[R-sig-Geo] reading HDF5 files

Fri Aug 10 11:09:00 CEST 2007

Paul,

I have added a CC to the R-sig-geo list, since I myself have no experiece 
of using this format in practice. If you are not a member, please join at:

https://stat.ethz.ch/mailman/listinfo/r-sig-geo

so that you will see any replies.

Did you try gdalinfo on the output file?

The error message suggests that the output file has a geographical 
coordinate reference system, with coordinate values outside the feasible 
range. From the HDF5 description, however, it ought to be projected, 
right? Do you need to make more use of the arguments taken by gdalinfo to 
give the output file the correct projected CRS?

Roger

On Fri, 10 Aug 2007, Paul Hiemstra wrote:

> Dear Roger,
>
> I tried the route through a GTiff before I sent you the e-mail but somehow it 
> did not work. When I use gdalinfo on one of the .h5 files I get this:
>
> PS E:\LSO data\Regenbui 20-7\regenradar_rasters\regenradar_hdf5> gdalinfo 
> RAD_NL21_PCP_NA_200707200000.h5
> Driver: HDF5/Hierarchical Data Format Release 5
> Files: RAD_NL21_PCP_NA_200707200000.h5
> Size is 512, 512
> Coordinate System is `'
> Metadata:
>  map_projection:projection_indication=Y
>  map_projection:projection_name=STEREOGRAPHIC
>  map_projection:projection_proj4_params=+proj=stere +lat_0=90 
> +lon_0=0.0 +lat_ts=60.0 +a=6378.388 +b=6356.912 +x_0=0 +y_0=0
> geographic: geo_number_rows=256
> geographic: geo_number_columns=256
> geographic: geo_pixel_size_x=2.500000
> geographic: geo_pixel_size_y=-2.500000
> geographic: geo_par_pixel=X,Y
> geographic: geo_dim_pixel=KM,KM
> geographic: geo_column_offset=0.000000
> geographic: geo_row_offset=1490.906006
> geographic: geo_pixel_def=LU
> geographic: geo_product_corners=0.000000 49.769001 0.000000 55.296001 
> 9.743000 54.818001 8.337000 49.373001
> calibration: calibration_flag=Y
> calibration: calibration_formulas=GEO = 0.5 * PV + -31.5
> calibration: calibration_missing_data=255
> calibration: calibration_out_of_image=255
> statistics: stat_min_value=-1.500000
> statistics: stat_max_value=45.000000
> image1: image_product_name=RAD_NL21_PCP_H0.8_NA
> image1: image_geo_parameter=REFLECTIVITY_[DBZ]
> image1: image_size=65536d
> image1: image_bytes_per_pixel=1d
> overview: product_group_name=RAD_NL21_PCP_NA
> overview: products_missing=N/A
> overview: hdftag_version_number=3.5
> overview: number_image_groups=1
> overview: number_satellite_groups=0d
> overview: number_radar_groups=2d
> overview: number_station_groups=0
> overview: product_datetime_start=20-JUL-2007;00:00:11.000
> overview: product_datetime_end=20-JUL-2007;00:00:11.000
> overview: number_lightning_groups=0d
> overview: number_classification_groups=0d
> overview: number_grid_groups=0d
> overview: number_point_groups=0d
> overview: number_vector_groups=0d
> radar1: radar_name=De_Bilt
> radar1: radar_location=5.179000 52.103001
> radar2: radar_name=Den_Helder
> radar2: radar_location=4.790000 52.955002
> Subdatasets:
> SUBDATASET_0_NAME=HDF5:"RAD_NL21_PCP_NA_200707200000.h5"://image1/image_data
> SUBDATASET_0_DESC=[256x256] //image1/image_data (8-bit unsigned character)
> Corner Coordinates:
> Upper Left  (    0.0,    0.0)
> Lower Left  (    0.0,  512.0)
> Upper Right (  512.0,    0.0)
> Lower Right (  512.0,  512.0)
> Center      (  256.0,  256.0)
>
> Then I use gdal_translate:
> PS E:\LSO data\Regenbui 20-7\regenradar_rasters\regenradar_hdf5> 
> gdal_translate -of GTiff 
> HDF5:"RAD_NL21_PCP_NA_200707200000.h5"://image1/image_data 
> RAD_NL21_PCP_NA_200707200000.img
>
> Then I try to read the file using rgdal produces the following error:
>
>>  test = readGDAL("regenradar_hdf5/RAD_NL21_PCP_NA_200707200000.tif")
> regenradar_hdf5/RAD_NL21_PCP_NA_200707200000.tif has GDAL driver GTiff
> and has 256 rows and 256 columns
> Closing GDAL dataset handle 0x0130b898...  destroyed ... done.
> Error in `proj4string<-`(`*tmp*`, value = <S4 object of class "CRS">) :
>        Geographical CRS given to non-conformant data
>
> Do you have an idea how to solve this?
>
> kind regards,
>
> Paul
>
>
> Roger Bivand schreef:
>>  Dear Paul,
>>
>>  There is information in the README.windows file in the package, this
>>  should display it:
>>
>>  file.show(system.file("README.windows", package="rgdal"))
>>
>>  If you do not want to build against the FWTools binary, then just install
>>  FWTools, and use the gdal_translate command line tool to convert your data
>>  to a format that the standard rgdal windows binary can read, such as
>>  gTiff. You'll need to play around a bit to find out what the data are
>>  called.
>>
>>  On Linux, this is easier, because you can build GDAL against HDF5 before
>>  installing rgdal, and there it "just works".
>>
>>  Hope this helps,
>>
>>  Roger
>>
>>  On Thu, 9 Aug 2007, Paul Hiemstra wrote:
>> 
>> >  Dear mr. Bivand
>> > 
>> >  My name is Paul Hiemstra, a PhD student of Edzer. I am trying to read 
>> >  HDF5 files through rgdal. If I use GDALinfo() on one of the files it 
>> >  produces the following error:
>> > 
>> >  Error in .local(.Object, ...) :
>> >        GDAL Error 4: `RAD_NL21_PCP_NA_200707200000.h5' not recognised as 
>> >  a supported file format.
>> > 
>> >  On the mailing list 
>> >  (http://finzi.psych.upenn.edu/R/Rhelp02a/archive/92270.html) you 
>> >  metioned using the dll files from FWTools to get support for HDF5 into 
>> >  rgdal. How can this be done?
>> > 
>> >  I also tried the hdf5 package on CRAN, but that does not seem to work, 
>> >  returning an empty object.
>> > 
>> >  many thanks,
>> > 
>> >  Paul
>> > 
>> > 
>> 
>
>
>

-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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