[GRASS-user] trouble with netCDF input arguments for r.in.gdal

Kirk_Wythers · October 1, 2012, 6:02pm

I am trying to read some netCDF data (from the CRU climate database) into grass. I am looking at the netcdf wiki page and having a little trouble translating the instructions there to the output I am getting from “gdalinfo”. Here is the

If I am trying to use syntax that looks something like:

r.in.gdal input=NETCDF:"sst.nc":time_bnds output=sst

I am getting the following error:

ERROR 4: `NETCDF:~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc:time_bnds’ does not exist in the file system,
and is not recognised as a supported dataset name.

In my case, the PATH_TO_FILE is

“~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc”

However, I can’t tell what to use in the place of “:time_bnds”. Any ideas from the pasted text below of what my input argument should look like?

Thanks in advance,

Kirk

Here is output I am looking at from gdalinfo:

GRASS 6.4.1 (globe_30min):~ > gdalinfo ~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc
ERROR 1: GDAL/GRASS57 driver was compiled against GDAL 1.8 but current library version is 1.9

ERROR 1: GDAL/GRASS57 driver was compiled against GDAL 1.8 but current library version is 1.9

Driver: netCDF/Network Common Data Format
Files: /Network/Servers/truffula.fr.umn.edu/Volumes/disk1/home1/kirkw/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc
Size is 720, 360
Coordinate System is `’
Origin = (-180.000000000000000,90.000000000000000)
Pixel Size = (0.500000000000000,-0.500000000000000)
Metadata:
lat#long_name=latitude
lat#units=degrees_north
lon#long_name=longitude
lon#units=degrees_east
NC_GLOBAL#comment=Data restrictions: for academic research use only.Contact BADC for details
NC_GLOBAL#contact=BADC <badc@rl.ac.uk>
NC_GLOBAL#Conventions=CF-1.4
NC_GLOBAL#history=Wed Feb 2 03:32:36 GMT 2011 : User badc : Program makegridsauto.for called by update.for
NC_GLOBAL#institution=Data held at British Atmospheric Data Centre, RAL, UK.
NC_GLOBAL#references=Information on the data is available at http://badc.nerc.ac.uk/data/cru/
NC_GLOBAL#source=Run ID = 1102011219
Data generated by BADC from:
tmp.1009221824.dtb
dtr.1009221824.dtb
vap.1009221824.dtb
cld.1009221824.dtb
NC_GLOBAL#title=CRU TS 3.10 Potential Evapotranspiration
pet#_FillValue=9.969209968386869e+36
pet#correlation_decay_distance=-999
pet#long_name=potential evapotranspiration
pet#missing_value=9.969209968386869e+36
pet#units=mm
time#calendar=gregorian
time#long_name=time
time#units=days since 1900-1-1
Corner Coordinates:
Upper Left (-180.0000000, 90.0000000)
Lower Left (-180.0000000, -90.0000000)
Upper Right ( 180.0000000, 90.0000000)
Lower Right ( 180.0000000, -90.0000000)
Center ( 0.0000000, 0.0000000)
Band 1 Block=720x1 Type=Float64, ColorInterp=Undefined
NoData Value=9.96920996838686905e+36
Metadata:
_FillValue=9.969209968386869e+36
correlation_decay_distance=-999
long_name=potential evapotranspiration
missing_value=9.969209968386869e+36
NETCDF_DIMENSION_time=380
NETCDF_time_units=days since 1900-1-1
NETCDF_VARNAME=pet
units=mm
Band 2 Block=720x1 Type=Float64, ColorInterp=Undefined
NoData Value=9.96920996838686905e+36
Metadata:
_FillValue=9.969209968386869e+36
correlation_decay_distance=-999
long_name=potential evapotranspiration
missing_value=9.969209968386869e+36
NETCDF_DIMENSION_time=410
NETCDF_time_units=days since 1900-1-1
NETCDF_VARNAME=pet
units=mm

.
.
.
.

