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To remove the zeros from an xarray DataArray called da, you can use the where method to create a new array with only the non-zero values:
da_nonzero = da.where(da != 0)
This creates a new DataArray da_nonzero that only contains the non-zero values of da. If you want to modify the original array da in place, you can assign the result back to da:
da = da.where(da != 0)