts automagically.My environment is: Windows 10 VS 2019 v16.11.32 Python v3.8.18 Ninja v1.11.1