gdcmSerieHelper.h not found on Ubuntu 18.04 despite ITKGDCM module enabled

[KrisThielemans]

Description

Installing ITK 5.0.1 via conda leads to a compilation problem when using gdcm IO despite a system gdcm being present. See conda-forge/libitk-feedstock#42

This seems to say that in whatever way ITK was built for conda, it doesn't find the system GDCM. Nevertheless, /home/sirfuser/miniconda3/lib/cmake/ITK-5.0/ITKConfig.cmake sets ITK_MODULES_ENABLED to include ITKGDCM.

Steps to Reproduce

conda install libitk-dev
sudo apt install libgdcm2-dev
git clone https://github.com/UCL/STIR.git
mkdir build; cd build; cmake ../STIR; make

Actual behavior

output

In file included from /home/sirfuser/devel/STIR/src/IO/ITKImageInputFileFormat.cxx:41:0:
/home/sirfuser/miniconda3/include/ITK-5.0/itkGDCMSeriesFileNames.h:25:10: fatal error: gdcmSerieHelper.h: No such file or directory
 #include "gdcmSerieHelper.h"
          ^~~~~~~~~~~~~~~~~~~
compilation terminated.

This is despite /usr/include/gdcm-2.8/gdcmSerieHelper.h existing.

Reproducibility

always

Versions

5.0.1

Environment

Ubuntu 18.04, cmake version 3.13.1

Additional Information

[stale]

This issue has been automatically marked as stale because it has not had recent activity. Thank you for your contributions.

[thewtex]

ITK provides GDCM by default, and a quick glance at the conda libitk recipe indicates that this GDCM is used in the conda recipe.

Where is the relevant find_package(ITK [...] of the dependent project?

[blowekamp]

There are some know issues with Conda not fixing up the paths in the CMake files correctly, but that is known to only happen on windows:
conda-forge/libitk-feedstock#43

It may be working grep-ing around the installation director as done in the above issue to see if something similar is occurring on your platform.

[KrisThielemans]

thanks for picking this up. I'll try to reproduce this with current conda on Ubuntu 18.04 using our VM https://doi.org/10.5281/zenodo.3552234

Our find_package is quite simple :-)

   find_package(ITK QUIET)
   if (ITK_FOUND)
      include(${ITK_USE_FILE})
   endif()

We use target_link_libraries here but this is a compilation error, so I guess that line is irrelevant.

[blowekamp]

It looks like you are including "itkGDCMSeriesFileNames.h" in the project, which includes "gdcmSerieHelper.h". This does not follow best practices of encapsulation, this PR #1768 addressed that issue.

The Conda-forge has two packages, libitk and itk-devel. I believe the GDCM "Headers" component used by GDCM. This PR should address it:
conda-forge/libitk-feedstock#44

[KrisThielemans]

@blowekamp both PRs look good to me. thanks a lot!

@rijobro, maybe we can try the new const itk-devel package once that PR is merged.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. Thank you for your contributions.

[dzenanz]

That PR is merged. Reopen if it didn't fix the issue.