A set of utilities called netCDF operators (NCOs) are available on most of the linux machines, and they permit you to perform simple calculations and manipulations of netCDF or HDF4 files at the operating system (for example, linux) level with only a minimimal knowledge of the netcdf files.
Useful information on each command can be obtained by just typing the name of the command in your linux session, for example, "ncatted" (no quotes), followed by carriage return. The NCO User's Guide is available in several formats: HTML and PostScript, PDF, and other, and the users guide is very useful subject to the caveat that not all of the features included in the users guide have actually been implemented, and you are encouraged to check the calculations so that you can build confidence in what the operators are doing.
Examples of commands:
Examples of combinations of commands used to perform common calculations:
Please contribute to this WWW page. This file is
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1) The usefulness of these routines is best demonstrated with
an example. We get NCEP / NCAR reanalysis data
from NOAA CDC in files where values of the variable, for example,
geopotential height, are given for all 17 of the model levels. For
simplicity it would be nice to have a file of just 500 mb geopotential
height. Creating such a file can be done with:
2) "ncra" could be used to calculate the January climatology of
monthly mean data:
3) Calculate thickness.
4) A more complex calcultaion is to compute pentad-mean (5-day
averages) horizontal momentum fluxes, the average of u'v', from the
reanalysis daily-average files. The time average momentum flux,
[u'v'], can be written as:
With the exception of ncrcat, there are always only one input and one output file in a NCO
operation. One way to include two or more input variables in a calculation is
to append additional variable files to a file. The reanalysis daily-average data is
stored as one year per file. Append vwnd to the uwnd file:
Calculate the product uv for a year of daily-average data.
Beginning of pentad loop:
Calculate u'v'.
Concatenate the pentad files in a single file for
the
year.
A more detailed (and harder to follow) cshell script
for this calculation has been written by Ioana Dima. Please write to
Ioana (ioana@atmos.washington.edu)
to obtain this script.
5) How to change the variable type:
For air temperature the add_offset and scale_factor are 512.81 and
0.01, respectively:
7) For files to be accepted by the Live Access Software,
a file cannot use the word "data" as a variable name.
8) NCO differentiates between concatenating and appending.
If you want to put two variables with the same time dimension
into the same file, use
If you have yearly files that you want to concatenate, use
* There is a special problem that can arise with the time dimension
in the concatenated files. I write time as "so many units
since some reference time" where the reference time is the first time
period present in a file. ncrcat, at present, doesn't calculate the time correctly for files written with the above
time prescription, and it provides a non-fatal error. I have come
up with a matlab5 work-around where I write correct time values into
the time variable inside a matlab session. For example,
1) Calculate a monthly climatology:
ncea -d level,6,6 -F hgt.mon.mean.nc hgt500.mon.mean.nc
where:
1000, 925, 850, 700, 600, 500, 400, 300, 250, 200, 150, 100, 70, 50, 30, 20, 10
and the 500mb level is the 6th level under FORTRAN-indexing (5th level
under C-indexing). The "-F" specfication says to use FORTRAN-indexing.
ncra -d time,1,nmonths,12 -F hgt.mon.mean.nc
hgt.mon.mean.clim.nc
where it now takes the average of every twelfth month and "nmonths"
is the total number of months in the file. More generally, the maps
to average are specified by
"-d dimension,minimum,maximum,stride", type "ncra" for more
information.
ncea -d level,8,8 -F hgt.mon.mean.nc hgt300.mon.mean.ncThe NCEP / NCAR reanalysis comes with data for 17 vertical
levels. Pick off the data for the 300 and 850 mb pressure levels. -F
means use FORTRAN-indexing (indexing begins with 1). C-indexing
begins with 0.
ncea -d level,3,3 -F hgt.mon.mean.nc hgt850.mon.mean.nc
ncdiff hgt300.mon.mean.nc hgt850.mon.mean.nc
thickness300850.mon.mean.nc
Subtract hgt850 from hgt300, and write it out to thickness...
[u'v'] = [uv] - [u][v]
where [] and ()' denote time averages and deviations from the time
average respectively. In this case the time averages are the
averages over 5 days.
ncks -A vwnd.1948.nc uwnd.1948.nc
ncap -s "uv=uwnd*vwnd" uwnd.1948.nc product.nc
where product.nc will contain uv, uwnd, and vwnd.
Calculate the pentad means of uv.
ncra -O -F -d time,day1,day2 product.nc product.pentad.nc
where day1 and day2 are the first and last Julian days of the pentad, respectively.
ncap -s "upvp=uv-uwnd*vwnd" -v product.pentad.nc
upvp.pentad.nc
where -v forces only upvp (and not uv, uwnd,
or vwnd) to be output to upvp.pentad.nc
End of pentad loop
ncrcat -h -O upvp.pentad.nc upvp.1948.nc
The NCEP / NCAR reanalysis comes as short integers, and NCO tends to
write outputs as floating point numbers (which take up twice as much
disk space). To convert the floating point numbers back to packed
integers, first look at the packing in the original files from CDC,
and use these as the add_offset and scale_factor for packing.
ncap -O -s "air=(air-512.81)/0.01" filename.nc temp.nc
6) For files to be intelligently handled by the Live Access Software,
a file needs to have the following defined: units, long_name, and
title. In addition, I like to put in an extended history variable.
ncap -O -s
"air=short(air);air@add_offset=512.81;air@scale_factor=0.01"
temp.nc filename.nc
ncatted -O -a units,air,c,c,"units goes here" filename.nc
where "-a" is followed by "attribute name, variable name, mode
(append, create, delete, modify, overwrite), attribute variable type
(float, character, ...), attribute value"
ncatted -O -a long_name,air,c,c,"long_name goes here" filename.nc
"\n" (no quotes) can be used to put in a carriage return.
ncatted -O -h -a title,global,o,c,"title goes here" filename.nc
ncatted -O -h -a history,global,o,c,'history goes here'
filename.nc
ncrename -h -O -v old_variable_name,new_variable_name
filename.nc
-h: do not add to the history variable
-O: (upper case) overwrite the file.
will make the Live Access Server software happy.
ncap -h -A file_a file_b
will put variables a and b into file file_b
ncrcat -h file_1979 file_1980 file_1981 file_197919801981
-h: do not add to the history variable.* f = netcdf( filename, 'write' ) % You have to "ncclose" the file to write
the
changes.
f{'time'}(:) = correct_time_values;
f{'time'}(penultimate:last) = (penultimate and last
correct_time_values);
% For reasons that make no sense to me I had to do the previous line.
ncclose( filename )
Combinations of commands:
"foreach/end" is a UNIX command line construction to perform looping.
"ncra" calculates the mean for each calendar month. "ncrcat" concatenates the
monthly climatologies. "/bin/rm temp??.nc" deletes the temporary files.
foreach month ( 01 02 03 04 05 06 07 08 09 10 11 12 )
foreach? ncra -F -d time,$month,,12 file_with_years_and_months.nc temp$month.nc
foreach? end
ncrcat -h temp*nc monthly_climatology.nc
/bin/rm temp??.nc
August 2008
Todd Mitchell ( mitchell@atmos.washington.edu
)
JISAO data