[R-sig-Geo] reading .hdf files
dododave
dododave at gmail.com
Fri Mar 28 17:11:53 CET 2014
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.
> rast <- raster("2011_P01.tif")
> mean.ndvi <- extract(rast, poly, fun=mean)
> mean.ndvi
[[1]]
NULL
Here is the output when I call rast;
> 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
> 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@
> > 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@
> > 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.
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>>
> R-sig-Geo@
>>> 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@
> , 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@
> , Gchat: jgrn307, Skype: jgrn3007
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo@
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Jonathan Greenberg-3 wrote
> 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@
> > 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@
> > 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.
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>>
> R-sig-Geo@
>>> 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@
> , 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@
> , Gchat: jgrn307, Skype: jgrn3007
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo@
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
--
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