ENH: Bump elastix for ITK_MODULE_TEMPLATE additions #102

thewtex · 2021-02-12T21:14:35Z

elastix develop branch, 2021-02-12.

ViktorvdValk

The notebook tests suddenly fail on this branch, due to an itk import error. A similar failure occurs on the #101 PR. I suppose the errors occur due to an erroneous build on dockerhub (v0.10.0), will one of these PRs fix these issues as well?

thewtex · 2021-02-15T15:40:34Z

The notebook tests suddenly fail on this branch, due to an itk import error. A similar failure occurs on the #101 PR. I suppose the errors occur due to an erroneous build on dockerhub (v0.10.0), will one of these PRs fix these issues as well?

These failures appear to be related to a lack of 4D support in the ITK package -- which indicates it is 5.1 instead of 5.2. I will also bump the versions in the Binder requirements.txt to address this.

thewtex · 2021-02-15T15:42:35Z

@N-Dekker we are observing a few small changes in the result on Linux:

https://open.cdash.org/test/342115602

Any ideas why?

Since it essentially the same result, I will increase the image comparison. tolerance.

Account for slight variations in the result on Linux between elastix versions.

ViktorvdValk · 2021-02-15T16:14:27Z

The segfault still occurs on this PR, so I think this elastix PR should be changed to the first version made by @thewtex, before this branch should be merged. Because @N-Dekker you changed Matts draft right?

N-Dekker · 2021-02-15T16:43:30Z

The segfault still occurs on this PR, so I think this elastix PR should be changed to the first version made by @thewtex, before this branch should be merged. Because @N-Dekker you changed Matts draft right?

I only excluded the dynamic_cast related changes from Matt's draft. Because I assumed that dynamic_cast should work fine if all classes are properly exported,

Now I wonder: are all elastix classes now indeed properly exported?

thewtex · 2021-02-15T16:53:46Z

Now I wonder: are all elastix classes now indeed properly exported?

We made progress on the exports, but there are still a lot of missing ITK_TEMPLATE_EXPORT declarations. Quick find:

https://github.com/SuperElastix/elastix/blob/develop/Common/ImageSamplers/itkImageGridSampler.h

While the exports could be addressed in the future, the patch will prevent crashing on macOS for now:

SuperElastix/elastix#419

N-Dekker · 2021-02-15T16:54:17Z

@thewtex

@N-Dekker we are observing a few small changes in the result on Linux:
https://open.cdash.org/test/342115602
Any ideas why?

Thanks for asking, Matt. I'm not sure but we started using itk::NumberToString last month, to convert floating point parameter values to string: SuperElastix/elastix@e1f5dae Which might have increased the precision of the elastix registration results (the transform parameters), compared to previous versions of elastix. Could that have caused the changes that you observed?

thewtex · 2021-02-15T16:55:23Z

Thanks for asking, Matt. I'm not sure but we started using itk::NumberToString last month, to convert floating point parameter values to string: SuperElastix/elastix@e1f5dae Which might have increased the precision of the elastix registration results (the transform parameters), compared to previous versions of elastix. Could that have caused the changes that you observed?

Thanks for the note, Neils. Yes, that would make sense.

thewtex · 2021-02-15T19:12:35Z

@N-Dekker we are getting the build error with the OpenCL builds:

