[Paraview] HDF5 and Paraview

[Pradeep Jha]

Thanks for the response everyone and thanks for the detailed response Ken.
It made things a bit more clearer.

But still I dont understand that once I create a Hdf5 data, and even I
create a XDMF file, how can I be sure which reader to use for the data? So
every time I switch to a new data, chances are I might have to try out all
the readers one by one, till one of them plots it fine?
Is there something I am missing?

Thanks,
Pradeep


2012/12/21 Moreland, Kenneth <kmorel at sandia.gov>

> 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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