[R-sig-Geo] Read HDF files

[Roger Bivand]

On Sat, 3 Sep 2011, Arnaud Mosnier wrote:

> Hi Jan,
>
> Thanks for you answer.
> I tried your script but unfortunatly it does not work for my case.

No, you did not. He is using rgdal built against an OSX framework GDAL 
that includes an HDF driver. If you type gdalDrivers() on your CRAN rgdal 
built statically against a minimal GDAL, you will see that you do not have 
an HDF driver. You need either to install rgdal from source linked to a 
GDAL that has the HDF driver (which I assume you do not want to do - see 
file.show(system.file("README.windows", package="rgdal")) for details if 
you do), or to use external software, such as a Windows version of 
gdal_translate to convert your HDF file to for example GTiff outside R, 
and then use the minimal set of drivers included in the CRAN rgdal to read 
the data.

GDAL potentially has well over 100 drivers, many of which must be linked 
against external libraries. It is not practically possible to build the 
CRAN Windows rgdal binaries (or the CRAN Extras OSX rgdal binaries) for 
more than a minimal set with very few external dependencies. A source of 
Windows GDAL binaries is:

http://www.gisinternals.com/sdk/

linked from:

http://trac.osgeo.org/gdal/wiki/DownloadingGdalBinaries

from:

http://www.gdal.org/

Hope this helps,

Roger

> If someone want to make some test with the kind of image I want to use, just
> try this script to download and uncompress it.
>
> TestFolder <- choose.dir()
>
> download.file("
> http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/A20072132007243.L3m_MO_CHL_chlor_a_4km.bz2",
> f<-paste(TestlFolder, "/hdf4test.bz2", sep = "")
> library(R.utils)
> gunzip(f, f2<-paste(TestFolder, "/testhdf4.hdf", sep = "")
> GDALinfo(f2) # in my case it results on this message
> `C:/test/testhdf4.hdf' not recognised as a supported file format.
>
>
>
> Here is my sessionInfo() result.
>
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=French_Canada.1252  LC_CTYPE=French_Canada.1252
> LC_MONETARY=French_Canada.1252 LC_NUMERIC=C
> LC_TIME=French_Canada.1252
>
> attached base packages:
> [1] grDevices datasets  splines   graphics  stats     tcltk     utils
> methods   base
>
> other attached packages:
> [1] R.utils_1.7.8     R.oo_1.8.1        R.methodsS3_1.2.1 rgdal_0.7-1
> raster_1.9-5      sp_0.9-84         svSocket_0.9-51   TinnR_1.0.3
> R2HTML_2.2        Hmisc_3.8-3       survival_2.35-8
>
> loaded via a namespace (and not attached):
> [1] cluster_1.14.0  grid_2.12.0     lattice_0.19-33 svMisc_0.9-61
> tools_2.12.0
>
>
> Thanks for any help !
>
> Arnaud
>
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>
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-- 
Roger Bivand
Department of Economics, NHH Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no