When trying to mask a NetCDF (a daily time series of 31 days) with the code below, I get the following error related to the part of writing the CRS to the rio NetCDF data:

CRSError: The WKT could not be parsed. OGR Error code 6

Here is the code I am using (taken from snowman2's answer here: How to mask NetCDF time series data from a shapefile in Python?):

import rioxarray
import xarray
from shapely.geometry import mapping

ERA5_daily = xarray.open_dataarray('ERA5_VIMD_2018_08_Daily.nc')
ERA5_daily.rio.set_spatial_dims(x_dim="longitude", y_dim="latitude", inplace=True)
ERA5_daily.rio.write_crs("epsg:4326", inplace=True)
shapefile = geopandas.read_file('Cluster_34586.shp', crs="epsg:4326")

clipped = ERA5_daily.rio.clip(shapefile.geometry.apply(mapping), shapefile.crs, drop=False)

Does anyone know how to fix it?

  • What is the output of python -c "import rioxarray; rioxarray.show_versions()"? What is the CRS?
    – snowman2
    Sep 9, 2020 at 20:19
  • Hi, @snowman2! This is what I get: Traceback (most recent call last): File "<ipython-input-65-54d7e150b1f6>", line 1, in <module> rioxarray.show_versions() AttributeError: module 'rioxarray' has no attribute 'show_versions'
    – Camila
    Sep 9, 2020 at 21:16
  • @snowman2: It looks like there is no CRS (couldn't find it either when opening the netcdf file in python with netcdf library, rioxarray or when opening with QGIS)
    – Camila
    Sep 9, 2020 at 21:23
  • I think that you have an old version of rioxarray. Mind updating and trying again?
    – snowman2
    Sep 9, 2020 at 22:02
  • Are you able to share the file? Or the output of ncdump -h file.nc?
    – snowman2
    Sep 9, 2020 at 22:05

1 Answer 1


Using this code:

import geopandas
import rioxarray
import xarray
from shapely.geometry import mapping

ERA5_daily = xarray.open_dataarray('ERA5_VIMD_2018_08.nc')
ERA5_daily.rio.write_crs("EPSG:4326", inplace=True)
shapefile = geopandas.read_file('Cluster_34586.shp', crs="EPSG:4326")
clipped = ERA5_daily.rio.clip(shapefile.geometry.apply(mapping), shapefile.crs, drop=False)

It works with this setup (from: rioxarray.show_versions()):

rioxarray (0.0.31) deps:
  rasterio: 1.1.5
    xarray: 0.16.0
      GDAL: 3.0.4

Other python deps:
     scipy: 1.5.2
    pyproj: 2.6.1.post1

    python: 3.7.8 | packaged by conda-forge | (default, Jul 31 2020, 02:25:08)  [GCC 7.5.0]

I would recommend upgrading the versions you have on your system.

  • I've uninstalled rioxarray and installed again using pip install and it is now with the same version as yours. The code is now working just fine! Thank you very much!
    – Camila
    Sep 10, 2020 at 16:12
  • Glad to hear that it worked 👍
    – snowman2
    Sep 10, 2020 at 23:23

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