Error while reading h5 file using MoMoIO

[Aalap Shah]

Hi All,

I am trying to use the scalismo-faces repository to load some morphable models stored in h5 files. Irrespective of the java version I use, I consistently got "java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path" error. with scala 2.13.8 and scalismo-faces 0.90.0. I tried both Java 8 as well as java 11 but nothing has worked so far. I am on an Ubuntu 20.04 system.

Things I have tried so far:

1. I downloaded the source code from HDF5 and also downloaded HDFView but unfortunately, providing paths from these folders is not helping with the error. 
2. I was able to solve the error by downloading the .so files available in OMX-Java but that lead to another issue: cannot find HDF5Constants.

I am able to see the required files under the ExtendedLibrary section of the IDE i.e., they are all stored in the .cache but somehow, they are all inaccessible to the scala code.

At this point, I am out of any ideas and therefore am reaching out to you for help. Please let me know if you'd need any additional information from my end.

Thank you

[Andreas Morel-Forster]

Hi Aalap Shah

The libraries should be loaded automatically, because scalismo-faces has a dependency to scalismo-natives trough the scalismo library.

If you are trying to write your own software, maybe you have forgotten to add in the beginning the scalismo.initialize() call. This usually unpacks the libraries which are in scalismo-natives into a temporary directory from where they should be found afterwards.

You can find more information at: https://scalismo.org/docs/Tutorials/tutorial01

Best regards
Andreas

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