[gradsusr] Opening up NASA GSSTF.3 HDF-EOS5 data in GrADS
James E. Johnson
James.Johnson at nasa.gov
Fri Oct 18 14:08:44 EDT 2013
You have to write a GrADS control (.ctl) file for the HDF-EOS5 file, the
sdfopen command won't work as GrADS / CF convention doesn't understand the
HDF-EOS conventions for geolocation. Make sure your version of GrADS supports
the HDF5 file format.
----------------------------- <start .ctl file> ------------------------------
DSET GSSTF.3.%y4.%m2.%d2.he5
DTYPE hdf5_grid
TITLE Goddard Satellite-Based Surface Turbulent Fluxes (GSSTF), 0.25x0.25
degree Daily Grid, Set1 of Combined Satellites, Version 3
UNDEF -999.0 _FillValue
OPTIONS template
XDEF 1440 linear -180 0.25
YDEF 720 linear -90 0.25
ZDEF 1 levels 1
TDEF 7847 linear 09jul1987 1dy
VARS 8
/HDFEOS/GRIDS/SET1/Data~Fields/E=>E 0 y,x latent heat flux (W/m^^2)
/HDFEOS/GRIDS/SET1/Data~Fields/STu=>STu 0 y,x zonal wind stress (N/m^^2)
/HDFEOS/GRIDS/SET1/Data~Fields/STv=>STv 0 y,x meridional wind stress
(N/m^^2)
/HDFEOS/GRIDS/SET1/Data~Fields/H=>H 0 y,x sensible heat flux (W/m^^2)
/HDFEOS/GRIDS/SET1/Data~Fields/Qair=>Qair 0 y,x surface air (~10-m)
specific humidity (g/kg)
/HDFEOS/GRIDS/SET1/Data~Fields/U=>U 0 y,x 10-m wind speed (m/s)
/HDFEOS/GRIDS/SET1/Data~Fields/DQ=>DQ 0 y,x sea-air humidity difference
(g/kg)
/HDFEOS/GRIDS/SET1/Data~Fields/Tot_Precip_Water=>Tot_Precip_Water 0 y,x
total precipitable water (g/cm^^2)
ENDVARS
------------------------------ <end .ctl file> -------------------------------
Then run grads, and open the .ctl file using the open command:
$ grads
Grid Analysis and Display System (GrADS) Version 2.0.2
Copyright (c) 1988-2011 by Brian Doty and the
Institute for Global Environment and Society (IGES)
GrADS comes with ABSOLUTELY NO WARRANTY
See file COPYRIGHT for more information
Config: v2.0.2 little-endian readline printim grib2 netcdf hdf4-sds hdf5
opendap-grids,stn geotiff shapefile
Issue 'q config' command for more detailed configuration information
Landscape mode? ('n' for portrait):
GX Package Initialization: Size = 11 8.5
ga-> open gsstf3-he5
Scanning description file: gsstf3-he5
Data file GSSTF.3.%y4.%m2.%d2.he5 is open as file 1
LON set to 0 360
LAT set to -90 89.75
LEV set to 1 1
Time values set: 1987:7:9:0 1987:7:9:0
E set to 1 1
ga-> q file
File 1 : Goddard Satellite-Based Surface Turbulent Fluxes (GSSTF), 0.25x0.25
degree Daily Grid, Set1 of Combined Satellites, Version 3
Descriptor: gsstf3-he5.ctl
Binary: GSSTF.3.%y4.%m2.%d2.he5
Type = Gridded
Xsize = 1440 Ysize = 720 Zsize = 1 Tsize = 7850 Esize = 1
Number of Variables = 8
e 0 y,x latent heat flux (W/m^^2)
stu 0 y,x zonal wind stress (N/m^^2)
stv 0 y,x meridional wind stress (N/m^^2)
h 0 y,x sensible heat flux (W/m^^2)
qair 0 y,x surface air (~10-m) specific humidity (g/kg)
u 0 y,x 10-m wind speed (m/s)
dq 0 y,x sea-air humidity difference (g/kg)
tot_precip_wate 0 y,x total precipitable water (g/cm^^2)
ga-> set time 28dec1998
Time values set: 1998:12:28:0 1998:12:28:0
ga-> set lat -90 90
LAT set to -90 90
ga-> set lon -180 180
LON set to -180 180
ga-> set gxout grfill
ga-> d e
Contouring: -0 to 650 interval 50
ga->
On Friday 18 October 2013 01:07:27 pm Vizy, Edward K wrote:
> Hi,
>
> I am trying to view the Goddard Satellite-Based Surface Turbulent Fluxes,
> Daily Grid from MEaSUREs site at:
> http://disc.gsfc.nasa.gov/daac-bin/DataHoldingsMEASURES.pl in GrADS.
>
> When I go to open the file in GrADS using the following I get the following
> error message: ga-> sdfopen GSSTF.3.1998.12.28.he5
> Scanning self-describing file: GSSTF.3.1998.12.28.he5
> gadsdf: SDF file has no discernable X coordinate.
> To open this file with GrADS, use a descriptor file with an XDEF entry.
> Documentation is at http://iges.org/grads/gadoc/SDFdescriptorfile.html
>
> However, when I use opendap to open the file it works fine and all of the
> fields are appropriate magnitudes. That is:
>
> ga-> sdfopen
> http://measures.gsfc.nasa.gov/opendap/GSSTF/GSSTF.3/1998/GSSTF.3.1998.12.2
> 8.he5 Scanning self-describing file:
> http://measures.gsfc.nasa.gov/opendap/GSSTF/GSSTF.3/1998/GSSTF.3.1998.12.2
> 8.he5 SDF file has no discernable time coordinate -- using default values.
> SDF file
> http://measures.gsfc.nasa.gov/opendap/GSSTF/GSSTF.3/1998/GSSTF.3.1998.12.2
> 8.he5 is open as file 1 LON set to -179.875 179.875
> LAT set to -89.875 89.875
> LEV set to 0 0
> Time values set: 1:1:1:0 1:1:1:0
> E set to 1 1
>
> So using the q ctlinfo command I was able to extract and construct a
> control file for the downloaded HDF-EOS5 data file:
>
> dset ^./GSSTF.3.1998.12.28.he5
> title
> undef -999
> dtype netcdf
> xdef 1440 levels -179.875 -179.625 -179.375 -179.125 -178.875 -178.625
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> -54.375 -54.125 -53.875 -53.625 -53.375 -53.125 -52.875 -52.625 -52.375
> -52.125 -51.875 -51.625 -51.375 -51.125 -50.875 -50.625 -50.375 -50.125
> -49.875 -49.625 -49.375 -49.125 -48.875 -48.625 -48.375 -48.125 -47.875
> -47.625 -47.375 -47.125 -46.875 -46.625 -46.375 -46.125 -45.875 -45.625
> -45.375 -45.125 -44.875 -44.625 -44.375 -44.125 -43.875 -43.625 -43.375
> -43.125 -42.875 -42.625 -42.375 -42.125 -41.875 -41.625 -41.375 -41.125
> -40.875 -40.625 -40.375 -40.125 -39.875 -39.625 -39.375 -39.125 -38.875
> -38.625 -38.375 -38.125 -37.875 -37.625 -37.375 -37.125 -36.875 -36.625
> -36.375 -36.125 -35.875 -35.625 -35.375 -35.125 -34.875 -34.625 -34.375
> -34.125 -33.875 -33.625 -33.375 -33.125 -32.875 -32.625 -32.375 -32.125
> -31.875 -31.625 -31.375 -31.125 -30.875 -30.625 -30.375 -30.125 -29.875
> -29.625 -29.375 -29.125 -28.875 -28.625 -28.375 -28.125 -27.875 -27.625
> -27.375 -27.125 -26.875 -26.625 -26.375 -26.125 -25.875 -25.625 -25.375
> -25.125 -24.875 -24.625 -24.375 -24.125 -23.875 -23.625 -23.375 -23.125
> -22.875 -22.625 -22.375 -22.125 -21.875 -21.625 -21.375 -21.125 -20.875
> -20.625 -20.375 -20.125 -19.875 -19.625 -19.375 -19.125 -18.875 -18.625
> -18.375 -18.125 -17.875 -17.625 -17.375 -17.125 -16.875 -16.625 -16.375
> -16.125 -15.875 -15.625 -15.375 -15.125 -14.875 -14.625 -14.375 -14.125
> -13.875 -13.625 -13.375 -13.125 -12.875 -12.625 -12.375 -12.125 -11.875
> -11.625 -11.375 -11.125 -10.875 -10.625 -10.375 -10.125 -9.875 -9.625
> -9.375 -9.125 -8.875 -8.625 -8.375 -8.125 -7.875 -7.625 -7.375 -7.125
> -6.875 -6.625 -6.375 -6.125 -5.875 -5.625 -5.375 -5.125 -4.875 -4.625
> -4.375 -4.125 -3.875 -3.625 -3.375 -3.125 -2.875 -2.625 -2.375 -2.125
> -1.875 -1.625 -1.375 -1.125 -0.875 -0.625 -0.375 -0.125 0.125 0.375 0.625
> 0.875 1.125 1.375 1.625 1.875
> 2.125 2.375 2.625 2.875 3.125 3.375 3.625 3.875 4.125 4.375
> 4.625 4.875 5.125 5.375 5.625 5.875 6.125 6.375 6.625 6.875
> 7.125 7.375 7.625 7.875 8.125 8.375 8.625 8.875 9.125 9.375
> 9.625 9.875 10.125 10.375 10.625 10.875 11.125 11.375 11.625 11.875
> 12.125 12.375 12.625 12.875 13.125 13.375 13.625 13.875 14.125 14.375
> 14.625 14.875 15.125 15.375 15.625 15.875 16.125 16.375 16.625 16.875
> 17.125 17.375 17.625 17.875 18.125 18.375 18.625 18.875 19.125 19.375
> 19.625 19.875 20.125 20.375 20.625 20.875 21.125 21.375 21.625 21.875
> 22.125 22.375 22.625 22.875 23.125 23.375 23.625 23.875 24.125 24.375
> 24.625 24.875 25.125 25.375 25.625 25.875 26.125 26.375 26.625 26.875
> 27.125 27.375 27.625 27.875 28.125 28.375 28.625 28.875 29.125 29.375
> 29.625 29.875 30.125 30.375 30.625 30.875 31.125 31.375 31.625 31.875
> 32.125 32.375 32.625 32.875 33.125 33.375 33.625 33.875 34.125 34.375
> 34.625 34.875 35.125 35.375 35.625 35.875 36.125 36.375 36.625 36.875
> 37.125 37.375 37.625 37.875 38.125 38.375 38.625 38.875 39.125 39.375
> 39.625 39.875 40.125 40.375 40.625 40.875 41.125 41.375 41.625 41.875
> 42.125 42.375 42.625 42.875 43.125 43.375 43.625 43.875 44.125 44.375
> 44.625 44.875 45.125 45.375 45.625 45.875 46.125 46.375 46.625 46.875
> 47.125 47.375 47.625 47.875 48.125 48.375 48.625 48.875 49.125 49.375
> 49.625 49.875 50.125 50.375 50.625 50.875 51.125 51.375 51.625 51.875
> 52.125 52.375 52.625 52.875 53.125 53.375 53.625 53.875 54.125 54.375
> 54.625 54.875 55.125 55.375 55.625 55.875 56.125 56.375 56.625 56.875
> 57.125 57.375 57.625 57.875 58.125 58.375 58.625 58.875 59.125 59.375
> 59.625 59.875 60.125 60.375 60.625 60.875 61.125 61.375 61.625 61.875
> 62.125 62.375 62.625 62.875 63.125 63.375 63.625 63.875 64.125 64.375
> 64.625 64.875 65.125 65.375 65.625 65.875 66.125 66.375 66.625 66.875
> 67.125 67.375 67.625 67.875 68.125 68.375 68.625 68.875 69.125 69.375
> 69.625 69.875 70.125 70.375 70.625 70.875 71.125 71.375 71.625 71.875
> 72.125 72.375 72.625 72.875 73.125 73.375 73.625 73.875 74.125 74.375
> 74.625 74.875 75.125 75.375 75.625 75.875 76.125 76.375 76.625 76.875
> 77.125 77.375 77.625 77.875 78.125 78.375 78.625 78.875 79.125 79.375
> 79.625 79.875 80.125 80.375 80.625 80.875 81.125 81.375 81.625 81.875
> 82.125 82.375 82.625 82.875 83.125 83.375 83.625 83.875 84.125 84.375
> 84.625 84.875 85.125 85.375 85.625 85.875 86.125 86.375 86.625 86.875
> 87.125 87.375 87.625 87.875 88.125 88.375 88.625 88.875 89.125 89.375
> 89.625 89.875
> zdef 1 linear 0 1
> tdef 1 linear 00Z01JAN0001 1mn
> vars 8
> DQ=>dq 0 y,x sea-air humidity difference
> E=>e 0 y,x latent heat flux
> H=>h 0 y,x sensible heat flux
> Qair=>qair 0 y,x surface air (~10-m) specific humidity
> STu=>stu 0 y,x zonal wind stress
> STv=>stv 0 y,x meridional wind stress
> Tot_Precip_Water=>tot_precip_wate 0 y,x total precipitable water
> U=>u 0 y,x 10-m wind speed
> endvars
>
> This control file allows me to open the data file up, but when I go to
> display any variable I get the following error message: ga-> d u
> Error: Variable U not in netcdf file
> Data Request Error: Error for variable 'u'
> Error ocurred at column 1
> DISPLAY error: Invalid expression
> Expression = u
>
> I then tried to change dtype netcdf to read dtype hdf5_grid. When I do
> this then try to display a variable I get the following: ga-> d u
> HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
> #000: H5D.c line 334 in H5Dopen2(): not found
> major: Dataset
> minor: Object not found
> #001: H5Gloc.c line 430 in H5G_loc_find(): can't find object
> major: Symbol table
> minor: Object not found
> #002: H5Gtraverse.c line 905 in H5G_traverse(): internal path traversal
> failed major: Symbol table
> minor: Object not found
> #003: H5Gtraverse.c line 688 in H5G_traverse_real(): traversal operator
> failed major: Symbol table
> minor: Callback failed
> #004: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'U' doesn't exist
> major: Symbol table
> minor: Object not found
> Error: H5Dopen2 failed for variable U
> Error: Variable U not in HDF5 file
> Data Request Error: Error for variable 'u'
> Error ocurred at column 1
> DISPLAY error: Invalid expression
> Expression = u
>
> Does anyone have any suggestions about what may be wrong and/or how the
> control file should read so as to be able to open up this data? My GrADS
> build information is as follows:
>
> Config: v2.0.2 little-endian readline printim grib2 netcdf hdf4-sds hdf5
> opendap-grids,stn geotiff shapefile Grid Analysis and Display System
> (GrADS) Version 2.0.2
> Copyright (c) 1988-2011 by Brian Doty and the
> Institute for Global Environment and Society (IGES)
> This program is distributed WITHOUT ANY WARRANTY
> See file COPYRIGHT for more information.
>
> Built Thu Nov 8 13:55:26 EST 2012 for x86_64-unknown-linux-gnu
>
> This version of GrADS has been configured with the following options:
> o Built on a LITTLE ENDIAN machine
> o Athena Widget GUI DISABLED
> o Command line editing ENABLED
> http://tiswww.case.edu/php/chet/readline/rltop.html
> o printim command for image output ENABLED
> http://www.zlib.net
> http://www.libpng.org/pub/png/libpng.html
> http://www.libgd.org/Main_Page
> o GRIB2 interface ENABLED
> http://www.ijg.org
> http://www.ece.uvic.ca/~mdadams/jasper
> http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2
> g2clib-1.4.0
> o NetCDF interface ENABLED
> http://www.unidata.ucar.edu/software/netcdf
> netcdf 4.1.2 of Oct 5 2011 11:54:30 $
> o OPeNDAP gridded data interface ENABLED
> o OPeNDAP station data interface ENABLED
> http://iges.org/grads/gadoc/supplibs.html
> libgadap 2.0
> o HDF4 and HDF5 interfaces ENABLED
> http://hdfgroup.org
> HDF 4.2r3
> HDF5 1.8.7
> o GeoTIFF and KML/TIFF output ENABLED
> http://www.libtiff.org
> http://geotiff.osgeo.org
> o KML contour output ENABLED
> o Shapefile interface ENABLED
> http://shapelib.maptools.org
>
>
> Many thanks
> Ned
>
>
> Dr. Edward "Ned" Vizy
> Research Engineer/Scientist Associate V
> Jackson School of Geosciences
> Department of Geological Sciences
> The University of Texas at Austin
> 2275 Speedway C9000
> Austin, Texas 78712
> e-mail: ned at jsg.utexas.edu<mailto:ned at jsg.utexas.edu>
> phone: 512-585-1937
>
------------------------------------------------------------------------------
| James E. Johnson | address: |
| ADNET Systems, Inc. | NASA Goddard Space Flight Center |
| e-mail: james.johnson at nasa.gov | Data and Information Services Center |
| phone: 301-614-5121 | Code 610.2, Bldg 32, Room S130G |
| fax: 301-614-5268 | Greenbelt, MD 20771 |
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