Band 1308 Block=720x1 Type=Float64, ColorInterp=Undefined
NoData Value=9.96920996838686905e+36
Metadata:
_FillValue=9.969209968386869e+36
correlation_decay_distance=-999
long_name=potential evapotranspiration
missing_value=9.969209968386869e+36
NETCDF_DIMENSION_time=40161
NETCDF_time_units=days since 1900-1-1
NETCDF_VARNAME=pet
units=mm

Jennifer_Boehnert · October 1, 2012, 6:22pm

Hi Kirk,
in your r.in.gdal syntax the time_bnds is the variable you want to read. My guess would be the variable you want to read is pet.

I would suggestion executing the following commands to read your file metadata before running the r.in.gdal.

/gdalinfo D:\data\projects\courses2012\IAI\data\B1_tas.nc
/

This will give you the variable names in your dataset. In your case I see PET

Then to find the dimensions on the variable of interest execute The syntax is your netCDF name : variable name

/gdalinfo NETCDF:D:\data\projects\courses2012\IAI\data\A2_tas.nc:tasC /

In my example the netCDF name is A2_tas.nc an the variable I want is tasC (temperature in degrees celsius). My data has 10 temporal dimensions.
You should put <netCDF Name>:PET

Now that I know this I run the r.in.gdal

/r.in.gdal -o -e input=NETCDF: D:\data\projects\courses2012\IAI\data\A2_tas.nc:tasC output=SRESA2_tas/

In this example I am bringing in all times if you want specify just 1 time you can do so by using the BAND number.
Jennifer
On 10/1/2012 12:02 PM, Kirk Wythers wrote:

I am trying to read some netCDF data (from the CRU climate database) into grass. I am looking at the netcdf wiki page and having a little trouble translating the instructions there to the output I am getting from "gdalinfo". Here is the

If I am trying to use syntax that looks something like:
r.in.gdal input=NETCDF:"sst.nc":time_bnds output=sst
I am getting the following error:

ERROR 4: `NETCDF:~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc:time_bnds' does not exist in the file system,
and is not recognised as a supported dataset name.

In my case, the PATH_TO_FILE is

"~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc"

However, I can't tell what to use in the place of ":time_bnds". Any ideas from the pasted text below of what my input argument should look like?

Thanks in advance,

Kirk

Here is output I am looking at from gdalinfo:

GRASS 6.4.1 (globe_30min):~ > gdalinfo ~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc
ERROR 1: GDAL/GRASS57 driver was compiled against GDAL 1.8 but current library version is 1.9

ERROR 1: GDAL/GRASS57 driver was compiled against GDAL 1.8 but current library version is 1.9

