[R-sig-Geo] reading HDF5 files

Paul Hiemstra p.hiemstra at geo.uu.nl
Tue Aug 14 11:59:42 CEST 2007


Dear Roger,

It works! The following command did the trick (adding -a_srs as you 
suggested):
E:\LSO data\Regenbui 
20-7\regenradar_rasters\regenradar_hdf5>gdal_translate -of GTiff -a_srs 
"+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" 
HDF5:"RAD_NL21_PCP_NA_200707202345.h5"://image1/image_data 
RAD_NL21_PCP_NA_20070720234.tif

thanks very much for helping me out.

cheers,

Paul

Roger Bivand schreef:
> On Tue, 14 Aug 2007, Paul Hiemstra wrote:
>
>> Mike,
>>
>> This is the result of using gdalinfo (FWTools) on the .tif file,
>>
>> E:\LSO data\Regenbui 20-7\regenradar_rasters\regenradar_tif>gdalinfo
>> RAD_NL21_PCP_NA_200707200000.tif
>> Driver: GTiff/GeoTIFF
>> Files: RAD_NL21_PCP_NA_200707200000.tif
>>       RAD_NL21_PCP_NA_200707200000.aux
>> Size is 256, 256
>> Coordinate System is:
>> GEOGCS["WGS 84",
>>    DATUM["WGS_1984",
>>        SPHEROID["WGS 84",6378137,298.2572235630016,
>>            AUTHORITY["EPSG","7030"]],
>>        AUTHORITY["EPSG","6326"]],
>>    PRIMEM["Greenwich",0],
>>    UNIT["degree",0.0174532925199433],
>>    AUTHORITY["EPSG","4326"]]
>> Metadata:
>>  AREA_OR_POINT=Area
>>  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_product_corners=0.000000 49.769001 0.000000 55.296001
>> 9.743000 54.818001 8.337000 49.373001
>>  calibration=calibration_out_of_image=255
>>  statistics=stat_max_value=45.000000
>>  image1=image_bytes_per_pixel=1d
>>  overview=number_vector_groups=0d
>>  radar1=radar_location=5.179000 52.103001
>>  radar2=radar_location=4.790000 52.955002
>> Corner Coordinates:
>> Upper Left  (    0.0,    0.0)
>> Lower Left  (    0.0,  256.0)
>> Upper Right (  256.0,    0.0)
>> Lower Right (  256.0,  256.0)
>> Center      (  128.0,  128.0)
>> Band 1 Block=256x32 Type=Byte, ColorInterp=Gray
>>  Metadata:
>>    image_data=DISPLAY_ORIGIN=UL
>
> The metadata records the correct srs, but the file has the wrong one - 
> it is staring you in the face, isn't it?
>
> Try adding
>
> -a_srs "+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"
>
> (all in one line, no line breaks) to the gdal_translate call (untried).
>
> Roger
>
>
>>
>> cheers, Paul
>>
>> Michael Sumner schreef:
>>> Note that readGDAL can read the subdataset directly (escaping the 
>>> quotes
>>> appropriately):
>>>
>>> d <- 
>>> readGDAL("HDF5:\"RAD_NL21_PCP_NA_200707200000.h5\"://image1/image_data") 
>>>
>>>
>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>


-- 
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone: 	+31302535773
Fax:	+31302531145
http://intamap.geo.uu.nl/~paul




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