Is something changed in "from_c_grid_dataset" for time-varying depth in Parcels 3 version?

[RomanIMMSP]

Dear Parcels developers,
thank you for your continuous improvement of the Parcels. I tried to move to the Parcels 3 version and found a lot of changes. Most of them I can manage myself but several questions remain.

First of all, when I try to run the code that worked on the previous version I have an error. The code and error follow. I would be very grateful if someone could advise me.

filenames = {'U': {'lon': path+'coordinates.nc', 'lat': path+'coordinates.nc', 'depth': path+'U/U_001.nc', 'data': path+'U/U_0*.nc'}, 
             'V': {'lon': path+'coordinates.nc', 'lat': path+'coordinates.nc', 'depth': path+'V/V_001.nc', 'data': path+'V/V_0*.nc'},
             'W': {'lon': path+'coordinates.nc', 'lat': path+'coordinates.nc', 'depth': path+'W/W_001.nc', 'data': path+'W/W_0*.nc'},
             'z_w': {'lon': path+'coordinates.nc', 'lat': path+'coordinates.nc', 'depth': path+'W/W_001.nc', 'data': path+'/Zw/Zw_0*.nc'}}
variables = {'U': 'u', 'V': 'v', 'W': 'w', 'z_w': 'z_w'}
indices = {'U': {'lon': range(0, 1441), 'lat': range(0, 429)},
           'V': {'lon': range(0, 1441), 'lat': range(0, 429)}}
dimensions = {'U': {'lon': 'lon_psi', 'lat': 'lat_psi', 'depth': 'not_yet_set', 'time': 'ocean_time'},
              'V': {'lon': 'lon_psi', 'lat': 'lat_psi', 'depth': 'not_yet_set', 'time': 'ocean_time'},
              'W': {'lon': 'lon_psi', 'lat': 'lat_psi', 'depth': 'not_yet_set', 'time': 'ocean_time'},
              'z_w': {'lon': 'lon_psi', 'lat': 'lat_psi', 'depth': 's_w', 'time': 'ocean_time'}}

fieldset = FieldSet.from_c_grid_dataset(filenames, variables, dimensions, indices={'depth': range(0,30)},  
           allow_time_extrapolation=False, time_periodic=delta(days=1095))

fieldset.U.set_depth_from_field(fieldset.z_w)
fieldset.V.set_depth_from_field(fieldset.z_w)
fieldset.W.set_depth_from_field(fieldset.z_w)

Error message: "depth dimension has a wrong format. It should be [tdim, zdim, ydim, xdim]"

Thanks in advance!

[erikvansebille]

Thanks for raising this, @RomanIMMSP. Could you provide me (via email?) a subset of your data where this error can be seen? That is the easiest way for me to check/fix the issue

[RomanIMMSP]

The solution by @erikvansebille is in the following changes

indices = {'lon': range(0, 1441), 'lat': range(0, 429), 'depth': range(0,30)}
fieldset = FieldSet.from_c_grid_dataset(filenames, variables, dimensions, indices=indices,  
           allow_time_extrapolation=False, time_periodic=delta(days=1095))

[quai20]

I jump in the conversation before opening an issue myself. I'm facing the same problem (or at least the same error) :
I have multiple data file in sigma coordinates with depth_rho calculated in the datasets. If I load only 1 file (so 1 timestep), the fieldset is created properly, but if I put multiple files as input, FieldSet.from_c_grid_dataset fails with the same error as @RomanIMMSP (AssertionError: depth dimension has the wrong format. It should be [tdim, zdim, ydim, xdim])

variables = {'U': 'u', 'V': 'v', 'depth_rho':'depth_rho'}

dimensions = {'U': {'lon': 'lon_u', 'lat': 'lat_u', 'depth': 'depth_rho', 'time': 'time'},
              'V': {'lon': 'lon_u', 'lat': 'lat_u', 'depth': 'depth_rho', 'time': 'time'},
              'depth_rho' : {'lon': 'lon_rho', 'lat': 'lat_rho', 'depth': 'depth_rho', 'time': 'time'}}

fieldset = FieldSet.from_c_grid_dataset(files,variables,dimensions)

I have parcels v3.0.4
I don't really understand how indices work and how @erikvansebille 's solution would fix my issue.
Some sample files can be found here : https://ubocloud.univ-brest.fr/s/qoWRMZeNsk5ooW8
Thanks for your help !

[quai20]

I might be more successful with this, I'll let you know 🥁

variables = {'U': 'u', 'V': 'v', 'depth_rho':'depth_rho', 'bathy':'bathy'}

dimensions = {'U': {'lon': 'lon_rho', 'lat': 'lat_rho', 'depth': 'not_yet_set', 'time': 'time'},
              'V': {'lon': 'lon_rho', 'lat': 'lat_rho', 'depth': 'not_yet_set', 'time': 'time'},
              'depth_rho' : {'lon': 'lon_rho', 'lat': 'lat_rho', 'depth': 'not_yet_set', 'time': 'time'},
              'bathy' :  {'lon': 'lon_rho', 'lat': 'lat_rho', 'time':'time'}}

fieldset = FieldSet.from_c_grid_dataset(files,variables,dimensions,allow_time_extrapolation=True)
fieldset.U.set_depth_from_field(fieldset.depth_rho)
fieldset.V.set_depth_from_field(fieldset.depth_rho)

[quai20]

seems to work 👍