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

Fri Oct 24 09:45:45 CEST 2014

On Wed, 22 Oct 2014, Jonathan Greenberg wrote:

> I think Roger has mentioned a few times over the years his reticence
> to build in the HDF4 drivers into the Windows gdal binary (Roger,
> perhaps you can discuss why this is a problem)-- I actually built
> gdalUtils for this exact purpose -- the need to access MODIS and
> Landsat HDFs in Windows.

The CRAN Windows binaries are built by statically linking to both 32-bit 
and 64-bit builds of GDAL, PROJ.4, and a small selection of (partly 
platform dependent) other libraries. These GDAL etc. binaries are prepared 
by Brian Ripley and Uwe Ligges, as they have write access to the 
win-builder and CRAN servers (the same relationship exists for rgeos). 
Some years ago, I prepared 32-bit DLLs, which were then used in a CRAN 
binary that shipped with those libraries. The CRAN administrators found 
that this was much less satisfactory than a static build, to avoid 
possible interference between multiple installs of DLLs on this platform 
among other reasons. HDF and NetCDF are seen as substantially more complex 
external dependencies, so have not been seriously considered for inclusion 
in the GDAL binaries used in preparing rgdal for Windows.

This isn't impossible, but volunteering other peoples' time and insight 
seems unfortunate. If interested people would like to work up a route to 
including these extra libraries, in the knowledge that both have had 
portability issues (see clang), then in time it might be possible to make 
progress.

Another avenue is to support the OSGeo4W project in its attempts to 
provide R with rgdal and rgeos, and thus get the drivers that way.

Neither will happen without a longer term commitment.

Roger

>
> One thing that may be worth considering is if Roger is open to it is
> having someone work to get the Windows binaries that come along with
> rgdal so they support a wider range of formats (specifically getting
> HDF4 and 5 and NetCDF functional)?  Others have already solved this
> satisfactorily (osgeo4w has all of the key formats supported, for
> instance), so it should be doable.
>
> Also, to respond to your question about why have gdalUtils at all -- I
> don't think every function that the base gdal utilities is available
> in rgdal (correct me if I'm wrong), so I wanted a way to bring them to
> R users in a (relatively) easy to use fashion -- I've seen gdalUtills
> as a complementary package to rgdal.
>
> --j
>
> On Tue, Oct 21, 2014 at 2:17 AM, Michael Sumner <mdsumner at gmail.com> wrote:
>> I have, and it's good but it's not what I am after here.
>>
>> I really want access to HDF4 via tight-coupling. It does work well in
>> R when you build GDAL right, especially with raster over the top to
>> clean everything up. If you can compile those drivers into GDAL it
>> does beg the question why have a wrapper like gdalUtils. (My take on
>> this is that Windows-support stops at the CRAN binary, and again this
>> is why raster has its own NetCDF wrapper).
>>
>> Ultimately the logic for these rogue files belongs in GDAL and
>> rgdal/raster should just reflect that: rgdal2 is essentially that, but
>> doesn't offer much more and it's not clear how to "rasterize"
>> everything again.
>>
>> :)
>>
>>
>>
>> On Thu, Oct 16, 2014 at 2:27 AM, Jonathan Greenberg <jgrn at illinois.edu> wrote:
>>> 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
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>>
>>>
>>> --
>>> 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
>>
>>
>>
>> --
>> Michael Sumner
>> Software and Database Engineer
>> Australian Antarctic Division
>> Hobart, Australia
>> e-mail: mdsumner at gmail.com
>
>
>
>

-- 
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