Changes between Version 9 and Version 10 of Documentation/UserGuide/StudyNetCDF

Timestamp:

2020-02-28T14:35:36+01:00 (4 years ago)

Author:

bguenet

Comment:

--

Documentation/UserGuide/StudyNetCDF

@@ -5 +5 @@
 Last revision: 2020/02/28, B. Guenet [[BR]]
 
-
-The quickest way of all to look at NetCDF files is to use '''ncview''', i.e.:
-
-{{{
-ncview myJob_20060101_20061231_1M_sechiba_history.nc
-}}}
-
-Unfortunately the ncview application can be a little unstable (at least on my system anyway).
-
-'''ncdump''' is more flexible, and is a great way to look at header information:
+== nco ==
+
+
+nco is a very powerful tool to print data, modify variable names, concatenate, etc on netcdf file. A detailled documentation can be found here http://nco.sourceforge.net/
+We will just summarize here some of the most useful nco commands often used in the orchidee context.
+
+ * '''ncdump''' 
+This command print all the informations stored in your netcdf file. Some prefix can extract only the information you need.
+
+   * To look at header information:
 
 {{{
@@ -20 +20 @@
 }}}
 
-or, for example to extract one column of data in a tabulated text format (here for 'fluxlat', the latent heat flux):
-
-
-{{{
-ncdump -v fluxlat -f fortran -n fluxlat myJob_20060101_20061231_1M_sechiba_history.nc > myJob_fluxlat.cdl
-}}}
-
-
-But there's a really useful script that can be used in '''IDL''' to import all of the data series at once, without having to spend time writing scripts to define input arrays first. First of all, download [http://aos.princeton.edu/WWWPUBLIC/PROFS/pom_gfdex/idl_lib/cdf2idl.pro cdf2idl.pro], compile it within IDL and then input the following:
-
-{{{
-
-cdf2idl, '/home/rest_of_the_path/myJob_20060101_20061231_1M_sechiba_history.nc'
-
-@myJob_20060101_20061231_1M_sechiba_history.idl
-}}}
-
-And then you have all of your variables automatically imported, each into arrays of an appropriate size, and they can be quickly plotted, e.g:
-
-
-{{{
-plot, tstep, tair(0,0,0,*)
-}}}
-
-(remember that IDL by default defines arrays as starting from 0, instead of from 1)
-
-'''ncks''': If you would like to remove a certain time series from a netcdf file (for instance, in this example, all data from 'temp_atmos_pres' in the file jamescdf.nc for which the height dimension is 20) with the output written to jamestest.nc
+   * To extract one variable (here for 'fluxlat', the latent heat flux)
+
+{{{
+ncdump -v fluxlat myJob_20060101_20061231_1M_sechiba_history.nc 
+}}}
+
+   * To extract one variable and show them in a tabulated way (here for 'fluxlat', the latent heat flux)
+
+{{{
+ncdump -v fluxlat -f fortran -n fluxlat myJob_20060101_20061231_1M_sechiba_history.nc 
+}}}
+
+ * '''ncrename''' 
+
+This command change the name of a given variable/dimension depending on the prefix you are using
+
+   * To rename a variable within the file (here for 'fluxlat', the latent heat flux)
+{{{
+ncrename -v fluxlat,latent_heat_flux myJob_20060101_20061231_1M_sechiba_history.nc 
+}}}
+
+   * To rename a variable a creating a new file (here for 'fluxlat', the latent heat flux)
+{{{
+ncrename -v fluxlat,latent_heat_flux myJob_20060101_20061231_1M_sechiba_history.nc mynewfile.nc
+}}}
+
+   * To rename a dimension within the file (here for 'lon', the longitude)
+{{{
+ncrename -d lon,longitude myJob_20060101_20061231_1M_sechiba_history.nc 
+}}}
+
+   * To rename a variable a creating a new file (here for 'lon', the longitude)
+{{{
+ncrename -d lon,longitude myJob_20060101_20061231_1M_sechiba_history.nc mynewfile.nc
+}}}
+
+  * '''ncks''' 
+
+If you would like to remove a certain time series from a netcdf file (for instance, in this example, all data from 'temp_atmos_pres' in the file jamescdf.nc for which the height dimension is 20) with the output written to jamestest.nc
 
 {{{
 ncks -H -d height,20 -d temp_atmos_pres,: jamescdf.nc jamestest.nc
 }}}
+
+ * '''ncap2''' 
+
+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]]
+
+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)
+
+{{{
+ 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
+}}}
+
+
+
 
 
@@ -72 +100 @@
 }}}
 
-
-
-== 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>
 
 
@@ -180 +194 @@
 </code>
 
-
+== ncview: a quick alternative ==
+The quickest way of all to look at NetCDF files and to quickly plot some outputs is to use ncview:
+
+{{{
+ncview myJob_20060101_20061231_1M_sechiba_history.nc
+}}}
+
+Unfortunately the ncview application can be sometimes a little unstable.