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Installing pyhdf

pyhdf has been successfully installed under Python 2.4 and above on several platforms, including

  • Windows XP
  • Linux 2.4.19
  • Tru64 4.0.f
  • Solaris 8
  • AIX 4
  • MacOSX 10.5.

Please open an issue here if you encounter any problems during installation: https://github.com/fhs/python-hdf4/issues

There are several available options for installing pyhdf:

  • Download and install EPD (Enthought Python Distribution) which includes pyhdf 0.8.3 . This makes sense if Python isn't already installed on you computer.
  • Download and install pyhdf 0.8.3 from PyPi / the cheeseshop.
  • Download and install pyhdf 0.8.3 from source

Installing EPD

EPD (The Enthought Python Distribution) is a python release which includes many of the major python packages (such as NumPy, SciPy, etc), along with pyhdf. As such, you don't need to worry about install other packages. The EPD is available at the Enthought website. Follow the instructions on the page.

Please note that the Enthought Python Distribution is a commercial product. If you have questions about the license, please see this page.

Installing from the Cheeseshop

Requirements:

The Python Package Index, also known as the Cheeseshop, is a site on the web where many open-source python packages are stored. To install PyHDF v0.8+: open a command prompt in the main python directory and type:

easy_install pyhdf

Quick install from Source for Windows Users

Requirements:

  1. Download the complete HDF4 binary package from the link given below. These packages include all libraries needed to compile pyhdf. There are two binary packages to choose from depending on whether or not you want to compile pyhdf with SZIP encoding enabled or disabled. There are different licensing implications for each choice (see the HDF page for more details on the licensing of SZIP).

  2. Unzip the selected package into a directory of your choice (e.g. C:HDF4).

  3. Go to the pyhdf source directory.

  4. Build the package in one of the two following ways:

    • Set the HDF4 environment variable to the directory where you unpacked the binary and (e.g. C:HDF4). Then run the following:

      python setup.py build

    • Run python setup.py build --hdf4 <directory of unzipped package> where <directory of unzipped package> is the location where you unzipped the downloaded HDF4 binary (e.g. C:HDF4).

    NOTE: If you are using the mingw32 compiler and are using the standard Python binary distribution, then you need to specify -c mingw32 on the command line as well.

  5. Install pyhdf or build a binary distribution (bdist_msi, bdist_wininst, bdist_egg, etc.) then run one of the following commands:

    python setup.py install
python setup.py bdist_msi
python setup.py bdist_wininst
python setup.py bdist_egg

Install from Source

Requirements:

NOTE: OS X users can obtain jpeg libraries here. Once the above packages are installed, you are ready to download and install pyhdf. Binaries and source tarballs can be downloaded from the SourceForge project page.

To download pyhdf using Subversion, enter the following at the the command prompt:

svn checkout https://pysclint.svn.sourceforge.net/svnroot/pysclint/trunk/pyhdf

Step-by-step instructions for installing pyhdf

  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 python setup.py install
$ python setup.py install --prefix=/usr/local (or prefix of choice)

    Or, you might prefer to make a package (msi, rpm, egg, etc.) and install the package:

    $ python setup.py bdist_<package>

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 NCSA hdf site. Source code and binaries are available for download.

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.