CDO

You can use sellonlatbox or selindexbox to select a rectangular region and mergegrid to merge the data of the selected region with an other file. Here is an example:

cdo sellonlatbox,-2,2,-2,2 emiss2014012620_toCUT.nc select_region.nc
cdo mergegrid emiss2014012620_toPASTE.nc select_region.nc result

Unfortunately your netcdf files doesn't follow the CF standard. Therefor the coordinate variable level_bnds is handled as a data variable. You have to set the correct netCDF attributes or remove this variable:

cdo sellonlatbox,-2,2,-2,2 -delname,level_bnds emiss2014012620_toCUT.nc select_region.nc
cdo mergegrid -delname,level_bnds emiss2014012620_toPASTE.nc select_region.nc result

Uwe thanks a lot for your help.

Sorry I have not responded sooner but our HPC down for maintenance. I believe it will be up again some time today and I will try your solution.
With respect to level_bnds, I am not sure if this will create an issue in my pre-processor. I will delete it and see what happens next.

As far as the mergegrid operator is concerned, I read from the online CDO User Guide that "Only rectilinear grids are supported". Is this a problem for my case?

Uwe,

I am happy to report that the elegant procedure worked nicely!
However, the pre-processor exits with an error as it expects this (very small in size variable)level_bnds.

Can I put it back in somehow when I am finished with the merging?

Once again, thank you.

Hello again!

I used the merge operator and successfully re-introduced the level_bnds. However, the pre-processor still exits with the same error.
Till now, I've used:
cdo sellonlatbox
cdo mergegrid
cdo merge (I created a separate file of level_bnds and merged it in the final file)

I looked into the two files using ncdump -h and saw that some things are completely missed by CDO and also some smaller changes in some of the variables:
-The char rotated_pole(time, level, rlat, rlon) ;
rotated_pole:grid_mapping_name = "rotated_latitude_longitude" ;
rotated_pole:grid_north_pole_latitude = 52.3f ;
rotated_pole:grid_north_pole_longitude = -156.5f ;
rotated_pole:north_pole_grid_longitude = 0.f ;
is completely missing

-The original has
float level_bnds(bnds, level) ;
level_bnds:units = "meters" ;
while the processed has
float level_bnds(x, level) ;
level_bnds:units = "meters" ;

-Under Dimensions:
the processed has x = 2 ; instead of bnds =2 ;

-The processed under each variable has attributes added:
missing_value and axis for the rlat, rlon, level variables

The problem with the renaming of bnds is fixed since CDO release 1.8.0.
The variable rotated_pole is missing because the attribute

grid_mapping = "rotated_pole" ;

is missing on all data variables.

I am in the process of compiling version 1.8.0 with our IT guy.

With respect to the missing attribute, do you suggest I should add this attribute to all or some of the variables? Should I do this before the first cdo sellonlatbox? Could you provide an example on how to do so?

Thanks,
Orestis

I now have version 1.9.6!

I added the attribute grid_mapping in all data variables (both of the CUT file and the PASTE file) as follows:

ncatted -a grid_mapping,,a,c,rotated_pole emiss2014011900.nc (to add the attribute in all variables)

ncatted -O -a grid_mapping,rotated_pole,d,, emiss2014011900.nc
ncatted -O -a grid_mapping,rlon,d,, emiss2014011900.nc
ncatted -O -a grid_mapping,rlat,d,, emiss2014011900.nc
ncatted -O -a grid_mapping,level,d,, emiss2014011900.nc
ncatted -O -a grid_mapping,time,d,, emiss2014011900.nc (to leave it only in the data variables)

I then proceeded with cutting a region:
cdo sellonlatbox,-0.025,0.475,-0.025,0.425 -delname,level_bnds CUT/emiss2014011900.nc CUT/select_region.nc
and then merging it with the PASTE file into the final file:
cdo mergegrid -delname,level_bnds PASTE/emiss2014011900.nc CUT/select_region.nc FINAL/emiss2014011900_final.nc

but I get an ERROR:
cdo mergegrid (Abort): Unsupported grid type: projection

Indeed, when I look at the cdo sinfon of the original file before changing anything I get:
Grid coordinates :
1 : generic : points=2
2 : lonlat : points=131040 (390x336)
rlon : -4.875 to 4.85 by 0.025 degrees
rlat : -4.075 to 4.3 by 0.025 degrees

and after the ncatted:
Grid coordinates :
1 : projection : points=2
mapping : rotated_latitude_longitude
2 : projection : points=131040 (390x336)
mapping : rotated_latitude_longitude
rlon : -4.875 to 4.85 by 0.025 degrees
rlat : -4.075 to 4.3 by 0.025 degrees

Finally, I would like to note that the file, although it uses rlat and rlon, does not follow the format lat(rlat, rlon). It only has rlon(rlon) and rlat(rlat).

[SOLVED]

Hi Uwe, everyone, I would just like to let you know that I used both NCO and CDO and managed to solve my problem. A synopsis of what I did:

I use NCO to cut static (same variables for all files), "cdo-dirty" variables that cdo cannot handle onto an out.nc file to put back at the end of the procedure:

$ncks -v level_bnds emiss2014011900.nc out.nc
$ncks -v rotated_pole emiss2014011900.nc out.nc

Again with NCO, I remove these undesired variables (I do this for all my files with a bash do loop, the -O option answers the interactive question that pops up with an "overwrite"):

$ncks -x -O -v rotated_pole,level_bnds emiss2014011900.nc emiss2014011900.nc

Using CDO, I first cut out a desired region from the CUT files and temporarily store it in the select_region.nc. Then, I merge the PASTE file and the selected_region file into the FINAL file:

$cdo sellonlatbox,-0.025,0.475,-0.025,0.425 CUT/emiss2014011900.nc CUT/select_region.nc
$cdo mergegrid PASTE/emiss2014011900.nc CUT/select_region.nc FINAL/emiss2014011900.nc

Finally, again with NCO, I "return" the two variables I had cut in the beginning into the FINAL files:
$ncks -h -A out.nc FINAL/emiss2014011900.nc

I am sure there are more efficient ways to do this (e.g. using pipe) but this is the best I could manage.

Cheers to all,
Orestis