NiftyPET version 2

[KrisThielemans]

upgraded to version 2.

Also added CUDA and NiftyPET to GitHub Actions.

@gschramm @casperdcl @pjmark please check

[KrisThielemans]

I've got the non-CUDA jobs to run again (phew) (minor correction to come). Turns out that github actions conditional steps are a bit fragile, or I misunderstand the doc, anyway.

I still have a problem letting CMake find NiftyPET (after installation from PyPy). I followed recommendations from
https://github.com/NiftyPET/NIPET/blob/master/README.rst.:

install

             export PATHTOOLS=${GITHUB_WORKSPACE}/NiftyPET_tools
             export HMUDIR=${GITHUB_WORKSPACE}/mmr_hardwareumaps
             python -m pip install "nipet>=2"
             niftypet_cmake_prefix=$(python -c "from niftypet.nipet import cmake_prefix; print(cmake_prefix)")
             ls -R "$niftypet_cmake_prefix"
             echo NiftyPET_PREFIX="$niftypet_cmake_prefix" >> $GITHUB_ENV

gives

niftypet_cmake_prefix=/home/runner/work/STIR/STIR/my-env/lib/python3.10/site-packages/niftypet/nipet/cmake
ls -R /home/runner/work/STIR/STIR/my-env/lib/python3.10/site-packages/niftypet/nipet/cmake
/home/runner/work/STIR/STIR/my-env/lib/python3.10/site-packages/niftypet/nipet/cmake:
NiftyPETmmr_auxeTargets-release.cmake
NiftyPETmmr_auxeTargets.cmake
NiftyPETmmr_lmprocTargets-release.cmake
NiftyPETmmr_lmprocTargets.cmake
NiftyPETnifty_scatterTargets-release.cmake
NiftyPETnifty_scatterTargets.cmake
NiftyPETnipetConfig.cmake
NiftyPETnipetConfigVersion.cmake
NiftyPETpetprjTargets-release.cmake
NiftyPETpetprjTargets.cmake

which surprised me a bit as that doesn't seem to be the prefix, but the actual location of the config files.

Using CMAKE_PREFIX_DIR leads to

cmake -S .. <snip> -DCMAKE_PREFIX_DIR=/home/runner/work/STIR/STIR/my-env/lib/python3.10/site-packages/niftypet/nipet/cmake <snip>

CMake isn't happy:

By not providing "FindNiftyPETnipet.cmake" in CMAKE_MODULE_PATH this
  project has asked CMake to find a package configuration file provided by
  "NiftyPETnipet", but CMake did not find one.

  Could not find a package configuration file provided by "NiftyPETnipet"
  with any of the following names:

    NiftyPETnipetConfig.cmake
    niftypetnipet-config.cmake

  Add the installation prefix of "NiftyPETnipet" to CMAKE_PREFIX_PATH or set
  "NiftyPETnipet_DIR" to a directory containing one of the above files.  If
  "NiftyPETnipet" provides a separate development package or SDK, be sure it
  has been installed.

so it seems we need to set NiftyPETnipet_DIR instead. NiftyPET doc bug?

[KrisThielemans]

forgot to mention @casperdcl in the above.

[KrisThielemans]

setting NiftyPETnipet_DIR works fine.

Currently struggling with g++ not finding prbj.h

[KrisThielemans]

I cannot find prbj.h: https://github.com/UCL/STIR/actions/runs/6992200721/job/19023543893#step:6:773

niftypet_cmake_prefix=/home/runner/work/STIR/STIR/my-env/lib/python3.10/site-packages/niftypet/nipet/cmake
find /home/runner/work/STIR/STIR/my-env/ -name prjb.h

returns nothing

https://github.com/UCL/STIR/actions/runs/6992200721/job/19023543893#step:9:978 shows that the include path set by CMake is likely correct

/usr/bin/g++-12 -DITK_IO_FACTORY_REGISTER_MANAGER -I/home/runner/work/STIR/STIR/src/include -I/home/runner/work/STIR/STIR/build/src/include -I/home/runner/work/STIR/STIR/build/src/ITKFactoryRegistration -I/home/runner/work/STIR/STIR/build/ITKFactoryRegistration -isystem /usr/include/hdf5/serial -isystem /usr/include/gdcm-3.0 -isystem /usr/include/ITK-5.2
 -isystem /home/runner/work/STIR/STIR/my-env/lib/python3.10/site-packages/niftypet/nipet/include -isystem /usr/local/cuda-12.1/include -isystem /home/runner/work/STIR/STIR/install/include -O3 -DNDEBUG -ffast-math -std=gnu++14 -fPIC   -Wall -Wno-deprecated -fopenmp -fopenmp -MD -MT src/recon_buildblock/CMakeFiles/recon_buildblock.dir/NiftyPET_projector/NiftyPETHelper.cxx.o -MF CMakeFiles/recon_buildblock.dir/NiftyPET_projector/NiftyPETHelper.cxx.o.d -o CMakeFiles/recon_buildblock.dir/NiftyPET_projector/NiftyPETHelper.cxx.o -c /home/runner/work/STIR/STIR/src/recon_buildblock/NiftyPET_projector/NiftyPETHelper.cxx
/home/runner/work/STIR/STIR/src/recon_buildblock/NiftyPET_projector/NiftyPETHelper.cxx:41:10: fatal error: prjb.h: No such file or directory

NiftyPET installation bug?

[KrisThielemans]

@casperdcl @pjmark I created NiftyPET/NIPET#51.

I suppose this might still work with a self-installed NIPET, but I have run out of steam.

[KrisThielemans]

As NiftyPET 2 is not compatible with C++, I will essentially abandon this PR, only keeping the CI cuda stuff

[pjmark]

the core of NIPET is written in C, so should be easy to add it to C++, no?

[KrisThielemans]

The problem is that all the set-up is in Python (where it used to be in C). See NiftyPET/NIPET#52 for more information.

[KrisThielemans]

Non-NiftyPET commits are now in #1300. I'm abandoning the rest.