[gradsusr] GCOM-W1(AMSR2) HDF5 data

Tue Mar 28 13:53:11 EDT 2017

Dear Toshiyuki Tanaka,
Thank you very much for providing all the information I needed to solve this problem! I downloaded a copy of your data file, and can confirm the following issues with your descriptor file:

1. You simply misspelled the variable name in your descriptor file, omitting the ‘o’ in “Geophysical Data”.
2. The scale factor attribute name has a space in it and GrADS is not set up to handle spaces in attribute names the way it handles them in variable names. You will have to apply the scale factor manually when you display the variable.
3. An ‘options yrev' was needed, along with an adjustment to the initial value in the ydef entry.
4. There is no attribute named _FillValue, and there are two actual undef values in this file,  -32767 and -32768. I picked the former because it masked out the gaps between swaths and the data at the pole, but in order to get a good display, you will need to use maskout():

ga-> d maskout(0.1*smc,smc)
[cid:3AA7296F-C4F7-4E28-913B-8B871EEFC8DC]

Here is my revised descriptor:

DSET ^GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300.h5
DTYPE hdf5_grid
TITLE GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300
options yrev
UNDEF -32767
XDEF 3600 LINEAR 0.05 0.1
YDEF 1800 LINEAR -89.95 0.1
ZDEF 1 LEVELS 1000
TDEF 1 LINEAR 0Z01JAN2017 1DY
vars 2
Geophysical~Data=>smc 1 y,x,z Soil Moisture Content (%)
Time~Information=>ti 0 y,x   Time Information (min)
ENDVARS

―Jennifer

On Mar 28, 2017, at 2:20 AM, 田中俊行 <priustoshi at gmail.com<mailto:priustoshi at gmail.com>> wrote:

Dear GrADS users,

I want to open GCOM-W1(AMSR2) HDF5 format data with GrADS.
(The sensor observes precipitation, water vapor, sea surface wind speed, SST, soil moisture and snow depth. See, http://gcom-w1.jaxa.jp/ )
I have never worked on HDF 5 data with GrADS.

The ncdump output of soil moisture data is as follows:

$ ncdump -c GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300.h5
netcdf GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300 {
dimensions:
phony_dim_0 = 1800 ;
phony_dim_1 = 3600 ;
phony_dim_2 = 1 ;
variables:
short Geophysical\ Data(phony_dim_0, phony_dim_1, phony_dim_2) ;
Geophysical\ Data:SCALE\ FACTOR = 0.1f ;
string Geophysical\ Data:UNIT = "%" ;
short Time\ Information(phony_dim_0, phony_dim_1) ;
Time\ Information:SCALE\ FACTOR = 1.f ;
string Time\ Information:UNIT = "min" ;

// global attributes:
string :ProductName = "AMSR2-L3" ;
string :GeophysicalName = "Soil Moisture Content" ;
string :MeanType = "DayMean" ;
string :Projection = "EQR" ;
string :Resolution = "0.1deg" ;
string :ProductVersion = "3" ;
string :AlgorithmVersion = "300" ;
string :ParameterVersion = "300" ;
string :ProductSize_MByte = "24.7" ;
string :AlgorithmDeveloper = "_" ;
string :GranuleID = "GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300" ;
string :ProductionDateTime = "2017-03-03T04:36:06.000Z" ;
string :ObservationStartDateTime = "2017-01-01T00:00:00.303Z" ;
string :ObservationEndDateTime = "2017-01-01T23:42:37.604Z" ;
string :PGEName = "GCOM-W1 Mission Operation System" ;
string :InputFileName = "GW1AM2_201612312348_172A_L2SGSMCLF3300300.h5,GW1AM2_201701010127_188A_L2SGSMCLF3300300.h5,GW1AM2_201701010306_204A_L2SGSMCLF3300300.h5,GW1AM2_201701010445_220A_L2SGSMCLF3300300.h5,GW1AM2_201701010624_003A_L2SGSMCLF3300300.h5,GW1AM2_201701010803_019A_L2SGSMCLF3300300.h5,GW1AM2_201701010942_035A_L2SGSMCLF3300300.h5,GW1AM2_201701011120_051A_L2SGSMCLF3300300.h5,GW1AM2_201701011259_067A_L2SGSMCLF3300300.h5,GW1AM2_201701011438_083A_L2SGSMCLF3300300.h5,GW1AM2_201701011617_099A_L2SGSMCLF3300300.h5,GW1AM2_201701011756_115A_L2SGSMCLF3300300.h5,GW1AM2_201701011935_131A_L2SGSMCLF3300300.h5,GW1AM2_201701012114_147A_L2SGSMCLF3300300.h5,GW1AM2_201701012253_163A_L2SGSMCLF3300300.h5" ;
string :ProcessingCenter = "JAXA GCOM Project" ;
string :ContactOrganizationName = "JAXA GCOM Project" ;
string :ContactOrganizationTelephone = "" ;
string :StartOrbitNumber = "24605" ;
string :StopOrbitNumber = "24620" ;
string :OrbitDirection = "Ascending" ;
string :PlatformShortName = "GCOM-W1" ;
string :SensorShortName = "AMSR2" ;
string :ECSDataModel = "B.0" ;
data:
}

And then, I made a descriptor file like this:

$ more GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300.ctl
DSET ^GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300.h5
DTYPE hdf5_grid
TITLE GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300
UNDEF -32768 _FillValue
UNPACK scale_factor
XDEF 3600 LINEAR 0.0 0.1
YDEF 1800 LINEAR 0.0 0.1
TDEF 1 LINEAR 0Z01JAN2017 1DY
ZDEF 1 LEVELS 1000
vars 1
Gephysical~Data=>smc 1 z,y,x Soil Moisture Content (%)
ENDVARS

My GrADS (Version 2.1.0 on macOS 10.12.3)  open the descriptor file with no error. But, it has a warning
"Descriptor File Warning: No offset attribute name in unpack record”
and cannot plot correctly:

ga-> open GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300.ctl
Scanning description file:  GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300.ctl
Descriptor File Warning: No offset attribute name in unpack record
Data file GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300.h5 is open as file 1
LON set to 0 360
LAT set to 0 179.9
LEV set to 1000 1000
Time values set: 2017:1:1:0 2017:1:1:0
E set to 1 1
ga->  q file
File 1 : GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300
 Descriptor: GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300.ctl
 Binary: GW1AM2_20170101_01D_EQMA_L3SGSMCHF3300300.h5
 Type = Gridded
 Xsize = 3600  Ysize = 1800  Zsize = 1  Tsize = 1  Esize = 1
 Number of Variables = 1
    smc  1  z,y,x  Soil Moisture Content (%)
ga-> d smc
HDF5-DIAG: Error detected in HDF5 (1.8.12) 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 861 in H5G_traverse(): internal path traversal failed
   major: Symbol table
   minor: Object not found
 #003: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed
   major: Symbol table
   minor: Callback failed
 #004: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'Gephysical Data' doesn't exist
   major: Symbol table
   minor: Object not found
Error: H5Dopen2 failed for variable Gephysical Data
Error: Variable Gephysical Data not in HDF5 file
Data Request Error:  Error for variable 'smc'
 Error ocurred at column 1
DISPLAY error:  Invalid expression
 Expression = smc

Could you suggest some tips for open correctly?

Toshiyuki Tanaka
priustoshi at gmail.com<mailto:priustoshi at gmail.com>

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--
Jennifer Miletta Adams
Center for Ocean-Land-Atmosphere Studies (COLA)
George Mason University

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