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reading .hdf files

6 messages · Barry Rowlingson, Jonathan Greenberg, dododave

Original
Jonathan Greenberg
# 
Dave:

We wrote a package initially inspired by this issue -- gdalUtils,
which are wrappers for the GDAL/OGR utilities.  There are even some
hdf helper functions we included (e.g. ?get_subdatasets).  Note that
if you are on a Windows or Mac box, it is important you install the
correct version of GDAL first.

Currently, you'll need to extract out the subdataset you want via
?gdal_translate -- there is an example using an HDF4 file in the help.

I would recommend grabbing the R-forge version, since I have a few
fixes in there that aren't on the latest CRAN:

install.packages("gdalUtils", repos="http://R-Forge.R-project.org")

Good luck!

--j

On Tue, Mar 25, 2014 at 11:54 AM, Barry Rowlingson
<b.rowlingson at lancaster.ac.uk> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      dododave
    

    

      
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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



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      Jonathan Greenberg
    

    

      
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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:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Jonathan Greenberg
    

    

      
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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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    
2 days later

    

      
      

        


  

        

      dododave
    

    

      
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I am now able to convert the hdf files into GeoTiffs. I have a follow-up
question though. 

I now need to extract the mean ndvi value from within a polygon overlaid on
that GeoTiff. The issue I am having is that the code is returning NULL when
I do.

            

      
      
      
    

        
[[1]]
NULL


Here is the output when I call rast;

            

      
      
      
    

        
class       : RasterLayer 
dimensions  : 904, 2500, 2260000  (nrow, ncol, ncell)
resolution  : 1, 1  (x, y)
extent      : 0, 2500, 0, 904  (xmin, xmax, ymin, ymax)
coord. ref. : NA 
data source : /Volumes/GOLONDRINA/tiff/2011_P01.tif 
names       : X2011_P01 
values      : -32768, 32767  (min, max)

Help appreciated!
Dave








Jonathan Greenberg-3 wrote

            

      
      
      
    

        

      
      
    

        

            

      
      
      
    

        

        

      
      
    

            

      
      
      
    

        

      
      
    

        

            

      
      
      
    

        

        

      
      
    

        
Jonathan Greenberg-3 wrote

            

      
      
      
    

        

      
      
    

        

            

      
      
      
    

        

        

      
      
    

            

      
      
      
    

        

      
      
    

        

            

      
      
      
    

        

        

      
      
    

        
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