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Installation

pyhdf supports installation on Python 2 and Python 3. Please open an issue here if you encounter any problems during installation: https://github.com/fhs/pyhdf/issues

The recommended method of installing pyhdf is to use conda. See the Conda user guide on how to install conda and activate your conda environment. Once you're in the conda environment, install pyhdf from conda-forge:

conda install -c conda-forge pyhdf

If you don't want to use conda, the instructions below describes how you can compile pyhdf from source. Version 0.10.3 also includes static linked wheels for linux with cpython 3.6-3.9. If compatible, pip install pyhdf will include the necessary libraries for you. If you don't want to use the built manylinux distribution, follow instructions below to build from source downloading from pypi with pip install pyhdf --no-binary :all:.

Download the source

The source code of the latest release of pyhdf can be obtained from either of these two location:

Requirements

The following packages are required to build and install pyhdf:

On Debian and Debian-based Linux distributions (e.g. Ubuntu), you can install all the requirements for Python 3 using this command:

apt-get install build-essential python3-dev python3-numpy libhdf4-dev -y

Installing from the source archive

  1. Go to the pyhdf source directory.

  2. If your HDF4 libraries or include files reside in directories that are not searched by default on your system, the installation script will complain about missing files.

    Add to the search path by exporting INCLUDE_DIRS and LIBRARY_DIRS, e.g.:

    export INCLUDE_DIRS=/usr/local/hdf-4.2r3/include
export LIBRARY_DIRS=/usr/local/hdf-4.2r3/lib

    or on Windows something like (replace with actual location):

    set INCLUDE_DIRS=C:\hdf4\include
set LIBRARY_DIRS=C:\hdf4\lib;C:\hdf4\dll;C:\hdf4\jpeg6\lib;C:\hdf4\szip21\lib;C:\hdf4\zlib123\lib

    Note that jpeg, zlib, and (optionally) szip libraries must be found as well. If they are not in a standard place for the compiler, their location must be specified. On Mac OS X, /usr/local/lib and /usr/local/include may need to be specified if the libraries were installed there. You may need to install the devel versions of these packages to get the statically-linked libraries if your HDF binary is statically linked.

    If you are using the binary HDF4 library available from the HDF4 site, you must also have szlib installed. Then, you will also need to set SZIP:

    export SZIP=1

(or on Windows:  set SZIP=1)

    If you do not wish to use szlib, you will need to compile HDF4 from source.

    If anything goes wrong, read the detailed notes below. Warning messages about implicit declarations of some functions may be produced. Those are due to SWIG, and may be safely ignored.

  3. Install system-wide or locally:

    # sudo pip install .
$ pip install -e .

    Or, you might prefer to make a python wheel and install it:

    $ python -m build

To make sure everything works as expected, run the hdfstruct.py script (under examples/hdfstruct) on one of your HDF4 files. The script should display the file structure. This is a handy tool to have around when you want to explore the contents of any HDF4 file.

Further notes

External libraries

HDF4.2 no longer provides its own copies of the jpeg and z libraries. Those must be installed separately (on Linux, they should be part of any standard distribution).

The sz library (versions 2.0 or higher) must be installed if the SZIP compression method is to be used with SDsetcompress(). HDF v4.2 must also then be compiled with SZIP support. The binaries available from NCSA are (at the time of this writing) compiled with SZIP support (including encoding). To use these binaries, you must have SZIP installed. The binaries Enthought has produced and which are available in EPD and for download from Sourceforge are compiled with SZIP support without encoding capability.

Getting an SZIP enabled HDF library may require compiling the library from source with the "--with-szlib" configuration option. Note that you must install SZIP in a separate step. For more details, see the HDF Group site.

In case your HDF library was compiled with SZIP support and you abide by the szip licensing terms, set the environment variable SZIP to 1.

If you get error messages related to the SDgetcompress() / SDsetcompress() functions, e.g. "undefined symbol: SDgetcompress", set the environment variable NO_COMPRESS to "1". This will transform SDgetcompress() and SDsetcompress() into no-ops, which will immediately raise an exception, and will not be resolved against the HDF library symbols. This may make it possible to work with an HDF library earlier than v4.2.

Swig-generated interface files

Interface files hdfext.py and hdfext_wrap.c (located under the pyhdf subdirectory) have been generated using the SWIG tool. Those two files should be usable as is on most environments. It could happen however that, for reasons related to your environment, your C compiler does not accept the '.c' file and raises a compilation error. If so, the interface needs to be regenerated. To do so, install SWIG, then run:

$ cd pyhdf
$ swig -python hdfext.i

SWIG should silently regenerate the two interface files, after which installation should proceed correctly.

TRU64 note

The HDF installation creates its libraries as archive (.a) files, not shareable (.so) ones. On TRU64, the linker by default first looks for shareable libraries in every directory, then in a second round for archive files. This means that if there is a libjpeg.so somewhere on the standard linker search paths, it will be found first, even if the HDF libjpeg.a file exists in the directory pointed by "library_dirs". To solve the problem, set the environment variable LINK_ARGS:

export LINK_ARGS="-oldstyle_liblookup"

This will tell the linker to look for .so then for .a files in each visited directory.