FAILED: _deps/elx-build/Components/ImageSamplers/MultInputRandomCoordinate/CMakeFiles/MultiInputRandomCoordinateSampler.dir/elxMultiInputRandomCoordinateSampler.cxx.o 
/opt/rh/devtoolset-2/root/usr/bin/g++  -DELASTIX_USE_OPENCL -DITK_IO_FACTORY_REGISTER_MANAGER -I_deps/elx-src/Common/OpenCL/Kernels -I_deps/elx-src/Common/OpenCL/Filters -I_deps/elx-src/Common/OpenCL/ITKimprovements -I_deps/elx-src/Common/OpenCL/Factories -I_deps/elx-src/Common/OpenCL -I_deps/elx-build/ITKFactoryRegistration -I../../../ITK-source/ITK/Modules/IO/MeshVTK/include -I../../../ITK-source/ITK/Modules/IO/MeshOFF/include -I../../../ITK-source/ITK/Modules/IO/MeshGifti/include -I../../../ITK-source/ITK/Modules/IO/MeshFreeSurfer/include -I../../../ITK-source/ITK/Modules/IO/MeshBYU/include -I../../../ITK-source/ITK/Modules/IO/Mesh/include -I../../../ITK-source/ITK/Modules/IO/TransformMatlab/include -I../../../ITK-source/ITK/Modules/IO/TransformInsightLegacy/include -I../../../ITK-source/ITK/Modules/IO/TransformHDF5/include -I../../../ITK-source/ITK/Modules/IO/VTK/include -I../../../ITK-source/ITK/Modules/IO/Stimulate/include -I../../../ITK-source/ITK/Modules/IO/PNG/include -I../../../ITK-source/ITK/Modules/IO/NRRD/include -I../../../ITK-source/ITK/Modules/IO/NIFTI/include -I../../../ITK-source/ITK/Modules/IO/MRC/include -I../../../ITK-source/ITK/Modules/IO/MINC/include -I../../../ITK-source/ITK/Modules/IO/TIFF/include -I../../../ITK-source/ITK/Modules/IO/LSM/include -I../../../ITK-source/ITK/Modules/IO/JPEG2000/include -I../../../ITK-source/ITK/Modules/IO/JPEG/include -I../../../ITK-source/ITK/Modules/IO/HDF5/include -I../../../ITK-source/ITK/Modules/IO/GIPL/include -I../../../ITK-source/ITK/Modules/IO/IPL/include -I../../../ITK-source/ITK/Modules/IO/GE/include -I../../../ITK-source/ITK/Modules/IO/GDCM/include -I../../../ITK-source/ITK/Modules/IO/Bruker/include -I../../../ITK-source/ITK/Modules/IO/BioRad/include -I../../../ITK-source/ITK/Modules/IO/BMP/include -I../../../ITK-source/ITK/Modules/Core/GPUCommon/include -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/DoubleConversion/src/double-conversion -I../../../ITK-source/ITK/Modules/ThirdParty/DoubleConversion/src -I../../../ITK-source/ITK/Modules/Core/TestKernel/include -I../../../ITK-source/ITK/Modules/Filtering/ImageSources/include -I../../../ITK-source/ITK/Modules/Filtering/ImageFeature/include -I../../../ITK-source/ITK/Modules/Registration/Common/include -I../../../ITK-source/ITK/Modules/Numerics/Optimizers/include -I../../../ITK-source/ITK/Modules/IO/XML/include -I../../../ITK-source/ITK/Modules/IO/TransformFactory/include -I../../../ITK-source/ITK/Modules/IO/TransformBase/include -I../../../ITK-source/ITK/Modules/IO/Meta/include -I../../../ITK-source/ITK/Modules/IO/MeshOBJ/include -I../../../ITK-source/ITK/Modules/Segmentation/Voronoi/include -I../../../ITK-source/ITK/Modules/Core/QuadEdgeMesh/include -I../../../ITK-source/ITK/Modules/Core/Mesh/include -I../../../ITK-source/ITK/Modules/IO/MeshBase/include -I../../../ITK-source/ITK/Modules/IO/ImageBase/include -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/IO/ImageBase -I../../../ITK-source/ITK/Modules/Filtering/ImageGradient/include -I../../../ITK-source/ITK/Modules/ThirdParty/Expat/src/expat -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/Expat/src/expat -I../../../ITK-source/ITK/Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition -I../../../ITK-source/ITK/Modules/ThirdParty/GDCM/src/gdcm/Source/MessageExchangeDefinition -I../../../ITK-source/ITK/Modules/ThirdParty/GDCM/src/gdcm/Source/InformationObjectDefinition -I../../../ITK-source/ITK/Modules/ThirdParty/GDCM/src/gdcm/Source/Common -I../../../ITK-source/ITK/Modules/ThirdParty/GDCM/src/gdcm/Source/DataDictionary -I../../../ITK-source/ITK/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/GDCM/src/gdcm/Source/Common -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/GDCM -I../../../ITK-source/ITK/Modules/Core/FiniteDifference/include -I../../../ITK-source/ITK/Modules/Filtering/CurvatureFlow/include -I../../../ITK-source/ITK/Modules/Numerics/NarrowBand/include -I../../../ITK-source/ITK/Modules/Filtering/Thresholding/include -I../../../ITK-source/ITK/Modules/Segmentation/ConnectedComponents/include -I../../../ITK-source/ITK/Modules/Filtering/MathematicalMorphology/include -I../../../ITK-source/ITK/Modules/Filtering/ImageLabel/include -I../../../ITK-source/ITK/Modules/Filtering/LabelMap/include -I../../../ITK-source/ITK/Modules/Filtering/BinaryMathematicalMorphology/include -I../../../ITK-source/ITK/Modules/Filtering/DistanceMap/include -I../../../ITK-source/ITK/Modules/Filtering/Smoothing/include -I../../../ITK-source/ITK/Modules/Filtering/Path/include -I../../../ITK-source/ITK/Modules/ThirdParty/ZLIB/src -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/ZLIB/src -I../../../ITK-source/ITK/Modules/ThirdParty/MetaIO/src/MetaIO/src -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/MetaIO/src/MetaIO/src -I../../../ITK-source/ITK/Modules/Core/SpatialObjects/include -I../../../ITK-source/ITK/Modules/Filtering/ImageCompose/include -I../../../ITK-source/ITK/Modules/Filtering/ImageStatistics/include -I../../../ITK-source/ITK/Modules/Filtering/ImageIntensity/include -I../../../ITK-source/ITK/Modules/Filtering/ImageFilterBase/include -I../../../ITK-source/ITK/Modules/Core/Transform/include -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/Netlib -I../../../ITK-source/ITK/Modules/Numerics/Statistics/include -I../../../ITK-source/ITK/Modules/Core/ImageAdaptors/include -I../../../ITK-source/ITK/Modules/Core/ImageFunction/include -I../../../ITK-source/ITK/Modules/Filtering/ImageGrid/include -I../../../ITK-source/ITK/Modules/Filtering/DisplacementField/include -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/VNL/src/vxl/core -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/VNL/src/vxl/vcl -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -I../../../ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core -I../../../ITK-source/ITK/Modules/ThirdParty/KWIML/src -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/KWIML/src -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/Eigen3/src -I../../../ITK-source/ITK/Modules/Core/Common/include -I../../../ITK-cp37-cp37m-manylinux1_x64/Modules/Core/Common -I_deps/elx-src/Common -I_deps/elx-src/Common/CostFunctions -I_deps/elx-src/Common/ImageSamplers -I_deps/elx-src/Common/LineSearchOptimizers -I_deps/elx-src/Common/ParameterFileParser -I_deps/elx-src/Common/Transforms -I_deps/elx-src/Common/xout -I_deps/elx-src/Common/MevisDicomTiff -I_deps/elx-src/Core -I_deps/elx-src/Core/Install -I_deps/elx-src/Core/Kernel -I_deps/elx-src/Core/ComponentBaseClasses -I_deps/elx-src/Core/Configuration -I_deps/elx-src/Core/Main -I_deps/elx-src/Components/FixedImagePyramids -I_deps/elx-src/Components/ImageSamplers -I_deps/elx-src/Components/Interpolators -I_deps/elx-src/Components/Metrics -I_deps/elx-src/Components/MovingImagePyramids -I_deps/elx-src/Components/Optimizers -I_deps/elx-src/Components/Registrations -I_deps/elx-src/Components/ResampleInterpolators -I_deps/elx-src/Components/Resamplers -I_deps/elx-src/Components/Transforms -I_deps/elx-build -isystem ../../../ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/vcl -isystem ../../../ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/v3p/netlib -isystem ../../../ITK-cp37-cp37m-manylinux1_x64/Modules/ThirdParty/KWSys/src -isystem ../../../ITK-source/ITK/Modules/ThirdParty/Eigen3/src/itkeigen/.. -isystem ../../../ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo -isystem ../../../ITK-source/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl -Wno-aggressive-loop-optimizations  -Wno-array-bounds -O3 -DNDEBUG -fPIC   -std=gnu++11 -MD -MT _deps/elx-build/Components/ImageSamplers/MultInputRandomCoordinate/CMakeFiles/MultiInputRandomCoordinateSampler.dir/elxMultiInputRandomCoordinateSampler.cxx.o -MF _deps/elx-build/Components/ImageSamplers/MultInputRandomCoordinate/CMakeFiles/MultiInputRandomCoordinateSampler.dir/elxMultiInputRandomCoordinateSampler.cxx.o.d -o _deps/elx-build/Components/ImageSamplers/MultInputRandomCoordinate/CMakeFiles/MultiInputRandomCoordinateSampler.dir/elxMultiInputRandomCoordinateSampler.cxx.o -c _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx
In file included from ../../../ITK-source/ITK/Modules/Core/Common/include/itkSliceIterator.h:23:0,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhood.h:24,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageBoundaryCondition.h:22,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhoodAccessorFunctor.h:21,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImage.h:28,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageSource.h:32,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageToImageFilter.h:31,
                 from ../../../ITK-source/ITK/Modules/Filtering/ImageGrid/include/itkChangeInformationImageFilter.h:21,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:38,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/valarray: In instantiation of ‘class std::valarray<xoutlibrary::xoutbase>’:
_deps/elx-src/Common/CostFunctions/itkAdvancedImageToImageMetric.hxx:273:20:   required from here
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/valarray:926:5: error: cannot allocate an object of abstract type ‘xoutlibrary::xoutbase’
     valarray<_Tp>::sum() const
     ^
In file included from _deps/elx-src/Common/xout/xoutmain.h:22:0,
                 from _deps/elx-src/Core/Configuration/elxConfiguration.h:27,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:33,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
_deps/elx-src/Common/xout/xoutbase.h:40:7: note:   because the following virtual functions are pure within ‘xoutlibrary::xoutbase’:
 class xoutbase
       ^
_deps/elx-src/Common/xout/xoutbase.h:52:11: note: 	virtual xoutlibrary::xoutbase::~xoutbase()
   virtual ~xoutbase() = 0;
           ^
In file included from ../../../ITK-source/ITK/Modules/Core/Common/include/itkSliceIterator.h:23:0,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhood.h:24,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageBoundaryCondition.h:22,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhoodAccessorFunctor.h:21,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImage.h:28,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageSource.h:32,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageToImageFilter.h:31,
                 from ../../../ITK-source/ITK/Modules/Filtering/ImageGrid/include/itkChangeInformationImageFilter.h:21,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:38,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/valarray:1033:5: error: cannot allocate an object of abstract type ‘xoutlibrary::xoutbase’
     valarray<_Tp>::min() const
     ^
In file included from _deps/elx-src/Common/xout/xoutmain.h:22:0,
                 from _deps/elx-src/Core/Configuration/elxConfiguration.h:27,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:33,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
_deps/elx-src/Common/xout/xoutbase.h:40:7: note:   since type ‘xoutlibrary::xoutbase’ has pure virtual functions
