struggling to build CaPTk

[mschachter]

Describe the bug I want to be able to build CaPTk from source, but having trouble finding mutually consistent versions of OpenCV, VTK, and ITK that work. I've tried:

• OpenCV 3.4.12
• VTK 8.1
• ITK 4.13

With this combo, Module_ITKVtkGlue is not compatible with OpenCV 3.4.12.

I'm on Ubuntu 20 LTS - and I've also tried just using apt to install opencv, ITK, and VTK. In that case when I try to compile CaPTk there is a missing itk file, itkStripTsImageFilter.h, which is not present in the more recent version of ITK but required by CaPTk.

To Reproduce I don't think you should try to reproduce this behavior...

Expected behavior I would like the build page (https://cbica.github.io/CaPTk/tr_buildFromSource.html) to reflect known working versions of OpenCV, ITK, and VTK, instead of saying "Version x.x and above", because that's not working for me. Alternatively just some up-to-date dependency information in a BUILD file or as a comment in this issue would be useful!

Screenshots n/a

CaPTk Version Clone from master branch on github.

Desktop (please complete the following information):

• OS: Ubuntu 20.04.1 LTS
• Version (including Build information, if any): 5.4.0-52-generic

Additional context I can successfully start the CaPTk after downloading the .bin file, but I haven't extensively tried out functionality yet.

[sarthakpati]

Thanks for your interest in CaPTk and I apologize for the issues you are facing. Tagging @AlexanderGetka-cbica who recently tested CaPTk on Ubuntu 20.04.

[AlexanderGetka-cbica]

Hi @mschachter, thank you for the issue report. I will add a line to the documentation that mentions a good known set of versions once we can confirm. The following combination builds correctly on my machine: OpenCV 3.4.7 VTK 8.1 ITK 4.13

Please let us know if this set of versions works for you.

[mschachter]

Thanks! @AlexanderGetka-cbica - what version of Eigen are you building opencv against?

[AlexanderGetka-cbica]

@mschachter I have it built against Eigen 3.3.7.

[sarthakpati]

Hi @mschachter, thank you for the issue report. I will add a line to the documentation that mentions a good known set of versions once we can confirm. The following combination builds correctly on my machine: OpenCV 3.4.7 VTK 8.1 ITK 4.13

Please let us know if this set of versions works for you.

Hey @AlexanderGetka-cbica, what is the GCC version you used? I know that the all the dependencies are pulled using the Superbuild, BTW.

[AlexanderGetka-cbica]

Hey @AlexanderGetka-cbica, what is the GCC version you used? I know that the all the dependencies are pulled using the Superbuild, BTW.

Last GCC used according to my logs was 7.5.0.

[mschachter]

Thanks again for the quick response. I'm not having success with the combinations mentioned by @sarthakpati. There are some caveats to the versions reported:

VTK 8.1: the versions tagged on github are 8.1.x - I'm using 8.1.2, for example. I do not see VTK_USE_QT and VTK_USE_QVTK_QTOPENGL tags in the ccmake advanced config, although these flags were mentioned on the CaPTk build page. ITK 4.13: The most recent tag is 4.13.3, I'm using this version. I don't know what tag 4.13 corresponds to. Maybe 4.13.0? *OpenCV: I'm using 3.4.7, as suggested.

I can't compile ITK 4.13.3 against OpenCV 3.4.7, the Module_ITKVtkGlue code is again not compatible, it uses the C version of OpenCV.

@sarthakpati - if possible could you tell me the sub-sub-versions of VTK and ITK you are using? I can probably figure this out on my own, but don't have a ton of time to do so.

[AlexanderGetka-cbica]

@mschachter The versions I have (from our superbuild) are ITK 4.13.0 and VTK 8.1.0 specifically.

[sarthakpati]

Okay, so could you try this:

• Purge your environment of ITK/VTK/OpenCV (just keep a Qt installation of 5.12.X in your path)
  • there should be nothing from these libraries in PATH, LD_LIBRARY_PATH or CMAKE_PREFIX_PATH
• Add ${qt_install_path}/lib/cmake to the environment variable CMAKE_PREFIX_PATH
• Are you able to reproduce the error by following these steps:

  git clone https://github.com/cbica/captk.git
  latesttag=$(git describe --tags)
  echo checking out ${latesttag}
  git checkout ${latesttag}
  mkdir bin_depends; cd bin_depends
  cmake .. # this should add build targets for OpenCV, VTK, ITK (not Qt because you should have it in your environment already)
  make -j # this should build all the dependencies
  export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:`pwd`/ITK-build:`pwd`/VTK-build:`pwd`/OpenCV-build
  cd ..; mkdir bin; cd bin
  cmake .. # this should add build targets for CaPTk by linking against previous dependencies
  make -j

[mschachter]

Thanks @sarthakpati - I'm using GCC 9 and building dependencies fails with this error:

In file included from /home/mschachter/code/3p/captk/bin_depends/ITK-source/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_iostream.h:5, from /home/mschachter/code/3p/captk/bin_depends/ITK-source/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_deprecated.cxx:4: /home/mschachter/code/3p/captk/bin_depends/ITK-source/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h:101:4: error: #error "Dunno about this gcc" 101 | # error "Dunno about this gcc" | ^~~~~ make[5]: *** [Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/build.make:63: Modules/ThirdParty/VNL/src/vxl/vcl/CMakeFiles/itkvcl.dir/vcl_deprecated.cxx.o] Error 1

I think CaPTk should upgrade it's dependencies... Not making that statement lightly, because I know what a pain that can be :) Is that something the team needs help with? I can work on it in a branch and submit a PR if I get something working.

[sarthakpati]

I can work on it in a branch and submit a PR if I get something working

It would be amazing if you could submit a PR for this!

I am not very familiar with the error that you mention, do you think you could try with a lower GCC version (I think we have tested with around GCC 6 - perhaps @AlexanderGetka-cbica has tried something newer?).

[AlexanderGetka-cbica]

@sarthakpati I strongly believe it works on GCC 7.5.0 based on my last-used compiler on my Ubuntu workstation, but for versions beyond that I am not sure.

@mschachter This would be an awesome (and highly appreciated) change; thank you for the offer to help out!

[mschachter]

Thanks for the replies - yes it probably has much to do with my GCC version, but it wouldn't make sense for me to downgrade. I'll start looking into upgrading the dependencies (Eigen, OpenCV, VTK, ITK) and will make a new post on feasibility some time in the hopefully near future :)

Closing this bug for now, thanks again!