NetCDF is a file format primarily used for meteorological and oceanographic data. The NetCDF4 format is built on top of a subset of HDF5. The NetCDF format is maintained by Unidata. Unidata's C, C++, and Fortran implementations of NetCDF are available at Unidata NetCDF, and the Unidata Java reader for NetCDF is available at Unidata NetCDF Java.
HDF5 is a file format primarily used for gridded scientific and engineering data. The HDF5 format is maintained by the HDF Group, which currently has C, C++, and Fortran APIs for HDF5 files. The HDF group also supports a Java JNI (Java Native Interface) to their C code. While the JNI interface does support most of the native HDF5 features, it can be a problem to integrate with other Java packages. Hence the origins of Nujan.
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