Error in Plotting STOFS-3D-Atlantic Data about thalassa HOT 6 CLOSED

OK. I guess I will just close the issue.

from thalassa.

Hello Atieh

I am afraid we haven't really looked into 3D output.

Judging from the screenshots, my guess is that there is some issue with the element connectivity.

ds = xr.open_dataset("~/Downloads/stofs_3d_atl.t12z.n001_024.field2d.nc")
ds.dims
ds.SCHISM_hgrid_face_nodes.min().values
ds.SCHISM_hgrid_face_nodes.max().values

outputs

FrozenMappingWarningOnValuesAccess({'time': 24, 'nSCHISM_hgrid_node': 2654153, 'nSCHISM_hgrid_face': 5039151, 'nMaxSCHISM_hgrid_face_nodes': 3})
array(3, dtype=int32)
array(2653944, dtype=int32)

Do notice that the node connectivity only starts from 3 and only reaches up to 2653944 instead of 2654153.

So, it seems that these files don't contain the full mesh for whatever reason.

related: #61

from thalassa.

You can try to copy the mesh connectivity from the schout_adcirc_* file and then it should might work. You will probably need to rename a bunch of dimensions though.

from thalassa.

@pmav99 Thank you so much for the great suggestion. I tried to use the format and names inside the shout_adcirc file and rename and replace values and dimensions in field2d.nc files.

First I read the nc files.

Then I renamed and replaced the dimensions and variables in field2d.nc files.

ds2= ds2.rename({'nSCHISM_hgrid_node': 'node', 'nSCHISM_hgrid_face': 'nele', 'nMaxSCHISM_hgrid_face_nodes': 'nvertex'})
ds2 = ds2.drop_dims('nele')
ds2['nele'] = ds['nele']
ds2['nvertex']=ds['nvertex']
ds2['element']= ds['element']
ds2= ds2.rename({'SCHISM_hgrid_node_x': 'x', 'SCHISM_hgrid_node_y': 'y'})
ds2

I normalized and cropped the data using Thalassa.

When I plot the data the depth values look OK, but for the rest of variables, there are a lot of missing data.

The same happens when I copy each variable to shout_adcirc file.

from thalassa.

Hmm... The missing values seem to be on triangles that are over land. So it could be that some kind of mask is applied on the dataset. Have you checked if there are values there? I suspect that there are nans for elev etc.

Check the original netcdf files. Not the normalized datasets. E.g. with

ds_orig = xr.open_dataset(...)
ds_orig.isel(nSCHISM_hgrid_node=0).elev.values

If this is the case, this should also explain why these files contain a subset of the connectivity. The mask must have been applied there, too.

from thalassa.

@pmav99, you're correct. I looked into the nodes in the original dataset near the areas that show as nan in the plots, and it seems that most of them are nan. Thanks a lot for your help and time.

from thalassa.