 class xoutbase
       ^
In file included from ../../../ITK-source/ITK/Modules/Core/Common/include/itkSliceIterator.h:23:0,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhood.h:24,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageBoundaryCondition.h:22,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhoodAccessorFunctor.h:21,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImage.h:28,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageSource.h:32,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageToImageFilter.h:31,
                 from ../../../ITK-source/ITK/Modules/Filtering/ImageGrid/include/itkChangeInformationImageFilter.h:21,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:38,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/valarray:1041:5: error: cannot allocate an object of abstract type ‘xoutlibrary::xoutbase’
     valarray<_Tp>::max() const
     ^
In file included from _deps/elx-src/Common/xout/xoutmain.h:22:0,
                 from _deps/elx-src/Core/Configuration/elxConfiguration.h:27,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:33,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
_deps/elx-src/Common/xout/xoutbase.h:40:7: note:   since type ‘xoutlibrary::xoutbase’ has pure virtual functions
 class xoutbase
       ^
In file included from ../../../ITK-source/ITK/Modules/Core/Common/include/itkSliceIterator.h:23:0,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhood.h:24,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageBoundaryCondition.h:22,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhoodAccessorFunctor.h:21,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImage.h:28,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageSource.h:32,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageToImageFilter.h:31,
                 from ../../../ITK-source/ITK/Modules/Filtering/ImageGrid/include/itkChangeInformationImageFilter.h:21,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:38,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/valarray:1049:5: error: cannot allocate an object of abstract type ‘xoutlibrary::xoutbase’
     valarray<_Tp>::apply(_Tp func(_Tp)) const
     ^
In file included from _deps/elx-src/Common/xout/xoutmain.h:22:0,
                 from _deps/elx-src/Core/Configuration/elxConfiguration.h:27,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:33,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
_deps/elx-src/Common/xout/xoutbase.h:40:7: note:   since type ‘xoutlibrary::xoutbase’ has pure virtual functions
 class xoutbase
       ^
In file included from ../../../ITK-source/ITK/Modules/Core/Common/include/itkSliceIterator.h:23:0,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhood.h:24,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageBoundaryCondition.h:22,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhoodAccessorFunctor.h:21,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImage.h:28,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageSource.h:32,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageToImageFilter.h:31,
                 from ../../../ITK-source/ITK/Modules/Filtering/ImageGrid/include/itkChangeInformationImageFilter.h:21,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:38,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/valarray:1057:5: error: cannot allocate an object of abstract type ‘xoutlibrary::xoutbase’
     valarray<_Tp>::apply(_Tp func(const _Tp &)) const
     ^
In file included from _deps/elx-src/Common/xout/xoutmain.h:22:0,
                 from _deps/elx-src/Core/Configuration/elxConfiguration.h:27,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:33,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
_deps/elx-src/Common/xout/xoutbase.h:40:7: note:   since type ‘xoutlibrary::xoutbase’ has pure virtual functions
 class xoutbase
       ^
In file included from ../../../ITK-source/ITK/Modules/Core/Common/include/itkSliceIterator.h:23:0,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhood.h:24,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageBoundaryCondition.h:22,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkNeighborhoodAccessorFunctor.h:21,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImage.h:28,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageSource.h:32,
                 from ../../../ITK-source/ITK/Modules/Core/Common/include/itkImageToImageFilter.h:31,
                 from ../../../ITK-source/ITK/Modules/Filtering/ImageGrid/include/itkChangeInformationImageFilter.h:21,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:38,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
/opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/valarray:1016:5: error: cannot allocate an object of abstract type ‘xoutlibrary::xoutbase’
     valarray<_Tp>::resize(size_t __n, _Tp __c)
     ^
In file included from _deps/elx-src/Common/xout/xoutmain.h:22:0,
                 from _deps/elx-src/Core/Configuration/elxConfiguration.h:27,
                 from _deps/elx-src/Core/Kernel/elxElastixBase.h:33,
                 from _deps/elx-src/Core/Kernel/elxElastixTemplate.h:21,
                 from _deps/elx-src/Core/Install/elxIncludes.h:39,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.h:21,
                 from _deps/elx-src/Components/ImageSamplers/MultInputRandomCoordinate/elxMultiInputRandomCoordinateSampler.cxx:19:
_deps/elx-src/Common/xout/xoutbase.h:40:7: note:   since type ‘xoutlibrary::xoutbase’ has pure virtual functions
 class xoutbase

