[R-sig-Geo] reading HDF5 files

Roger Bivand Roger.Bivand at nhh.no
Tue Aug 14 11:22:45 CEST 2007


On Tue, 14 Aug 2007, Paul Hiemstra wrote:

> Mike,
>
> I tried, and failed, to directly load the HDF5 files into R using rgdal.
> The next thing I tried was to convert the .h5 file to a GTiff using
> FWTools. This seemed to work, but when I tried to load the file into R
> through rgdal I got the following error message:
>
> test = readGDAL("regenradar_hdf5/RAD_NL21_PCP_NA_200707200000.tif")
>
>> test = readGDAL("RAD_NL21_PCP_NA_200707200000.tif")
> RAD_NL21_PCP_NA_200707200000.tif has GDAL driver GTiff
> and has 256 rows and 256 columns
> Closing GDAL dataset handle 0x0226a220...  destroyed ... done.
> Error in `proj4string<-`(`*tmp*`, value = <S4 object of class "CRS">) :
>        Geographical CRS given to non-conformant data

Please state the gdalinfo of the input HDF5, and the output gTiff. Your 
use of gdal_translate seems to be mangling the (IIRC) projected 
coordinate reference system of the HDF5 to a geographical coordinate 
reference system, with the result that the coordinate values are "out of 
bounds". I think you need to show the full gdal_translate command, and to 
look at the help page:

http://www.gdal.org/gdal_translate.html

and try out the -a_srs option. Maybe also look at the -sds option if you 
are not sure that the subset is being chosen correctly.

Once gdalinfo on the output gTiff shows a geographical coordinate 
reference system, rgdal will work (unless this is near-polar and you have 
a raster cell boundary > |90|, which does happen sometimes - then you need 
to adjust the input data).

Roger


>> traceback()
> 8: stop("Geographical CRS given to non-conformant data")
> 7: `proj4string<-`(`*tmp*`, value = <S4 object of class "CRS">)
> 6: SpatialGrid(grid, proj4string)
> 5: initialize(value, ...)
> 4: initialize(value, ...)
> 3: new("SpatialGridDataFrame", SpatialGrid(grid, proj4string), data = data)
> 2: SpatialGridDataFrame(grid = grid, data = data.frame(df), proj4string = CRS(p4s))
> 1: readGDAL("RAD_NL21_PCP_NA_200707200000.tif")
>> sessionInfo()
> R version 2.5.1 (2007-06-27)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;LC_MONETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands.1252
>
> attached base packages:
> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"
>
> other attached packages:
>   rgdal       sp
> "0.5-14" "0.9-14"
>
> Do you have any idea what caused this error and how I can circumvent it?
>
> Many thanks in advance,
>
> 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
>>>>>
>>>>>
>>>>>
>>>
>>>
>>
>>
>
>
>

-- 
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




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