[Vv] Add HDF5 reading capability

[Simon Rit]

Hi,
I would suggest to open a draft PR on the GitHub repo
<https://vv.creatis.insa-lyon.fr/> with your code to see if we can
reproduce (and hopefully fix) the problem on Linux.
Cheers,
Simon

On Thu, Nov 13, 2025 at 8:32 AM Jerome Lesaint <lesaint.jerome at gmail.com>
wrote:

> Hi all,
> I am trying to add an Nexus/HDF5 file reader in vv but am struggling with
> the build configuration. The error I get at the end of the compilation is :
>
> ================
> [100%] Linking CXX executable ../bin/vv.app/Contents/MacOS/vv
> Undefined symbols for architecture arm64:
>   "_H5check_version", referenced from:
>       rtk::NexusHdf5ImageIO::ReadImageInformation() in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::CanReadFile(char const*) in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::Read(void*) in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>   "_H5open", referenced from:
>       rtk::NexusHdf5ImageIO::ReadImageInformation() in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::CanReadFile(char const*) in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::Read(void*) in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>   "H5::DSetAccPropList::DEFAULT", referenced from:
>       rtk::NexusHdf5ImageIO::ReadImageInformation() in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::ReadImageInformation() in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::Read(void*) in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>   "H5::FileAccPropList::DEFAULT", referenced from:
>       rtk::NexusHdf5ImageIO::ReadImageInformation() in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::CanReadFile(char const*) in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::Read(void*) in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>   "H5::FileCreatPropList::DEFAULT", referenced from:
>       rtk::NexusHdf5ImageIO::ReadImageInformation() in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::CanReadFile(char const*) in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::Read(void*) in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>   "H5::DSetMemXferPropList::DEFAULT", referenced from:
>       rtk::NexusHdf5ImageIO::ReadImageInformation() in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::ReadImageInformation() in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::Read(void*) in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>   "H5::PredType::NATIVE_FLOAT", referenced from:
>       rtk::NexusHdf5ImageIO::ReadImageInformation() in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
>       rtk::NexusHdf5ImageIO::ReadImageInformation() in
> libclitkCommon.a[17](rtkNexusHdf5ImageIO.cxx.o)
> ld: symbol(s) not found for architecture arm64
> clang++: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make[2]: *** [bin/vv.app/Contents/MacOS/vv] Error 1
> make[1]: *** [vv/CMakeFiles/vv.dir/all] Error 2
> ===========
>
> What I've done :
> - added files common/rtkNexusHdf5ImageIO.cxx(and .h) and
> common/rtkNexusHdf5ImageIOFactory.cxx( and .h)
> - added #include <H5Cpp.h> in the common/rtkNexusHdf5ImageIO.h
> - updated clitkIO.cxx and (root) CMakeLists.txt.
>
> If I run `file /opt/homebrew/opt/hdf5/lib/libhdf5_cpp.dylib`, I get
> `/opt/homebrew/opt/hdf5/lib/libhdf5_cpp.dylib: Mach-O 64-bit dynamically
> linked shared library arm64`.
>
> I guess the ITK - HDF5 installation interferes badly somewhere, but cannot
> figure it out properly.
> Any help would be much appreciated.
> Thanks in advance,
> Jerome
>
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