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Problem: I want to clip a basin (e.g. Nena) from a global netcdf file (e.g. global.nc) and output a new .nc file (nena.nc). What I have is a shapefile of this basin.

Step1: Generate a set of coordinates of the basin boundary. In ArcGIS, use “Feature Vertices To Points” and then “Export Feature Attribute to ASCII” to output the coordinates file (lena.txt), which looks like

 113.25000000 52.25000000 1
 113.25000000 52.50000000 2
 113.00000000 52.50000000 3
 113.00000000 52.25000000 4
 112.75000000 52.25000000 5
 112.75000000 52.50000000 6
 112.50000000 52.50000000 7
 112.50000000 52.25000000 8
 ......

then use “cut” in shell to cut the last column.

Step2: Using cdo to clip the basin.

$ cdo maskregion,lena.txt global.nc lena.nc