Unable to successfully compile LesionSizingToolkit module

[artitj]

I am unable to successfully compile the LesionSizingToolkit module using ITK 5.12. I am building the module in tree by enabling the Module_LesionSizingToolkit option, setting LSTK_USE_VTK=ON. I have tried VTK 9.0.1 and VTK 7.1.1. I am using Ubuntu 20.04.2.

I receive the following errors:
`[ 80%] Building CXX object Modules/Remote/LesionSizingToolkit/Examples/CMakeFiles/LesionSegmentation.dir/LesionSegmentation.cxx.o

In file included from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:40:

/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h: In member function ‘double* LesionSegmentationCLI::GetROI()’:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:128:37: error: ‘__gnu_cxx::__alloc_traits<std::allocator<itk::SpatialObjectPoint<3> >, itk::SpatialObjectPoint<3> >::value_type’ {aka ‘class itk::SpatialObjectPoint<3>’} has no member named ‘GetPosition’
128 | this->ROI[2 * i] = seeds[0].GetPosition()[i] - this->GetValueAsFloat("MaximumRadius");
| ^~~~~~~~~~~
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:129:41: error: ‘__gnu_cxx::__alloc_traits<std::allocator<itk::SpatialObjectPoint<3> >, itk::SpatialObjectPoint<3> >::value_type’ {aka ‘class itk::SpatialObjectPoint<3>’} has no member named ‘GetPosition’
129 | this->ROI[2 * i + 1] = seeds[0].GetPosition()[i] + this->GetValueAsFloat("MaximumRadius");
| ^~~~~~~~~~~
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h: In member function ‘LesionSegmentationCLI::LandmarkPointListType LesionSegmentationCLI::GetSeeds()’:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:255:16: error: ‘__gnu_cxx::__alloc_traits<std::allocator<itk::SpatialObjectPoint<3> >, itk::SpatialObjectPoint<3> >::value_type’ {aka ‘class itk::SpatialObjectPoint<3>’} has no member named ‘SetPosition’
255 | seeds[i].SetPosition(sx, sy, sz);
| ^~~~~~~~~~~
In file included from /usr/include/dirent.h:245,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:17,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:40:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx: In function ‘itk::Image<short int, 3>::Pointer GetImage(std::string, bool)’:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:154:14: error: conversion from ‘long int’ to ‘itk::Image<short int, 3>::Pointer’ {aka ‘itk::SmartPointer<itk::Image<short int, 3> >’} is ambiguous
154 | return NULL;
| ^~~~
In file included from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkExceptionObject.h:25,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkMacro.h:1272,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReaderException.h:22,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReader.h:20,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:1:
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:99:3: note: candidate: ‘itk::SmartPointer::SmartPointer(itk::SmartPointer::ObjectType*) [with TObjectType = itk::Image<short int, 3>; itk::SmartPointer::ObjectType = itk::Image<short int, 3>]’
99 | SmartPointer(ObjectType * p) noexcept
| ^~~~~~~~~~~~
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:71:13: note: candidate: ‘constexpr itk::SmartPointer::SmartPointer(std::nullptr_t) [with TObjectType = itk::Image<short int, 3>; std::nullptr_t = std::nullptr_t]’
71 | constexpr SmartPointer(std::nullptr_t p) noexcept
| ^~~~~~~~~~~~
In file included from /usr/include/dirent.h:245,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:17,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:40:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:175:12: error: conversion from ‘long int’ to ‘itk::Image<short int, 3>::Pointer’ {aka ‘itk::SmartPointer<itk::Image<short int, 3> >’} is ambiguous
175 | return NULL;
| ^~~~
In file included from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkExceptionObject.h:25,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkMacro.h:1272,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReaderException.h:22,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReader.h:20,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:1:
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:99:3: note: candidate: ‘itk::SmartPointer::SmartPointer(itk::SmartPointer::ObjectType*) [with TObjectType = itk::Image<short int, 3>; itk::SmartPointer::ObjectType = itk::Image<short int, 3>]’
99 | SmartPointer(ObjectType * p) noexcept
| ^~~~~~~~~~~~
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:71:13: note: candidate: ‘constexpr itk::SmartPointer::SmartPointer(std::nullptr_t) [with TObjectType = itk::Image<short int, 3>; std::nullptr_t = std::nullptr_t]’
71 | constexpr SmartPointer(std::nullptr_t p) noexcept
| ^~~~~~~~~~~~
In file included from /usr/include/dirent.h:245,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentationCLI.h:17,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:40:
/home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:178:10: error: conversion from ‘long int’ to ‘itk::Image<short int, 3>::Pointer’ {aka ‘itk::SmartPointer<itk::Image<short int, 3> >’} is ambiguous
178 | return NULL;
| ^~~~
In file included from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkExceptionObject.h:25,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkMacro.h:1272,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReaderException.h:22,
from /home/artit/src/InsightToolkit-5.1.2/Modules/IO/ImageBase/include/itkImageFileReader.h:20,
from /home/artit/src/InsightToolkit-5.1.2/Modules/Remote/LesionSizingToolkit/Examples/LesionSegmentation.cxx:1:
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:99:3: note: candidate: ‘itk::SmartPointer::SmartPointer(itk::SmartPointer::ObjectType*) [with TObjectType = itk::Image<short int, 3>; itk::SmartPointer::ObjectType = itk::Image<short int, 3>]’
99 | SmartPointer(ObjectType * p) noexcept
| ^~~~~~~~~~~~
/home/artit/src/InsightToolkit-5.1.2/Modules/Core/Common/include/itkSmartPointer.h:71:13: note: candidate: ‘constexpr itk::SmartPointer::SmartPointer(std::nullptr_t) [with TObjectType = itk::Image<short int, 3>; std::nullptr_t = std::nullptr_t]’
71 | constexpr SmartPointer(std::nullptr_t p) noexcept
| ^~~~~~~~~~~~
make[2]: *** [Modules/Remote/LesionSizingToolkit/Examples/CMakeFiles/LesionSegmentation.dir/build.make:63: Modules/Remote/LesionSizingToolkit/Examples/CMakeFiles/LesionSegmentation.dir/LesionSegmentation.cxx.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:15615: Modules/Remote/LesionSizingToolkit/Examples/CMakeFiles/LesionSegmentation.dir/all] Error 2
make: *** [Makefile:152: all] Error 2`

