Changes between Version 7 and Version 8 of Documentation/UserGuide/StudyNetCDF

Timestamp:

2020-02-28T12:11:16+01:00 (4 years ago)

Author:

bguenet

Comment:

--

Documentation/UserGuide/StudyNetCDF

@@ -48 +48 @@
 ncks -H -d height,20 -d temp_atmos_pres,: jamescdf.nc jamestest.nc
 }}}
+
+
+XXXXXXXXXXXXXX
+
+Similar to Ferret (see also How To), CDO can also be used to regrid NetCDF files. It is very straight and fast. Contrary to Ferret I [SL] did not find how to increase the memory allocation for CDO. Thus for very large files Ferret seems to be the software of your choice.
+
+The call has the following structure:
+{{{
+cdo -f nc -regriddingMethod,gridTemplate.nc input.nc output.nc
+}}}
+
+There are three regridding methods: remapbil (bilinear interpolation), remapbic (bicubic interpolation), remapnn (nearest neighbour), remapcon (conservative regridding). Use remapnn and remapcon to avoid weird values if your variable is heterogeneous.
+
+For the template file with your target grid, it can be any netcdf with regular lat/lon. A trick here is to use "full paths" and not relative paths to the files in order to work.
+
+Some examples:
+{{{
+cdo -f nc -remapbil,/gpfs/cru/rst08auu/code/target.0.5degree.gpp.grid.45N.nc esa.ecv.smo.0.25deg.grid.monthly.1979.2010.nc esa.ecv.smo.0.25deg.grid.monthly.1979.2010.cdo.remapped.0.5deg.remapbil.45N.nc
+cdo -f nc -remapnn,/gpfs/cru/rst08auu/code/target.0.5degree.gpp.grid.45N.nc esa.ecv.smo.0.25deg.grid.monthly.1979.2010.nc esa.ecv.smo.0.25deg.grid.monthly.1979.2010.cdo.remapped.0.5deg.remapnn.45N.nc
+}}}
+
+
+
+== ncap2 ==
+
+The most powerful and quickly evolving tool from the nco set of functions
+
+See the file of exemples : {{:reunions_orchidee:ncap2.pdf| ncap2 file}} or search what you are looking on this growing list of answers [[http://sourceforge.net/search/index.php?words=&sort=posted_date&sortdir=desc&offset=0&group_id=3331&type_of_search=forums|forum nco]]
+
+A simple exemple showing different capacities (creation of a variable, use of a mask, call to an attribute, count the total and the size of the field (we can restrict this operation to a dimension as shown on the second line)
+
+<code>
+ ncap2 -O -s 'missing_flag[$y,$x]=0;where(t2m_daily!=t2m_daily@missing_value) missing_flag=1;missing_count=float(missing_flag.total())/missing_flag.size();print(missing_count)' stomate_restart.nc  ~/foo.nc
+ ncap2 -O -s 'missing_flag[$y,$x]=0;where(t2m_daily!=t2m_daily@missing_value) missing_flag=1;missing_count=float(missing_flag.total($x))/missing_flag.size($x);print(missing_count)' stomate_restart.nc  ~/foo.nc
+</code>
+
+
+== cdo ==
+
+A command that handle many operations one would like to do when working on outputs of models of the Earth System :
+  * changing of time axis
+  * regridding (many grid are already implemented and it is an even more versatile tool)
+  * complex operations...
+
+See the website of the project {{https://code.zmaw.de/projects/cdo/wiki}} or the doc : {{:reunions_orchidee:cdo-manual.pdf| CDO Manual}} and  the  {{:reunions_orchidee:cdo_refcard.pdf | quickref}}
+
+<code> 
+
+   cdo -v # print list of available operators [[BR]]
+   cdo -V # version (if very old, think of downloading the source and install a new version, as it is a tool that is evolving quickly [[BR]]
+   cdo -h remapcon # informations about a command [[BR]]
+   cdo remapcon,my_grid my_climatology.nc my_regridded_climatology.nc # conservative regridding to an other resolution [[BR]]
+
+</code>
+
+my_grid could be a file like :
+
+<code>  
+   gridtype  = lonlat
+   gridsize  = 220
+   xname     = longitude
+   xunits    = degrees_east
+   yname     = latitude
+   yunits    = degrees_north
+   xsize     = 20
+   ysize     = 11
+   xfirst    = -18.75
+   xinc      = 3.75
+   yfirst    = 20
+</code>
+
+
+
+
+<code>
+   cdo sinfov my_file.nc #most info on the file
+   cdo griddes my_file.nc #grid description (check that the type is not generic (which means unrecognised and thus not useable for mapping
+</code>
+
+Sometimes, one just need to add the attribute coordinates (linking to the variables defining the longitude and latitude positions) to enable the recognition of the grid that is used (see https://code.zmaw.de/boards/1/topics/55)
+<code>
+   ncatted -a coordinates,my_var,o,c,"nav_lon nav_lat" sst_data.nc
+</code>
+
+or to correct a wrong spelling of an attribute
+
+<code>
+   ncatted -a units,latitude,m,c,"degrees_north" force2002.nc
+</code>
+
+== Operator chaining ==
+It is one of the main features of CDO. Use it as often as possible. But Note: Operatos with a arbitrary list of input files cannot be combined with other operators
+
+# Simple combination:
+<code>
+   cdo sub -dayavg ifile2 -timavg ifile1 ofile
+</code>
+
+
+instead of :
+
+<code>
+  cdo timavg ifile1 tmp1
+
+  cdo dayavg ifile2 tmp2
+
+  cdo sub tmp2 tmp1 ofile
+
+  rm tmp1 tmp2
+</code>
+
+
+== To install a newer version than the default one on asterix/obelix ==
+
+<code>
+   get files from https://code.zmaw.de/projects/cdo/files
+   ./configure --prefix=/home/users/your_ACCOUNT/ --with-netcdf=/usr
+
+   make clean
+   make
+   make install
+</code>
+
+If you installed proj and hdf5 libraries somewhere, their can also be support for these file formats :
+
+<code>
+   ./configure --prefix=/home/users/your_ACCOUNT/ --with-netcdf=/usr --with-proj=/path/to/install --with-hdf5=/path/where/installed
+</code>
+
+