[Rd] HDF5 compound data types and h5r/hdf5 R packages

[Bernd Fischer]

Dear Jeremy!

I have written a package rhdf5 that can handle compound data types as well. The 
H5T_UNIX_TIME type is not yet supported, but it should be possible to read the floats
into a data.frame.

I put the H5T_UNIX_TIME type on my list and will add it in the next weeks.

Currently, you can download the package from
http://www-huber.embl.de/users/befische/rhdf5/
It will appear on bioconductor in the next couple of days.

Best,

Bernd



> From: Jeremy Reeve <jeremy.reeve1 at gmail.com>
> Date: Wed, Nov 30, 2011 at 10:22 PM
> Subject: [Rd] HDF5 compound data types and h5r/hdf5 R packages
> To: r-devel at r-project.org
> 
> 
> Hi there,
> 
> 
> I have a Java process that writes HDF5 files with the following
> approximate structure:
> 
> group "xxx" {
> 
>   group "yyy" {
> 
>       dataset {}
>       dataset {}
> 
>   }
> 
>   group "zzz" {
> 
>       dataset {}
>       dataset {}
> 
>   }
> 
> }
> 
> where dataset is a rank one dataspace having a compound datatype defined as:
> 
> H5T_UNIX_TIME, float, float, float, float
> 
> I have tried R packages h5r and hdf5 in an attempt to read the file
> but examining the source of h5r and reading documentation for hdf5
> here:  http://xweb.geos.ed.ac.uk/~hcp/Rhdf5.html  leads me to believe
> that compound datatypes are not supported by these packages.  My guess
> is that mapping arbitrary type definitions in HDF5 to available types
> in R might be somewhat tricky.  Incidentally, h5dump has trouble
> displaying the data in the dataset but I think this is to do with the
> time 'field':
> 
>     DATASPACE  SIMPLE { ( 33 ) / ( H5S_UNLIMITED ) }
>     DATA {
>        h5dump error: unable to print data
>     }
> 
> Since I am new to both HDF5 and R I wonder if there are better
> approaches to storing the information I have that will allow me to use
> either h5r or hdf5 packages unmodified.  I expect I can contribute
> changes to either of the packages that will allow me to do what I
> describe but fall short of general compound datatype support.
> 
> Any comments or advice gratefully received.
> 
> Regards...Jeremy
> 
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> 
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--
Bernd Fischer
EMBL Heidelberg
Meyerhofstraße 1
69117 Heidelberg
Tel: +49 [0] 6221 387-8131
E-Mail: bernd.fischer at embl.de
Homepage: http://www.ebi.ac.uk/~bfischer