Does this ring a bell?

ViktorvdValk · 2021-02-16T14:32:26Z

If this branch can point to the most recent elastix update . The MacOS issue will at least be fixed wrt the segfault and issue #52 can finally be closed :).
And I'll then update the import statements in the example notebooks accordingly.
Great effort @thewtex and @N-Dekker!

To address macOS crashes.

N-Dekker · 2021-02-19T16:43:12Z

@thewtex

we are getting the build error with the OpenCL builds:
FAILED: _deps/elx-build/Components/ImageSamplers/MultInputRandomCoordinate/CMakeFiles/MultiI
...
Does this ring a bell?

Honestly no. Can you give me another clue, please? So the compilation of various valarray<_Tp> member function calls appears to fail, just because xoutbase has become an abstract base class?

thewtex · 2021-02-20T02:07:02Z

@N-Dekker with the update to ITK 5.2, the manylinux2014 compiler we no longer have the error.

ENH: Bump elastix for ITK_MODULE_TEMPLATE additions

20a0d10

elastix develop branch, 2021-02-12.

thewtex requested review from N-Dekker and ViktorvdValk February 12, 2021 21:14

ViktorvdValk approved these changes Feb 15, 2021

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ViktorvdValk reviewed Feb 15, 2021

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thewtex added 2 commits February 15, 2021 10:43

BUG: Bump Binder requirements for ITK 5.2 RC 2

833022b

BUG: Set itkElastixRegistrationMethodTest number of pixel tolerance

a75a5b0

Account for slight variations in the result on Linux between elastix versions.

COMP: Bump elastix version to 2021-02-16 develop

bde1870

To address macOS crashes.

ViktorvdValk mentioned this pull request Feb 16, 2021

STYLE:Remove unnecessary notebook imports #103

Merged

COMP: Update Linux OpenCL wheel builds for manylinux2014

5be1812

thewtex force-pushed the elastix-bump branch 2 times, most recently from 7c24311 to f6714e2 Compare February 19, 2021 16:25

COMP: Address elastix OpenCL build errors

e13b306

thewtex force-pushed the elastix-bump branch from f6714e2 to e13b306 Compare February 19, 2021 16:52

ENH: Bump CI to ITK 5.2 RC 2

4045f0c

thewtex force-pushed the elastix-bump branch from 1667f7a to 4045f0c Compare February 19, 2021 21:11

thewtex merged commit 314df2f into master Feb 20, 2021

thewtex deleted the elastix-bump branch February 20, 2021 02:07

thewtex mentioned this pull request Feb 20, 2021

ENH: Bump CI to ITK 5.2 RC 2 #101

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ENH: Bump elastix for ITK_MODULE_TEMPLATE additions #102

ENH: Bump elastix for ITK_MODULE_TEMPLATE additions #102

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thewtex commented Feb 20, 2021

ENH: Bump elastix for ITK_MODULE_TEMPLATE additions #102

ENH: Bump elastix for ITK_MODULE_TEMPLATE additions #102

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