EDIT: I tried ITK 4.13.3 with VTK 7.1 and it compiled successfully. So the problem seems to be with the latest versions of ITK.

[dzenanz]

The original author (@karthikkrishnan?) has abandoned this nearly 10 years ago. ITK 5 had a significant SpatialObject refactoring, and I don't think anyone updated this remote properly. Does it build if you build without VTK?

[artitj]

Thanks for the quick reply! If I set LSTK_USE_VTK=OFF, the LesionSegmentation binary doesn't get built.

[dzenanz]

I meant, are there compile errors?

Yes, this module is in serious need of maintenance. Contributions are welcome. If anyone wants to do it, they should follow the migration guide:
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/ITK5MigrationGuide.md

[artitj]

I meant, are there compile errors?

Yes, this module is in serious need of maintenance. Contributions are welcome. If anyone wants to do it, they should follow the migration guide:
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/ITK5MigrationGuide.md

Sorry I wasn't clear. While there are no compile errors, it doesn't look like the LegionSegmentation binary is actually part of the build; only its dependencies get built.

Thank you for your help though! I was confused since even the latest 5.2 rc 3 release notes specifically say the LesionSizingToolkit module is updated (https://github.com/InsightSoftwareConsortium/ITK/releases).

[dzenanz]

I guess it was only updated to build in default configuration. By build, I mean have no compile errors.

[romangrothausmann]

Hi @dzenanz!
Just came across this issue when trying to make use of itkVesselEnhancingDiffusion3DImageFilter.
I noticed that quite a bit of work has gone on LesionSizingToolkit since the last post here.
What is the last know combination of ITK-4.x and VTK-y to work for compiling ITK with Module_LesionSizingToolkit=ON?
Is there a known version combination that works for ITK-5.z?
Adding -DLSTK_USE_VTK=OFF did not seem to have any (positive) effect.

[dzenanz]

@hjmjohnson has PR #51 open, he might be up to date and be able to answer your questions.

[romangrothausmann]

Found a working combination:
VTK-7.1.1 with ITK-4.12.2:
https://gitlab.com/romangrothausmann/ITK-VTK_CLIs/-/blob/03b952cf4389972057fab5b088b5334671b5a0bb/Dockerfile#L58
https://gitlab.com/romangrothausmann/ITK-VTK_CLIs/-/pipelines/1820809559