[R] R and HDF5 Question

[Paul Hiemstra]

Hi,

You can also read the hdf5 files with the rgdal package. This loads them 
into sp-objects, see the sp-package for more info. In the archives of 
the r-sig-geo mailing list there have been some other people (including 
myself :)) that have asked this question:

https://stat.ethz.ch/pipermail/r-sig-geo/2009-January/004828.html
http://markmail.org/message/ypsr77vl3qscq72f#query:r-sig-geo%20read%20hdf5+page:1+mid:ivkt5qxroeh3z646+state:results
http://www.mail-archive.com/r-sig-geo@stat.math.ethz.ch/msg01871.html

cheers,
Paul

Scott MacDonald wrote:
> That did it, boy do I feel silly.
>
> Thanks!
>
> On Fri, Nov 13, 2009 at 10:16 PM, Berwin A Turlach
> <berwin at maths.uwa.edu.au>wrote:
>
>   
>> G'day Scott,
>>
>> On Fri, 13 Nov 2009 09:52:43 -0700
>> Scott MacDonald <scott.p.macdonald at gmail.com> wrote:
>>
>>     
>>> I am trying to load an hdf5 file into R and running into some
>>> problems.
>>>       
>> It's a while that I used hdf5 files and that package in R, but:
>>
>>     
>>> This builds fine. The library seems to load without issue, but no
>>> data is returned when I try to load a file:
>>>
>>>     > library(hdf5)
>>>     > hdf5load("test.h5")
>>>     > NULL
>>>       
>> Is NULL the return of the hdf5load command or are you typing it on the
>> command line?
>>
>> Anyway, .hdf5 files can contain several objects, just as R's .rda
>> file.  load() will load an .rda file and put all objects in that file
>> into the workspace.  Likewise, hdf5load() loads an hdf5 file and puts
>> all objects in that file into the workspace.
>>
>>     
>>> Yet,
>>>
>>>     osx:data scott$ h5dump test.h5 HDF5 "test.h5" { GROUP
>>> "/" { DATASET "dset" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE
>>> { ( 31 ) / ( 31 ) } DATA { (0): 1, 2, 4, 8, 16, 32, 64, 128, 256,
>>> 512, 1024, 2048, 4096, 8192, (14): 16384, 32768, 65536, 131072,
>>> 262144, 524288, 1048576, 2097152, (22): 4194304, 8388608, 16777216,
>>> 33554432, 67108864, 134217728, (28): 268435456, 536870912,
>>> 1073741824 } } } }
>>>
>>> Any thoughts?
>>>       
>> Did you try an ls() after the hdf5load() command?  If the hdf5load()
>> command was successfull, an ls() should show you that an object with
>> name "dset" is now in your workspace; if I read the output above
>> correctly.
>>
>> HTH.
>>
>> Cheers,
>>
>>        Berwin
>>
>>
>>
>>     
>
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>
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-- 
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul