[gradsusr] HDF5 control file help
Jennifer M Adams
jadams21 at gmu.edu
Wed Dec 23 08:11:30 EST 2015
Hi, Joyce —
Try changing the variable declaration from “y,x” to “x,y” and see if that fixes it.
—Jennifer
On Dec 22, 2015, at 9:28 PM, Meyerson, Joyce <hobo at atmos.ucla.edu<mailto:hobo at atmos.ucla.edu>> wrote:
Hi Jennifer,
I removed _FillValue and most of the errors resolved however I'm left with the error below. The grid attributes are from 20N, 50N, -180, 180. Is there something I'm not seeing in the control file?
ga-> d pr
HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
#000: ../../src/H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
HDF5 read error for float data
Data Request Error: Error for variable 'pr'
Error ocurred at column 1
DISPLAY error: Invalid expression
Expression = pr
*********************
DSET ^3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5
OPTIONS template
DTYPE hdf5_grid
TITLE GPM precip
UNDEF -9999.9
XDEF 3600 linear -180 0.1
YDEF 300 linear 20 0.1
ZDEF 1 levels 1000
TDEF 100 linear 00Z01jan2015 6hr
VARS 1
Grid/precipitation=>pr 0 y,x precipitation mm/hr
ENDVARS
********************
> h5dump 3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5 |more
HDF5 "3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5" {
GROUP "/" {
ATTRIBUTE "FileHeader" {
DATATYPE H5T_STRING {
STRSIZE 563;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
DATA {
(0): "DOI=10.5067/GPM/IMERG/HH/3B;
DOIauthority=http://dx.doi/org/;
DOIshortName=3IMERGM;
AlgorithmID=3IMERGMCAG;
AlgorithmVersion=3IMERGM_1.0;
FileName=3B-MO.MS.MRG.3IMERG.20150101-S000000-E235959.01.V03D.HDF5.ps.hdf;
SatelliteName=MULTI;
InstrumentName=MERGED;
GenerationDateTime=2015-12-03T21:21:48.000Z;
StartGranuleDateTime=2015-01-01T00:00:00.000Z;
StopGranuleDateTime=2015-01-31T23:59:59.999Z;
GranuleNumber=;
NumberOfSwaths=0;
NumberOfGrids=1;
GranuleStart=;
TimeInterval=MONTH;
ProcessingSystem=PPS;
ProductVersion=V03D;
EmptyGranule=NOT_EMPTY;
MissingData=;
"
}
}
ATTRIBUTE "FileInfo" {
DATATYPE H5T_STRING {
STRSIZE 228;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
DATA {
(0): "DataFormatVersion=bh;
TKCodeBuildVersion=1;
MetadataVersion=bh;
FormatPackage=HDF5-1.8.9;
BlueprintFilename=GPM.V1.3IMERGM.blueprint.xml;
BlueprintVersion=BV_42;
TKIOVersion=3.60.8;
MetadataStyle=PVL;
EndianType=LITTLE_ENDIAN;
"
}
}
GROUP "Grid" {
ATTRIBUTE "GridHeader" {
DATATYPE H5T_STRING {
STRSIZE 257;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
DATA {
(0): "BinMethod=ARITHMETIC_MEAN;
Registration=CENTER;
LatitudeResolution=0.1;
LongitudeResolution=0.1;
NorthBoundingCoordinate=50.000000;
SouthBoundingCoordinate=20.000000;
EastBoundingCoordinate=180.000000;
WestBoundingCoordinate=-180.000000;
Origin=SOUTHWEST;
"
}
}
On Dec 10, 2015, at 4:59 AM, Jennifer M Adams <jadams21 at gmu.edu<mailto:jadams21 at gmu.edu>> wrote:
Hi, Joyce —
The first thing to try is set up aliases for those variable names, which are not GrADS-compliant. Something like this:
Grid/precipitation=>p 0 y,x precipitation
Grid/probabilityLiquidPrecipitation=>lp 0 y,x liquid precip
—Jennifer
On Dec 9, 2015, at 7:06 PM, Meyerson, Joyce <hobo at atmos.ucla.edu<mailto:hobo at atmos.ucla.edu>> wrote:
Hi Users,
I have a hdf5 data file from NASA's Global Precipitation Measurement project and I'm having trouble writing the control file. I don't know what I'm doing wrong. Any help would be greatly appreciated. The error I'm getting is
open test.ctl
Open Error: Invalid variable record
--> The invalid description file record is:
--> Grid/precipitation 0 y,x precipitation
DSET ^3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5
OPTIONS template
DTYPE hdf5_grid
TITLE GPM precip
UNDEF -999.0 _FillValue
XDEF 3600 linear -180 0.1
YDEF 300 linear -20 0.1
ZDEF 1 levels 1000
TDEF 1 linear 01dec2015 1dy
VARS 2
Grid/precipitation 0 y,x precipitation
Grid/probabilityLiquidPrecipitation 0 y,x liquid precip
ENDVARS
Here's the file contents of
h5dump -n 3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5
HDF5 "3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5" {
FILE_CONTENTS {
group /
group /Grid
dataset /Grid/gaugeRelativeWeighting
dataset /Grid/lat
dataset /Grid/lon
dataset /Grid/precipitation
dataset /Grid/probabilityLiquidPrecipitation
dataset /Grid/randomError
}
}
and the dataset
h5dump -H -d/Grid/precipitation 3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5
HDF5 "3B-MO-CA-180W50N180E20N.MS.MRG.3IMERG.20150101-S000000-E235959.000001.V03D.HDF5" {
DATASET "/Grid/precipitation" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 3600, 300 ) / ( 3600, 300 ) }
ATTRIBUTE "CodeMissingValue" {
DATATYPE H5T_STRING {
STRSIZE 8;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "DIMENSION_LIST" {
DATATYPE H5T_VLEN { H5T_REFERENCE}
DATASPACE SIMPLE { ( 2 ) / ( 2 ) }
}
ATTRIBUTE "DimensionNames" {
DATATYPE H5T_STRING {
STRSIZE 8;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "Units" {
DATATYPE H5T_STRING {
STRSIZE 6;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "_FillValue" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SCALAR
}
ATTRIBUTE "coordinates" {
DATATYPE H5T_STRING {
STRSIZE 8;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
ATTRIBUTE "units" {
DATATYPE H5T_STRING {
STRSIZE 6;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
}
}
}
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