Actions

NetCDF Operators

From BAWiki


About NCO

The NCO toolkit manipulates and analyzes data stored in NetCDF-accessible formats, including DAP, HDF4, and HDF5. It exploits the geophysical expressivity of many CF (Climate & Forecast) metadata conventions, the flexible description of physical dimensions translated by UDUnits, the network transparency of OPeNDAP, the storage features (e.g., compression, chunking, groups) of HDF (the Hierarchical Data Format), and many powerful mathematical and statistical algorithms of GSL (the GNU Scientific Library). NCO is fast, powerful, and free.

For more information see nco.sourceforge.net.


Typical applications at BAW

Concatenation of several NetCDF files converted from boewrt.dat files into one cf-netcdf.nc file

  1. Verify original data for correctness and completeness;
  2. (optional) Transform boewrt.dat using ZEITRIO into equidistant time-series of identical length;
  3. Convert several boewrt.dat files using DATACONVERT to equivalent cf-netcdf.nc files (with identical dates and times);
  4. With ncrcat several files can be concatenated into one cf-netcdf.nc file;
  5. Typical post processors: NCANALYSE;
  6. Example: ncrcat -h f1.nc f2.nc ... fn.nc result.nc (-h suppresses the modification or creation of a history attribute);
  7. More information: ncrcat-netCDF-Record-Concatenator.

Reduction of a NetCDF file along its dimensions

General

  • ncks -d dim, min, max,[ stride] in_file out_file
  • more options see [1].

Typical reduction of UnTRIM results in time

  • ncks -d nMesh2_data_time,1,19,6 in_file out_file
  • extracts the first, seventh, thirteenth and nineteenth timestep

Typical reduction of meteorological data in space

  • ncks -d rlon,600,900 iconeu.nc tmp_reduced_rlon.nc
  • ncks -d rlat,200,500 tmp_reduced_rlon.nc iconeu.reduced_in_space.nc
  • extracts a "square" of 301 * 301 values in longitude and latitude direction in a two-step procedure

Availability at the BAW in Hamburg

  • Linux: nco-4.6.1 from 06.08.2016
  • Windows: at console level. Status 04.02.2015

"Recipe" for execution on Windows systems

  • Open the console in the data directory, e.g. in the TotalCommander:
 -> Befehle -> Kommandozeilenfenster öffnen (TotalCommander language = German):
  • Extend the search path:
 set PATH = %PATH%;\\themis\system\akprog\bin\win
  • Get help on the command, for example:
 ncrcat
  • Execute the command with options, file names etc.:
 ncrcat -h file1.nc file2.nc result.nc
  • The option -h eliminates the attributes history and nco_openmp_thread_number. The latter causes an error when processing the output file with BAW programs as NCANALYSE.
  • Example directory $PROGHOME/examples/ncdelta/data/emderfahrwasser-1/mes/wl. The time series of eleven different stations have been concatenated to 2010_0608_0708.aequi5.nc with ncrcat.


Citations

The recommended citations for NCO software are

  1. Zender, C. S. (2008), Analysis of Self-describing Gridded Geoscience Data with netCDF Operators (NCO), Environ. Modell. Softw., 23(10), 1338-1342, doi:10.1016/j.envsoft.2008.03.004.
  2. Zender, C. S. (2014), netCDF Operator (NCO) User Guide, Version 4.4.8, http://nco.sf.net/nco.pdf.

Use the former when referring to overall design, purpose, and optimization of NCO, and use the latter when referring to specific features and/or the User Guide itself.


back to Standard-Software-Applications (Add-ons)


Overview