I've downloaded a netcdf from the Climate Data Store and would like to write a CRS to it, so I can clip it for a shapefile. However, I get an error when assigning a CRS. Below my script and what is being printed. I receive this error after trying to write a crs:

MissingSpatialDimensionError: y dimension (lat) not found. Data variable: lon_bnds

# load netcdf with xarray
dset = xr.open_dataset(netcdf_fn)

# add projection system to nc
dset = dset.rio.write_crs("EPSG:4326", inplace=True)

# mask CMIP6 data with shapefile
dset_shp = dset.rio.clip(shp.geometry.apply(mapping), shp.crs)

Dimensions:      (time: 1825, bnds: 2, lat: 2, lon: 1)
  * time         (time) object 2021-01-01 12:00:00 ... 2025-12-31 12:00:00
  * lat          (lat) float64 0.4712 1.414
  * lon          (lon) float64 31.25
    spatial_ref  int32 0
Dimensions without coordinates: bnds
Data variables:
    time_bnds    (time, bnds) object ...
    lat_bnds     (lat, bnds) float64 0.0 0.9424 0.9424 1.885
    lon_bnds     (lon, bnds) float64 ...
    pr           (time, lat, lon) float32 ...
Attributes: (12/48)
    Conventions:            CF-1.7 CMIP-6.2
    activity_id:            ScenarioMIP
    branch_method:          standard
    branch_time_in_child:   60225.0
    branch_time_in_parent:  60225.0
    comment:                none
    title:                  CMCC-ESM2 output prepared for CMIP6
    variable_id:            pr
    variant_label:          r1i1p1f1
    license:                CMIP6 model data produced by CMCC is licensed und...
    cmor_version:           3.6.0
    tracking_id:            hdl:21.14100/0c6732f7-2cdd-4296-99a0-7952b7ca911e

1 Answer 1


You are attempting to clip the whole dataset, but only the pr data var can be clipped. This is because it is the only one with both x and y dimensions. This should work:

dset_shp = dset.pr.rio.clip(shp.geometry, shp.crs)
  • Thanks, but then I get the following error: NoDataInBounds: No data found in bounds. Data variable: pr.
    – CrossLord
    May 16 at 7:59
  • That means that there was no data when you performed the clip operation.
    – snowman2
    May 16 at 12:07
  • There seems to be data though.. When I print dset.pr this is what I get: array([[[7.368938e-07], ... [1.653116e-07]]], dtype=float32) Coordinates: * time (time) object 2021-01-01 12:00:00 ... 2025-12-31 12:00:00 * lat (lat) float64 0.4712 1.414 * lon (lon) float64 31.25
    – CrossLord
    May 16 at 15:00
  • I thought it might had something to do with the size of the polygon compared to the pixel, since the pixels are much larger than the polygon. However, adding all_touched = True does not help. See: gis.stackexchange.com/questions/390777/…
    – CrossLord
    May 16 at 15:03
  • Might be that the data in the cell is filled with the no data value.
    – snowman2
    May 16 at 20:15

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.