CODEWITHSUNDEEP
netcdfnco
Brian Mapes
Brian Mapes

Reputation: 21

dimension called "time" exists, but variable "time" uses a different dimension

How can one give this peculiar netCDF file a proper time axis?

"time" exists as both a dimension and a variable, but the time variable uses "serial\ date\ number" as its dimension.

There are two challenges: 1. the variables vs. dimensions issue; and 2. "serial\ date\ number" appears to indicate spaces (with backslash delimiters) on some systems, but has underscores ("serial_date_number") on other systems. 

netcdf 
dimensions:
 lon = 80 ;
 lat = 41 ;
 pres = 27 ;
 time = 12053 ;
 serial\ date\ number = 12053 ;
variables:
 double u_mjo(time, pres, lat, lon) ;
 double lon(lon) ;
 lon:units = "degrees_east" ;
 double lat(lat) ;
 lat:units = "degrees_north" ;
 double p_level(pres) ;
 p_level:units = "hPa" ;
 double time(serial\ date\ number) ;
 time:units = "days since 0000-01-01 00:00 UTC" ;
  ...

Upvotes: 1

Views: 2040

Answers (3)

chillwx
chillwx

Reputation: 31

On Ubuntu 14.04 I was able to do: 

ncrename -v variable\ with\ whitespace,variable_with_whitespace filein.nc fileout.nc

Upvotes: 0

Rich Signell
Rich Signell

Reputation: 16365

Here's the procedure that worked for me using only NCO commands (no ncdump/manual edit/ncgen step):

Extract 4 time steps from OPeNDAP dataset to local netCDF file allfields.nc:

   ncks -d time,0,3 -d serial_date_number,0,3
    http://weather.rsmas.miami.edu/repository/opendap/synth:100ae90b-71ac-4d38-add9-f8982a976322:L2FsbGZpZWxkcy5uYw==/entry
    -O allfields.nc

Extract the time variable into a separate file time.nc:

ncks -v time allfields.nc time.nc

Extract everything except the time variable to a separate file fixed.nc (which also removes the problematic serial_date_number dimension`):

ncks -C -x -v time allfields.nc fixed.nc

Rename the dimension serial_data_number to time:

ncrename -O -d serial_date_number,time time.nc

Append the file with fixed time to the file without time:

ncks -A time.nc fixed.nc

The files I used and created in this workflow may be seen here: http://geoport.whoi.edu/thredds/catalog/usgs/data2/rsignell/models/mapes/catalog.html

Upvotes: 2

Brian Mapes
Brian Mapes

Reputation: 21

The solution to convert original.nc to fixed.nc, addressing the 2 challenges, was (after much wrangling) this: 

# 1. extract time from the original.nc file to create a new file with only time:
 ncks -v time original.nc time.nc

# 2. remove the time variable from original.nc (which removes the problematic `serial_date_number dimension`)
 ncks -C -x -v time original.nc fixed.nc

#3. Fix the time.nc file manually, with a text editor:
 ncdump time.nc > time.txt   # dump netCDF to text
    ## text-edit time.txt to fix up header, 
    ## creating time = UNLIMITED ; // (12053 currently)
 ncgen -o newtime.nc < time.txt   # remake netCDF from text

# 4. Finally, concatenate the new time variable file into fixed.nc
 ncks -A newtime.nc fixed.nc

Upvotes: 0

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