Adding Chl to reader and module

[AndresSepulveda]

Hello,

I will be using larvalfish model to track a particle and I want to add the Chlorophyll from a CROCO-PISCES run which is divided in

   float NCHL(time, s_rho, eta_rho, xi_rho) ;
            NCHL:long_name = "averaged Chlorophyll in nano" ;
            NCHL:units = "mg Chl m-3" ;
            NCHL:field = "NCHL, scalar, series" ;
            NCHL:coordinates = "lat_rho lon_rho" ;
    float DCHL(time, s_rho, eta_rho, xi_rho) ;
            DCHL:long_name = "averaged Chlorophyll in diatoms" ;
            DCHL:units = "mg Chl m-3" ;
            DCHL:field = "DCHL, scalar, series" ;

my guess this needs a modification in both reader reader_ROMS_native.py and larvalfish.py. Has anyone done it?

[knutfrode]

Hi,
If the actual variables had standard_name attribute, you would not need to make any changes in the reader, only adding the given variable (standard_name) to the actual module.

As an alternative to updating the reader, one can also open dataset with Xarray, add needed attributes, and create a reader from this:

ds = xr.open_dataset(<files.nc>)
ds['NCHL'] = ds.NCHL.assign_attrs(standard_name='mass_concentration_of_chlorophyll_in_sea_water')
reader = reader_ROMS_native(ds)