[R-sig-Geo] reading HDF5 files

Sat Aug 11 13:02:06 CEST 2007

On Sat, 11 Aug 2007, Michael Sumner wrote:

> Note that readGDAL can read the subdataset directly (escaping the quotes
> appropriately):
>
> d <- readGDAL("HDF5:\"RAD_NL21_PCP_NA_200707200000.h5\"://image1/image_data")

The original questioner does not have an rgdal build against FWTools, and 
is just using FWTools gdal_translate outside R to get to a format that 
standard Windows rgdal can read, if I understand correctly.

Roger

>
> It also seems that your gdal_translate to TIFF output has the extension
> .img, but then you attempt to read from a tif.
>
> Just a thought.
>
> Cheers, Mike.
>
> ==============Original message text===============
> On Fri, 10 Aug 2007 19:09:00 +1000 Roger Bivand wrote:
>
> 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