Driver: netCDF/Network Common Data Format
Files: /Network/Servers/truffula.fr.umn.edu/Volumes/disk1/home1/kirkw/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc <http://truffula.fr.umn.edu/Volumes/disk1/home1/kirkw/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc>
Size is 720, 360
Coordinate System is `'
Origin = (-180.000000000000000,90.000000000000000)
Pixel Size = (0.500000000000000,-0.500000000000000)
Metadata:
  lat#long_name=latitude
  lat#units=degrees_north
  lon#long_name=longitude
  lon#units=degrees_east
  NC_GLOBAL#comment=Data restrictions: for academic research use only.Contact BADC for details
  NC_GLOBAL#contact=BADC <badc@rl.ac.uk <mailto:badc@rl.ac.uk>>
  NC_GLOBAL#Conventions=CF-1.4
  NC_GLOBAL#history=Wed Feb 2 03:32:36 GMT 2011 : User badc : Program makegridsauto.for called by update.for
  NC_GLOBAL#institution=Data held at British Atmospheric Data Centre, RAL, UK.
  NC_GLOBAL#references=Information on the data is available at http://badc.nerc.ac.uk/data/cru/
  NC_GLOBAL#source=Run ID = 1102011219
Data generated by BADC from:
tmp.1009221824.dtb
dtr.1009221824.dtb
vap.1009221824.dtb
cld.1009221824.dtb
  NC_GLOBAL#title=CRU TS 3.10 Potential Evapotranspiration
  pet#_FillValue=9.969209968386869e+36
  pet#correlation_decay_distance=-999
  pet#long_name=potential evapotranspiration
  pet#missing_value=9.969209968386869e+36
  pet#units=mm
  time#calendar=gregorian
  time#long_name=time
  time#units=days since 1900-1-1
Corner Coordinates:
Upper Left (-180.0000000, 90.0000000)
Lower Left (-180.0000000, -90.0000000)
Upper Right ( 180.0000000, 90.0000000)
Lower Right ( 180.0000000, -90.0000000)
Center ( 0.0000000, 0.0000000)
Band 1 Block=720x1 Type=Float64, ColorInterp=Undefined
  NoData Value=9.96920996838686905e+36
  Metadata:
    _FillValue=9.969209968386869e+36
    correlation_decay_distance=-999
    long_name=potential evapotranspiration
    missing_value=9.969209968386869e+36
    NETCDF_DIMENSION_time=380
    NETCDF_time_units=days since 1900-1-1
    NETCDF_VARNAME=pet
    units=mm
Band 2 Block=720x1 Type=Float64, ColorInterp=Undefined
  NoData Value=9.96920996838686905e+36
  Metadata:
    _FillValue=9.969209968386869e+36
    correlation_decay_distance=-999
    long_name=potential evapotranspiration
    missing_value=9.969209968386869e+36
    NETCDF_DIMENSION_time=410
    NETCDF_time_units=days since 1900-1-1
    NETCDF_VARNAME=pet
    units=mm
.
Band 1308 Block=720x1 Type=Float64, ColorInterp=Undefined
  NoData Value=9.96920996838686905e+36
  Metadata:
    _FillValue=9.969209968386869e+36
    correlation_decay_distance=-999
    long_name=potential evapotranspiration
    missing_value=9.969209968386869e+36
    NETCDF_DIMENSION_time=40161
    NETCDF_time_units=days since 1900-1-1
    NETCDF_VARNAME=pet
    units=mm

_______________________________________________
grass-user mailing list
grass-user@lists.osgeo.org
http://lists.osgeo.org/mailman/listinfo/grass-user

Kirk_Wythers · October 1, 2012, 6:46pm

Thanks Jennifer,

In my case I want all 1308 time dimensions… so I tried:

GRASS 6.4.1 (globe_30min):~ > r.in.gdal input=NETCDF:“~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc”:PET output=cru_pet

but got the same error:

ERROR 4: `NETCDF:~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc:PET’ does not exist in the file system,
and is not recognised as a supported dataset name.

I also tried single instead of double quotes, and give the full pathname instead of the ~/ for my home directory… still not working.

Also, if you specify PET as the variable of interest, do you still pull in the lat and lon data?

Thanks

···

Hi Kirk,
in your r.in.gdal syntax the time_bnds is the variable you want to read. My guess would be the variable you want to read is pet.

I would suggestion executing the following commands to read your file metadata before running the r.in.gdal.

gdalinfo D:\data\projects\courses2012\IAI\data\B1_tas.nc

On 10/1/2012 12:02 PM, Kirk Wythers wrote:

This will give you the variable names in your dataset. In your case I see PET

Then to find the dimensions on the variable of interest execute The syntax is your netCDF name : variable name

gdalinfo NETCDF:D:\data\projects\courses2012\IAI\data\A2_tas.nc:tasC

In my example the netCDF name is A2_tas.nc an the variable I want is tasC (temperature in degrees celsius). My data has 10 temporal dimensions.
You should put :PET

Now that I know this I run the r.in.gdal

r.in.gdal -o -e input=NETCDF: D:\data\projects\courses2012\IAI\data\A2_tas.nc:tasC output=SRESA2_tas

In this example I am bringing in all times if you want specify just 1 time you can do so by using the BAND number.
Jennifer

I am trying to read some netCDF data (from the CRU climate database) into grass. I am looking at the netcdf wiki page and having a little trouble translating the instructions there to the output I am getting from “gdalinfo”. Here is the

If I am trying to use syntax that looks something like:
r.in.gdal input=NETCDF:"sst.nc":time_bnds output=sst
I am getting the following error:

ERROR 4: `NETCDF:~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc:time_bnds’ does not exist in the file system,
and is not recognised as a supported dataset name.

