[R-sig-Geo] subdatasets in rgdal/raster

[Jonathan Greenberg]

Mike:

Have you taken a look at gdalUtils?  This is a wrapper for all the
GDAL binaries (I am still working on adding in all those new tools
that were recently released with version 1.11.1, but it should be up
to date as of v 1.10.1).  gdalinfo that is part of gdalUtils gives you
the full info dump (more, if less clean, output than rgdal's gdalInfo
will give you), which you could parse for the info you wanted.  I also
have a custom function "get_subdatasets" which sounds a lot like what
you are describing.

Give it a shot!  You will need to install GDAL yourself first -- check
the help for suggestions on which flavor of GDAL I recommend.

--j

On Wed, Oct 15, 2014 at 6:23 AM, Michael Sumner <mdsumner at gmail.com> wrote:
> Thanks Roger, I'm still hoping to be able to code at this level one day.
>
> I have gone off half-cocked, confusing things. I can get SDS from
> NetCDF and HDF files with GDALinfo() with no problems - I just had to
> turn off returnScaleOffset, which I think has a confounding of nbands
> and subdatasets - since a datasource with SDS has no bands, but I need
> to explore this more to be sure.
>
> Cheers, Mike.
>
>
>
>
>
> On Wed, Oct 15, 2014 at 5:50 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
>> On Wed, 15 Oct 2014, Michael Sumner wrote:
>>
>>> Hello,
>>>
>>> As far as I know there's nothing in rgdal to determine existing
>>> subdatasets (SDS) in HDF (or NetCDF for that matter).
>>>
>>> In raster, raster(x) will read from the first candidate *variable*,
>>> and list the others with a warning, which is analogous to an SDS but
>>> of course it's always providing this via ncdf/ncdf4 rather than via
>>> rgdal.
>>>
>>> Is it true there's no way to find out SDS from HDF or NetCDF in rgdal?
>>
>>
>> Because these formats are poorly organised (an XML tree describing the
>> internal structure would be easy to parse, but self-descriptive metadata
>> isn't usual here), GDALinfo() does not provide much.
>>
>> If you start by identifying the incantation used by command line gdalinfo to
>> report the SDS metadata, then look at its source code, it should be possible
>> to make some progress. I don't use either if I can help it, and do not have
>> the necessary trial set of sample files. You'd need to find a robust route
>> covering a wide range of files seen in the wild to allow for oddities in the
>> ways things are organised. It is unfortunate to have to branch code on the
>> selected driver, but here it is hard to avoid. Once GDALinfo is reporting
>> the metadata in a predictable way, the other functions can be given
>> appropriate argument values.
>>
>> Also consider looking at this from the point of view of rgdal2 in addition
>> to rgdal; it could possibly be "closer" there and looking at both may make
>> it easier to spot:
>>
>> https://github.com/thk686/rgdal2
>>
>> Contributions welcome!
>>
>> Roger
>>
>>
>>>
>>> I've not really explored this before much since compiling HDF was
>>> unavailable to me. gdalUtils fills a gap but only by running the
>>> installed command line tools, which obviously can be avoided with the
>>> right features in rgdal/raster. I personally have always run the
>>> command line tools and then jumped back to R (if I could).
>>>
>>> (The vector analogy in rgdal to listing SDS would be ogrListLayers).
>>>
>>> This is a missing capability in the raster package, somewhat disguised
>>> because of the independent support for NetCDF. I guess hardly anyone
>>> is using HDF? That's a shame since these R tools really help.  It's a
>>> pretty complicated story all round and I keep re/discovering
>>> interesting corners. If anyone is writing anything significant about
>>> all this I'd be keen to be involved.
>>>
>>> Cheers, Mike.
>>>
>>>
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; fax +47 55 95 91 00
>> e-mail: Roger.Bivand at nhh.no
>>
>
>
>
> --
> Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> Hobart, Australia
> e-mail: mdsumner at gmail.com
>
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-- 
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
259 Computing Applications Building, MC-150
605 East Springfield Avenue
Champaign, IL  61820-6371
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007