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

From: Bernd Fischer <bernd.fischer_at_embl.de>
Date: Fri, 02 Dec 2011 08:48:25 +0100

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
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

--
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

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Received on Fri 02 Dec 2011 - 11:22:14 GMT

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