In my case, the PATH_TO_FILE is

“~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc”

However, I can’t tell what to use in the place of “:time_bnds”. Any ideas from the pasted text below of what my input argument should look like?

Thanks in advance,

Kirk

Here is output I am looking at from gdalinfo:

GRASS 6.4.1 (globe_30min):~ > gdalinfo ~/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc
ERROR 1: GDAL/GRASS57 driver was compiled against GDAL 1.8 but current library version is 1.9

ERROR 1: GDAL/GRASS57 driver was compiled against GDAL 1.8 but current library version is 1.9

Driver: netCDF/Network Common Data Format
Files: /Network/Servers/truffula.fr.umn.edu/Volumes/disk1/home1/kirkw/Downloads/cru_ts_3_10.1901.2009.pet.dat.nc
Size is 720, 360
Coordinate System is `’
Origin = (-180.000000000000000,90.000000000000000)
Pixel Size = (0.500000000000000,-0.500000000000000)
Metadata:
lat#long_name=latitude
lat#units=degrees_north
lon#long_name=longitude
lon#units=degrees_east
NC_GLOBAL#comment=Data restrictions: for academic research use only.Contact BADC for details
NC_GLOBAL#contact=BADC <badc@rl.ac.uk>
NC_GLOBAL#Conventions=CF-1.4
NC_GLOBAL#history=Wed Feb 2 03:32:36 GMT 2011 : User badc : Program makegridsauto.for called by update.for
NC_GLOBAL#institution=Data held at British Atmospheric Data Centre, RAL, UK.
NC_GLOBAL#references=Information on the data is available at http://badc.nerc.ac.uk/data/cru/
NC_GLOBAL#source=Run ID = 1102011219
Data generated by BADC from:
tmp.1009221824.dtb
dtr.1009221824.dtb
vap.1009221824.dtb
cld.1009221824.dtb
NC_GLOBAL#title=CRU TS 3.10 Potential Evapotranspiration
pet#_FillValue=9.969209968386869e+36
pet#correlation_decay_distance=-999
pet#long_name=potential evapotranspiration
pet#missing_value=9.969209968386869e+36
pet#units=mm
time#calendar=gregorian
time#long_name=time
time#units=days since 1900-1-1
Corner Coordinates:
Upper Left (-180.0000000, 90.0000000)
Lower Left (-180.0000000, -90.0000000)
Upper Right ( 180.0000000, 90.0000000)
Lower Right ( 180.0000000, -90.0000000)
Center ( 0.0000000, 0.0000000)
Band 1 Block=720x1 Type=Float64, ColorInterp=Undefined
NoData Value=9.96920996838686905e+36
Metadata:
_FillValue=9.969209968386869e+36
correlation_decay_distance=-999
long_name=potential evapotranspiration
missing_value=9.969209968386869e+36
NETCDF_DIMENSION_time=380
NETCDF_time_units=days since 1900-1-1
NETCDF_VARNAME=pet
units=mm
Band 2 Block=720x1 Type=Float64, ColorInterp=Undefined
NoData Value=9.96920996838686905e+36
Metadata:
_FillValue=9.969209968386869e+36
correlation_decay_distance=-999
long_name=potential evapotranspiration
missing_value=9.969209968386869e+36
NETCDF_DIMENSION_time=410
NETCDF_time_units=days since 1900-1-1
NETCDF_VARNAME=pet
units=mm

.
.
.
.

Band 1308 Block=720x1 Type=Float64, ColorInterp=Undefined
NoData Value=9.96920996838686905e+36
Metadata:
_FillValue=9.969209968386869e+36
correlation_decay_distance=-999
long_name=potential evapotranspiration
missing_value=9.969209968386869e+36
NETCDF_DIMENSION_time=40161
NETCDF_time_units=days since 1900-1-1
NETCDF_VARNAME=pet
units=mm
_______________________________________________
grass-user mailing list
[grass-user@lists.osgeo.org](mailto:grass-user@lists.osgeo.org)
[http://lists.osgeo.org/mailman/listinfo/grass-user](http://lists.osgeo.org/mailman/listinfo/grass-user)