Changes between Version 10 and Version 11 of Documentation/UserGuide/StudyNetCDF

Timestamp:

2020-02-28T15:22:22+01:00 (4 years ago)

Author:

bguenet

Comment:

--

Documentation/UserGuide/StudyNetCDF

@@ -68 +68 @@
 The most powerful and quickly evolving tool from the nco set of functions
 
-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]]
+search what you are looking on this growing list of answers [[https://sourceforge.net/p/nco/discussion/|forum nco]]
 
 A simple example 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)
@@ -78 +78 @@
 
 
-
-
-
-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
-}}}
-
+ * '''ncatted'''
+
+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. In that cases the ncatted command might be useful
+
+
+{{{
+   ncatted -a coordinates,my_var,o,c,"nav_lon nav_lat" sst_data.nc
+}}}
+
+or to correct a wrong spelling of an attribute
+
+{{{
+   ncatted -a units,latitude,m,c,"degrees_north" force2002.nc
+}}}
 
 
 == cdo ==
 
-A command that handle many operations one would like to do when working on outputs of models of the Earth System :
+An alternative to nco is cdo. They are basically doing similar things but dependending on what you want to do the command line might be easier with one or another. Details on cdo are here https://code.mpimet.mpg.de/projects/cdo cdo is useful for :
   * 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>
+Below a list of classical command:
+
+
+ * print list of available operators [[BR]]
+{{{ 
+   cdo -v 
+}}} 
+
+ * print the version you are using (if very old, think of downloading the source and install a new version, as it is a tool that is evolving quickly)
+{{{
+   cdo -V
+}}}
+
+ * more info on the file
+{{{
+   cdo sinfov my_file.nc
+}}}
+
+ * grid description
+{{{ 
+   cdo griddes my_file.nc 
+}}}
+
+
+* print some information about the command remapcon
+{{{
+   cdo -h remapcon
+}}}
+
+* an example of a conservative regridding to an other resolution
+{{{
+   cdo remapcon,my_grid my_climatology.nc my_regridded_climatology.nc 
+}}}
 
 my_grid could be a file like :
 
-<code>  
+{{{
    gridtype  = lonlat
    gridsize  = 220
@@ -134 +149 @@
    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 ==
@@ -177 +178 @@
 
 
-== 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>
+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
+}}}
 
 == ncview: a quick alternative ==