unable to locate HDF5 header file at hdf5.h stack traceback: about sagan

[xinario]

Is the hdf5.h file inside your include path?
The path can be found in [your torch folder]/install/share/lua/5.1/hdf5/config.lua specified as HDF5_INCLUDE_PATH

[flystarhe]

I try:

luarocks install hdf5

or:

sudo apt-get install libhdf5-serial-dev hdf5-tools
git clone https://github.com/deepmind/torch-hdf5
cd torch-hdf5
luarocks make hdf5-0-0.rockspec LIBHDF5_LIBDIR="/usr/lib/x86_64-linux-gnu/"

not find hdf5*/**/include for ~/torch/install/share/lua/5.1/hdf5/config.lua:

hdf5._config = {
    HDF5_INCLUDE_PATH = "",
    HDF5_LIBRARIES = "/home/hejian/anaconda3/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so"
}

installed hdf5 dir:

hejian@xlab:~$ tree -L 3 /home/hejian/torch/install/lib/luarocks/rocks/hdf5/
/home/hejian/torch/install/lib/luarocks/rocks/hdf5/
└── 0-0
    ├── doc
    │   ├── hdf5.md
    │   └── usage.md
    ├── hdf5-0-0.rockspec
    └── rock_manifest

2 directories, 4 files

[flystarhe]

thx, find it at /usr/lib/x86_64-linux-gnu/hdf5/serial/. I'll try it again.
@ubuntu 16.04

[xinario]

Great, just specify the include path in config.lua. For example in my case it is:
HDF5_INCLUDE_PATH = "/usr/include/hdf5/serial"

[flystarhe]

Thank you very much for your contribution.

I ran your model, the effect is amazing. I also want to do some experiments in this area, but the paired CT scan data provided by the doctor are difficult to align. How did your paired training data get?

[xinario]

Most likely you'll have to register the images by yourself. Actually, we are trying to release our scanned piglet data for research purpose. Please stay tuned:)