[R-sig-Geo] reading .hdf files

[Jonathan Greenberg]

Ok, I actually think you probably got it working somewhat correctly
(if it returns something in the previous step) -- I think the issue
you are having is a few things:

1) Don't use the system.file for your own file -- the system.file()
call is specifically for demo files within a package.  Set the working
directory to where your HDF file is located and do:
setwd("path/to/your/hdf/files")
hdf_file <- "GVIX_NL_G16_C07_NVI_Y2005_P26.hdf"

Note you should be able to now do:
gdalinfo(hdf_file)

2) You are using an oddly formatted hdf file -- the get_subdatasets()
routine and the sd_index= parameter only work when the subdatasets are
named following a generally agreed-upon standard, the
"SUBDATASET_n_NAME" format (common to e.g. MODIS, Landsat LEDAPS, and
a lot of other products).  In your case, since it doesn't follow these
conventions, you can instead use the sds=TRUE parameter which will
extract ALL subdatasets it finds.  The one annoying part about this is
that GDAL won't append the correct suffix (at least, not with version
1.10.0 and earlier), so you will need to rename the output:
outfile="testout"
gdal_translate(hdf_file,outfile,sds=TRUE,verbose=TRUE)
# Notice you now have a file named "testout" with no extension.  Let's
rename it:
file.rename(outfile,paste(outfile,".tif",sep="")) # Only if a tif.
Mod this if a different output format.

Hope this helps!  I'll make it more clear in future documentation when
the sd_index parameter works.

--j



On Tue, Mar 25, 2014 at 1:52 PM, Jonathan Greenberg <jgrn at illinois.edu> wrote:
> Hi Dave:
>
> In all likelihood, it couldn't find your GDAL install.  What OS are
> you using?  What GDAL install did you use?  Can you restart R, and
> then paste the output of:
>
> library("gdalUtils")
> gdal_setInstallation(verbose=TRUE)
>
> And then the output of:
>
> getOption("gdalUtils_gdalPath")
>
> Thanks!
>
> --j
>
> On Tue, Mar 25, 2014 at 12:40 PM, dododave <dododave at gmail.com> wrote:
>> Thank-you Jonathan. I have done as you suggested and installed the latest
>> version of GDAL and gdalUtils, and then followed the example in the
>> gdal_translate help.
>>
>> To convert the hdf file test.hdf to .tif format, I use the following code;
>>
>> hdf4_dataset <- system.file("test.hdf", package="gdalUtils")
>> gdal_translate(hdf4_dataset,"test.tif",sd_index=1)
>> #I renamed the file to test.hdf for simplicity
>>
>> But this did not work. I got this error;
>>
>> Error in split1[[1]] : subscript out of bounds
>> In addition: Warning message:
>> running command '"C:\Program Files\QGIS Dufour\bin\gdalinfo.exe" ""' had
>> status 1
>>
>> The hdf file I was trying to load was;
>> ftp://ftp.orbit.nesdis.noaa.gov/pub/corp/scsb/wguo/GVIx/GVIx_VH_16km/NVI/GVIX_NL_G16_C07_NVI_Y2005_P26.hdf
>>
>> Thanks,
>> Dave
>>
>>
>>
>> --
>> View this message in context: http://r-sig-geo.2731867.n2.nabble.com/reading-hdf-files-tp7586038p7586041.html
>> Sent from the R-sig-geo mailing list archive at Nabble.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



-- 
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