unstructured netcdf file not compatible with CDO

Hi all,

I have a python-based tool that via xarray creates a NetCDF file which then need must be processed by CDO. I can easily play with attributes and properties of the file since I am creating it via python, and in most of the situation I can get it through. However, the following file - a 3D oceanic mask - does not seems to be compatible with CDO (I tried version 2.2.0 through mamba). I guess there is something in CF-compliant file structure which I am missing.

The netcdf look like this:

netcdf bounds {
dimensions:
    cell = 120184 ;
    bnds = 4 ;
    lev = 75 ;
variables:
    double lon(cell) ;
        lon:standard_name = "longitude" ;
        lon:units = "degrees East" ;
        lon:bounds = "lon_bnds" ;
    double lat(cell) ;
        lat:standard_name = "latitude" ;
        lat:units = "degrees North" ;
        lat:bounds = "lat_bnds" ;
    double lat_bnds(cell, bnds) ;
    double lon_bnds(cell, bnds) ;
    double lev(lev) ;
        lev:standard_name = "Depth" ;
        lev:units = "m" ;
    double tmask(lev, cell) ;
        tmask:_FillValue = NaN ;
        tmask:coordinates = "lev lat lon" ;

Indeed, every CDO operations ends with:

cdi  warning (cdfInqContents): Coordinates variable lev can't be assigned!
cdi  warning (cdf_read_ycoord): Unsupported array structure, skipped variable tmask!
cdi  warning (cdfInqContents): No data arrays found!
cdo    sinfo: Open failed on >Desktop/bounds.nc<
              Unsupported file structure

The file is quite big, but if it is not something trivial I can try to produce a subsample of it...

many thanks!
Paolo

Replies (5)

RE: unstructured netcdf file not compatible with CDO - Added by Karin Meier-Fleischer 11 months ago

Hi Paolo,

the warning says that something is wrong assigning lev at some point. I guess you have to change the tmask coordinates attribute to

coordinates = "lat lon"

RE: unstructured netcdf file not compatible with CDO - Added by Paolo Davini 11 months ago

Thanks Karin,

if I remove the lev from the coordinate, you are right, the warning disappear. However, the `unsupported array structure` remains :-(

cdi  warning (cdf_read_ycoord): Unsupported array structure, skipped variable tmask!
cdi  warning (cdfInqContents): No data arrays found!
cdo    sinfo: Open failed on >bounds.nc<
              Unsupported file structure

I suspect the issue is somewhere else... I created a sample file, you can find here attached in case you want to check yourself! Thanks again

bounds.nc (20.2 MB) bounds.nc

RE: unstructured netcdf file not compatible with CDO - Added by Karin Meier-Fleischer 11 months ago

The attribute grid_type has to be set to unstructured:

ncatted -a grid_type,tmask,c,c,"unstructured" bounds.nc

RE: unstructured netcdf file not compatible with CDO - Added by Uwe Schulzweida 11 months ago

The problem here is that the content of the attribute lev:standard_name is not recognized by CDO. If you change this to lowercase it works without problems:

ncatted -a standard_name,lev,m,c,"depth" bounds.nc

RE: unstructured netcdf file not compatible with CDO - Added by Paolo Davini 11 months ago

Many thanks! Both the suggestions are great, in this way CDO can deal with the data.

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