[Paraview] HDF5 and Paraview

[Moreland, Kenneth]

Perhaps I'll elaborate on John's response a little bit.

As John alluded to, Hdf5 is not really a file format in that it does not
specify any semantic meaning to the data.  Hdf5 is just a storage
mechanism for arrays of data.  It is self describing in that it provides
enough metadata to determine the basic data type, dimensions, name,
attributes, and hierarchical namespace, but this is not enough for any
reader to reliably build mesh structures from.  For example, say there is
an array stored in an Hdf5 file called "pts".  Is this a list of point
indices?  Is this a collection of point coordinates that form a
curvilinear grid?  A list of point coordinates around triangles?  A bag of
point coordinates that will be indexed by some other array?  Maybe pts
doesn't mean points at all.

The relevance of this discussion is that simply providing the Hdf5 is not
sufficient to present data.  The data has to follow some convention (or
have that convention otherwise specified).

But not to worry.  This question of reading Hdf5 files comes up a lot on
the ParaView mailing list and there exists a general solution: XDMF.  XDMF
is a simple XML descriptor file that you place next to your h5 file.  The
XDMF file describes what is called the schema for the data in the Hdf5
file: That is, it defines the structure of the data.

XDMF files can be created through the XDMF library or you can create the
XML file to describe an existing h5 file by hand.  Based on the fact that
the generic NetCDF reader works (a coincidence whose technical details I
won't go into), I expect the describing XDMF file to be small and easy to
write.  See the XDMF documentation at www.xdmf.org for more details.

-Ken



On 12/20/12 2:30 AM, "Biddiscombe, John A." <biddisco at cscs.ch> wrote:

>Hdf5 is very flexible so one reader cannot cope with all possibilities.
>You need to know which hdf5 reader you need and target that format
>
>Sent from my Phone
>________________________________
>From: Pradeep Jha
>Sent: 20/12/2012 08:33
>To: paraview at paraview.org
>Subject: [Paraview] HDF5 and Paraview
>
>Hello,
>
>I dont understand something. In all of Paraview manuals it says that it
>is compatible with HDF5 file format. I am using Paraview 3.98.
>I wrote a data file using HDF for fortran and generated a file
>(filename.h5). But when I am tried to open it, "*.h5" was not in the list
>of supported
>file formats.
>
>Paraview gives me the message "A reader for filename.h5 could not be
>found. Please choose one: <followed by a long list of readers>".
>Even in that long list there are no HDF5 readers, so I just started
>trying everything and finally succeeded with "NetCDF files generic and
>CF conventions" (I don't even know what it is).
>
>But it is not reassuring. I don't know if this will work for any other
>data set. Am I missing something here?
>
>Thanks
>Pradeep
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